Publications

Departmental Publications

2023

Mutate or die: Atomic structures explain bacterial SOS induction. Egelman EH. Proc Natl Acad Sci U S A. 2023 Jan 31;120(5):e2221605120. doi: 10.1073/pnas.2221605120. Epub 2023 Jan 24. PMID: 36693092 No abstract available.

ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by promoting apoptosis resistance and metabolic dysregulation. Przanowski P, Przanowska RK, Guertin MJ. Commun Biol. 2023 Mar 1;6(1):231. doi: 10.1038/s42003-023-04611-w. PMID: 36859531 Free PMC article.

Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis. Dutta AB, Lank DS, Przanowska RK, Przanowski P, Wang L, Nguyen B, Walavalkar NM, Duarte FM, Guertin MJ. Genome Res. 2023 Feb 21:gr.277559.122. doi: 10.1101/gr.277559.122. Online ahead of print. MID: 36810156

Hollow Octadecameric Self-Assembly of Collagen-like Peptides. Yu LT, Hancu MC, Kreutzberger MAB, Henrickson A, Demeler B, Egelman EH, Hartgerink JD. J Am Chem Soc. 2023 Feb 22. doi: 10.1021/jacs.2c12931. Online ahead of print. PMID: 36812303

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery. Beltran LC, Cvirkaite-Krupovic V, Miller J, Wang F, Kreutzberger MAB, Patkowski JB, Costa TRD, Schouten S, Levental I, Conticello VP, Egelman EH, Krupovic M. Nat Commun. 2023 Feb 7;14(1):666. doi: 10.1038/s41467-023-36349-8. PMID: 36750723 Free PMC article.

Interpretable Meta-learning of Multi-omics Data for Survival Analysis and Pathway Enrichment. Cho HJ, Shu M, Bekiranov S, Zang C, Zhang A. Bioinformatics. 2023 Mar 2:btad113. doi: 10.1093/bioinformatics/btad113. Online ahead of print. PMID: 36864611

Cryptic lncRNA-encoded ORFs: A hidden source of regulatory proteins. Dutta A, Li H, Abounader R. J Clin Invest. 2023 Mar 1;133(5):e167271. doi: 10.1172/JCI167271. PMID: 36856112 Free PMC article.

Models are useful until high-resolution structures are available. Wang F, Craig L, Liu X, Rensing C, Egelman EH. Trends Microbiol. 2023 Mar 31:S0966-842X(23)00087-2. doi: 10.1016/j.tim.2023.03.007. Online ahead of print. PMID: 37005159 No abstract available.

Hollow Octadecameric Self-Assembly of Collagen-like Peptides. Yu LT, Hancu MC, Kreutzberger MAB, Henrickson A, Demeler B, Egelman EH, Hartgerink JD. J Am Chem Soc. 2023 Mar 8;145(9):5285-5296. doi: 10.1021/jacs.2c12931. Epub 2023 Feb 22. PMID: 36812303

Microbial nanowires: type IV pili or cytochrome filaments? Wang F, Craig L, Liu X, Rensing C, Egelman EH. Trends Microbiol. 2023 Apr;31(4):384-392. doi: 10.1016/j.tim.2022.11.004. Epub 2022 Nov 26. PMID: 36446702 Review.

Aurora kinases: Generators of spatial control during mitosis. Ali A, Stukenberg PT. Front Cell Dev Biol. 2023 Mar 13;11:1139367. doi: 10.3389/fcell.2023.1139367. eCollection 2023. PMID: 36994100 Free PMC article. Review.

Rituximab induced cytokine release with high serum IP-10 (CXCL10) concentrations is associated with infusion reactions. Moore JE, Bloom PC, Chu CC, Bruno JE, Herne CA, Baran AM, Quataert SA, Mosmann TR, Taylor RP, Wallace DS, Elliott MR, Barr PM, Zent CS. Leuk Res. 2023 Mar 29;129:107072. doi: 10.1016/j.leukres.2023.107072. Online ahead of print. PMID: 37003030

Phagocytosis via complement receptor 3 enables microbes to evade killing by neutrophils. Smirnov A, Daily KP, Gray MC, Ragland SA, Werner LM, Johnson MB, Eby JC, Hewlett EL, Taylor RP, Criss AK. J Leukoc Biol. 2023 Mar 7:qiad028. doi: 0.1093/jleuko/qiad028. Online ahead of print. PMID: 36882066

Increased alcohol dehydrogenase 1 activity promotes longevity. Ghaddar A, Mony VK, Mishra S, Berhanu S, Johnson JC, Enriquez-Hesles E, Harrison E, Patel A, Horak MK, Smith JS, O’Rourke EJ. Curr Biol. 2023 Mar 27;33(6):1036-1046.e6. doi: 10.1016/j.cub.2023.01.059. Epub 2023 Feb 17. PMID: 36805847

Genomic mapping of metastatic organotropism in lung adenocarcinoma. Lengel HB, Mastrogiacomo B, Connolly JG, Tan KS, Liu Y, Fick CN, Dunne EG, He D, Lankadasari MB, Satravada BA, Sun Y, Kundra R, Fong C, Smith S, Riely GJ, Rudin CM, Gomez DR, Solit DB, Berger MF, Li BT, Mayo MW, Matei I, Lyden DC, Adusumilli PS, Schultz N, Sanchez-Vega F, Jones DR. Cancer Cell. 2023 May 8;41(5):970-985.e3. doi: 10.1016/j.ccell.2023.03.018. Epub 2023 Apr 20. PMID: 37084736

An unbroken network of interactions connecting flagellin domains is required for motility in viscous environments. Nedeljković M, Kreutzberger MAB, Postel S, Bonsor D, Xing Y, Jacob N, Schuler WJ, Egelman EH, Sundberg EJ. PLoS Pathog. 2023 May 30;19(5):e1010979. doi: 10.1371/journal.ppat.1010979. Online ahead of print. PMID: 37253071

Cell spheroid creation by transcytotic intercellular gelation. Guo J, Wang F, Huang Y, He H, Tan W, Yi M, Egelman EH, Xu B. Nat Nanotechnol. 2023 May 22. doi: 10.1038/s41565-023-01401-7. Online ahead of print. PMID: 37217766

Models are useful until high-resolution structures are available: (Trends in Microbiology 31(6), 550-551; 2023). Wang F, Craig L, Liu X, Rensing C, Egelman EH. Trends Microbiol. 2023 May 11:S0966-842X(23)00119-1. doi: 10.1016/j.tim.2023.04.005. Online ahead of print. PMID: 37179126 No abstract available.

Models are useful until high-resolution structures are available. Wang F, Craig L, Liu X, Rensing C, Egelman EH. Trends Microbiol. 2023 Jun;31(6):550-551. doi: 10.1016/j.tim.2023.03.007. Epub 2023 Mar 31. PMID: 37005159 No abstract available.

Vulnerable newborn types: analysis of subnational, population-based birth cohorts for 541 285 live births in 23 countries, 2000-2021. Erchick DJ, Hazel EA, Katz J, Lee ACC, Diaz M, Wu LSF, Yoshida S, Bahl R, Grandi C, Labrique AB, Rashid M, Ahmed S, Roy AD, Haque R, Shaikh S, Baqui AH, Saha SK, Khanam R, Rahman S, Shapiro R, Zash R, Silveira MF, Buffarini R, Kolsteren P, Lachat C, Huybregts L, Roberfroid D, Zeng L, Zhu Z, He J, Qiu X, Gebreyesus SH, Tesfamariam K, Bekele D, Chan G, Baye E, Workneh F, Asante KP, Kaali EB, Adu-Afarwuah S, Dewey KG, Gyaase S, Wylie BJ, Kirkwood BR, Manu A, Thulasiraj RD, Tielsch J, Chowdhury R, Taneja S, Babu GR, Shriyan P, Ashorn P, Maleta K, Ashorn U, Mangani C, Acevedo-Gallegos S, Rodriguez-Sibaja MJ, Khatry SK, LeClerq SC, Mullany LC, Jehan F, Ilyas M, Rogerson SJ, Unger HW, Ghosh R, Musange S, Ramokolo V, Zembe-Mkabile W, Lazzerini M, Rishard M, Wang D, Fawzi WW, Minja DTR, Schmiegelow C, Masanja H, Smith E, Lusingu JPA, Msemo OA, Kabole FM, Slim SN, Keentupthai P, Mongkolchati A, Kajubi R, Kakuru A, Waiswa P, Walker D, Hamer DH, Semrau KEA, Chaponda EB, Chico RM, Banda B, Musokotwane K, Manasyan A, Pry JM, Chasekwa B, Humphrey J, Black RE; Subnational Vulnerable Newborn Prevalence Collaborative Group and Vulnerable Newborn Measurement Core Group. BJOG. 2023 May 8. doi: 10.1111/1471-0528.17510. Online ahead of print. PMID: 37156239

XRN2 suppresses aberrant entry of tRNA trailers into argonaute in humans and Arabidopsis. Wilson B, Su Z, Kumar P, Dutta A. PLoS Genet. 2023 May 5;19(5):e1010755. doi: 10.1371/journal.pgen.1010755. eCollection 2023 May. PMID: 37146074

Rituximab induced cytokine release with high serum IP-10 (CXCL10) concentrations is associated with infusion reactions. Moore JE, Bloom PC, Chu CC, Bruno JE, Herne CA, Baran AM, Quataert SA, Mosmann TR, Taylor RP, Wallace DS, Elliott MR, Barr PM, Zent CS. Leuk Res. 2023 Jun;129:107072. doi: 10.1016/j.leukres.2023.107072. Epub 2023 Mar 29. PMID: 37003030

2022

Assessing acute myeloid leukemia susceptibility in rearrangement-driven patients by DNA breakage at topoisomerase II and CCCTC-binding factor/cohesin binding sites. Atkin ND, Raimer HM, Wang Z, Zang C, Wang YH. Genes Chromosomes Cancer. 2021 Dec;60(12):808-821. doi: 10.1002/gcc.22993. Epub 2021 Aug 26. PMID: 34405474

Genetic ablation of Pim1 or pharmacologic inhibition with TP-3654 ameliorates myelofibrosis in murine models. Dutta A, Nath D, Yang Y, Le BT, Rahman MF, Faughnan P, Wang Z, Stuver M, He R, Tan W, Hutchison RE, Foulks JM, Warner SL, Zang C, Mohi G. Leukemia. 2022 Mar;36(3):746-759. doi: 10.1038/s41375-021-01464-2. Epub 2021 Nov 5. PMID: 34741118

Correlation of ATP7B gene mutations with clinical phenotype and radiological features in Indian Wilson disease patients. Chaudhuri J, Biswas S, Gangopadhyay G, Biswas T, Datta J, Biswas A, Pandit A, Datta AK, Mukherjee A, Dutta AK, Bhattacharya P, Hazra A. Acta Neurol Belg. 2022 Feb;122(1):181-190. doi: 10.1007/s13760-021-01816-w. Epub 2021 Oct 13. PMID: 34643937

Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome. Wang F, Cvirkaite-Krupovic V, Vos M, Beltran LC, Kreutzberger MAB, Winter JM, Su Z, Liu J, Schouten S, Krupovic M, Egelman EH. Cell. 2022 Mar 17:S0092-8674(22)00199-4. doi: 10.1016/j.cell.2022.02.019. Online ahead of print. PMID: 35325592

Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments. Kreutzberger MAB, Sobe RC, Sauder AB, Chatterjee S, Peña A, Wang F, Giron JA, Kiessling V, Costa TRD, Conticello VP, Frankel G, Kendall MM, Scharf BE, Egelman EH. Nat Commun. 2022 Mar 17;13(1):1422. doi: 10.1038/s41467-022-29069-y.PMID: 35301306Free PMC article.

CDK6 Is a Therapeutic Target in Myelofibrosis. Dutta A, Nath D, Yang Y, Le BT, Mohi G. Cancer Res. 2021 Aug 15;81(16):4332-4345. doi: 10.1158/0008-5472.CAN-21-0590. Epub 2021 Jun 18. PMID: 34145036.

PEPPRO: quality control and processing of nascent RNA profiling data. Smith JP, Dutta AB, Sathyan KM, Guertin MJ, Sheffield NC. Genome Biol. 2021 May 15;22(1):155. doi: 10.1186/s13059-021-02349-4. PMID: 33992117

Atomic structure of Lanreotide nanotubes revealed by cryo-EM. Pieri L, Wang F, Arteni AA, Vos M, Winter JM, Le Du MH, Artzner F, Gobeaux F, Legrand P, Boulard Y, Bressanelli S, Egelman EH, Paternostre M. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2120346119. doi: 10.1073/pnas.2120346119. PMID: 35042822

A Genomic-Pathologic Annotated Risk Model to Predict Recurrence in Early-Stage Lung Adenocarcinoma. Jones GD, Brandt WS, Shen R, Sanchez-Vega F, Tan KS, Martin A, Zhou J, Berger M, Solit DB, Schultz N, Rizvi H, Liu Y, Adamski A, Chaft JE, Riely GJ, Rocco G, Bott MJ, Molena D, Ladanyi M, Travis WD, Rekhtman N, Park BJ, Adusumilli PS, Lyden D, Imielinski M, Mayo MW, Li BT, Jones DR. JAMA Surg. 2021 Feb 1;156(2):e205601. doi: 10.1001/jamasurg.2020.5601. Epub 2021 Feb 10.

HPVE6-USP46 Mediated Cdt2 Stabilization Reduces Set8 Mediated H4K20-Methylation to Induce Gene Expression Changes. Kiran S, Wilson B, Saha S, Graff JA, Dutta A. Cancers (Basel). 2021 Dec 22;14(1):30. doi: 10.3390/cancers14010030. PMID: 35008200

The tumor-suppressive long noncoding RNA DRAIC inhibits protein translation and induces autophagy by activating AMPK. Saha S, Zhang Y, Wilson B, Abounader R, Dutta A. J Cell Sci. 2021 Dec 15;134(24):jcs259306. doi: 10.1242/jcs.259306. Epub 2021 Dec 20. PMID: 34746949

Chk1 promotes non-homologous end joining in G1 through direct phosphorylation of ASF1A. Lee KY, Dutta A. Cell Rep. 2021 Jan 26;34(4):108680. doi: 10.1016/j.celrep.2020.108680. PMID: 33503415

Reconstitution of the DTX3L-PARP9 complex reveals determinants for high-affinity heterodimerization and multimeric assembly. Ashok Y, Vela-Rodríguez C, Yang C, Alanen HI, Liu F, Paschal BM, Lehtiö L.Biochem J. 2022 Feb 11;479(3):289-304. doi: 10.1042/BCJ20210722. PMID: 35037691

Inhibition of DYRK1a Enhances Cardiomyocyte Cycling After Myocardial Infarction. Young A, Bradley LA, Farrar E, Bilcheck HO, Tkachenko S, Saucerman JJ, Bekiranov S, Wolf MJ. Circ Res. 2022 Apr 29;130(9):1345-1361. doi: 10.1161/CIRCRESAHA.121.320005. Epub 2022 Apr 4. PMID: 35369706

TRMT6/61A-dependent base methylation of tRNA-derived fragments regulates gene-silencing activity and the unfolded protein response in bladder cancer. Su Z, Monshaugen I, Wilson B, Wang F, Klungland A, Ougland R, Dutta A. Nat Commun. 2022 Apr 20;13(1):2165. doi: 10.1038/s41467-022-29790-8. PMID: 35444240

Integrated bioinformatic pipeline using whole-exome and RNAseq data to identify germline variants correlated with cancer. Sahu D, Chatrath A, Ratan A, Dutta A. STAR Protoc. 2022 Apr 4;3(2):101273. doi: 10.1016/j.xpro.2022.101273. eCollection 2022 Jun 17. PMID: 35403010

ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines. Kumar P, Kiran S, Saha S, Su Z, Paulsen T, Chatrath A, Shibata Y, Shibata E, Dutta A. Sci Adv. 2020 May 15;6(20):eaba2489. doi: 10.1126/sciadv.aba2489. eCollection 2020 May. PMID: 32440553

DeepTracer ID: De Novo Protein Identification from Cryo-EM Maps. Chang L, Wang F, Connolly K, Meng H, Su Z, Cvirkaite-Krupovic V, Krupovic M, Egelman EH, Si D. Biophys J. 2022 Jun 28:S0006-3495(22)00511-2. doi: 10.1016/j.bpj.2022.06.025. Online ahead of print. PMID: 35769006

Archaeal bundling pili of Pyrobaculum calidifontis reveal similarities between archaeal and bacterial biofilms. Wang F, Cvirkaite-Krupovic V, Krupovic M, Egelman EH. Proc Natl Acad Sci U S A. 2022 Jun 28;119(26):e2207037119. doi: 10.1073/pnas.2207037119. Epub 2022 Jun 21. PMID: 35727984

Mating pair stabilization mediates bacterial conjugation species specificity. Low WW, Wong JLC, Beltran LC, Seddon C, David S, Kwong HS, Bizeau T, Wang F, Peña A, Costa TRD, Pham B, Chen M, Egelman EH, Beis K, Frankel G. Nat Microbiol. 2022 Jul;7(7):1016-1027. doi: 10.1038/s41564-022-01146-4. Epub 2022 Jun 13. PMID: 35697796

Allosteric regulation controls actin-bundling properties of human plastins. Schwebach CL, Kudryashova E, Agrawal R, Zheng W, Egelman EH, Kudryashov DS. Nat Struct Mol Biol. 2022 Jun;29(6):519-528. doi: 10.1038/s41594-022-00771-1. Epub 2022 May 19. PMID: 35589838

The long and short of rDNA and yeast replicative aging. Smith JS. Proc Natl Acad Sci U S A. 2022 Jun 7;119(23):e2205124119. doi: 10.1073/pnas.2205124119. Epub 2022 Jun 3. PMID: 35658078

The impact of lumbar alignment targets on mechanical complications after adult lumbar scoliosis surgery. Dial BL, Hills JM, Smith JS, Sardi JP, Lazaro B, Shaffrey CI, Bess S, Schwab FJ, Lafage V, Lafage R, Kelly MP, Bridwell KH. Eur Spine J. 2022 Jun;31(6):1573-1582. doi: 10.1007/s00586-022-07200-3. Epub 2022 Apr 15. PMID: 35428916Clinical Trial.

Development of consensus-based best practice guidelines for response to intraoperative neuromonitoring events in high-risk spinal deformity surgery. Lenke LG, Fano AN, Iyer RR, Matsumoto H, Sucato DJ, Samdani AF, Smith JS, Gupta MC, Kelly MP, Kim HJ, Sciubba DM, Cho SK, Polly DW, Boachie-Adjei O, Lewis SJ, Angevine PD, Vitale MG. Spine Deform. 2022 Jul;10(4):745-761. doi: 10.1007/s43390-022-00485-w. Epub 2022 Mar 15. PMID: 35290626

Is frailty responsive to surgical correction of adult spinal deformity? An investigation of sagittal re-alignment and frailty component drivers of postoperative frailty status. Passias PG, Segreto FA, Moattari KA, Lafage R, Smith JS, Line BG, Eastlack RK, Burton DC, Hart RA, Bess S, Shaffrey CI, Ames CP, Lafage V; International Spine Study Group. Spine Deform. 2022 Jul;10(4):901-911. doi: 10.1007/s43390-022-00476-x. Epub 2022 Mar 9. PMID: 35262879

Establishing consensus: determinants of high-risk and preventative strategies for neurological events in complex spinal deformity surgery. Iyer RR, Vitale MG, Fano AN, Matsumoto H, Sucato DJ, Samdani AF, Smith JS, Gupta MC, Kelly MP, Kim HJ, Sciubba DM, Cho SK, Polly DW, Boachie-Adjei O, Angevine PD, Lewis SJ, Lenke LG. Spine Deform. 2022 Jul;10(4):733-744. doi: 10.1007/s43390-022-00482-z. Epub 2022 Feb 23. PMID: 35199320

Are the Arbeitsgemeinschaft Für Osteosynthesefragen (AO) Principles for Long Bone Fractures Applicable to 3-Column Osteotomy to Reduce Rod Fracture Rates? Virk S, Lafage R, Bess S, Shaffrey C, Kim HJ, Ames C, Burton D, Gupta M, Smith JS, Eastlack R, Klineberg E, Mundis G, Schwab F, Lafage V; International Spine Study Group. Clin Spine Surg. 2022 Jun 1;35(5):E429-E437. doi: 10.1097/BSD.0000000000001289. Epub 2021 Dec 29. PMID: 34966036

Transcription-associated DNA DSBs activate p53 during hiPSC-based neurogenesis. Michel N, Young HMR, Atkin ND, Arshad U, Al-Humadi R, Singh S, Manukyan A, Gore L, Burbulis IE, Wang YH, McConnell MJ. Sci Rep. 2022 Jul 15;12(1):12156. doi: 10.1038/s41598-022-16516-5. PMID: 35840793

Tip60 acetylation of histone H3K4 temporally controls chromosome passenger complex localization. Niedzialkowska E, Liu L, Kuscu C, Mayo Z, Minor W, Strahl BD, Adli M, Stukenberg PT. Mol Biol Cell. 2022 Aug 1;33(9):br15. doi: 10.1091/mbc.E21-06-0283. Epub 2022 Jun 2. PMID: 35653296

DNA-guided lattice remodeling of carbon nanotubes. Lin Z, Beltrán LC, De Los Santos ZA, Li Y, Adel T, Fagan JA, Hight Walker AR, Egelman EH, Zheng M. Science. 2022 Jul 29;377(6605):535-539. doi: 0.1126/science.abo4628. Epub 2022 Jul 28. PMID: 35901135

Enzyme Responsive Rigid-Rod Aromatics Target “Undruggable” Phosphatases to Kill Cancer Cells in a Mimetic Bone Microenvironment. Yi M, Wang F, Tan W, Hsieh JT, Egelman EH, Xu B. J Am Chem Soc. 2022 Jul 27;144(29):13055-13059. doi: 0.1021/jacs.2c05491. Epub 2022 Jul 18. PMID: 35849554

Photorhabdus luminescens TccC3 Toxin Targets the Dynamic Population of F-Actin and Impairs Cell Cortex Integrity. Dong S, Zheng W, Pinkerton N, Hansen J, Tikunova SB, Davis JP, Heissler SM, Kudryashova E, Egelman EH, Kudryashov DS. Int J Mol Sci. 2022 Jun 24;23(13):7026. doi: 10.3390/ijms23137026. PMID: 35806028

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing. Wang F, Mustafa K, Suciu V, Joshi K, Chan CH, Choi S, Su Z, Si D, Hochbaum AI, Egelman EH, Bond DR. Nat Microbiol. 2022 Jul 7. doi: 10.1038/s41564-022-01159-z. Online ahead of print. PMID: 35798889

FcγR-Mediated Trogocytosis 2.0: Revisiting History Gives Rise to a Unifying Hypothesis. Lindorfer MA, Taylor RP. Antibodies (Basel). 2022 Jul 5;11(3):45. doi: 10.3390/antib11030045. PMID: 35892705 Review.

Convergent evolution in the supercoiling of prokaryotic flagellar filaments. Kreutzberger MAB, Sonani RR, Liu J, Chatterjee S, Wang F, Sebastian AL, Biswas P, Ewing C, Zheng W, Poly F, Frankel G, Luisi BF, Calladine CR, Krupovic M, Scharf BE, Egelman EH. Cell. 2022 Aug 30:S0092-8674(22)00996-5. doi: 10.1016/j.cell.2022.08.009. Online ahead of print. PMID: 36057255

DNA-guided lattice remodeling of carbon nanotubes. Lin Z, Beltran LC, De Los Santos ZA, Li Y, Adel T, Fagan JA, Hight Walker AR, Egelman EH, Zheng M. Science. 2022 Jul 29;377(6605):535-539. doi: 10.1126/science.abo4628. Epub 2022 Jul 28. PMID: 35901135

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing. Wang F, Mustafa K, Suciu V, Joshi K, Chan CH, Choi S, Su Z, Si D, Hochbaum AI, Egelman EH, Bond DR. Nat Microbiol. 2022 Aug;7(8):1291-1300. doi: 10.1038/s41564-022-01159-z. Epub 2022 Jul 7. PMID: 35798889

DeepTracer-ID: De novo protein identification from cryo-EM maps. Chang L, Wang F, Connolly K, Meng H, Su Z, Cvirkaite-Krupovic V, Krupovic M, Egelman EH, Si D. Biophys J. 2022 Aug 2;121(15):2840-2848. doi: 10.1016/j.bpj.2022.06.025. Epub 2022 Jun 28. PMID: 35769006

Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times. Wang F, Chan CH, Suciu V, Mustafa K, Ammend M, Si D, Hochbaum AI, Egelman EH, Bond DR. Elife. 2022 Sep 5;11:e81551. doi: 10.7554/eLife.81551. PMID: 36062910

Convergent evolution in the supercoiling of prokaryotic flagellar filaments.Kreutzberger MAB, Sonani RR, Liu J, Chatterjee S, Wang F, Sebastian AL, Biswas P, Ewing C, Zheng W, Poly F, Frankel G, Luisi BF, Calladine CR, Krupovic M, Scharf BE, Egelman EH. Cell. 2022 Sep 15;185(19):3487-3500.e14. doi:0.1016/j.cell.2022.08.009. Epub 2022 Sep 2. PMID: 36057255

Cryo-EM of Helical Polymers. Wang F, Gnewou O, Solemanifar A, Conticello VP, Egelman EH. Chem Rev. 2022 Sep 14;122(17):14055-14065. doi: 10.1021/acs.chemrev.1c00753. Epub 2022 Feb 8. PMID: 35133794 Review.

Interleukin-1 contributes to clonal expansion and progression of bone marrow fibrosis in JAK2V617F-induced myeloproliferative neoplasm. Rahman MF, Yang Y, Le BT, Dutta A, Posyniak J, Faughnan P, Sayem MA, Aguilera NS, Mohi G. Nat Commun. 2022 Sep 13;13(1):5347. doi: 10.1038/s41467-022-32928-3. PMID: 36100596

Rotavirus Infection with Systemic Dissemination in an Infant. Prasad S, Chandelia S, Tiwari MK, Angurana SK, Nallasamy K, Ratho RK, Sarkar S, Mohi GK, Vyas S. Indian J Pediatr. 2022 Oct;89(10):1056. doi: 10.1007/s12098-022-04320-y. Epub 2022 Aug 10. PMID: 35947270 No abstract available.

Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA. Hu SS, Liu L, Li Q, Ma W, Guertin MJ, Meyer CA, Deng K, Zhang T, Zang C. Nat Commun. 2022 Sep 21;13(1):5533. doi: 10.1038/s41467-022-33194-z. PMID: 36130957

Avian influenza revisited: concerns and constraints. Kanaujia R, Bora I, Ratho RK, Thakur V, Mohi GK, Thakur P. Virusdisease. 2022 Oct 28:1-10. doi: 10.1007/s13337-022-00800-z. Online ahead of print. PMID: 36320191 Free PMC article. Review.

A germline SNP in BRMS1 predisposes patients with lung adenocarcinoma to metastasis and can be ameliorated by targeting c-fos. Liu Y, Chudgar N, Mastrogiacomo B, He D, Lankadasari MB, Bapat S, Jones GD, Sanchez-Vega F, Tan KS, Schultz N, Mukherjee S, Offit K, Bao Y, Bott MJ, Rekhtman N, Adusumilli PS, Li BT, Mayo MW, Jones DR. Sci Transl Med. 2022 Oct 5;14(665):eabo1050. doi: 10.1126/scitranslmed.abo1050. Epub 2022 Oct 5. PMID: 36197962

Replicative Instability Drives Cancer Progression. Morris BB, Smith JP, Zhang Q, Jiang Z, Hampton OA, Churchman ML, Arnold SM, Owen DH, Gray JE, Dillon PM, Soliman HH, Stover DG, Colman H, Chakravarti A, Shain KH, Silva AS, Villano JL, Vogelbaum MA, Borges VF, Akerley WL, Gentzler RD, Hall RD, Matsen CB, Ulrich CM, Post AR, Nix DA, Singer EA, Larner JM, Stukenberg PT, Jones DR, Mayo MW. Biomolecules. 2022 Oct 26;12(11):1570. doi: 10.3390/biom12111570. PMID: 36358918 Free PMC article.

Aurora A phosphorylates Ndel1 to reduce the levels of Mad1 and NuMA at spindle poles. Janczyk PŁ, Żyłkiewicz E, De Hoyos H, West T, Matson DR, Choi WC, Young HMR, Derewenda ZS, Stukenberg PT. Mol Biol Cell. 2022 Nov 9:mbcE21090438. doi: 10.1091/mbc.E21-09-0438. Online ahead of print. PMID: 36350697

Generalization Performance of Quantum Metric Learning Classifiers. Kim J, Bekiranov S. Biomolecules. 2022 Oct 27;12(11):1576. doi: 10.3390/biom12111576. PMID: 36358927 Free PMC article.

Microbial nanowires: type IV pili or cytochrome filaments? Wang F, Craig L, Liu X, Rensing C, Egelman EH. Trends Microbiol. 2022 Nov 26:S0966-842X(22)00312-2. doi: 10.1016/j.tim.2022.11.004. Online ahead of print. PMID: 36446702 Review.

Opa1 and Drp1 reciprocally regulate cristae morphology, ETC function, and NAD⁺ regeneration in KRas-mutant lung adenocarcinoma. Sessions DT, Kim KB, Kashatus JA, Churchill N, Park KS, Mayo MW, Sesaki H, Kashatus DF. Cell Rep. 2022 Dec 13;41(11):111818. doi: 10.1016/j.celrep.2022.111818. PMID: 36516772

A Step Toward Personalized Surgical Decision Making: Machine Learning Predicts One Versus Numerous Melanoma Lymph Node Metastases Using RNA-Sequencing.

Meneveau MO, Vavolizza RD, Mohammad A, Kumar P, Manderfield JT, Callahan C, Lynch KT, Abbas T, Slingluff CL Jr, Bekiranov S. Ann Surg. 2022 Nov 25. doi: 10.1097/SLA.0000000000005761. Online ahead of print. PMID: 36538614

ADP-ribosyltransferases, an update on function and nomenclature. Lüscher B, Ahel I, Altmeyer M, Ashworth A, Bai P, Chang P, Cohen M, Corda D, Dantzer F, Daugherty MD, Dawson TM, Dawson VL, Deindl S, Fehr AR, Feijs KLH, Filippov DV, Gagné JP, Grimaldi G, Guettler S, Hoch NC, Hottiger MO, Korn P, Kraus WL, Ladurner A, Lehtiö L, Leung AKL, Lord CJ, Mangerich A, Matic I, Matthews J, Moldovan GL, Moss J, Natoli G, Nielsen ML, Niepel M, Nolte F, Pascal J, Paschal BM, Pawłowski K, Poirier GG, Smith S, Timinszky G, Wang ZQ, Yélamos J, Yu X, Zaja R, Ziegler M. FEBS J. 2022 Dec;289(23):7399-7410. doi: 10.1111/febs.16142. Epub 2021 Sep 13. PMID: 34323016

Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes. Triant DA, Pearson WR. Front Genet. 2022 Nov 22;13:984513. doi: 10.3389/fgene.2022.984513. eCollection 2022. PMID: 36482890

Aurora A phosphorylates Ndel1 to reduce the levels of Mad1 and NuMA at spindle poles. Janczyk PŁ, Żyłkiewicz E, De Hoyos H, West T, Matson DR, Choi WC, Young HMR, Derewenda ZS, Stukenberg PT. Mol Biol Cell. 2023 Jan 1;34(1):br1. doi: 10.1091/mbc.E21-09-0438. Epub 2022 Nov 9. PMID: 36350697

Induction of PARP7 Creates a Vulnerability for Growth Inhibition by RBN2397 in Prostate Cancer Cells. Yang C, Wierbiłowicz K, Dworak NM, Bae SY, Tengse SB, Abianeh N, Drake JM, Abbas T, Ratan A, Wotton D, Paschal BM. Cancer Res Commun. 2023 Apr 17;3(4):592-606. doi: 10.1158/2767-9764.CRC-23-0086. eCollection 2023 Apr. PMID: 37077937

Genomic mapping of metastatic organotropism in lung adenocarcinoma.Lengel HB, Mastrogiacomo B, Connolly JG, Tan KS, Liu Y, Fick CN, Dunne EG, He D, Lankadasari MB, Satravada BA, Sun Y, Kundra R, Fong C, Smith S, Riely GJ, Rudin CM, Gomez DR, Solit DB, Berger MF, Li BT, Mayo MW, Matei I, Lyden DC, Adusumilli PS, Schultz N, Sanchez-Vega F, Jones DR. Cancer Cell. 2023 Apr 8:S1535-6108(23)00091-0. doi: 10.1016/j.ccell.2023.03.018. Online ahead of print. PMID: 37084736

Patient and procedural risk factors for decline in lower-extremity motor scores following adult spinal deformity surgery. Mohanty S, Hassan FM, Lenke LG, Burton D, Daniels AH, Gupta MC, Kebaish KM, Kelly M, Kim HJ, Klineberg EO, Passias PG, Protopsaltis T, Schwab F, Shaffrey CI, Smith JS, Line BG, Lafage R, Lafage V, Bess S. J Neurosurg Spine. 2023 Apr 28:1-11. doi: 10.3171/2023.3.SPINE221311. Online ahead of print. PMID: 37119105

Incremental benefits of circumferential minimally invasive surgery for increasingly frail patients with adult spinal deformity. Passias PG, Tretiakov PS, Nunley PD, Wang MY, Park P, Kanter AS, Okonkwo DO, Eastlack RK, Mundis GM, Chou D, Agarwal N, Fessler RG, Uribe JS, Anand N, Than KD, Brusko G, Fu KM, Turner JD, Le VP, Line BG, Ames CP, Smith JS, Shaffrey CI, Hart RA, Burton D, Lafage R, Lafage V, Schwab F, Bess S, Mummaneni PV. J Neurosurg Spine. 2023 Apr 21:1-7. doi: 10.3171/2023.2.SPINE221278. Online ahead of print. PMID: 37086158

Natural history of adult spinal deformity: how do patients with suboptimal surgical outcomes fare relative to nonoperative counterparts? Passias PG, Joujon-Roche R, Mir JM, Williamson TK, Tretiakov PS, Imbo B, Krol O, Passfall L, Ahmad S, Lebovic J, Owusu-Sarpong S, Lanre-Amos T, Protopsaltis T, Lafage R, Lafage V, Park P, Chou D, Mummaneni PV, Fu KG, Than KD, Smith JS, Janjua MB, Schoenfeld AJ, Diebo BG, Vira S. J Neurosurg Spine. 2023 Apr 14:1-9. doi: 10.3171/2023.2.SPINE22559. Online ahead of print. PMID: 37060316

Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III. Dinda M, Fine RD, Saha S, Wang Z, Zang C, Li M, Smith JS. PLoS Genet. 2023 Apr 14;19(4):e1010705. doi: 10.1371/journal.pgen.1010705. eCollection 2023 Apr. PMID: 37058545

Changes in health-related quality of life measures associated with degree of proximal junctional kyphosis. Passias PG, Frangella NJ, Williamson TK, Moattari KA, Lafage R, Lafage V, Smith JS, Kebaish KM, Burton DC, Hart RA, Ames CP, Bess S, Shaffrey CI, Schwab FJ; International Spine Study Group. Spine Deform. 2023 May;11(3):699-706. doi: 10.1007/s43390-022-00607-4. Epub 2022 Dec 13. PMID: 36512314

Pelvic Nonresponse Following Treatment of Adult Spinal Deformity: Influence of Realignment Strategies on Occurrence. Passias PG, Pierce KE, Williamson TK, Krol O, Lafage R, Lafage V, Schoenfeld AJ, Protopsaltis TS, Vira S, Line B, Diebo BG, Ames CP, Kim HJ, Smith JS, Chou D, Daniels AH, Gum JL, Shaffrey CI, Burton DC, Kelly MP, Klineberg EO, Hart RA, Bess S, Schwab FJ, Gupta MC; International Spine Study Group. Spine (Phila Pa 1976). 2023 May 1;48(9):645-652. doi: 10.1097/BRS.0000000000004464. Epub 2022 Sep 14. PMID: 36102572

Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment. Cho HJ, Shu M, Bekiranov S, Zang C, Zhang A. Bioinformatics. 2023 Apr 3;39(4):btad113. doi: 10.1093/bioinformatics/btad113. PMID: 36864611

2021

The RNA helicase DHX36-G4R1 modulates C9orf72 GGGGCC hexanucleotide repeat-associated translation. Tseng YJ, Sandwith SN, Green KM, Chambers AE, Krans A, Raimer HM, Sharlow ME, Reisinger MA, Richardson AE, Routh ED, Smaldino MA, Wang YH, Vaughn JP, Todd PK, Smaldino PJ. J Biol Chem. 2021 Aug;297(2):100914. doi: 10.1016/j.jbc.2021.100914. Epub 2021 Jun 24.PMID: 34174288

MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage. Paulsen T, Malapati P, Shibata Y, Wilson B, Eki R, Benamar M, Abbas T, Dutta A. Nucleic Acids Res. 2021 Nov 18;49(20):11787-11799. doi: 10.1093/nar/gkab984. PMID: 34718766

Genomic analyses of the metastasis-derived prostate cancer cell lines LNCaP, VCaP, and PC3-AR. Sienkiewicz K, Yang C, Paschal BM, Ratan A. Prostate. 2021 Dec 24:e24290. doi: 10.1002/pros.24290. Online ahead of print. PMID: 34951700

PARP7 mono-ADP-ribosylates the agonist conformation of the androgen receptor in the nucleus. Kamata T, Yang CS, Paschal BM. Biochem J. 2021 Aug 13;478(15):2999-3014. doi: 10.1042/BCJ20210378. PMID: 34264286

A tumor suppressive long noncoding RNA, DRAIC, inhibits protein translation and induces autophagy by activating AMPK. Saha S, Zhang Y, Wilson B, Abounader R, Dutta A. J Cell Sci. 2021 Nov 8:jcs.259306. doi: 10.1242/jcs.259306. PMID: 34746949

Genetic ablation of Pim1 or pharmacologic inhibition with TP-3654 ameliorates myelofibrosis in murine models. Dutta A, Nath D, Yang Y, Le BT, Rahman MF, Faughnan P, Wang Z, Stuver M, He R, Tan W, Hutchison RE, Foulks JM, Warner SL, Zang C, Mohi G. Leukemia. 2021 Nov 5. doi: 10.1038/s41375-021-01464-2. PMID: 34741118

IGF1R and Src inhibition induce synergistic cytotoxicity in HNSCC through inhibition of FAK. Lehman CE, Spencer A, Hall S, Shaw JJP, Wulfkuhle J, Petricoin EF, Bekiranov S, Jameson MJ, Gioeli D. Sci Rep. 2021 May 24;11(1):10826. doi: 10.1038/s41598-021-90289-1. PMID: 34031486

Epigenetic condensates regulate chromatin activity and tumorigenesis. Shi B, Li W, Jiang H. Mol Cell Oncol. 2021 Nov 9;8(5):1997040. doi: 10.1080/23723556.2021.1997040. eCollection 2021. PMID: 34859151

Genetic ablation of Pim1 or pharmacologic inhibition with TP-3654 ameliorates myelofibrosis in murine models. Dutta A, Nath D, Yang Y, Le BT, Rahman MF, Faughnan P, Wang Z, Stuver M, He R, Tan W, Hutchison RE, Foulks JM, Warner SL, Zang C, Mohi G. Leukemia. 2021 Nov 5. doi: 10.1038/s41375-021-01464-2. PMID: 34741118

A patch of positively charged residues regulates the efficacy of clinical DR5 antibodies in solid tumors. Shivange G, Mondal T, Lyerly E, Bhatnagar S, Landen CN, Reddy S, Kim J, Doan B, Riddle P, Tushir-Singh J. Cell Rep. 2021 Nov 2;37(5):109953. doi: 10.1016/j.celrep.2021.109953.PMID: 34731630
Unexpected PD-L1 immune evasion mechanism in TNBC, ovarian, and other solid tumors by DR5 agonist antibodies. Mondal T, Shivange GN, Tihagam RG, Lyerly E, Battista M, Talwar D, Mosavian R, Urbanek K, Rashid NS, Harrell JC, Bos PD, Stelow EB, Stack MS, Bhatnagar S, Tushir-Singh J. EMBO Mol Med. 2021 Mar 5;13(3):e12716. doi: 10.15252/emmm.202012716. Epub 2021 Feb 15. PMID: 33587338

Deterministic chaos in the self-assembly of β sheet nanotubes from an amphipathic oligopeptide. Wang F, Gnewou O, Wang S, Osinski T, Zuo X, Egelman EH, Conticello VP. Matter. 2021 Oct 6;4(10):3217-3231. doi: 10.1016/j.matt.2021.06.037. Epub 2021 Jul 27. PMID: 34632372

Cryoelectron-Microscopic Structure of the pKpQIL Conjugative Pili from Carbapenem-Resistant Klebsiella pneumoniae. Zheng W, Pena A, Low WW, Wong JLC, Frankel G, Egelman EH. Structure. 2020 Dec 1;28(12):1321-1328.e2. doi: 10.1016/j.str.2020.08.010. Epub 2020 Sep 10. PMID: 32916103

MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage. Paulsen T, Malapati P, Shibata Y, Wilson B, Eki R, Benamar M, Abbas T, Dutta A. Nucleic Acids Res. 2021 Oct 30:gkab984. doi: 10.1093/nar/gkab984. PMID: 34718766

Post-Transcriptional Regulation of PARP7 Protein Stability Is Controlled by Androgen Signaling. Kamata T, Yang CS, Melhuish TA, Frierson HF Jr, Wotton D, Paschal BM. Cells. 2021 Feb 9;10(2):363. doi: 10.3390/cells10020363. PMID: 33572475

Genomic and evolutionary portraits of disease relapse in acute myeloid leukemia. Rapaport F, Neelamraju Y, Baslan T, Hassane D, Gruszczynska A, Robert de Massy M, Farnoud N, Haddox S, Lee T, Medina-Martinez J, Sheridan C, Thurmond A, Becker M, Bekiranov S, Carroll M, Moses Murdock H, Valk PJM, Bullinger L, D’Andrea R, Lowe SW, Neuberg D, Levine RL, Melnick A, Garrett-Bakelman FE. Leukemia. 2021 Sep;35(9):2688-2692. doi: 10.1038/s41375-021-01153-0. Epub 2021 Feb 12. PMID: 33580203

Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis. Alencar GF, Owsiany KM, Karnewar S, Sukhavasi K, Mocci G, Nguyen AT, Williams CM, Shamsuzzaman S, Mokry M, Henderson CA, Haskins R, Baylis RA, Finn AV, McNamara CA, Zunder ER, Venkata V, Pasterkamp G, Björkegren J, Bekiranov S, Owens GK. Circulation. 2020 Nov 24;142(21):2045-2059. doi: 10.1161/CIRCULATIONAHA.120.046672. Epub 2020 Jul 17. PMID: 32674599

Associations of immune cell homing gene signatures and infiltrates of lymphocyte subsets in human melanomas: discordance with CD163⁺ myeloid cell infiltrates. Kwak M, Erdag G, Leick KM, Bekiranov S, Engelhard VH, Slingluff CL. J Transl Med. 2021 Aug 28;19(1):371. doi: 10.1186/s12967-021-03044-5. PMID: 34454518

Quantum computing at the frontiers of biological sciences. Emani PS, Warrell J, Anticevic A, Bekiranov S, Gandal M, McConnell MJ, Sapiro G, Aspuru-Guzik A, Baker JT, Bastiani M, Murray JD, Sotiropoulos SN, Taylor J, Senthil G, Lehner T, Gerstein MB, Harrow AW. PMID: 33398186

Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism. Kupkova K, Shetty SJ, Haque R, Petri WA Jr, Auble DT. Clin Epigenetics. 2021 Sep 26;13(1):182. doi: 10.1186/s13148-021-01173-8. PMID: 34565452

Structure and assembly of archaeal viruses. Baquero DP, Liu Y, Wang F, Egelman EH, Prangishvili D, Krupovic M. Adv Virus Res. 2020;108:127-164. doi: 10.1016/bs.aivir.2020.09.004. Epub 2020 Oct 5. PMID: 33837715 Review.

A small-molecule screen reveals novel modulators of MeCP2 and X-chromosome inactivation maintenance. Lee HM, Kuijer MB, Ruiz Blanes N, Clark EP, Aita M, Galiano Arjona L, Kokot A, Sciaky N, Simon JM, Bhatnagar S, Philpot BD, Cerase A. J Neurodev Disord. 2020 Nov 10;12(1):29. doi: 10.1186/s11689-020-09332-3. PMID: 33172406

Special Issue: The Role of Complement in Cancer Immunotherapy. Taylor RP. Antibodies (Basel). 2021 Jul 23;10(3):29. doi: 10.3390/antib10030029. PMID: 34449550

Risk-adapted, ofatumumab-based chemoimmunotherapy and consolidation in treatment-naïve chronic lymphocytic leukemia: a phase 2 study. Desai S, Mo C, Gaglione EM, Yuan CM, Stetler-Stevenson M, Tian X, Maric I, Wake L, Farooqui MZ, Drinkwater DC, Soto S, Valdez J, Hughes TE, Nierman P, Lotter J, Marti GE, Pleyer C, Sun C, Superata J, Nichols C, Herman SEM, Lindorfer MA, Taylor RP, Wiestner A, Ahn IE. Leuk Lymphoma. 2021 Aug;62(8):1816-1827. doi: 10.1080/10428194.2021.1888379. Epub 2021 Mar 2. PMID: 33653216Clinical Trial.

U2af1 is required for survival and function of hematopoietic stem/progenitor cells. Dutta A, Yang Y, Le BT, Zhang Y, Abdel-Wahab O, Zang C, Mohi G. Leukemia. 2021 Aug;35(8):2382-2398. doi: 10.1038/s41375-020-01116-x. Epub 2021 Jan 7. PMID: 33414485

Germline Variants That Affect Tumor Progression. Chatrath A, Ratan A, Dutta A. Trends Genet. 2021 May;37(5):433-443. doi: 10.1016/j.tig.2020.10.005. Epub 2020 Nov 14. PMID: 33203571

Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes. Krupovic M, Kuhn JH, Wang F, Baquero DP, Dolja VV, Egelman EH, Prangishvili D, Koonin EV. J Virol. 2021 Jul 12;95(15):e0067321. doi: 10.1128/JVI.00673-21. Epub 2021 Jul 12. PMID: 34011550

A cell-nonautonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism. Enriquez-Hesles E, Smith DL Jr, Maqani N, Wierman MB, Sutcliffe MD, Fine RD, Kalita A, Santos SM, Muehlbauer MJ, Bain JR, Janes KA, Hartman JL 4th, Hirschey MD, Smith JS. J Biol Chem. 2021 Jan-Jun;296:100125. doi: 10.1074/jbc.RA120.015402. Epub 2020 Dec 2. PMID: 33243834

Comparative interactomes of HSF1 in stress and disease reveal a role for CTCF in HSF1-mediated gene regulation. Burchfiel ET, Vihervaara A, Guertin MJ, Gomez-Pastor R, Thiele DJ. J Biol Chem. 2021 Jan-Jun;296:100097. doi: 10.1074/jbc.RA120.015452. Epub 2020 Nov 24. PMID: 33208463

ARF-AID: A Rapidly Inducible Protein Degradation System That Preserves Basal Endogenous Protein Levels. Sathyan KM, Scott TG, Guertin MJ. Curr Protoc Mol Biol. 2020 Sep;132(1):e124. doi: 10.1002/cpmb.124. PMID: 32757370

C3(H2O) prevents rescue of complement-mediated C3 glomerulopathy in Cfh-/- Cfd-/- mice. Zhang Y, Keenan A, Dai DF, May KS, Anderson EE, Lindorfer MA, Henrich JB, Pitcher GR, Taylor RP, Smith RJ. JCI Insight. 2020 May 7;5(9):e135758. doi: 10.1172/jci.insight.135758. PMID: 32376801

A Machine Learning Model Utilizing a Novel SNP Shows Enhanced Prediction of Coronary Artery Disease Severity. Pattarabanjird T, Cress C, Nguyen A, Taylor A, Bekiranov S, McNamara C. Genes (Basel). 2020 Dec 1;11(12):1446. doi: 10.3390/genes11121446. PMID: 33271747

tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model. Su Z, Frost EL, Lammert CR, Przanowska RK, Lukens JR, Dutta A. RNA Biol. 2020 Aug;17(8):1183-1195. doi: 10.1080/15476286.2020.1721047. Epub 2020 Jan 31. PMID: 31983265

PARP7 mono-ADP-ribosylates the Agonist Conformation of the Androgen Receptor in the Nucleus. Kamata T, Yang CS, Paschal BM. Biochem J. 2021 Jul 15:BCJ20210378. doi: 10.1042/BCJ20210378. Online ahead of print. PMID: 34264286

COCOA: coordinate covariation analysis of epigenetic heterogeneity. Lawson JT, Smith JP, Bekiranov S, Garrett-Bakelman FE, Sheffield NC. Genome Biol. 2020 Sep 7;21(1):240. doi: 10.1186/s13059-020-02139-4. PMID: 32894181

Upregulation of human endogenous retrovirus-K (HML-2) mRNAs in hepatoblastoma: Identification of potential new immunotherapeutic targets and biomarkers. Grabski DF, Ratan A, Gray LR, Bekiranov S, Rekosh D, Hammarskjold ML, Rasmussen SK. J Pediatr Surg. 2021 Feb;56(2):286-292. doi: 10.1016/j.jpedsurg.2020.05.022. Epub 2020 May 27. PMID: 32682541

A Condensed View of the Chromosome Passenger Complex. Trivedi P, Stukenberg PT. Trends Cell Biol. 2020 Sep;30(9):676-687. doi: 10.1016/j.tcb.2020.06.005. Epub 2020 Jul 17. PMID: 32684321 Review.

The RNA helicase DHX36/G4R1 modulates C9orf72 GGGGCC hexanucleotide repeat- associated translation. Tseng YJ, Sandwith SN, Green KM, Chambers AE, Krans A, Raimer HM, Sharlow ME, Reisinger MA, Richardson AE, Routh ED, Smaldino MA, Wang YH, Vaughn JP, Todd PK, Smaldino PJ. J Biol Chem. 2021 Jun 23:100914. doi: 10.1016/j.jbc.2021.100914. PMID: 34174288

CDK6 is a therapeutic target in myelofibrosis. Dutta A, Nath D, Yang Y, Le BT, Mohi G. Cancer Res. 2021 Jun 18:canres.0590.2021. doi: 10.1158/0008-5472.CAN-21-0590. PMID: 34145036

ATAC-Seq-based Identification of Extrachromosomal Circular DNA in Mammalian Cells and Its Validation Using Inverse PCR and FISH. Su Z, Saha S, Paulsen T, Kumar P, Dutta A. Bio Protoc. 2021 May 5;11(9):e4003. doi: 10.21769/BioProtoc.4003. eCollection 2021 May 5. PMID: 34124304

Noncanonical Roles of tRNAs: tRNA Fragments and Beyond. Su Z, Wilson B, Kumar P, Dutta A. Annu Rev Genet. 2020 Nov 23;54:47-69. doi: 10.1146/annurev-genet-022620-101840. Epub 2020 Aug 25. PMID: 32841070.

A Functional Variant on 9p21.3 Related to Glioma Risk Affects Enhancer Activity and Modulates Expression of CDKN2B-AS1. Ali MW, Patro CPK, Devall M, Dampier CH, Plummer SJ, Kuscu C, Adli M, Lai RK, Casey G. Hum Mutat. 2021 Jun 21. doi: 10.1002/humu.24244. PMID: 34153138

Mutation of complement factor B causing massive fluid-phase dysregulation of the alternative complement pathway can result in atypical hemolytic uremic syndrome. Zhang Y, Kremsdorf RA, Sperati CJ, Henriksen KJ, Mori M, Goodfellow RX, Pitcher GR, Benson CL, Borsa NG, Taylor RP, Nester CM, Smith RJH. Kidney Int. 2020 Nov;98(5):1265-1274. doi: 10.1016/j.kint.2020.05.028. Epub 2020 Jun 12. PMID: 32540405

Adnaviria: a new realm for archaeal filamentous viruses with linear A-form double-stranded DNA genomes. Krupovic M, Kuhn JH, Wang F, Baquero DP, Dolja VV, Egelman EH, Prangishvili D, Koonin EV. J Virol. 2021 May 19:JVI.00673-21. doi: 10.1128/JVI.00673-21. PMID: 34011550

Distinct axial and lateral interactions within homologous filaments dictate the signaling specificity and order of the AIM2-ASC inflammasome. Matyszewski M, Zheng W, Lueck J, Mazanek Z, Mohideen N, Lau AY, Egelman EH, Sohn J. Nat Commun. 2021 May 12;12(1):2735. doi: 10.1038/s41467-021-23045-8. PMID: 33980849

Cryoelectron-microscopy structure of the enteropathogenic Escherichia coli type III secretion system EspA filament. Zheng W, Peña A, Ilangovan A, Clark JN, Frankel G, Egelman EH, Costa TRD. Proc Natl Acad Sci U S A. 2021 Jan 12;118(2):e2022826118. doi: 10.1073/pnas.2022826118. PMID: 33397726

Structural Determination of a Filamentous Chaperone to Fabricate Electronically Conductive Metalloprotein Nanowires. Chen YX, Ing NL, Wang F, Xu D, Sloan NB, Lam NT, Winter DL, Egelman EH, Hochbaum AI, Clark DS, Glover DJ. ACS Nano. 2020 Jun 23;14(6):6559-6569. doi: 10.1021/acsnano.9b09405. Epub 2020 May 7. PMID: 32347705

Single-cell sequencing of the small and AT-skewed genome of malaria parasites. Liu S, Huckaby AC, Brown AC, Moore CC, Burbulis I, McConnell MJ, Güler JL. Genome Med. 2021 May 4;13(1):75. doi: 10.1186/s13073-021-00889-9. PMID: 33947449

Altering mammalian transcription networking with ADAADi: An inhibitor of ATP-dependent chromatin remodeling. Rakesh R, Chanana UB, Hussain S, Sharma S, Goel K, Bisht D, Patne K, Swer PB, Hockensmith JW, Muthuswami R. PLoS One. 2021 May 17;16(5):e0251354. doi: 10.1371/journal.pone.0251354. eCollection 2021. PMID: 33999958

Androgen signaling uses a writer and a reader of ADP-ribosylation to regulate protein complex assembly. Yang CS, Jividen K, Kamata T, Dworak N, Oostdyk L, Remlein B, Pourfarjam Y, Kim IK, Du KP, Abbas T, Sherman NE, Wotton D, Paschal BM. Nat Commun. 2021 May 11;12(1):2705. doi: 10.1038/s41467-021-23055-6. PMID: 33976187

High nuclear TPX2 expression correlates with TP53 mutation and poor clinical behavior in a large breast cancer cohort, but is not an independent predictor of chromosomal instability. Matson DR, Denu RA, Zasadil LM, Burkard ME, Weaver BA, Flynn C, Stukenberg PT. BMC Cancer. 2021 Feb 23;21(1):186. doi: 10.1186/s12885-021-07893-7. PMID: 33622270

DuoHexaBody-CD37^®, a novel biparatopic CD37 antibody with enhanced Fc-mediated hexamerization as a potential therapy for B-cell malignancies. Oostindie SC, van der Horst HJ, Kil LP, Strumane K, Overdijk MB, van den Brink EN, van den Brakel JHN, Rademaker HJ, van Kessel B, van den Noort J, Chamuleau MED, Mutis T, Lindorfer MA, Taylor RP, Schuurman J, Parren PWHI, Beurskens FJ, Breij ECW.Blood Cancer J. 2020 Apr 28;10(3):30. doi: 10.1038/s41408-020-0292-7. PMID: 32341336

A human cancer cell line initiates DNA replication normally in the absence of ORC5 and ORC2 proteins. Shibata E, Dutta A. J Biol Chem. 2020 Dec 11;295(50):16949-16959. doi: 10.1074/jbc.RA120.015450. Epub 2020 Sep 28. PMID: 32989049

Risk-adapted, ofatumumab-based chemoimmunotherapy and consolidation in treatment-naïve chronic lymphocytic leukemia: a phase 2 study. Desai S, Mo C, Gaglione EM, Yuan CM, Stetler-Stevenson M, Tian X, Maric I, Wake L, Farooqui MZ, Drinkwater DC, Soto S, Valdez J, Hughes TE, Nierman P, Lotter J, Marti GE, Pleyer C, Sun C, Superata J, Nichols C, Herman SEM, Lindorfer MA, Taylor RP, Wiestner A, Ahn IE. Leuk Lymphoma. 2021 Mar 2:1-17. doi: 10.1080/10428194.2021.1888379. PMID: 33653216

Cryo-EM is a powerful tool, but helical applications can have pitfalls. Egelman EH , Wang F .Soft Matter. 2021 Mar 28;17(12):3291-3293. doi: 10.1039/d1sm00282a. Epub 2021 Mar 17. PMID: 33729271

Germline variants predictive of tumor mutational burden and immune checkpoint inhibitor efficacy. Chatrath A, Ratan A, Dutta A. iScience. 2021 Mar 4;24(3):102248. doi: 10.1016/j.isci.2021.102248. eCollection 2021 Mar 19. PMID: 33786423

What Is Extrachromosomal Circular DNA and What Does It Do? Chiu RWK, Dutta A, Hensson AG, Lo YMD, Mischel P, Regenberg B. Clin Chem. 2020 Jun 1;66(6):754-759. doi: 10.1093/clinchem/hvaa096. PMID: 32470125

Gut microbiome communication with bone marrow regulates susceptibility to amebiasis. Burgess SL, Leslie JL, Uddin J, Oakland DN, Gilchrist C, Moreau GB, Watanabe K, Saleh M, Simpson M, Thompson BA, Auble DT, Turner SD, Giallourou N, Swann J, Pu Z, Ma JZ, Haque R, Petri WA Jr. J Clin Invest. 2020 Aug 3;130(8):4019-4024. doi: 10.1172/JCI133605. PMID: 32369444

NOTCH1-driven UBR7 stimulates nucleotide biosynthesis to promote T cell acute lymphoblastic leukemia. Srivastava S, Sahu U, Zhou Y, Hogan AK, Sathyan KM, Bodner J, Huang J, Wong KA, Khalatyan N, Savas JN, Ntziachristos P, Ben-Sahra I, Foltz DR. Sci Adv. 2021 Jan 27;7(5):eabc9781. doi: 10.1126/sciadv.abc9781. Print 2021 Jan. PMID: 33571115

Genomic and evolutionary portraits of disease relapse in acute myeloid leukemia. Rapaport F, Neelamraju Y, Baslan T, Hassane D, Gruszczynska A, Robert de Massy M, Farnoud N, Haddox S, Lee T, Medina-Martinez J, Sheridan C, Thurmond A, Becker M, Bekiranov S, Carroll M, Moses Murdock H, Valk PJM, Bullinger L, D’Andrea R, Lowe SW, Neuberg D, Levine RL, Melnick A, Garrett-Bakelman FE. Leukemia. 2021 Feb 12. doi: 10.1038/s41375-021-01153-0. PMID: 33580203

Oncogenic TRIM37 Links Chemoresistance and Metastatic Fate in Triple-Negative Breast Cancer. Przanowski P, Lou S, Tihagam RD, Mondal T, Conlan C, Shivange G, Saltani I, Singh C, Xing K, Morris BB, Mayo MW, Teixeira L, Lehmann-Che J, Tushir-Singh J, Bhatnagar S. Cancer Res. 2020 Nov 1;80(21):4791-4804. doi: 10.1158/0008-5472.CAN-20-1459. Epub 2020 Aug 27. PMID: 32855208

The Underlying Tumor Genomics of Predominant Histologic Subtypes in Lung Adenocarcinoma. Caso R, Sanchez-Vega F, Tan KS, Mastrogiacomo B, Zhou J, Jones GD, Nguyen B, Schultz N, Connolly JG, Brandt WS, Bott MJ, Rocco G, Molena D, Isbell JM, Liu Y, Mayo MW, Adusumilli PS, Travis WD, Jones DR. J Thorac Oncol. 2020 Dec;15(12):1844-1856. doi: 10.1016/j.jtho.2020.08.005. Epub 2020 Aug 10. PMID: 32791233

Effects of working posture and roof slope on activation of lower limb muscles during shingle installation. Dutta A, Breloff SP, Dai F, Sinsel EW, Warren CM, Carey RE, Wu JZ. Ergonomics. 2020 Sep;63(9):1182-1193. doi: 10.

MYBL2-Driven Transcriptional Programs Link Replication Stress and Error-prone DNA Repair With Genomic Instability in Lung Adenocarcinoma. Morris BB, Wages NA, Grant PA, Stukenberg PT, Gentzler RD, Hall RD, Akerley WL, Varghese TK, Arnold SM, Williams TM, Coppola V, Jones DR, Auble DT, Mayo MW. Front Oncol. 2021 Jan 8;10:585551. doi: 10.3389/fonc.2020.585551. eCollection 2020. PMID: 33489883

A cell-nonautonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism. Enriquez-Hesles E, Smith DL Jr, Maqani N, Wierman MB, Sutcliffe MD, Fine RD, Kalita A, Santos SM, Muehlbauer MJ, Bain JR, Janes KA, Hartman JL 4th, Hirschey MD, Smith JS. J Biol Chem. 2020 Dec 2;296:100125. doi: 10.1074/jbc.RA120.015402. Online ahead of print. PMID: 33460918

Targeted CRISPR screening identifies PRMT5 as synthetic lethality combinatorial target with gemcitabine in pancreatic cancer cells. Wei X, Yang J, Adair SJ, Ozturk H, Kuscu C, Lee KY, Kane WJ, O’Hara PE, Liu D, Demirlenk YM, Habieb AH, Yilmaz E, Dutta A, Bauer TW, Adli M. Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28068-28079. doi: 10.1073/pnas.2009899117. Epub 2020 Oct 23.PMID: 33097661

Chk1 promotes non-homologous end joining in G1 through direct phosphorylation of ASF1A. Lee KY, Dutta A. Cell Rep. 2021 Jan 26;34(4):108680. doi: 10.1016/j.celrep.2020.108680. PMID: 33503415

U2af1 is required for survival and function of hematopoietic stem/progenitor cells. Dutta A, Yang Y, Le BT, Zhang Y, Abdel-Wahab O, Zang C, Mohi G. Leukemia. 2021 Jan 7. doi: 10.1038/s41375-020-01116-x. Online ahead of print. PMID: 33414485

miR-206 family is important for mitochondrial and muscle function, but not essential for myogenesis in vitro. Przanowska RK, Sobierajska E, Su Z, Jensen K, Przanowski P, Nagdas S, Kashatus JA, Kashatus DF, Bhatnagar S, Lukens JR, Dutta A. FASEB J. 2020 Jun;34(6):7687-7702. doi: 10.1096/fj.201902855RR. Epub 2020 Apr 11. PMID: 32277852

The pan-cancer landscape of prognostic germline variants in 10,582 patients. Chatrath A, Przanowska R, Kiran S, Su Z, Saha S, Wilson B, Tsunematsu T, Ahn JH, Lee KY, Paulsen T, Sobierajska E, Kiran M, Tang X, Li T, Kumar P, Ratan A, Dutta A. Genome Med. 2020 Feb 17;12(1):15. doi: 10.1186/s13073-020-0718-7. PMID: 32066500

Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials. Wang F, Gnewou O, Modlin C, Beltran LC, Xu C, Su Z, Juneja P, Grigoryan G, Egelman EH, Conticello VP. Nat Commun. 2021 Jan 18;12(1):407. doi: 10.1038/s41467-020-20689-w. PMID: 33462223

2020

Label-Free Quantification of Cell Cycle Synchronicity of Human Neural Progenitor Cells Based on Electrophysiology Phenotypes. Honrado C, Michel N, Moore JH, Salahi A, Porterfield V, McConnell MJ, Swami NS. ACS Sens. 2020 Dec 16. doi: 10.1021/acssensors.0c02022. PMID: 33325234

An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding. Oostdyk LT, Wang Z, Zang C, Li H, McConnell MJ, Paschal BM. Sci Rep. 2020 Mar 16;10(1):4844. doi: 10.1038/s41598-020-61369-5. PMID: 32179771

Role of SPTSSB-Regulated de Novo Sphingolipid Synthesis in Prostate Cancer Depends on Androgen Receptor Signaling. Costa-Pinheiro P, Heher A, Raymond MH, Jividen K, Shaw JJ, Paschal BM, Walker SJ, Fox TE, Kester M. iScience. 2020 Nov 23;23(12):101855. doi: 10.1016/j.isci.2020.101855. eCollection 2020 Dec 18. PMID: 33313495

A Genomic-Pathologic Annotated Risk Model to Predict Recurrence in Early-Stage Lung Adenocarcinoma. Jones GD, Brandt WS, Shen R, Sanchez-Vega F, Tan KS, Martin A, Zhou J, Berger M, Solit DB, Schultz N, Rizvi H, Liu Y, Adamski A, Chaft JE, Riely GJ, Rocco G, Bott MJ, Molena D, Ladanyi M, Travis WD, Rekhtman N, Park BJ, Adusumilli PS, Lyden D, Imielinski M, Mayo MW, Li BT, Jones DR. JAMA Surg. 2020 Dec 23:e205601. doi: 10.1001/jamasurg.2020.5601. PMID: 33355651

Pausing sites of RNA polymerase II on actively transcribed genes are enriched in DNA double-stranded breaks. Singh S, Szlachta K, Manukyan A, Raimer HM, Dinda M, Bekiranov S, Wang YH. J Biol Chem. 2020 Mar 20;295(12):3990-4000. doi: 10.1074/jbc.RA119.011665. Epub 2020 Feb 6. PMID: 32029477

Molecular imaging of prostate cancer targeting CD46 using immunoPET. Wang S, Li J, Hua J, Su Y, Beckford Vera DR, Zhao W, Jayaraman M, Huynh TL, Zhao N, Wang YH, Huang Y, Qin F, Shen S, Gioeli D, Dreicer R, Sriram R, Egusa EA, Chou J, Feng FY, Aggarwal R, Evans MJ, Seo Y, Liu B, Flavell RR, He J. Clin Cancer Res. 2020 Dec 8:clincanres.3310.2020. doi: 10.1158/1078-0432.CCR-20-3310 PMID: 33293372

Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R. Anderson WD, Duarte FM, Civelek M, Guertin MJ. Bioinformatics. 2020 May 1;36(9):2926-2928. doi: 10.1093/bioinformatics/btaa011. PMID: 31917388

Targeted CRISPR screening identifies PRMT5 as synthetic lethality combinatorial target with gemcitabine in pancreatic cancer cells. Wei X, Yang J, Adair SJ, Ozturk H, Kuscu C, Lee KY, Kane WJ, O’Hara PE, Liu D, Demirlenk YM, Habieb AH, Yilmaz E, Dutta A, Bauer TW, Adli M. Proc Natl Acad Sci U S A. 2020 Oct 23:202009899. doi: 10.1073/pnas.2009899117. PMID: 33097661

The inositol pyrophosphate 5-InsP₇ drives sodium-potassium pump degradation by relieving an autoinhibitory domain of PI3K p85α. Chin AC, Gao Z, Riley AM, Furkert D, Wittwer C, Dutta A, Rojas T, Semenza ER, Felder RA, Pluznick JL, Jessen HJ, Fiedler D, Potter BVL, Snyder SH, Fu C. Sci Adv. 2020 Oct 28;6(44):eabb8542. doi: 10.1126/sciadv.abb8542. Print 2020 Oct. PMID: 33115740

Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments. Wang F, Baquero DP, Beltran LC, Su Z, Osinski T, Zheng W, Prangishvili D, Krupovic M, Egelman EH. Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):19643-19652. doi: 10.1073/pnas.2011125117. Epub 2020 Aug 5. PMID: 32759221

Cryo-EM: Ice Is Nice, but Good Ice Can Be Hard to Find. Egelman EH.Biophys

A three-dimensional dementia model reveals spontaneous cell cycle re-entry and a senescence-associated secretory phenotype. Porterfield V, Khan SS, Foff EP, Koseoglu MM, Blanco IK, Jayaraman S, Lien E, McConnell MJ, Bloom GS, Lazo JS, Sharlow ER. Neurobiol Aging. 2020 Jun;90:125-134. doi: 10.1016/j.neurobiolaging.2020.02.011. Epub 2020 Feb 19. PMID: 32184029 J. 2020 Mar 24;118(6):1238-1239. doi: 10.1016/j.bpj.2020.01.026. Epub 2020 Feb 1. PMID: 32061273No abstract available.

The Role of Complement in the Mechanism of Action of Therapeutic Anti-Cancer mAbs. Golay J, Taylor RP. Antibodies (Basel). 2020 Oct 28;9(4):E58. doi: 10.3390/antib9040058. PMID: 33126570Review.

A human cancer cell line initiates DNA replication normally in the absence of ORC5 and ORC2 proteins. Shibata E, Dutta A. J Biol Chem. 2020 Sep 28:jbc.RA120.015450. doi: 10.1074/jbc.RA120.015450. PMID: 32989049

Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation. Saha S, Kiran M, Kuscu C, Chatrath A, Wotton D, Mayo MW, Dutta A. Cancer Res. 2020 Mar 1;80(5):950-963. doi: 10.1158/0008-5472.CAN-19-3460. Epub 2020 Jan 3. PMID: 31900260

Antitumor effect of insulin-like growth factor-1 receptor inhibition in head and neck squamous cell carcinoma. Lehman CE, Khalil AA, Axelrod MJ, Dougherty MI, Schoeff SS, Taniguchi LE, Mendez RE, David AP, McGarey PO Jr,, Hubbard MA, Donaldson L, Frierson HF Jr,, Stelow EB, Bekiranov S, Wulfkuhle JD, Petricoin EF, Gioeli DG, Jameson MJ. Laryngoscope. 2020 Jun;130(6):1470-1478. doi: 10.1002/lary.28236. Epub 2019 Aug 21. PMID: 31433065

Topoisomerase II contributes to DNA secondary structure-mediated double-stranded breaks. Szlachta K, Manukyan A, Raimer HM, Singh S, Salamon A, Guo W, Lobachev KS, Wang YH. Nucleic Acids Res. 2020 Jul 9;48(12):6654-6671. doi: 10.1093/nar/gkaa483. PMID: 32501506

Cryoelectron-Microscopic Structure of the pKpQIL Conjugative Pili from Carbapenem-Resistant Klebsiella pneumoniae. Zheng W, Pena A, Low WW, Wong JLC, Frankel G, Egelman EH. Structure. 2020 Sep 8:S0969-2126(20)30292-6. doi: 10.1016/j.str.2020.08.010. PMID: 32916103

Atomic structure of the Campylobacter jejuni flagellar filament reveals how ε Proteobacteria escaped Toll-like receptor 5 surveillance. Kreutzberger MAB, Ewing C, Poly F, Wang F, Egelman EH. Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):16985-16991. doi: 10.1073/pnas.2010996117. Epub 2020 Jul 8.PMID: 32641510

How Do mAbs Make Use of Complement to Kill Cancer Cells? The Role of Ca². Taylor RP, Lindorfer MA. Antibodies (Basel). 2020 Sep 4;9(3):E45. doi: 10.3390/antib9030045. PMID: 32899722.

Oncogenic TRIM37 links chemoresistance and metastatic fate in triple-negative breast cancer. Przanowski P, Lou S, Tihagam RD, Mondal T, Conlan C, Shivange G, Saltani I, Singh C, Xing K, Morris BB, Mayo MW, Teixeira L, Lehmann-Che J, Tushir-Singh J, Bhatnagar S.Cancer Res. 2020 Aug 27:canres.1459.2020. doi: 10.1158/0008-5472.CAN-20-1459. PMID: 32855208

Implementation of a Hamming distance-like genomic quantum classifier using inner products on ibmqx2 and ibmq_16_melbourne. Kathuria K, Ratan A, McConnell M, Bekiranov S. Quantum Mach Intell. 2020;2(1):1-26. doi: 10.1007/s42484-020-00017-7. Epub 2020 Jul 17. PMID: 32879908

The Novel ReNu Region of TAF12 Regulates Gcn5 Nucleosomal Acetylation. Torok MS, Pray-Grant MG, Grant BM, Josephs ME, Grant PA. J Mol Genet (Isleworth). 2019Nov;2(1):https://researchopenworld.com/wp content/uploads/2019/07/JMG-2019-105-Patrick-Grant-USA.pdf. Epub 2019 Jun 10. PMID: 32832935

Clearance of amyloid-beta with bispecific antibody constructs bound to erythrocytes. Taylor RP, Lindorfer MA, Atkinson JP. Alzheimers Dement (N Y). 2020 Aug 27;6(1):e12067. doi: 10.1002/trc2.12067. eCollection 2020. PMID: 32885023

Oncogenic TRIM37 links chemoresistance and metastatic fate in triple-negative breast cancer. Przanowski P, Lou S, Tihagam RD, Mondal T, Conlan C, Shivange G, Saltani I, Singh C, Xing K, Morris BB, Mayo MW, Teixeira L, Lehmann-Che J, Tushir-Singh J, Bhatnagar S. Cancer Res. 2020 Aug 27:canres.1459.2020. doi: 10.1158/0008-5472.CAN-20-1459. Online ahead of print. PMID: 32855208

The Underlying Tumor Genomics of Predominant Histologic Subtypes in Lung Adenocarcinoma. Caso R, Sanchez-Vega F, Tan KS, Mastrogiacomo B, Zhou J, Jones GD, Nguyen B, Schultz N, Connolly JG, Brandt WS, Bott MJ, Rocco G, Molena D, Isbell JM, Liu Y, Mayo MW, Adusumilli PS, Travis WD, Jones DR. J Thorac Oncol. 2020 Aug 10:S1556-0864(20)30636-5. doi: 10.1016/j.jtho.2020.08.005. Online ahead of print. PMID: 32791233

Artificial Intracellular Filaments. Feng Z, Wang H, Wang F, Oh Y, Berciu C, Cui Q, Egelman EH, Xu B.Cell Rep Phys Sci. 2020 Jul 22;1(7):100085. doi: 10.1016/j.xcrp.2020.100085. Epub 2020 Jul 1. PMID: 32776017

The structures of two archaeal type IV pili illuminate evolutionary relationships. Wang F, Baquero DP, Su Z, Beltran LC, Prangishvili D, Krupovic M, Egelman EH. Nat Commun. 2020 Jul 9;11(1):3424. doi: 10.1038/s41467-020-17268-4. PMID: 32647180

Noncanonical Roles of tRNAs: tRNA Fragments and Beyond. Su Z, Wilson B, Kumar P, Dutta A. Annu Rev Genet. 2020 Aug 25. doi: 10.1146/annurev-genet-022620-101840. Online ahead of print. PMID: 32841070

Imaging Flow Cytometry Quantifies Neural Genome Dynamics. Michel N, Majumdar UB, Lannigan J, McConnell MJ. Cytometry A. 2019 Aug;95(8):825-835. doi: 10.1002/cyto.a.23783. Epub 2019 May 7. PMID: 31063256

CD20 and CD37 antibodies synergize to activate complement by Fc-mediated clustering. Oostindie SC van der Horst HJ, Lindorfer MA, Cook EM, Tupitza JC, Zent CS, Burack R, VanDerMeid KR, Strumane K, Chamuleau MED, Mutis T, de Jong RN, Schuurman J, Breij ECW, Beurskens FJ, Parren PWHI, Taylor RP. Haematologica. 2019 Sep;104(9):1841-1852. doi: 10.3324/haematol.2018.207266. Epub 2019 Feb 21. PMID: 30792198

The structure of helical lipoprotein lipase reveals an unexpected twist in lipase storage. Gunn KH, Roberts BS, Wang F, Strauss JD, Borgnia MJ, Egelman EH, Neher SB. Proc Natl Acad Sci U S A. 2020 May 12;117(19):10254-10264. doi: 10.1073/pnas.1916555117. Epub 2020 Apr 24. PMID: 32332168

Characterization of the Importin-β binding domain in nuclear import receptor KPNA7. Oostdyk LT, McConnell MJ, Paschal BM. Biochem J. 2019 Nov 15;476(21):3413-3434. doi: 10.1042/BCJ20190717. PMID: 31642884

A Condensed View of the Chromosome Passenger Complex. Trivedi P, Stukenberg PT. Trends Cell Biol.2020 Jul 16:S0962-8924(20)30123-9. doi: 10.1016/j.tcb.2020.06.005. Online ahead of print. PMID: 32684321 Review.

Upregulation of human endogenous retrovirus-K (HML-2) mRNAs in hepatoblastoma: Identification of potential new immunotherapeutic targets and biomarkers. Grabski DF, Ratan A, Gray LR, Bekiranov S, Rekosh D, Hammarskjold ML, Rasmussen SK. J Pediatr Surg. 2020 May 27:S0022-3468(20)30353-5. doi: 10.1016/j.jpedsurg.2020.05.022. Online ahead of print. PMID: 32682541

The Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis. Alencar GF, Owsiany KM, K S, Sukhavasi K, Mocci G, Nguyen A, Williams CM, Shamsuzzaman S, Mokry M, Henderson CA, Haskins R, Baylis RA, Finn AV, McNamara CA, Zunder ER, Venkata V, Pasterkamp G, Björkegren J, Bekiranov S, Owens GK. Circulation. 2020 Jul 17. doi: 10.1161/CIRCULATIONAHA.120.046672. Online ahead of print. PMID: 32674599

Human endogenous retrovirus-K mRNA expression and genomic alignment data in hepatoblastoma. Grabski DF, Ratan A, Gray LR, Bekiranov S, Rekosh D, Hammarskjold ML, Rasmussen SK. Data Brief. 2020 Jun 18;31:105895. doi: 10.1016/j.dib.2020.105895. eCollection 2020 Aug. PMID: 32637500

Deletion of Topoisomerase 1 in excitatory neurons causes genomic instability and early onset neurodegeneration. Fragola G, Mabb AM, Taylor-Blake B, Niehaus JK, Chronister WD, Mao H, Simon JM, Yuan H, Li Z, McConnell MJ, Zylka MJ. Nat Commun. 2020 Apr 23;11(1):1962. doi: 10.1038/s41467-020-15794-9. PMID: 32327659

Mutation of complement factor B causing massive fluid-phase dysregulation of the alternative complement pathway can result in atypical hemolytic uremic syndrome. Zhang Y, Kremsdorf R, Sperati CJ, Henriksen KJ, Mori M, Goodfellow RX, Pitcher GR, Benson C, Borsa NG, Taylor RP, Nester CM, Smith RJ. Kidney Int. 2020 Jun 12. pii: S0085-2538(20)30637-2. doi: 10.1016/j.kint.2020.05.028. PMID: 32540405

Osteogenesis imperfecta mutations in plastin 3 lead to impaired calcium regulation of actin bundling. Schwebach CL, Kudryashova E, Zheng W, Orchard M, Smith H, Runyan LA, Egelman EH, Kudryashov DS. Bone Res. 2020 May 22;8:21. doi: 10.1038/s41413-020-0095-2. eCollection 2020. PMID: 32509377

Angiogenin generates specific stress-induced tRNA halves and is not involved in tRF-3-mediated gene silencing. Su Z, Kuscu C, Malik A, Shibata E, Dutta A. J Biol Chem. 2019 Nov 8;294(45):16930-16941. doi: 10.1074/jbc.RA119.009272. Epub 2019 Oct 3. PMID: 31582561

Mapping and Making Sense of Noncoding Mutations in the Genome. Yang J, Adli M. Cancer Res. 2019 Sep 1;79(17):4309-4314. doi: 10.1158/0008-5472.CAN-19-0905. Epub 2019 Aug 6. Review. PMID: 31387922

Topoisomerase II contributes to DNA secondary structure-mediated double-stranded breaks. Szlachta K, Manukyan A, Raimer HM, Singh S, Salamon A, Guo W, Lobachev KS, Wang YH. Nucleic Acids Res. 2020 Jun 5. pii: gkaa483. doi: 10.1093/nar/gkaa483. PMID: 32501506

CNCC: an analysis tool to determine genome-wide DNA break end structure at single-nucleotide resolution. Szlachta K, Raimer HM, Comeau LD, Wang YH. BMC Genomics. 2020 Jan 8;21(1):25. doi: 10.1186/s12864-019-6436-0. PMID: 31914926

Corticosteroids to prevent kidney scarring in children with a febrile urinary tract infection: a randomized trial. Shaikh N, Shope TR, Hoberman A, Muniz GB, Bhatnagar S, Nowalk A, Hickey RW, Michaels MG, Kearney D, Rockette HE, Charron M, Lim R, Majd M, Shalaby-Rana E, Kurs-Lasky M, Cohen DM, Wald ER, Lockhart G, Pohl HG, Martin JM. Pediatr Nephrol. 2020 Jun 15. doi: 10.1007/s00467-020-04622-3. PMID: 32556960

The Biology and Application Areas of CRISPR Technologies. Adli M. J Mol Biol. 2019 Jan 4;431(1):1-2. doi: 10.1016/j.jmb.2018.11.012. Epub 2018 Nov 14. No abstract available. PMID: 30447221

Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells.Kuscu C, Mammadov R, Czikora A, Unlu H, Tufan T, Fischer NL, Arslan S, Bekiranov S, Kanemaki M, Adli M. J Mol Biol. 2019 Jan 4;431(1):111-121. doi: 10.1016/j.jmb.2018.08.001. Epub 2018 Aug 9. PMID: 30098338

CRISPR Ethics: Moral Considerations for Applications of a Powerful Tool. Brokowski C, Adli M. J Mol Biol. 2019 Jan 4;431(1):88-101. doi: 10.1016/j.jmb.2018.05.044. Epub 2018 Jun 7. Review. PMID: 29885329

Neurons with Complex Karyotypes Are Rare in Aged Human Neocortex. Chronister WD, Burbulis IE, Wierman MB, Wolpert MJ, Haakenson MF, Smith ACB, Kleinman JE, Hyde TM, Weinberger DR, Bekiranov S, McConnell MJ. Cell Rep. 2019 Jan 22;26(4):825-835.e7. doi: 10.1016/j.celrep.2018.12.107. PMID: 30673605

An epilepsy-associated mutation in the nuclear import receptor KPNA7 reduces nuclear localization signal binding. Oostdyk LT, Wang Z, Zang C, Li H, McConnell MJ, Paschal BM Sci Rep. 2020 Mar 16;10(1):4844. doi: 10.1038/s41598-020-61369-5. PMID: 32179771

A nuclear lamina-chromatin-Ran GTPase axis modulates nuclear import and DNA damage signaling. Dworak N, Makosa D, Chatterjee M, Jividen K, Yang CS, Snow C, Simke WC, Johnson IG, Kelley JB, Paschal BM. Aging Cell. 2019 Feb;18(1):e12851. doi: 10.1111/acel.12851. Epub 2018 Dec 19. PMID: 30565836

A three-dimensional dementia model reveals spontaneous cell cycle re-entry and a senescence-associated secretory phenotype. Porterfield V, Khan SS, Foff EP, Koseoglu MM, Blanco IK, Jayaraman S, Lien E, McConnell MJ, Bloom GS, Lazo JS, Sharlow ER. Neurobiol Aging. 2020 Feb 19. pii: S0197-4580(20)30038-5. doi: 10.1016/j.neurobiolaging.2020.02.011. PMID: 32184029

A deletion in Eml1 leads to bilateral subcortical heterotopia in the tish rat. Grosenbaugh DK, Joshi S, Fitzgerald MP, Lee KS, Wagley PK, Koeppel AF, Turner SD, McConnell MJ, Goodkin HP. Neurobiol Dis. 2020 Mar 13:104836. doi: 10.1016/j.nbd.2020.104836. PMID: 32179177

Ant-icipating Change: An Epigenetic Switch in Reprogramming the Social Lives of Ants. Pray-Grant MG, Grant PA. Mol Cell. 2020 Jan 16;77(2):205-206. doi: 10.1016/j.molcel.2019.12.006. PMID: 31951544

Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs. Hughes SA, Wang F, Wang S, Kreutzberger MAB, Osinski T, Orlova A, Wall JS, Zuo X, Egelman EH, Conticello VP. Proc Natl Acad Sci U S A. 2019 Jul 16;116(29):14456-14464. doi: 10.1073/pnas.1903910116. Epub 2019 Jul 1. PMID: 31262809

A Non-random Mouse Model for Pharmacological Reactivation of Mecp2 on the Inactive X Chromosome.Przanowski P, Zheng Z, Wasko U, Bhatnagar S. J Vis Exp. 2019 May 22;(147). doi: 10.3791/59449. PMID: 31180354

Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction. Williams JJ, Drew JC, Galindo-Gonzalez S, Robic S, Dinsdale E, Morgan WR, Triplett EW, Burnette JM 3rd, Donovan SS, Fowlks ER, Goodman AL, Grandgenett NF, Goller CC, Hauser C, Jungck JR, Newman JD, Pearson WR, Ryder EF, Sierk M, Smith TM, Tosado-Acevedo R, Tapprich W, Tobin TC, Toro-Martínez A, Welch LR, Wilson MA, Ebenbach D, McWilliams M, Rosenwald AG, Pauley MA. PLoS One. 2019 Nov 18;14(11):e0224288. doi: 10.1371/journal.pone.0224288. eCollection 2019. PMID: 31738797

Cryo-EM: Ice Is Nice, but Good Ice Can Be Hard to Find. Egelman EH. Biophys J. 2020 Feb 1. pii: S0006-3495(20)30099-0. doi: 10.1016/j.bpj.2020.01.026. No abstract available. PMID: 32061273

Hooked on motility. Egelman EH. Nat Struct Mol Biol. 2019 Oct;26(10):848-849. doi: 10.1038/s41594-019-0302-2. No abstract available. PMID: 31570876

Pausing sites of RNA polymerase II on actively transcribed genes are enriched with DNA double-stranded breaks. Singh S, Szlachta K, Manukyan A, Raimer HM, Dinda M, Bekiranov S, Wang YH. J Biol Chem. 2020 Feb 6. pii: jbc.RA119.011665. doi: 10.1074/jbc.RA119.011665.

PMID: 32029477

Broken by the Cut: A Journey into the Role of Topoisomerase II in DNA Fragility. Atkin ND, Raimer HM, Wang YH. Genes (Basel). 2019 Oct 12;10(10). pii: E791. doi: 10.3390/genes10100791. Review. PMID: 31614754

Ant-icipating Change: An Epigenetic Switch in Reprogramming the Social Lives of Ants. Pray-Grant MG, Grant PA. Mol Cell. 2020 Jan 16;77(2):205-206. doi: 10.1016/j.molcel.2019.12.006.PMID: 31951544

An extensively glycosylated archaeal pilus survives extreme conditions. Wang F, Cvirkaite-Krupovic V, Kreutzberger MAB, Su Z, de Oliveira GAP, Osinski T, Sherman N, DiMaio F, Wall JS, Prangishvili D, Krupovic M, Egelman EH. Nat Microbiol. 2019 Aug;4(8):1401-1410. doi: 10.1038/s41564-019-0458-x. Epub 2019 May 20. PMID: 31110358

Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Wang F, Gu Y, O’Brien JP, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Cell. 2019 Apr 4;177(2):361-369.e10. doi: 10.1016/j.cell.2019.03.029. PMID: 30951668

tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model. Su Z, Frost EL, Lammert CR, Przanowska RK, Lukens JR, Dutta A. RNA Biol. 2020 Jan 31:1-13. doi: 10.1080/15476286.2020.1721047. PMID: 31983265

A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure. Li M, Fine RD, Dinda M, Bekiranov S, Smith JS. PLoS Genet. 2019 Aug 28;15(8):e1008339. doi: 10.1371/journal.pgen.1008339. eCollection 2019 Aug. PMID: 31461456

High-content phenotypic assay for proliferation of human iPSC-derived cardiomyocytes identifies L-type calcium channels as targets. Woo LA, Tkachenko S, Ding M, Plowright AT, Engkvist O, Andersson H, Drowley L, Barrett I, Firth M, Akerblad P, Wolf MJ, Bekiranov S, Brautigan DL, Wang QD, Saucerman JJ. J Mol Cell Cardiol. 2019 Feb;127:204-214. doi: 10.1016/j.yjmcc.2018.12.015. Epub 2018 Dec 28. PMID: 30597148

Complement alone drives efficacy of a chimeric antigonococcal monoclonal antibody. Gulati S, Beurskens FJ, de Kreuk BJ, Roza M, Zheng B, DeOliveira RB, Shaughnessy J, Nowak NA, Taylor RP, Botto M, He X, Ingalls RR, Woodruff TM, Song WC, Schuurman J, Rice PA, Ram S. PLoS Biol. 2019 Jun 19;17(6):e3000323. doi: 10.1371/journal.pbio.3000323. eCollection 2019 Jun. PMID: 31216278

Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R. Anderson WD, Duarte FM, Civelek M, Guertin MJ. Bioinformatics. 2020 Jan 9. pii: btaa011. doi: 10.1093/bioinformatics/btaa011. PMID: 31917388

2019

HIV-1 Rev interacts with HERV-K RcREs present in the human genome and promotes export of unspliced HERV-K proviral RNA. Gray LR, Jackson RE, Jackson PEH, Bekiranov S, Rekosh D, Hammarskjöld ML. Retrovirology. 2019 Dec 16;16(1):40. doi: 10.1186/s12977-019-0505-y. PMID: 31842941

Long noncoding RNA DRAIC inhibits prostate cancer progression by interacting with IKK to inhibit NF-κB activation. Saha S, Kiran M, Kuscu C, Chatrath A, Wotton D, Mayo MW, Dutta A. Cancer Res. 2020 Jan 3. pii: canres.3460.2019. doi: 10.1158/0008-5472.CAN-19-3460. PMID: 31900260

Critical role of C5a in sickle cell disease. Vercellotti GM, Dalmasso AP, Schaid TR Jr, Nguyen J, Chen C, Ericson ME, Abdulla F, Killeen T, Lindorfer MA, Taylor RP, Belcher JD. Am J Hematol. 2019 Mar;94(3):327-337. doi: 10.1002/ajh.25384. Epub 2019 Jan 3. PMID: 30569594

Bioprinting on sheet-based scaffolds applied to the creation of implantable tissue-engineered constructs with potentially diverse clinical applications: Tissue-Engineered Muscle Repair (TEMR) as a representative testbed. Bour RK, Sharma PR, Turner JS, Hess WE, Mintz EL, Latvis CR, Shepherd BR, Presnell SC, McConnell MJ, Highley C, Peirce SM, Christ GJ. Connect Tissue Res. 2020 Jan 3:1-13. doi: 10.1080/03008207.2019.1679800 PMID: 31899969

The AAA + ATPase TorsinA polymerizes into hollow helical tubes with 8.5 subunits per turn. Demircioglu FE, Zheng W, McQuown AJ, Maier NK, Watson N, Cheeseman IM, Denic V, Egelman EH, Schwartz TU. Nat Commun. 2019 Jul 22;10(1):3262. doi: 10.1038/s41467-019-11194-w.PMID: 31332180

Identification and characterization of extrachromosomal circular DNA in maternal plasma. Sin STK, Jiang P, Deng J, Ji L, Cheng SH, Dutta A, Leung TY, Chan KCA, Chiu RWK, Lo YMD. Proc Natl Acad Sci U S A. 2020 Jan 3. pii: 201914949. doi: 10.1073/pnas.1914949117. PMID: 31900366

A Prognostic Signature for Lower Grade Gliomas Based on Expression of Long Non-Coding RNAs. Kiran M, Chatrath A, Tang X, Keenan DM, Dutta A. Mol Neurobiol. 2019 Jul;56(7):4786-4798. doi: 10.1007/s12035-018-1416-y. Epub 2018 Nov 3. PMID: 30392137

AT-dinucleotide rich sequences drive fragile site formation. Irony-Tur Sinai M, Salamon A, Stanleigh N, Goldberg T, Weiss A, Wang YH, Kerem B. Nucleic Acids Res. 2019 Oct 10;47(18):9685-9695. doi: 10.1093/nar/gkz689. PMID: 31410468

Systems analysis of barrier molecule and ARNT-related gene expression regulation in melanoma. Leick KM, Obeid JM, Bekiranov S, Slingluff CL Jr. Oncoimmunology. 2019 Sep 24;8(12):e1665978. doi: 10.1080/2162402X.2019.1665978. eCollection 2019. PMID: 31741768

Null donors favor prepared immunologists. Taylor RP. Blood. 2019 Mar 28;133(13):1389-1390. doi: 10.1182/blood-2019-01-898775. No abstract available. PMID: 30923104

Endothelial Microparticles and Systemic Complement Activation in Patients With Chronic Kidney Disease. Jalal D, Renner B, Laskowski J, Stites E, Cooper J, Valente K, You Z, Perrenoud L, Le Quintrec M, Muhamed I, Christians U, Klawitter J, Lindorfer MA, Taylor RP, Holers VM, Thurman JM. J Am Heart Assoc. 2018 Jul 13;7(14). pii: e007818. doi: 10.1161/JAHA.117.007818. PMID: 30006493

Methods in Nuclear Architecture and Transport. Paschal BM. Methods. 2019 Mar 15;157:1-2. doi: 10.1016/j.ymeth.2019.02.020. No abstract available. PMID: 30832896

Fluorescence-based quantification of nucleocytoplasmic transport. Kelley JB, Paschal BM. Methods. 2019 Mar 15;157:106-114. doi: 10.1016/j.ymeth.2018.11.002. Epub 2018 Nov 10. PMID: 30419335

Towards improving proximity labeling by the biotin ligase BirA. Oostdyk LT, Shank L, Jividen K, Dworak N, Sherman NE, Paschal BM. Methods. 2019 Mar 15;157:66-79. doi: 10.1016/j.ymeth.2018.11.003. Epub 2018 Nov 10. PMID: 30419333

Mechanisms underlying the efficacy of exercise as an intervention for cocaine relapse: a focus on mGlu5 in the dorsal medial prefrontal cortex. Abel JM, Nesil T, Bakhti-Suroosh A, Grant PA, Lynch WJ. Psychopharmacology (Berl). 2019 Jul;236(7):2155-2171. doi: 10.1007/s00213-019-05208-0. Epub 2019 Jun 3. PMID: 31161451

Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters. Paulsen T, Shibata Y, Kumar P, Dillon L, Dutta A. Nucleic Acids Res. 2019 May 21;47(9):4586-4596. doi: 10.1093/nar/gkz155. PMID: 30828735

Conformational changes and catalytic inefficiency associated with Mot1-mediated TBP-DNA dissociation. Heiss G, Ploetz E, Voith von Voithenberg L, Viswanathan R, Glaser S, Schluesche P, Madhira S, Meisterernst M, Auble DT, Lamb DC. Nucleic Acids Res. 2019 Apr 8;47(6):2793-2806. doi: 10.1093/nar/gky1322. PMID: 30649478

The inner centromere is a biomolecular condensate scaffolded by the chromosomal passenger complex. Trivedi P, Palomba F, Niedzialkowska E, Digman MA, Gratton E, Stukenberg PT.Nat Cell Biol. 2019 Sep;21(9):1127-1137. doi: 10.1038/s41556-019-0376-4. Epub 2019 Sep 3. PMID: 31481798

Identification of Drivers of Aneuploidy in Breast Tumors. Pfister K, Pipka JL, Chiang C, Liu Y, Clark RA, Keller R, Skoglund P, Guertin MJ, Hall IM, Stukenberg PT. Cell Rep. 2018 May 29;23(9):2758-2769. doi: 10.1016/j.celrep.2018.04.102. PMID: 29847804

JAK2 V617F -Mediated Clonal Hematopoiesis Accelerates Pathological Remodeling in Murine Heart Failure. Sano S, Wang Y, Yura Y, Sano M, Oshima K, Yang Y, Katanasaka Y, Min KD, Matsuura S, Ravid K, Mohi G, Walsh K. JACC Basic Transl Sci. 2019 Sep 18;4(6):684-697. doi: 10.1016/j.jacbts.2019.05.013. eCollection 2019 Oct. PMID: 31709318

An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion. Sathyan KM, McKenna BD, Anderson WD, Duarte FM, Core L, Guertin MJ. Genes Dev. 2019 Oct 1;33(19-20):1441-1455. doi: 10.1101/gad.328237.119. Epub 2019 Aug 29. PMID: 31467088

Author Correction: ‘Stealth’ corporate innovation: an emerging threat for therapeutic drug development. Mastellos DC, Blom AM, Connolly ES, Daha MR, Geisbrecht BV, Ghebrehiwet B, Gros P, Hajishengallis G, Holers VM, Huber-Lang M, Kinoshita T, Mollnes TE, Montgomery RA, Morgan BP, Nilsson B, Pio R, Ricklin D, Risitano AM, Taylor RP, Mantovani A, Ioannidis JPA, Lambris JD. Nat Immunol. 2019 Oct 11. doi: 10.1038/s41590-019-0531-x. PMID: 31605100

Overexpression of transforming growth factor β induced factor homeobox 1 represses NPC1L1 and lowers markers of intestinal cholesterol absorption. Parini P, Melhuish TA, Wotton D, Larsson L, Ahmed O, Eriksson M, Pramfalk C. Atherosclerosis. 2018 Aug;275:246-255. doi: 10.1016/j.atherosclerosis.2018.06.867. Epub 2018 Jun 19. PMID: 29980051

Functions of TGIF homeodomain proteins and their roles in normal brain development and holoprosencephaly. Wotton D, Taniguchi K. Am J Med Genet C Semin Med Genet. 2018 Jun;178(2):128-139. doi: 10.1002/ajmg.c.31612. Epub 2018 May 11. PMID: 29749689

A packing for A-form DNA in an icosahedral virus. Wang F, Liu Y, Su Z, Osinski T, de Oliveira GAP, Conway JF, Schouten S, Krupovic M, Prangishvili D, Egelman EH. Proc Natl Acad Sci U S A. 2019 Oct 21. pii: 201908242. doi: 10.1073/pnas.1908242116. PMID: 31636205

Characterization of the Importin-β binding domain in nuclear import receptor KPNA7. Oostdyk LT, McConnell MJ, Paschal BM. Biochem J. 2019 Oct 23. pii: BCJ20190717. doi: 10.1042/BCJ20190717. PMID: 31642884

‘Stealth’ corporate innovation: an emerging threat for therapeutic drug development. Mastellos DC, Blom AM, Connolly ES, Daha MR, Geisbrecht BV, Ghebrehiwet B, Gros P, Hajishengallis G, Holers VM, Huber-Lang M, Kinoshita T, Mollnes TE, Montgomery RA, Morgan BP, Nilsson B, Pio R, Ricklin D, Risitano AM, Taylor RP, Mantovani A, Ioannidis JPA, Lambris JD. Nat Immunol. 2019 Sep 27. doi: 10.1038/s41590-019-0503-1. No abstract available. PMID: 31562490

Complement C1r serine protease contributes to kidney fibrosis. Xavier S, Sahu RK, Bontha SV, Mass V, Taylor RP, Megyesi J, Thielens NM, Portilla D. Am J Physiol Renal Physiol. 2019 Sep 11. doi: 10.1152/ajprenal.00357.2019. PMID: 31509012

Depletion of Limiting rDNA Structural Complexes Triggers Chromosomal Instability and Replicative Aging of Saccharomyces cerevisiae. Fine RD, Maqani N, Li M, Franck E, Smith JS. Genetics. 2019 May;212(1):75-91. doi: 10.1534/genetics.119.302047. Epub 2019 Mar 6. PMID: 30842210

Hooked on motility. Egelman EH. Nat Struct Mol Biol. 2019 Sep 30. doi: 10.1038/s41594-019-0302-2. No abstract available. PMID: 31570876

Angiogenin generates specific stress-induced tRNA halves and is not involved in tRF-3-mediated gene silencing. Su Z, Kuscu C, Malik A, Shibata E, Dutta A. J Biol Chem. 2019 Oct 3. pii: jbc.RA119.009272. doi: 10.1074/jbc.RA119.009272. PMID: 31582561

Super-enhancers maintain renin-expressing cell identity and memory to preserve multi-system homeostasis. Martinez MF, Medrano S, Brown EA, Tufan T, Shang S, Bertoncello N, Guessoum O, Adli M, Belyea BC, Sequeira-Lopez MLS, Gomez RA. J Clin Invest. 2018 Nov 1;128(11):4787-4803. doi: 10.1172/JCI121361. Epub 2018 Oct 2. PMID: 30130256

The inner centromere is a biomolecular condensate scaffolded by the chromosomal passenger complex Trivedi P, Palomba F, Niedzialkowska E, Digman MA, Gratton E, Stukenberg PT. Nat Cell Biol. 2019 Sep;21(9):1127-1137. doi: 10.1038/s41556-019-0376-4. Epub 2019 Sep 3. PMID: 31481798

A prediction model of military combat and training exposures on VA service-connected disability: a CENC study. Eggleston B, Dismuke-Greer CE, Pogoda TK, Denning JH, Eapen BC, Carlson KF, Bhatnagar S, Nakase-Richardson R, Troyanskaya M, Nolen T, Walker WC. Brain Inj. 2019 Sep 2:1-13. doi: 10.1080/02699052.2019.1655793. PMID: 31476880

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, Zang C. Bioinformatics. 2018 Aug 15;34(16):2867-2869. doi: 10.1093/bioinformatics/bty194. PMID: 29608647

Shah KK, Whitaker RH, Busby T, Hu J, Shi B, Wang Z, Zang C, Placzek WJ, Jiang H. Specific inhibition of DPY30 activity by ASH2L-derived peptides suppresses blood cancer cell growth. Exp Cell Res. 2019 Sep 15;382(2):111485. doi: 10.1016/j.yexcr.2019.06.030. Epub 2019 Jun 26. PubMed PMID: 31251903; PubMed Central PMCID: PMC6717027.

An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion. Sathyan KM, McKenna BD, Anderson WD, Duarte FM, Core L, Guertin MJ. Genes Dev. 2019 Aug 29. doi: 10.1101/gad.328237.119. PMID: 31467088

Mapping and Making Sense of Noncoding Mutations in the Genome.Yang J, Adli M. Cancer Res. 2019 Aug 6. doi: 10.1158/0008-5472.CAN-19-0905. Review. PMID: 31387922

Assessing work-related risk factors for musculoskeletal knee disorders in construction roofing tasks. Breloff SP, Dutta A, Dai F, Sinsel EW, Warren CM, Ning X, Wu JZ. Appl Ergon. 2019 Nov;81:102901. doi: 10.1016/j.apergo.2019.102901. Epub 2019 Jul 17. PMID: 31422268

Functional role of the type 1 pilus rod structure in mediating host-pathogen interactions. Spaulding CN, Schreiber HL 4th, Zheng W, Dodson KW, Hazen JE, Conover MS, Wang F, Svenmarker P, Luna-Rico A, Francetic O, Andersson M, Hultgren S, Egelman EH. Elife. 2018 Jan 18;7. pii: e31662. doi: 10.7554/eLife.31662. PMID: 29345620

NF-κB upregulates glutamine-fructose-6-phosphate transaminase 2 to promote migration in non-small cell lung cancer. Szymura SJ, Zaemes JP, Allison DF, Clift SH, D’Innocenzi JM, Gray LG, McKenna BD, Morris BB, Bekiranov S, LeGallo RD, Jones DR, Mayo MW. Cell Commun Signal. 2019 Mar 18;17(1):24. doi: 10.1186/s12964-019-0335-5. PMID: 30885209

Detection of ADP-Ribosylation of the Androgen Receptor Using the Recombinant Macrodomain AF1521 from Archaeoglobus fulgidus. Kamata T, Yang CS, Jividen K, Spencer A, Dworak N, Oostdyk LT, Paschal BM. Methods Mol Biol. 2019;1966:107-124. doi: 10.1007/978-1-4939-9195-2_9. PMID: 31041742

AT-dinucleotide rich sequences drive fragile site formation. Irony-Tur Sinai M, Salamon A, Stanleigh N, Goldberg T, Weiss A, Wang YH, Kerem B. Nucleic Acids Res. 2019 Aug 14. pii: gkz689. doi: 10.1093/nar/gkz689. PMID: 31410468

Complex DNA structures trigger copy number variation across the Plasmodium falciparum genome. Huckaby AC, Granum CS, Carey MA, Szlachta K, Al-Barghouthi B, Wang YH, Guler JL. Nucleic Acids Res. 2019 Feb 28;47(4):1615-1627. doi: 10.1093/nar/gky1268. PMID: 30576466

Antitumor effect of insulin-like growth factor-1 receptor inhibition in head and neck squamous cell carcinoma. Lehman CE, Khalil AA, Axelrod MJ, Dougherty MI, Schoeff SS, Taniguchi LE, Mendez RE, David AP, McGarey PO Jr.,, Hubbard MA, Donaldson L, Frierson HF Jr.,, Stelow EB, Bekiranov S, Wulfkuhle JD, Petricoin EF, Gioeli DG, Jameson MJ.Laryngoscope. 2019 Aug 21. doi: 10.1002/lary.28236. PMID: 31433065

Yang Z, Shah K, Khodadadi-Jamayran A, Jiang H. Control of Hematopoietic Stem and Progenitor Cell Function through Epigenetic Regulation of Energy Metabolism and Genome Integrity. Stem Cell Reports. 2019 Jul 9;13(1):61-75. doi: 10.1016/j.stemcr.2019.05.023. Epub 2019 Jun 20. PubMed PMID: 31231026; PubMed Central PMCID: PMC6627005.

Shah K, King GD, Jiang H. A chromatin modulator sustains self-renewal and enables differentiation of postnatal neural stem and progenitor cells. J Mol Cell Biol. 2019 May 8;. doi: 10.1093/jmcb/mjz036. PubMed PMID: 31065682.

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq. Guertin MJ, Cullen AE, Markowetz F, Holding AN. Nucleic Acids Res. 2018 Jul 6;46(12):e75. doi: 10.1093/nar/gky252. PMID: 29672735

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions. Martins AL, Walavalkar NM, Anderson WD, Zang C, Guertin MJ. Nucleic Acids Res. 2018 Jan 25;46(2):e9. doi: 10.1093/nar/gkx1053. PMID: 29126307

Chemotherapy-induced distal enhancers drive transcriptional program to maintain the chemoresistant state in ovarian cancer. Shang S, Yang J, Jazaeri AA, Duval AJ, Tufan T, Lopes Fischer N, Benamar M, Guessous F, Lee I, Campbell RM, Ebert PJ, Abbas T, Landen CN, DiFeo A, Scacheri PC, Adli M. Cancer Res. 2019 Jul 29. pii: canres.0215.2019. doi: 10.1158/0008-5472.CAN-19-0215. PMID: 31358529

LINC00152 Promotes Invasion through a 3′-Hairpin Structure and Associates with Prognosis in Glioblastoma. Reon BJ, Takao Real Karia B, Kiran M, Dutta A. Mol Cancer Res. 2018 Oct;16(10):1470-1482. doi: 10.1158/1541-7786.MCR-18-0322. Epub 2018 Jul 10. PMID: 29991527

Functional reconstitution of the type IVa pilus assembly system from enterohaemorrhagic Escherichia coli. Luna Rico A, Zheng W, Petiot N, Egelman EH, Francetic O. Mol Microbiol. 2019 Mar;111(3):732-749. doi: 10.1111/mmi.14188. Epub 2019 Jan 21. PMID: 30561149

Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome. Pincus D, Anandhakumar J, Thiru P, Guertin MJ, Erkine AM, Gross DS. Mol Biol Cell. 2018 Dec 15;29(26):3168-3182. doi: 10.1091/mbc.E18-06-0353. Epub 2018 Oct 17. PMID: 30332327

A Non-random Mouse Model for Pharmacological Reactivation of Mecp2 on the Inactive X Chromosome. Przanowski P, Zheng Z, Wasko U, Bhatnagar S. J Vis Exp. 2019 May 22;(147). doi: 10.3791/59449. PMID: 31180354

A Single-Agent Dual-Specificity Targeting of FOLR1 and DR5 as an Effective Strategy for Ovarian Cancer. Shivange G, Urbanek K, Przanowski P, Perry JSA, Jones J, Haggart R, Kostka C, Patki T, Stelow E, Petrova Y, Llaneza D, Mayo M, Ravichandran KS, Landen CN, Bhatnagar S, Tushir-Singh J. Cancer Cell. 2018 Aug 13;34(2):331-345.e11. doi: 10.1016/j.ccell.2018.07.005. PMID: 30107179

MUNC, an Enhancer RNA Upstream from the MYOD Gene, Induces a Subgroup of Myogenic Transcripts in trans Independently of MyoD. Cichewicz MA, Kiran M, Przanowska RK, Sobierajska E, Shibata Y, Dutta A. Mol Cell Biol. 2018 Sep 28;38(20). pii: e00655-17. doi: 10.1128/MCB.00655-17. Print 2018 Oct 15. PMID: 30037979

Mechanisms underlying the efficacy of exercise as an intervention for cocaine relapse: a focus on mGlu5 in the dorsal medial prefrontal cortex. Abel JM, Nesil T, Bakhti-Suroosh A, Grant PA, Lynch WJ. Psychopharmacology (Berl). 2019 Jun 3. doi: 10.1007/s00213-019-05208-0. PMID: 31161451

Myt1 and Myt1l transcription factors limit proliferation in GBM cells by repressing YAP1 expression. Melhuish TA, Kowalczyk I, Manukyan A, Zhang Y, Shah A, Abounader R, Wotton D. Biochim Biophys Acta Gene Regul Mech. 2018 Nov;1861(11):983-995. doi: 10.1016/j.bbagrm.2018.10.005. Epub 2018 Oct 10. PMID: 30312684

Imaging Flow Cytometry Quantifies Neural Genome Dynamics. Michel N, Majumdar UB, Lannigan J, McConnell MJ. Cytometry A. 2019 May 7. doi: 10.1002/cyto.a.23783. PMID: 31063256

An extensively glycosylated archaeal pilus survives extreme conditions. Wang F, Cvirkaite-Krupovic V, Kreutzberger MAB, Su Z, de Oliveira GAP, Osinski T, Sherman N, DiMaio F, Wall JS, Prangishvili D, Krupovic M, Egelman EH. Nat Microbiol. 2019 May 20. doi: 10.1038/s41564-019-0458-x. PMID: 31110358

The Deubiquitinase USP46 Is Essential for Proliferation and Tumor Growth of HPV-Transformed Cancers. Kiran S, Dar A, Singh SK, Lee KY, Dutta A. Mol Cell. 2018 Dec 6;72(5):823-835.e5. doi: 10.1016/j.molcel.2018.09.019. Epub 2018 Nov 8. PMID: 30415951

Targeting HER2 beyond breast cancer. Bhatnagar S, Tushir-Singh J. Mol Cell Oncol. 2019 Mar 20;6(3):1571984. doi: 10.1080/23723556.2019.1571984. eCollection 2019. PMID: 31131305

Visualization of Xist Long Noncoding RNA with a Fluorescent CRISPR/Cas9 System. Waśko U, Zheng Z, Bhatnagar S. Methods Mol Biol. 2019;1870:41-50. doi: 10.1007/978-1-4939-8808-2_3. PMID: 30539545

Molecular mechanism for NLRP6 inflammasome assembly and activation. Shen C, Lu A, Xie WJ, Ruan J, Negro R, Egelman EH, Fu TM, Wu H. Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2052-2057. doi: 10.1073/pnas.1817221116. Epub 2019 Jan 23. PMID: 30674671

Cryo-EM structure of the NLRC4CARD filament provides insights into how symmetric and asymmetric supramolecular structures drive inflammasome assembly. Matyszewski M, Zheng W, Lueck J, Antiochos B, Egelman EH, Sohn J. J Biol Chem. 2018 Dec 28;293(52):20240-20248. doi: 10.1074/jbc.RA118.006050. Epub 2018 Nov 1. PMID: 30385506

The binding of Borealin to microtubules underlies a tension independent kinetochore-microtubule error correction pathway. Trivedi P, Zaytsev AV, Godzi M, Ataullakhanov FI, Grishchuk EL, Stukenberg PT. Nat Commun. 2019 Feb 8;10(1):682. doi: 10.1038/s41467-019-08418-4. PMID: 30737408

TGIF transcription factors repress acetyl CoA metabolic gene expression and promote intestinal tumor growth. Shah A, Melhuish TA, Fox TE, Frierson HF Jr, Wotton D. Genes Dev. 2019 Apr 1;33(7-8):388-402. doi: 10.1101/gad.320127.118. Epub 2019 Feb 26. PMID: 30808659

Mechanisms of Complement-Mediated Damage in Hematological Disorders. Taylor RP, Lindorfer MA. Semin Hematol. 2018 Jul;55(3):118-123. doi: 10.1053/j.seminhematol.2018.02.003. Epub 2018 Feb 14. Review. PMID: Similar articles

Evaluation of various risk factors associated with multidrug-resistant organisms isolated from diabetic foot ulcer patients. Datta P, Chander J, Gupta V, Mohi GK, Attri AK. J Lab Physicians. 2019 Jan-Mar;11(1):58-62. doi: 10.4103/JLP.JLP_106_18. PMID: 30983804

Methods in Nuclear Architecture and Transport. Paschal BM. Methods. 2019 Mar 15;157:1-2. doi: 10.1016/j.ymeth.2019.02.020. No abstract available. PMID: 30832896

Depletion of Limiting rDNA Structural Complexes Triggers Chromosomal Instability and Replicative Aging of Saccharomyces cerevisiae. Fine RD, Maqani N, Li M, Franck E, Smith JS. Genetics. 2019 Mar 6. pii: genetics.302047.2019. doi: 10.1534/genetics.119.302047. PMID: 30842210

P190RhoGAP prevents mitotic spindle fragmentation and is required to activate Aurora A kinase at acentriolar poles. Manukyan A, Sargsyan L, Parsons SJ, Stukenberg PT. Chromosoma. 2018 Sep;127(3):375-386. doi: 10.1007/s00412-018-0670-0. Epub 2018 Apr 14. PMID: 29656322

Null donors favor prepared immunologists. Taylor RP. Blood. 2019 Mar 28;133(13):1389-1390. doi: 10.1182/blood-2019-01-898775. No abstract available. PMID: 30923104

Histone H3 lysine 4 methylation signature associated with human undernutrition. Uchiyama R, Kupkova K, Shetty SJ, Linford AS, Pray-Grant MG, Wagar LE, Davis MM, Haque R, Gaultier A, Mayo MW, Grant PA, Petri WA Jr, Bekiranov S, Auble DT. Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11264-E11273. doi: 10.1073/pnas.1722125115. Epub 2018 Nov 12. PMID: 30420518

Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promotersPaulsen T, Shibata Y, Kumar P, Dillon L, Dutta A. Nucleic Acids Res. 2019 Mar 4. pii: gkz155. doi: 10.1093/nar/gkz155. [Epub ahead of print] PMID: 30828735

Improved molecular karyotyping in glioblastoma. Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Mutat Res. 2018 Sep;811:16-26. doi: 10.1016/j.mrfmmm.2018.06.002. Epub 2018 Jul 8. PMID: 30055482

Dissecting the Genetics of Osteoporosis using Systems Approaches. Al-Barghouthi BM, Farber CR. Trends Genet. 2019 Jan;35(1):55-67. doi: 10.1016/j.tig.2018.10.004. Epub 2018 Nov 20. PMID: 30470485

TGIF transcription factors repress acetyl CoA metabolic gene expression and promote intestinal tumor growth. Shah A, Melhuish TA, Fox TE, Frierson HF Jr, Wotton D. Genes Dev. 2019 Feb 26. doi: 10.1101/gad.320127.118. PMID: 30808659

Analysis of transcriptional activity by the Myt1 and Myt1l transcription factors. Manukyan A, Kowalczyk I, Melhuish TA, Lemiesz A, Wotton D. J Cell Biochem. 2018 Jun;119(6):4644-4655. doi: 10.1002/jcb.26636. Epub 2018 Mar 9. PMID: 29291346

CD20 and CD37 antibodies synergize to activate complement by Fc-mediated clustering. Oostindie SC, van der Horst HJ, Lindorfer MA, Cook EM, Tupitza JC, Zent CS, Burack R, VanDerMeid KR, Strumane K, Chamuleau MED, Mutis T, de Jong RN, Schuurman J, Breij ECW, Beurskens FJ, Parren PWHI, Taylor RP. Haematologica. 2019 Feb 21. pii: haematol.2018.207266. doi: 10.3324/haematol.2018.207266. PMID: 30792198

Recurrent mutations at estrogen receptor binding sites alter chromatin topology and distal gene expression in breast cancer. Yang J, Wei X, Tufan T, Kuscu C, Unlu H, Farooq S, Demirtas E, Paschal BM, Adli M. Genome Biol. 2018 Nov 7;19(1):190. doi: 10.1186/s13059-018-1572-4. PMID: 30404658

STAT3 mutations are not sufficient to induce large granular lymphocytic leukaemia in mice. Dutta A, Yan D, Hutchison RE, Mohi G. Br J Haematol. 2018 Mar;180(6):911-915. doi: 10.1111/bjh.14487. Epub 2016 Dec 26. No abstract available. PMID: 28025836

BRG1 is a prognostic indicator and a potential therapeutic target for prostate cancer. Muthuswami R, Bailey L, Rakesh R, Imbalzano AN, Nickerson JA, Hockensmith JW J Cell Physiol. 2019 Jan 22. doi: 10.1002/jcp.28161. PMID: 30667054

Molecular mechanism for NLRP6 inflammasome assembly and activation. Shen C, Lu A, Xie WJ, Ruan J, Negro R, Egelman EH, Fu TM, Wu H. Proc Natl Acad Sci U S A. 2019 Jan 23. pii: 201817221. doi: 10.1073/pnas.1817221116. PMID: 30674671

The Germline Variants rs61757955 and rs34988193 are Predictive of Survival in Lower Grade Glioma Patients. Chatrath A, Kiran M, Kumar P, Ratan A, Dutta A. Mol Cancer Res. 2019 Jan 16. pii: molcanres.0996.2018. doi: 10.1158/1541-7786.MCR-18-0996. PMID: 30651372

Cryo-EM of Helical Polymers. Wang F, Gnewou O, Solemanifar A, Conticello VP, Egelman EH. Chem Rev. 2022 Feb 8. doi: 10.1021/acs.chemrev.1c00753. Online ahead of print. PMID: 35133794

Atomic structure of Lanreotide nanotubes revealed by cryo-EM. Pieri L, Wang F, Arteni AA, Vos M, Winter JM, Le Du MH, Artzner F, Gobeaux F, Legrand P, Boulard Y, Bressanelli S, Egelman EH, Paternostre M.Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2120346119. doi: 10.1073/pnas.2120346119.PMID: 35042822

Reconstitution of the DTX3L-PARP9 complex reveals determinants for high-affinity heterodimerization and multimeric assembly. Ashok Y, Vela-Rodríguez C, Yang C, Alanen HI, Liu F, Paschal BM, Lehtiö L. Biochem J. 2022 Feb 11;479(3):289-304. doi: 10.1042/BCJ20210722. PMID: 35037691

Genomic analyses of the metastasis-derived prostate cancer cell lines LNCaP, VCaP, and PC3-AR. Sienkiewicz K, Yang C, Paschal BM, Ratan A. Prostate. 2022 Mar;82(4):442-451. doi: 10.1002/pros.24290. Epub 2021 Dec 24. PMID: 34951700

Molecular Imaging of Prostate Cancer Targeting CD46 Using ImmunoPET. Wang S, Li J, Hua J, Su Y, Beckford-Vera DR, Zhao W, Jayaraman M, Huynh TL, Zhao N, Wang YH, Huang Y, Qin F, Shen S, Gioeli D, Dreicer R, Sriram R, Egusa EA, Chou J, Feng FY, Aggarwal R, Evans MJ, Seo Y, Liu B, Flavell RR, He J. Clin Cancer Res. 2021 Mar 1;27(5):1305-1315. doi: 10.1158/1078-0432.CCR-20-3310. Epub 2020 Dec 8. PMID: 33293372

Tip60 acetylation of histone H3K4 temporally controls Chromosome Passenger Complex localization. Niedzialkowska E, Liu L, Kuscu C, Mayo Z, Minor W, Strahl BD, Adli M, Stukenberg PT.Mol Biol Cell. 2022 Jun 2:mbcE21060283. doi: 10.1091/mbc.E21-06-0283. Online ahead of print. PMID: 35653296

Function and Therapeutic Implications of tRNA Derived Small RNAs. Wilson B, Dutta A. Front Mol Biosci. 2022 Apr 13;9:888424. doi: 10.3389/fmolb.2022.888424. eCollection 2022. PMID: 35495621

One- and Two-Year Analysis of a Five-Year Prospective Multicenter Study Assessing Radiographic and Patient-Reported Outcomes Following Triplanar First Tarsometatarsal Arthrodesis With Early Weightbearing for Symptomatic Hallux Valgus. Liu GT, Chhabra A, Dayton MJ, Dayton PD, Duke WJ, Farber DC, Hatch DJ, Kile DA, Koay J, McAleer JP, Raissi A, Raspovic KM, Santrock RD, Taylor RP, VanPelt MD, Wukich DK. J Foot Ankle Surg. 2022 Apr 27:S1067-2516(22)00118-1. doi: 10.1053/j.jfas.2022.04.008. Online ahead of print. PMID: 35613971

Allosteric regulation controls actin-bundling properties of human plastins.Schwebach CL, Kudryashova E, Agrawal R, Zheng W, Egelman EH, Kudryashov DS. Nat Struct Mol Biol. 2022 May 19. doi: 10.1038/s41594-022-00771-1. Online ahead of print. PMID: 35589838

Phenol-soluble modulins PSMα3 and PSMβ2 form nanotubes that are cross-α amyloids. Kreutzberger MAB, Wang S, Beltran LC, Tuachi A, Zuo X, Egelman EH, Conticello VP. Proc Natl Acad Sci U S A. 2022 May 17;119(20):e2121586119. doi: 10.1073/pnas.2121586119. Epub 2022 May 9. PMID: 35533283

The long and short of rDNA and yeast replicative aging. Smith JS. Proc Natl Acad Sci U S A. 2022 Jun 7;119(23):e2205124119. doi: 10.1073/pnas.2205124119. Epub 2022 Jun 3. PMID: 35658078 No abstract available.

2018

A nuclear lamina-chromatin-Ran GTPase axis modulates nuclear import and DNA damage signaling. Dworak N, Makosa D, Chatterjee M, Jividen K, Yang CS, Snow C, Simke WC, Johnson IG, Kelley JB, Paschal BM. Aging Cell. 2018 Dec 19:e12851. doi: 10.1111/acel.12851. PMID: 30565836

Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile. Liu Y, Osinski T, Wang F, Krupovic M, Schouten S, Kasson P, Prangishvili D, Egelman EH. Nat Commun. 2018 Aug 22;9(1):3360. doi: 10.1038/s41467-018-05684-6. PMID: 30135568

Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. Paulsen T, Kumar P, Koseoglu MM, Dutta A. Trends Genet. 2018 Apr;34(4):270-278. doi: 10.1016/j.tig.2017.12.010. Epub 2018 Jan 9. Review. PMID: 29329720

CRISPR knockout screening identifies combinatorial drug targets in pancreatic cancer and models cellular drug response. Szlachta K, Kuscu C, Tufan T, Adair SJ, Shang S, Michaels AD, Mullen MG, Fischer NL, Yang J, Liu L, Trivedi P, Stelow EB, Stukenberg PT, Parsons JT, Bauer TW, Adli M. Nat Commun. 2018 Oct 15;9(1):4275. doi: 10.1038/s41467-018-06676-2. PMID: 30323222

High-content phenotypic assay for proliferation of human iPSC-derived cardiomyocytes identifies L-type calcium channels as targets. Woo LA, Tkachenko S, Ding M, Plowright AT, Engkvist O, Andersson H, Drowley L, Barrett I, Firth M, Akerblad P, Wolf MJ, Bekiranov S, Brautigan DL, Wang QD, Saucerman JJ. J Mol Cell Cardiol. 2018 Dec 28. pii: S0022-2828(18)31309-9. doi: 10.1016/j.yjmcc.2018.12.015. PMID: 30597148

Inheritance of CENP-A Nucleosomes during DNA Replication Requires HJURP. Zasadzińska E, Huang J, Bailey AO, Guo LY, Lee NS, Srivastava S, Wong KA, French BT, Black BE, Foltz DR. Dev Cell. 2018 Nov 5;47(3):348-362.e7. doi: 10.1016/j.devcel.2018.09.003. Epub 2018 Oct 4. PMID: 30293838

Visualization of Xist Long Noncoding RNA with a Fluorescent CRISPR/Cas9 System. Waśko U, Zheng Z, Bhatnagar S. Methods Mol Biol. 2019;1870:41-50. doi: 10.1007/978-1-4939-8808-2_3. PMID: 30539545

The Biology and Application Areas of CRISPR Technologies.Adli M. J Mol Biol. 2018 Nov 14. pii: S0022-2836(18)31237-3. doi: 10.1016/j.jmb.2018.11.012. PMID: 30447221

Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. Qin P, Parlak M, Kuscu C, Bandaria J, Mir M, Szlachta K, Singh R, Darzacq X, Yildiz A, Adli M. Nat Commun. 2017 Mar 14;8:14725. doi: 10.1038/ncomms14725. PMID: 28290446

α-amino trimethylation of CENP-A by NRMT is required for full recruitment of the centromere. Sathyan KM, Fachinetti D, Foltz DR. Nat Commun. 2017 Mar 7;8:14678. doi: 10.1038/ncomms14678. PMID: 28266506

Fluorescence-based Quantification of Nucleocytoplasmic Transport. Kelley JB, Paschal BM. Methods. 2018 Nov 9. pii: S1046-2023(18)30123-3. doi: 10.1016/j.ymeth.2018.11.002. PMID: 30419335

Towards improving proximity labeling by the biotin ligase BirA. Oostdyk LT, Shank L, Jividen K, Dworak N, Sherman NE, Paschal BM. Methods. 2018 Nov 10. pii: S1046-2023(18)30115-4. doi: 10.1016/j.ymeth.2018.11.003. PMID: 30419333

The effect of rho kinase inhibition on morphological and electrophysiological maturity in iPSC-derived neurons. Harbom LJ, Rudisill TL, Michel N, Litwa KA, Beenhakker MP, McConnell MJ. Cell Tissue Res. 2018 Nov 8. doi: 10.1007/s00441-018-2942-7. PMID: 30406823

Cryo-EM structure of the NLRC4CARD filament provides insights into how symmetric and asymmetric supramolecular structures drive inflammasome assembly. Matyszewski M, Zheng W, Lueck J, Antiochos B, Egelman EH, Sohn J. J Biol Chem. 2018 Nov 1. pii: jbc.RA118.006050. doi: 10.1074/jbc.RA118.006050. PMID: 30385506

The Deubiquitinase USP46 Is Essential for Proliferation and Tumor Growth of HPV-Transformed Cancers. Kiran S, Dar A, Singh SK, Lee KY, Dutta A. Mol Cell. 2018 Oct 30. pii: S1097-2765(18)30790-1. doi: 10.1016/j.molcel.2018.09.019. PMID: 30415951

A Prognostic Signature for Lower Grade Gliomas Based on Expression of Long Non-Coding RNAs. Kiran M, Chatrath A, Tang X, Keenan DM, Dutta A. Mol Neurobiol. 2018 Nov 3. doi: 10.1007/s12035-018-1416-y. PMID: 3039213

Crystal structure of the full Swi2/Snf2 remodeler Mot1 in the resting state. Butryn A, Woike S, Shetty SJ, Auble DT, Hopfner KP. Elife. 2018 Oct 5;7. pii: e37774. doi: 10.7554/eLife.37774. PMID: 30289385

RNA synthesis is associated with multiple TBP-chromatin binding events. Zaidi HA, Auble DT, Bekiranov S. Sci Rep. 2017 Jan 4;7:39631. doi: 10.1038/srep39631. PMID: 28051102

Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human. Szlachta K, Thys RG, Atkin ND, Pierce LCT, Bekiranov S, Wang YH. Genome Biol. 2018 Jul 12;19(1):89. doi: 10.1186/s13059-018-1463-8. PMID: 30001206

Inheritance of CENP-A Nucleosomes during DNA Replication Requires HJURP. Zasadzińska E, Huang J, Bailey AO, Guo LY, Lee NS, Srivastava S, Wong KA, French BT, Black BE, Foltz DR. Dev Cell. 2018 Oct 3. pii: S1534-5807(18)30732-9. doi: 10.1016/j.devcel.2018.09.003. PMID: 30293838

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer. Jividen K, Kedzierska KZ, Yang CS, Szlachta K, Ratan A, Paschal BM. BMC Cancer. 2018 Oct 10;18(1):960. doi: 10.1186/s12885-018-4848-x. PMID: 30305041

Cryo-EM structure of the NLRC4CARD filament provides insights into how symmetric and asymmetric supramolecular structures drive inflammasome assembly. Matyszewski M, Zheng W, Lueck J, Antiochos B, Egelman EH, Sohn J. J Biol Chem. 2018 Nov 1. pii: jbc.RA118.006050. doi: 10.1074/jbc.RA118.006050. PMID: 30385506

Structure of the Neisseria meningitidis Type IV pilus. Kolappan S, Coureuil M, Yu X, Nassif X, Egelman EH, Craig L. Nat Commun. 2016 Oct 4;7:13015. doi: 10.1038/ncomms13015. PMID: 27698424

Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome. Pincus D, Anandhakumar J, Thiru P, Guertin MJ, Erkine AM, Gross DS. Mol Biol Cell. 2018 Oct 17:mbcE18060353. doi: 10.1091/mbc.E18-06-0353. PMID: 30332327

Structural basis for high-affinity actin binding revealed by a β-III-spectrin SCA5 missense mutation. Avery AW, Fealey ME, Wang F, Orlova A, Thompson AR, Thomas DD, Hays TS, Egelman EH. Nat Commun. 2017 Nov 7;8(1):1350. doi: 10.1038/s41467-017-01367-w. PMID: 29116080

CRISPR-Cas9-AID base editor is a powerful gain-of-function screening tool. Kuscu C, Adli M. Nat Methods. 2016 Nov 29;13(12):983-984. doi: 10.1038/nmeth.4076. No abstract available. PMID: 27898061

Pharmacological reactivation of inactive X-linked Mecp2 in cerebral cortical neurons of living mice. Przanowski P, Wasko U, Zheng Z, Yu J, Sherman R, Zhu LJ, McConnell MJ, Tushir-Singh J, Green MR, Bhatnagar S. Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):7991-7996. doi: 10.1073/pnas.1803792115. Epub 2018 Jul 16. PMID: 30012595

Hijacking a key chromatin modulator creates epigenetic vulnerability for MYC-driven cancer. Yang Z, Shah K, Busby T, Giles K, Khodadadi-Jamayran A, Li W, Jiang H. The Journal of clinical investigation. 2018; 128(8):3605-3618. PMID:29870403

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB. PLoS Biol. 2018 Aug 7;16(8):e2006352. doi: 10.1371/journal.pbio.2006352. eCollection 2018 Aug. PMID: 30086128

Single-cell analysis of diversity in human stem cell-derived neurons. Harbom LJ, Michel N, McConnell MJ. Cell Tissue Res. 2018 Jan;371(1):171-179. doi: 10.1007/s00441-017-2728-3. Epub 2017 Nov 29. Review. PMID: 29185070

Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells. Kuscu C, Mammeadov R, Czikora A, Unlu H, Tufan T, Fischer NL, Arslan S, Bekiranov S, Kanemaki M, Adli M. J Mol Biol. 2018 Aug 9. pii: S0022-2836(18)30892-1. doi: 10.1016/j.jmb.2018.08.001. PMID: 30098338

tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. Kuscu C, Kumar P, Kiran M, Su Z, Malik A, Dutta A. RNA. 2018 Aug;24(8):1093-1105. doi: 10.1261/rna.066126.118. Epub 2018 May 29. PMID: 29844106

Improved molecular karyotyping in glioblastoma. Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Mutat Res. 2018 Jul 8;811:16-26. doi: 10.1016/j.mrfmmm.2018.06.002. PMID: 30055482

Structure of the calcium-dependent type 2 secretion pseudopilus. López-Castilla A, Thomassin JL, Bardiaux B, Zheng W, Nivaskumar M, Yu X, Nilges M, Egelman EH, Izadi-Pruneyre N, Francetic O. Nat Microbiol. 2017 Dec;2(12):1686-1695. doi: 10.1038/s41564-017-0041-2. Epub 2017 Oct 9. PMID: 28993624

MUNC, an eRNA upstream from the MYOD gene, induces a subgroup of myogenic transcripts in trans, independently of MyoD. Cichewicz MA, Kiran M, Przanowska RK, Sobierajska E, Shibata Y, Dutta A. Mol Cell Biol. 2018 Jul 23. pii: MCB.00655-17. doi: 10.1128/MCB.00655-17. PMID: 30037979

LINC00152 Promotes Invasion Through a 3′-hairpin Structure and Associates with Prognosis in Glioblastoma. Reon BJ, Takao Real Karia B, Kiran M, Dutta A. Mol Cancer Res. 2018 Jul 10. pii: molcanres.0322.2018. doi: 10.1158/1541-7786.MCR-18-0322. PMID: 29991527

Regulation of Mammalian DNA Replication via the Ubiquitin-Proteasome System. Abbas T, Dutta A. Adv Exp Med Biol. 2017;1042:421-454. doi: 10.1007/978-981-10-6955-0_19. Review. PMID: 29357069

Overexpression of transforming growth factor β induced factor homeobox 1 represses NPC1L1 and lowers markers of intestinal cholesterol absorption. Parini P, Melhuish TA, Wotton D, Larsson L, Ahmed O, Eriksson M, Pramfalk C. Atherosclerosis. 2018 Jun 19;275:246-255. doi: 10.1016/j.atherosclerosis.2018.06.867. PMID: 29980051

Small molecule inhibition of the CBFβ/RUNX interaction decreases ovarian cancer growth and migration through alterations in genes related to epithelial-to-mesenchymal transition. Carlton AL, Illendula A, Gao Y, Llaneza DC, Boulton A, Shah A, Rajewski RA, Landen CN, Wotton D, Bushweller JH. Gynecol Oncol. 2018 May;149(2):350-360. doi: 10.1016/j.ygyno.2018.03.005. Epub 2018 Mar 16. PMID: 29551565

Differential Expression of Homing Receptor Ligands on Tumor-Associated Vasculature that Control CD8 Effector T-cell Entry. Woods AN, Wilson AL, Srivinisan N, Zeng J, Dutta AB, Peske JD, Tewalt EF, Gregg RK, Ferguson AR, Engelhard VH. Cancer Immunol Res. 2017 Dec;5(12):1062-1073. doi: 10.1158/2326-6066.CIR-17-0190. Epub 2017 Nov 2. PMID: 29097419

CRISPR Ethics: Moral Considerations for Applications of a Powerful Tool. Brokowski C, Adli M. J Mol Biol. 2018 Jun 7. pii: S0022-2836(18)30586-2. doi: 10.1016/j.jmb.2018.05.044. PMID: 29885329

Correction to: Multiple receptor tyrosine kinases converge on microRNA-134 to control KRAS, STAT5B, and glioblastoma. Zhang Y, Kim J, Mueller AC, Dey B, Yang Y, Lee DH, Hachmann J, Finderle S, Park DM, Christensen J, Schiff D, Purow B, Dutta A, Abounader R.

Cell Death Differ. 2018 Jun 13. doi: 10.1038/s41418-018-0145-0. PMID: 29899381 TGFβ signaling limits lineage plasticity in prostate cancer. Hao Y, Bjerke GA, Pietrzak K, Melhuish TA, Han Y, Turner SD, Frierson HF Jr, Wotton D. PLoS Genet. 2018 May 21;14(5):e1007409. doi: 10.1371/journal.pgen.1007409. eCollection 2018 May. PMID: 29782499

Cryo-EM of bacterial pili and archaeal flagellar filaments. Egelman EH. Curr Opin Struct Biol. 2017 Oct;46:31-37. doi: 10.1016/j.sbi.2017.05.012. Epub 2017 Jun 10. Review. PMID: 28609682

Deletion of Ptpn1 induces myeloproliferative neoplasm. Jobe F, Patel B, Kuzmanovic T, Makishima H, Yang Y, Przychodzen B, Hutchison RE, Bence KK, Maciejewski JP, Mohi G. Leukemia. 2017 May;31(5):1229-1234. doi: 10.1038/leu.2017.31. Epub 2017 Jan 23. No abstract available. PMID:

TGFβ signaling limits lineage plasticity in prostate cancer. Hao Y, Bjerke GA, Pietrzak K, Melhuish TA, Han Y, Turner SD, Frierson HF Jr, Wotton D. PLoS Genet. 2018 May 21;14(5):e1007409. doi: 10.1371/journal.pgen.1007409. eCollection 2018 May. PMID: 29782499

Functions of TGIF homeodomain proteins and their roles in normal brain development and holoprosencephaly. Wotton D, Taniguchi K. Am J Med Genet C Semin Med Genet. 2018 May 11. doi: 10.1002/ajmg.c.31612. PMID: 29749689

Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK. Maqani N, Fine RD, Shahid M, Li M, Enriquez-Hesles E, Smith JS. Microb Cell. 2018 Feb 19;5(5):233-248. doi: 10.15698/mic2018.05.630. PMID: 29796388

The RNA-editing enzyme ADAR promotes lung adenocarcinoma migration and invasion by stabilizing FAK. Amin EM, Liu Y, Deng S, Tan KS, Chudgar N, Mayo MW, Sanchez-Vega F, Adusumilli PS, Schultz N, Jones DR. Sci Signal. 2017 Sep 19;10(497). pii: eaah3941. doi: 10.1126/scisignal.aah3941. PMID: 28928239

tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer independent manner. Kuscu C, Kumar P, Kiran M, Su Z, Malik A, Dutta A. RNA. 2018 May 29. pii: rna.066126.118. doi: 10.1261/rna.066126.118. PMID: 29844106

Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation. Kumar P, Dillon LW, Shibata Y, Jazaeri AA, Jones DR, Dutta A. Mol Cancer Res. 2017 Sep;15(9):1197-1205. doi: 10.1158/1541-7786.MCR-17-0095. Epub 2017 May 26. PMID: 28550083

The CRISPR tool kit for genome editing and beyond. Adli M. Nat Commun. 2018 May 15;9(1):1911. doi: 10.1038/s41467-018-04252-2. Review. PMID: 29765029

An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking. Hoffman EA, Zaidi H, Shetty SJ, Bekiranov S, Auble DT. Bio Protoc. 2018 Feb 20;8(4). pii: e2905. doi: 10.21769/bioprotoc.2905. PMID: 29682595

P190RhoGAP prevents mitotic spindle fragmentation and is required to activate Aurora A kinase at acentriolar poles. Manukyan A, Sargsyan L, Parsons SJ, Stukenberg PT. Chromosoma. 2018 Apr 14. doi: 10.1007/s00412-018-0670-0. PMID: 29656322

Posttranslational mechanisms controlling centromere function and assembly. Srivastava S, Zasadzińska E, Foltz DR. Curr Opin Cell Biol. 2018 Apr 2;52:126-135. doi: 10.1016/j.ceb.2018.03.003. PMID: 29621654

Mislocalization of centromeric histone H3 variant CENP-A contributes to chromosomal instability (CIN) in human cells. Shrestha RL, Ahn GS, Staples MI, Sathyan KM, Karpova TS, Foltz DR, Basrai MA. Oncotarget. 2017 Jul 18;8(29):46781-46800. doi: 10.18632/oncotarget.18108. PMID: 28596481

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq. Guertin MJ, Cullen AE, Markowetz F, Holding AN. Nucleic Acids Res. 2018 Apr 17. doi: 10.1093/nar/gky252. PMID: 29672735

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, Zang C. Bioinformatics. 2018 Mar 28. doi: 10.1093/bioinformatics/bty194. PMID: 29608647

A structural model of flagellar filament switching across multiple bacterial species. Wang F, Burrage AM, Postel S, Clark RE, Orlova A, Sundberg EJ, Kearns DB, Egelman EH. Nat Commun. 2017 Oct 16;8(1):960. doi: 10.1038/s41467-017-01075-5. PMID: 29038601

Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution. Wang F, Coureuil M, Osinski T, Orlova A, Altindal T, Gesbert G, Nassif X, Egelman EH, Craig L. Structure. 2017 Sep 5;25(9):1423-1435.e4. doi: 10.1016/j.str.2017.07.016. PMID: 28877506

Refined Cryo-EM Structure of the T4 Tail Tube: Exploring the Lowest Dose Limit. Zheng W, Wang F, Taylor NMI, Guerrero-Ferreira RC, Leiman PG, Egelman EH. Structure. 2017 Sep 5;25(9):1436-1441.e2. doi: 10.1016/j.str.2017.06.017. Epub 2017 Jul 27. PMID: 28757144

Model for a novel membrane envelope in a filamentous hyperthermophilic virus. Kasson P, DiMaio F, Yu X, Lucas-Staat S, Krupovic M, Schouten S, Prangishvili D, Egelman EH. Elife. 2017 Jun 22;6. pii: e26268. doi: 10.7554/eLife.26268. PMID: 28639939

Small molecule inhibition of the CBFβ/RUNX interaction decreases ovarian cancer growth and migration through alterations in genes related to epithelial-to-mesenchymal transition. Carlton AL, Illendula A, Gao Y, Llaneza DC, Boulton A, Shah A, Rajewski RA, Landen CN, Wotton D, Bushweller JH. Gynecol Oncol. 2018 Mar 15. pii: S0090-8258(18)30174-4. doi: 10.1016/j.ygyno.2018.03.005. PMID: 29551565

Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain. Braun T, Vos MR, Kalisman N, Sherman NE, Rachel R, Wirth R, Schröder GF, Egelman EH. Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10352-7. doi: 10.1073/pnas.1607756113. Epub 2016 Aug 30. PMID: 27578865

Transgenerational Effects of Bisphenol A on Gene Expression and DNA Methylation of Imprinted Genes in Brain. Drobná Z, Henriksen AD, Wolstenholme JT, Montiel C, Lambeth PS, Shang S, Harris EP, Zhou C, Flaws JA, Adli M, Rissman EF. Endocrinology. 2018 Jan 1;159(1):132-144. doi: 10.1210/en.2017-00730. PMID: 29165653

Neutrophils: positive or negative? Taylor RP. Blood. 2017 May 11;129(19):2596-2597. doi: 10.1182/blood-2017-03-774695. No abstract available. PMID: 28495923

Functional role of the type 1 pilus rod structure in mediating host-pathogen interactions.

Spaulding CN, Schreiber HL, Zheng W, Dodson KW, Hazen JE, Conover MS, Wang F, Svenmarker P, Luna-Rico A, Francetic O, Andersson M, Hultgren S, Egelman EH.

Elife. 2018 Jan 18;7. pii: e31662. doi: 10.7554/eLife.31662. PMID: 29345620

Regulation of Mammalian DNA Replication via the Ubiquitin-Proteasome System. Abbas T, Dutta A. Adv Exp Med Biol. 2017;1042:421-454. doi: 10.1007/978-981-10-6955-0_19. PMID: 29357069

Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. Paulsen T, Kumar P, Koseoglu MM, Dutta A. Trends Genet. 2018 Jan 9. pii: S0168-9525(17)30230-5. doi: 10.1016/j.tig.2017.12.010. PMID: 29329720

Second-generation method for analysis of chromatin binding with formaldehyde-cross-linking kinetics. Zaidi H, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT. J Biol Chem. 2017 Nov 24;292(47):19338-19355. doi: 10.1074/jbc.M117.796441. Epub 2017 Sep 26. PMID: 28972159

Analysis of transcriptional activity by the Myt1 and Myt1l transcription factors. Manukyan A, Kowalczyk I, Melhuish TA, Lemiesz A, Wotton D. J Cell Biochem. 2018 Jan 1. doi: 10.1002/jcb.26636. PMID: 29291346

In Vitro Assay to Study Histone Ubiquitination During Transcriptional Regulation. Tushir-Singh J, Bhatnagar S. Methods Mol Biol. 2017;1507:235-244. PMID: 27832544

Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology. Mechanic LE, Lindström S, Daily KM, Sieberts SK, Amos CI, Chen HS, Cox NJ, Dathe M, Feuer EJ, Guertin MJ, Hoffman J, Liu Y, Moore JH, Myers CL, Ritchie MD, Schildkraut J, Schumacher F, Witte JS, Wang W, Williams SM; U4C Challenge Participants; U4C Challenge Data Contributors, Gillanders EM. PLoS Genet. 2017 Sep 28;13(9):e1006945. doi: 10.1371/journal.pgen.1006945. eCollection 2017 Sep. No abstract available. PMID: 28957327

Transcriptional response to stress is pre-wired by promoter and enhancer architecture. Vihervaara A, Mahat DB, Guertin MJ, Chu T, Danko CG, Lis JT, Sistonen L. Nat Commun. 2017 Aug 15;8(1):255. doi: 10.1038/s41467-017-00151-0. PMID: 28811569

2017

Resolution advances in cryo-EM enable application to drug discovery. Subramaniam S, Earl LA, Falconieri V, Milne JL, Egelman EH. Curr Opin Struct Biol. 2016 Dec;41:194-202. doi: 10.1016/j.sbi.2016.07.009. Epub 2016 Aug 20. Review PMID: 27552081

Noncoding RNAs in Glioblastoma. Zhang Y, Cruickshanks N, Pahuski M, Yuan F, Dutta A, Schiff D, Purow B, Abounader R. In: De Vleeschouwer S, editor. Glioblastoma [Internet]. Brisbane (AU): Codon Publications; 2017 Sep 27. PMID: 29251875

Cytotoxic mechanisms of immunotherapy: Harnessing complement in the action of anti-tumor monoclonal antibodies. Taylor RP, Lindorfer MA. Semin Immunol. 2016 Jun;28(3):309-16. doi: 10.1016/j.smim.2016.03.003. Epub 2016 Mar 19. Review. PMID: 27009480

Transgenerational effects of Bisphenol A on gene expression and DNA methylation of imprinted genes in brain. Drobná Z, Henriksen AD, Wolstenholme JT, Montiel C, Lambeth PS, Shang S, Harris EP, Zhou C, Flaws JA, Adli M, Rissman EF. Endocrinology. 2017 Nov 17. doi: 10.1210/en.2017-00730. PMID: 29165653

Corrigendum to: “Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers” [EBioMedicine 8 (2016) 117-131]. Illendula A, Gilmour J, Grembecka J, Tirumala VSS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH. EBioMedicine. 2017 Nov;25:188. doi: 10.1016/j.ebiom.2017.10.029. Epub 2017 Oct 31. No abstract available. PMID: 29104075

The protein kinase C super-family member PKN is regulated by mTOR and influences differentiation during prostate cancer progression. Yang CS, Melhuish TA, Spencer A, Ni L, Hao Y, Jividen K, Harris TE, Snow C, Frierson HF Jr, Wotton D, Paschal BM. Prostate. 2017 Nov;77(15):1452-1467. doi: 10.1002/pros.23400. Epub 2017 Sep 6. PMID: 28875501

The Impact of dUTPase on Ribonucleotide Reductase-Induced Genome Instability in Cancer Cells. Chen CW, Tsao N, Huang LY, Yen Y, Liu X, Lehman C, Wang YH, Tseng MC, Chen YJ, Ho YC, Chen CF, Chang ZF. Cell Rep. 2016 Aug 2;16(5):1287-1299. doi: 10.1016/j.celrep.2016.06.094. Epub 2016 Jul 21. PMID: 27452458

Using SQL Databases for Sequence Similarity Searching and Analysis. Pearson WR, Mackey AJ. Curr Protoc Bioinformatics. 2017 Sep 13;59:9.4.1-9.4.22. doi: 10.1002/cpbi.32. PMID: 28902397

Single-cell analysis of diversity in human stem cell-derived neurons. Harbom LJ, Michel N, McConnell MJ. Cell Tissue Res. 2017 Nov 29. doi: 10.1007/s00441-017-2728-3. PMID: 29185070

Identification of breast cancer associated variants that modulate transcription factor binding. Liu Y, Walavalkar NM, Dozmorov MG, Rich SS, Civelek M, Guertin MJ. PLoS Genet. 2017 Sep 28;13(9):e1006761. doi: 10.1371/journal.pgen.1006761. eCollection 2017 Sep. PMID: 28957321

Second-generation method for analysis of chromatin binding with formaldehyde crosslinking kinetics. Zaidi H, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT. J Biol Chem. 2017 Sep 26. pii: jbc.M117.796441. doi: 10.1074/jbc.M117.796441. PMID: 28972159

Echocardiographic Ischemic Memory Imaging Through Complement-Mediated Vascular Adhesion of Phosphatidylserine-Containing Microbubbles. Mott B, Packwood W, Xie A, Belcik JT, Taylor RP, Zhao Y, Davidson BP, Lindner JR. JACC Cardiovasc Imaging. 2016 Aug;9(8):937-46. doi: 10.1016/j.jcmg.2015.11.031. Epub 2016 Jun 15. PMID: 27318722

Microenvironmental agonists generate de novo phenotypic resistance to combined ibrutinib plus venetoclax in CLL and MCL. Jayappa KD, Portell CA, Gordon VL, Capaldo BJ, Bekiranov S, Axelrod MJ, Brett LK, Wulfkuhle JD, Gallagher RI, Petricoin EF, Bender TP, Williams ME, Weber MJ. Blood Adv. 2017 Jun 13;1(14):933-946. PMID: 29034364. Shibata E, Kiran M, Shibata Y, Singh S, Kiran S, Dutta A. Elife. 2016 Dec 1;5. pii: e19084. doi: 10.7554/eLife.19084. PMID: 27906128

SUMO and Chromatin Remodeling. Wotton D, Pemberton LF, Merrill-Schools J. Adv Exp Med Biol. 2017;963:35-50. doi: 10.1007/978-3-319-50044-7_3. Review. PMID: 28197905

Neonatal expression of RNA-binding protein IGF2BP3 regulates the human fetal-adult megakaryocyte transition. Elagib KE, Lu CH, Mosoyan G, Khalil S, Zasadzińska E, Foltz DR, Balogh P, Gru AA, Fuchs DA, Rimsza LM, Verhoeyen E, Sansó M, Fisher RP, Iancu-Rubin C, Goldfarb AN. J Clin Invest. 2017 Jun 1;127(6):2365-2377. doi: 10.1172/JCI88936. Epub 2017 May 8. PMID: 28481226

HJURP interaction with the condensin II complex during G1 promotes CENP-A deposition. Barnhart-Dailey MC, Trivedi P, Stukenberg PT, Foltz DR. Mol Biol Cell. 2017 Jan 1;28(1):54-64. doi: 10.1091/mbc.E15-12-0843. Epub 2016 Nov 2. PMID: 27807043

Differential Binding Partners of the Mis18α/β YIPPEE Domains Regulate Mis18 Complex Recruitment to Centromeres. Stellfox ME, Nardi IK, Knippler CM, Foltz DR. Cell Rep. 2016 Jun 7;15(10):2127-2135. doi: 10.1016/j.celrep.2016.05.004. Epub 2016 May 26. PMID: 27239045

Mechanism of Ska Recruitment by Ndc80 Complexes to Kinetochores. Janczyk PŁ, Skorupka KA, Tooley JG, Matson DR, Kestner CA, West T, Pornillos O, Stukenberg PT. Dev Cell. 2017 May 22;41(4):438-449.e4. doi: 10.1016/j.devcel.2017.04.020. PMID: 28535377

ASF1a Promotes Non-homologous End Joining Repair by Facilitating Phosphorylation of MDC1 by ATM at Double-Strand Breaks. Lee KY, Im JS, Shibata E, Dutta A. Mol Cell. 2017 Sep 13. pii: S1097-2765(17)30618-4. doi: 10.1016/j.molcel.2017.08.021. PMID: 28943310

Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling. Ve T, Vajjhala PR, Hedger A, Croll T, DiMaio F, Horsefield S, Yu X, Lavrencic P, Hassan Z, Morgan GP, Mansell A, Mobli M, O’Carroll A, Chauvin B, Gambin Y, Sierecki E, Landsberg MJ, Stacey KJ, Egelman EH, Kobe B. Nat Struct Mol Biol. 2017 Sep;24(9):743-751. doi: 10.1038/nsmb.3444. Epub 2017 Jul 31. PMID: 28759049

Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex. Fu TM, Li Y, Lu A, Li Z, Vajjhala PR, Cruz AC, Srivastava DB, DiMaio F, Penczek PA, Siegel RM, Stacey KJ, Egelman EH, Wu H. Mol Cell. 2016 Oct 20;64(2):236-250. doi: 10.1016/j.molcel.2016.09.009. Epub 2016 Oct 13. PMID: 27746017

Perfluorocarbon emulsions radiosensitise brain tumors in carbogen breathing mice with orthotopic GL261 gliomas. Feldman LA, Fabre MS, Grasso C, Reid D, Broaddus WC, Lanza GM, Spiess BD, Garbow JR, McConnell MJ, Herst PM. PLoS One. 2017 Sep 5;12(9):e0184250. doi: 10.1371/journal.pone.0184250. eCollection 2017. PMID: 28873460

Ubiquitin Modification by the E3 Ligase/ADP-Ribosyltransferase Dtx3L/Parp9. Yang CS, Jividen K, Spencer A, Dworak N, Ni L, Oostdyk LT, Chatterjee M, Kuśmider B, Reon B, Parlak M, Gorbunova V, Abbas T, Jeffery E, Sherman NE, Paschal BM. Mol Cell. 2017 May 18;66(4):503-516.e5. doi: 10.1016/j.molcel.2017.04.028. PMID: 28525742

Using SQL Databases for Sequence Similarity Searching and Analysis. Pearson WR, Mackey AJ. Curr Protoc Bioinformatics. 2017 Sep 13;59:9.4.1-9.4.22. doi: 10.1002/cpbi.32. PMID: 28902397

Caloric Restriction Extends Yeast Chronological Life Span by Optimizing the Snf1 (AMPK) Signaling Pathway. Wierman MB, Maqani N, Strickler E, Li M, Smith JS. Mol Cell Biol. 2017 Jun 15;37(13). pii: e00562-16. doi: 10.1128/MCB.00562-16. Print 2017 Jul 1. PMID: 28373292

Complement C5a-Induced Changes in Neutrophil Morphology During Inflammation. Denk S, Taylor RP, Wiegner R, Cook EM, Lindorfer MA, Pfeiffer K, Paschke S, Eiseler T, Weiss M, Barth E, Lambris JD, Kalbitz M, Martin T, Barth H, Messerer DAC, Gebhard F, Huber-Lang MS. Scand J Immunol. 2017 Sep;86(3):143-155. doi: 10.1111/sji.12580. PMID: 28671713

IgG Fc domains that bind C1q but not effector Fcγ receptors delineate the importance of complement-mediated effector functions. Lee CH, Romain G, Yan W, Watanabe M, Charab W, Todorova B, Lee J, Triplett K, Donkor M, Lungu OI, Lux A, Marshall N, Lindorfer MA, Goff OR, Balbino B, Kang TH, Tanno H, Delidakis G, Alford C, Taylor RP, Nimmerjahn F, Varadarajan N, Bruhns P, Zhang YJ, Georgiou G. Nat Immunol. 2017 Aug;18(8):889-898. doi: 10.1038/ni.3770. Epub 2017 Jun 12. PMID: 28604720

Hexamerization-enhanced CD20 antibody mediates complement-dependent cytotoxicity in serum genetically deficient in C9. Taylor RP, Lindorfer MA, Cook EM, Beurskens FJ, Schuurman J, Parren PWHI, Zent CS, VanDerMeid KR, Burack R, Mizuno M, Morgan BP. Clin Immunol. 2017 Aug;181:24-28. doi: 10.1016/j.clim.2017.05.016. Epub 2017 May 31. PMID: 28578024

Antibodies That Efficiently Form Hexamers upon Antigen Binding Can Induce Complement-Dependent Cytotoxicity under Complement-Limiting Conditions. Cook EM, Lindorfer MA, van der Horst H, Oostindie S, Beurskens FJ, Schuurman J, Zent CS, Burack R, Parren PW, Taylor RP. J Immunol. 2016 Sep 1;197(5):1762-75. doi: 10.4049/jimmunol.1600648. Epub 2016 Jul 29. PMID: 27474078

DNA fragile site breakage as a measure of chemical exposure and predictor of individual susceptibility to form oncogenic rearrangements. Lehman CE, Dillon LW, Nikiforov YE, Wang YH. Carcinogenesis. 2017 Mar 1;38(3):293-301. doi: 10.1093/carcin/bgw210. PMID: 28069693

Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective. Cherepanova OA, Gomez D, Shankman LS, Swiatlowska P, Williams J, Sarmento OF, Alencar GF, Hess DL, Bevard MH, Greene ES, Murgai M, Turner SD, Geng YJ, Bekiranov S, Connelly JJ, Tomilin A, Owens GK. Nat Med. 2016 Jun;22(6):657-65. doi: 10.1038/nm.4109. Epub 2016 May 16. PMID: 27183216

Orchestrating the Specific Assembly of Centromeric Nucleosomes. Zasadzińska E, Foltz DR. Prog Mol Subcell Biol. 2017;56:165-192. doi: 10.1007/978-3-319-58592-5_7. PMID: 28840237

CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations. Kuscu C, Parlak M, Tufan T, Yang J, Szlachta K, Wei X, Mammadov R, Adli M. Nat Methods. 2017 Jul;14(7):710-712. doi: 10.1038/nmeth.4327. Epub 2017 Jun 5. PMID: 28581493

Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). Kumar P, Kuscu C, Dutta A.Trends Biochem Sci. 2016 Aug;41(8):679-689. doi: 10.1016/j.tibs.2016.05.004. Epub 2016 Jun 1. Review. PMID: 27263052

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps. Frenz B, Walls AC, Egelman EH, Veesler D, DiMaio F. Nat Methods. 2017 Aug;14(8):797-800. doi: 10.1038/nmeth.4340. Epub 2017 Jun 19. PMID: 28628127

Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. Pearson WR, Li W, Lopez R. Nucleic Acids Res. 2017 Apr 20;45(7):e46. doi: 10.1093/nar/gkw1207. PMID: 27923999

CK2α’ Drives Lung Cancer Metastasis by Targeting BRMS1 Nuclear Export and Degradation. Liu Y, Amin EB, Mayo MW, Chudgar NP, Bucciarelli PR, Kadota K, Adusumilli PS, Jones DR. Cancer Res. 2016 May 1;76(9):2675-86. doi: 10.1158/0008-5472.CAN-15-2888. Epub 2016 Mar 15. PMID: 26980766

Refined Cryo-EM Structure of the T4 Tail Tube: Exploring the Lowest Dose Limit. Zheng W, Wang F, Taylor NMI, Guerrero-Ferreira RC, Leiman PG, Egelman EH. Structure. 2017 Jul 10. pii: S0969-2126(17)30213-7. doi: 10.1016/j.str.2017.06.017. PMID: 28757144

Genome-Wide Identification of Basic Helix-Loop-Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus. Pooley JR, Flynn BP, Grøntved L, Baek S, Guertin MJ, Kershaw YM, Birnie MT, Pellatt A, Rivers CA, Schiltz RL, Hager GL, Lightman SL, Conway-Campbell BL. Endocrinology. 2017 May 1;158(5):1486-1501. doi: 10.1210/en.2016-1929. PMID: 28200020

Complement C5a-induced changes in neutrophil morphology during inflammation. Denk S, Taylor RP, Wiegner R, Cook EM, Lindorfer MA, Pfeiffer K, Paschke S, Eiseler T, Weiss M, Barth E, Lambris JD, Kalbitz M, Martin T, Barth H, Messerer DAC, Gebhard F, Huber-Lang MS. Scand J Immunol. 2017 Jun 30. doi: 10.1111/sji.12580. PMID: 28671713

Pericytes and immune cells contribute to complement activation in tubulointerstitial fibrosis. Xavier S, Sahu RK, Landes SG, Yu J, Taylor RP, Ayyadevara S, Megyesi J, Stallcup WB, Duffield JS, Reis ES, Lambris JD, Portilla D. Am J Physiol Renal Physiol. 2017 Mar 1;312(3):F516-F532. doi: 10.1152/ajprenal.00604.2016. Epub 2017 Jan 4. PMID: 28052876

Tgif1 and Tgif2 Repress Expression of the RabGAP Evi5l. Anderson AE, Taniguchi K, Hao Y, Melhuish TA, Shah A, Turner SD, Sutherland AE, Wotton D. Mol Cell Biol. 2017 Feb 15;37(5). pii: e00527-16. doi: 10.1128/MCB.00527-16. Print 2017 Mar 1. PMID: 27956704

Genetic and Molecular Analyses indicate independent effects of TGIFs on Nodal and Gli3 in neural tube patterning. Taniguchi K, Anderson AE, Melhuish TA, Carlton AL, Manukyan A, Sutherland AE, Wotton D. Eur J Hum Genet. 2017 Feb;25(2):208-215. doi: 10.1038/ejhg.2016.164. Epub 2016 Dec 7. PMID: 27924807

Tgif1 and Tgif2 Regulate Axial Patterning in Mouse. Melhuish TA, Taniguchi K, Wotton D. PLoS One. 2016 May 17;11(5):e0155837. doi: 10.1371/journal.pone.0155837. eCollection 2016. PMID: 27187787

Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. Chen X, Poorey K, Carver MN, Müller U, Bekiranov S, Auble DT, Brow DA. PLoS Genet. 2017 Jun 30;13(6):e1006863. doi: 10.1371/journal.pgen.1006863. eCollection 2017 Jun. PMID: 28665995

RNA Polymerase I and Fob1 contributions to transcriptional silencing at the yeast rDNA locus.Buck SW, Maqani N, Matecic M, Hontz RD, Fine RD, Li M, Smith JS. Nucleic Acids Res. 2016 Jul 27;44(13):6173-84. doi: 10.1093/nar/gkw212. Epub 2016 Apr 8. PMID: 27060141

Model for a novel membrane envelope in a filamentous hyperthermophilic virus. Egelman EH, Kasson PM, DiMaio F, Yu X, Lucas-Staat S, Krupovic M, Schouten S, Prangishvili D. Elife. 2017 Jun 22;6. pii: e26268. doi: 10.7554/eLife.26268. PMID: 28639939

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps. Frenz B, Walls AC, Egelman EH, Veesler D, DiMaio F. Nat Methods. 2017 Jun 19. doi: 10.1038/nmeth.4340. PMID: 28628127

Cryo-EM of bacterial pili and archaeal flagellar filaments. Egelman EH. Curr Opin Struct Biol. 2017 Jun 10;46:31-37. doi: 10.1016/j.sbi.2017.05.012. Review. PMID: 28609682

Mislocalization of centromeric histone H3 variant CENP-A contributes to chromosomal instability (CIN) in human cells. Shrestha RL, Ahn GS, Staples MI, Sathyan KM, Karpova TS, Foltz DR, Basrai MA. Oncotarget. 2017 May 23. doi: 10.18632/oncotarget.18108. PMID: 28596481

The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization.

True JD, Muldoon JJ, Carver MN, Poorey K, Shetty SJ, Bekiranov S, Auble DT. J Biol Chem. 2016 Jul 15;291(29):15307-19. doi: 10.1074/jbc.M116.735134. Epub 2016 May 16. PMID: 27226635

Neutrophils: positive or negative? Taylor RP. Blood. 2017 May 11;129(19):2596-2597. doi: 10.1182/blood-2017-03-774695. PMID: 28495923

Ubiquitin Modification by the E3 Ligase/ADP-Ribosyltransferase Dtx3L/Parp9.Yang CS, Jividen K, Spencer A, Dworak N, Ni L, Oostdyk LT, Chatterjee M, Kuśmider B, Reon B, Parlak M, Gorbunova V, Abbas T, Jeffery E, Sherman NE, Paschal BM. Mol Cell. 2017 May 18;66(4):503-516.e5. doi: 10.1016/j.molcel.2017.04.028. PMID: 28525742

Normal and Cancerous Tissues Release extrachromosomal circular DNA (eccDNA) into the Circulation. Kumar P, Dillon L, Shibata Y, Jazaeri AA, Jones DR, Dutta A. Mol Cancer Res. 2017 May 26. pii: molcanres.0095.2016. doi: 10.1158/1541-7786.MCR-17-0095. PMID: 28550083

Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis. Reon BJ, Anaya J, Zhang Y, Mandell J, Purow B, Abounader R, Dutta A. PLoS Med. 2016 Dec 6;13(12):e1002192. doi: 10.1371/journal.pmed.1002192. eCollection 2016 Dec. PMID: 27923049

Molecular Mechanism of Mot1, a TATA-binding Protein (TBP)-DNA Dissociating Enzyme. Viswanathan R, True JD, Auble DT. J Biol Chem. 2016 Jul 22;291(30):15714-26. doi: 10.1074/jbc.M116.730366. Epub 2016 Jun 2. PMID: 27255709

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation. Duarte FM, Fuda NJ, Mahat DB, Core LJ, Guertin MJ, Lis JT. Genes Dev. 2016 Aug 1;30(15):1731-46. doi: 10.1101/gad.284430.116. Epub 2016 Aug 4. PMID: 27492368

Caloric restriction extends yeast chronological lifespan by optimizing the Snf1 (AMPK) signaling pathway. Wierman MB, Maqani N, Strickler E, Li M, Smith JS. Mol Cell Biol. 2017 Apr 3. pii: MCB.00562-16. doi: 10.1128/MCB.00562-16. PMID: 28373292

SUMO and Chromatin Remodeling. Wotton D, Pemberton LF, Merrill-Schools J. Adv Exp Med Biol. 2017;963:35-50. doi: 10.1007/978-3-319-50044-7_3. PMID: 28197905

Genome-wide identification of basic helix-loop helix and NF-1 motifs underlying GR binding sites in male rat hippocampus. Pooley JR, Flynn BP, Grøntved L, Baek S, Guertin MJ, Kershaw YM, Birnie MT, Pellatt A, Rivers CA, Schiltz RL, Hager GL, Lightman SL, Conway-Campbell BL. Endocrinology. 2017 Feb 13. doi: 10.1210/en.2016-1929. No abstract available. PMID: 28200020

Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers. Illendula A, Gilmour J, Grembecka J, Tirumala VS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH. EBioMedicine. 2016 Jun;8:117-31. doi: 10.1016/j.ebiom.2016.04.032. PMID: 27428424

The human SKA complex drives the metaphase-anaphase cell cycle transition by recruiting protein phosphatase 1 to kinetochores. Sivakumar S, Janczyk PŁ, Qu Q, Brautigam CA, Stukenberg PT, Yu H, Gorbsky GJ. Elife. 2016 Mar 16;5. pii: e12902. doi: 10.7554/eLife.12902. PMID: 26981768

DNA Fragile Site Breakage as a Measure of Chemical Exposure and Predictor of Individual Susceptibility to Form Oncogenic Rearrangements. Lehman CE, Dillon LW, Nikiforov YE, Wang YH. Carcinogenesis. 2017 Jan 9. pii: bgw210. doi: 10.1093/carcin/bgw210. PMID: 28069693

RNA synthesis is associated with multiple TBP-chromatin binding events. Zaidi HA, Auble DT, Bekiranov S. Sci Rep. 2017 Jan 4;7:39631. doi: 10.1038/srep39631. PMID: 28051102

Pericyte and immune cells contribute to complement activation in tubulointerstitial fibrosis.Xavier S, Sahu RK, Landes SG, Yu J, Taylor RP, Ayyadevara S, Megyesi J, Stallcup WB, Duffield JS, Reis ES, Lambris JD, Portilla D. Am J Physiol Renal Physiol. 2017 Jan 4:ajprenal.00604.2016. doi: 10.1152/ajprenal.00604.2016. PMID: 28052876

Single neuron transcriptome analysis can reveal more than cell type classification: Does it matter if every neuron is unique? Harbom LJ, Chronister WD, McConnell MJ. Bioessays. 2016 Feb;38(2):157-61. doi: 10.1002/bies.201500097. Review. PMID: 26749010

2016

Evolution of Osteocrin as an activity-regulated factor in the primate brain. Ataman B, Boulting GL, Harmin DA, Yang MG, Baker-Salisbury M, Yap EL, Malik AN, Mei K, Rubin AA, Spiegel I, Durresi E, Sharma N, Hu LS, Pletikos M, Griffith EC, Partlow JN, Stevens CR, Adli M, Chahrour M, Sestan N, Walsh CA, Berezovskii VK, Livingstone MS, Greenberg ME. Nature. 2016 Nov 10;539(7628):242-247. doi: 10.1038/nature20111. PMID: 27830782

The Current Revolution in Cryo-EM. Egelman EH. Biophys J. 2016 Mar 8;110(5):1008-12. doi: 10.1016/j.bpj.2016.02.001. Review. No abstract available. PMID: 26958874

Biophysical Journal Special Issue: Focus on Cryo-EM. Egelman EH, Engel A. Biophys J. 2016 Feb 23;110(4):E01. doi: 10.1016/j.bpj.2016.01.025. No abstract available. PMID: 26910436

Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. Pearson WR, Li W, Lopez R. Nucleic Acids Res. 2016 Dec 6. pii: gkw1207. PMID: 27923999

Finding Protein and Nucleotide Similarities with FASTA. Pearson WR. Curr Protoc Bioinformatics. 2016 Mar 24;53:3.9.1-25. doi: 10.1002/0471250953.bi0309s53. PMID: 27010337

Tgif1 and Tgif2 repress expression of the RabGAP, Evi5l. Anderson AE, Taniguchi K, Hao Y, Melhuish TA, Shah A, Turner SD, Sutherland AE, Wotton D. Mol Cell Biol. 2016 Dec 12. pii: MCB.00527-16. PMID: 27956704

Genetic and Molecular Analyses indicate independent effects of TGIFs on Nodal and Gli3 in neural tube patterning. Taniguchi K, Anderson AE, Melhuish TA, Carlton AL, Manukyan A, Sutherland AE, Wotton D. Eur J Hum Genet. 2016 Dec 7. doi: 10.1038/ejhg.2016.164. PMID: 27924807

In Vitro Assay to Study Histone Ubiquitination During Transcriptional Regulation. Tushir-Singh J, Bhatnagar S. Methods Mol Biol. 2017;1507:235-244. PMID: 27832544

Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas. Roller DG, Capaldo B, Bekiranov S, Mackey AJ, Conaway MR, Petricoin EF, Gioeli D, Weber MJ. Oncotarget. 2016 Jan 19;7(3):2734-53. doi: 10.18632/oncotarget.6548. PMID: 26673621

CRISPR-Cas9-AID base editor is a powerful gain-of-function screening tool. Kuscu C, Adli M. Nat Methods. 2016 Nov 29;13(12):983-984. doi: 10.1038/nmeth.4076. No abstract available. PMID: 27898061

Evolution of Osteocrin as an activity-regulated factor in the primate brain. Ataman B, Boulting GL, Harmin DA, Yang MG, Baker-Salisbury M, Yap EL, Malik AN, Mei K, Rubin AA, Spiegel I, Durresi E, Sharma N, Hu LS, Pletikos M, Griffith EC, Partlow JN, Stevens CR, Adli M, Chahrour M, Sestan N, Walsh CA, Berezovskii VK, Livingstone MS, Greenberg ME. Nature. 2016 Nov 9;539(7628):242-247. doi: 10.1038/nature20111. PMID: 27830782

Two subunits of human ORC are dispensable for DNA replication and proliferation. Shibata E, Kiran M, Shibata Y, Singh S, Kiran S, Dutta A. Elife. 2016 Dec 1;5. pii: e19084. doi: 10.7554/eLife.19084. PMID: 27906128

Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. Brennand KJ, Marchetto MC, Benvenisty N, Brüstle O, Ebert A, Izpisua Belmonte JC, Kaykas A, Lancaster MA, Livesey FJ, McConnell MJ, McKay RD, Morrow EM, Muotri AR, Panchision DM, Rubin LL, Sawa A, Soldner F, Song H, Studer L, Temple S, Vaccarino FM, Wu J, Vanderhaeghen P, Gage FH, Jaenisch R. Stem Cell Reports. 2015 Dec 8;5(6):933-45. doi: 10.1016/j.stemcr.2015.10.011. PMID: 26610635

Bacterial flagellar capping proteins adopt diverse oligomeric states. Postel S, Deredge D, Bonsor DA, Yu X, Diederichs K, Helmsing S, Vromen A, Friedler A, Hust M, Egelman EH, Beckett D, Wintrode PL, Sundberg EJ. Elife. 2016 Sep 24;5. pii: e18857. doi: 10.7554/eLife.18857. PMID: 27664419

Structure of the Neisseria meningitidis Type IV pilus. Kolappan S, Coureuil M, Yu X, Nassif X, Egelman EH, Craig L. Nat Commun. 2016 Oct 4;7:13015. doi: 10.1038/ncomms13015. PMID: 27698424

Structure of the Bacterial Sex F Pilus Reveals an Assembly of a Stoichiometric Protein-Phospholipid Complex. Costa TR, Ilangovan A, Ukleja M, Redzej A, Santini JM, Smith TK, Egelman EH, Waksman G. Cell. 2016 Sep 8;166(6):1436-1444.e10. doi: 10.1016/j.cell.2016.08.025. PMID: 27610568

A Pro-metastatic tRNA Pathway. Kuscu C, Dutta A. Cell. 2016 Jun 2;165(6):1314-5. doi: 10.1016/j.cell.2016.05.066. PMID: 27259143

Efficacy of Hybrid Tetrahydrobenzo[d]thiazole Based Aryl Piperazines D-264 and D-301 at D₂ and D₃ Receptors. Zhen J, Antonio T, Jacob JC, Grandy DK, Reith ME, Dutta AK, Selley DE. Neurochem Res. 2016 Feb;41(1-2):328-39. doi: 10.1007/s11064-015-1808-6.

HJURP interaction with the condensin II complex during G1 promotes CENP-A deposition. Barnhart-Dailey MC, Trivedi P, Stukenberg PT, Foltz DR. Mol Biol Cell. 2016 Nov 2. pii: mbc.E15-12-0843. PMID: 27807043

A Centromere-Signaling Network Underlies the Coordination among Mitotic Events. Trivedi P, Stukenberg PT. Trends Biochem Sci. 2016 Feb;41(2):160-74. doi: 10.1016/j.tibs.2015.11.002. Review. PMID: 26705896

Connecting the microtubule attachment status of each kinetochore to cell cycle arrest through the spindle assembly checkpoint. Stukenberg PT, Burke DJ. Chromosoma. 2015 Dec;124(4):463-80. doi: 10.1007/s00412-015-0515-z. Epub 2015 Apr 28. Review. PMID: 25917595

Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Lacar B, Linker SB, Jaeger BN, Krishnaswami S, Barron J, Kelder M, Parylak S, Paquola A, Venepally P, Novotny M, O’Connor C, Fitzpatrick C, Erwin J, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH. Nat Commun. 2016 Apr 19;7:11022. doi: 10.1038/ncomms11022. PMID: 27090946

Preventing the Androgen Receptor N/C Interaction Delays Disease Onset in a Mouse Model of SBMA. Zboray L, Pluciennik A, Curtis D, Liu Y, Berman-Booty LD, Orr C, Kesler CT, Berger T, Gioeli D, Paschal BM, Merry DE. Cell Rep. 2015 Dec 15;13(10):2312-23. doi: 10.1016/j.celrep.2015.11.019. Epub 2015 Dec 7. PMID: 26673324

Dutta A. Curr Biol. 2015 Dec 7;25(23):R1112-4. No abstract available. PMID: 27027134

Biological Processes Discovered by High-Throughput Sequencing. Reon BJ, Dutta A. Am J Pathol. 2016 Apr;186(4):722-32. doi: 10.1016/j.ajpath.2015.10.033. Epub 2016 Jan 30. Review. PMID: 26828742

Protein Function Prediction: Problems and Pitfalls. Pearson WR. Curr Protoc Bioinformatics. 2015 Sep 3;51:4.12.1-8. doi: 10.1002/0471250953.bi0412s51. Review. PMID: 26334923

Centromeres of a Different CAL-ibre. Zasadzińska E, Foltz DR. Dev Cell. 2016 Apr 18;37(2):105-6. doi: 10.1016/j.devcel.2016.04.006. PMID: 27093076

Resolution advances in cryo-EM enable application to drug discovery. Subramaniam S, Earl LA, Falconieri V, Milne JL, Egelman EH. Curr Opin Struct Biol. 2016 Aug 20;41:194-202. doi: 10.1016/j.sbi.2016.07.009. PMID: 27552081

Compstatin Cp40 blocks hematin-mediated deposition of C3b fragments on erythrocytes: Implications for treatment of malarial anemia. Lindorfer MA, Cook EM, Reis ES, Ricklin D, Risitano AM, Lambris JD, Taylor RP. Clin Immunol. 2016 Aug 18;171:32-35. doi: 10.1016/j.clim.2016.08.017. PMID: 27546448

Real-time analysis of the detailed sequence of cellular events in mAb-mediated complement-dependent cytotoxicity of B-cell lines and of chronic lymphocytic leukemia B-cells. Lindorfer MA, Cook EM, Tupitza JC, Zent CS, Burack R, de Jong RN, Beurskens FJ, Schuurman J, Parren PW, Taylor RP. Mol Immunol. 2016 Feb;70:13-23. doi: 10.1016/j.molimm.2015.12.007. Epub 2015 Dec 12. PMID: 26690706

Major histocompatibility complex class I molecules protect motor neurons from astrocyte-induced toxicity in amyotrophic lateral sclerosis. Song S, Miranda CJ, Braun L, Meyer K, Frakes AE, Ferraiuolo L, Likhite S, Bevan AK, Foust KD, McConnell MJ, Walker CM, Kaspar BK. Nat Med. 2016 Apr;22(4):397-403. doi: 10.1038/nm.4052. Epub 2016 Feb 29. PMID: 26928464

Selecting the Right Similarity-Scoring Matrix. Pearson WR. Curr Protoc Bioinformatics. 2013;43:3.5.1-9. doi: 10.1002/0471250953.bi0305s43. PMID: 24509512

The Impact of dUTPase on Ribonucleotide Reductase-Induced Genome Instability in Cancer Cells. Chen CW, Tsao N, Huang LY, Yen Y, Liu X, Lehman C, Wang YH, Tseng MC, Chen YJ, Ho YC, Chen CF, Chang ZF. Cell Rep. 2016 Jul 20. pii: S2211-1247(16)30863-4. doi: 10.1016/j.celrep.2016.06.094. PMID: 27452458

Licensing of Centromeric Chromatin Assembly through the Mis18α-Mis18β Heterotetramer. Nardi IK, Zasadzińska E, Stellfox ME, Knippler CM, Foltz DR. Mol Cell. 2016 Mar 3;61(5):774-87. doi: 10.1016/j.molcel.2016.02.014. PMID: 26942680

The Xenopus ORFeome: A resource that enables functional genomics. Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ. Dev Biol. 2015 Dec 15;408(2):345-57. doi: 10.1016/j.ydbio.2015.09.004. Epub 2015 Sep 29. PMID: 26391338

Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1. Butryn A, Schuller JM, Stoehr G, Runge-Wollmann P, Förster F, Auble DT, Hopfner KP. Elife. 2015 Aug 10;4. doi: 10.7554/eLife.07432. PMID: 26258880

Actin polymerization is stimulated by actin cross-linking protein palladin. Gurung R, Yadav R, Brungardt JG, Orlova A, Egelman EH, Beck MR. Biochem J. 2016 Feb 15;473(4):383-96. doi: 10.1042/BJ20151050. Epub 2015 Nov 25. PMID: 26607837

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. Nat Protoc. 2016 Mar;11(3):499-524. doi: 10.1038/nprot.2016.015. Epub 2016 Feb 18. PMID: 26890679

Echocardiographic Ischemic Memory Imaging Through Complement-Mediated Vascular Adhesion of Phosphatidylserine-Containing Microbubbles. Mott B, Packwood W, Xie A, Belcik JT, Taylor RP, Zhao Y, Davidson BP, Lindner JR. JACC Cardiovasc Imaging. 2016 Jun 10. pii: S1936-878X(16)30244-3. doi: 10.1016/j.jcmg.2015.11.031. PMID: 27318722

Molecular Mechanism of Mot1, a TATA-Binding Protein (TBP)-DNA Dissociating Enzyme. Viswanathan R, True JD, Auble DT. J Biol Chem. 2016 Jun 2. pii: jbc.M116.730366. PMID: 27255709

The Mot1 ATPase and Spt16 Histone Chaperone Co-Regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization. True JD, Muldoon JJ, Carver MN, Poorey K, Shetty SJ, Bekiranov S, Auble DT.J Biol Chem. 2016 May 16. pii: jbc.M116.735134. PMID: 27226635

Differential Binding Partners of the Mis18α/β YIPPEE Domains Regulate Mis18 Complex Recruitment to Centromeres. Stellfox ME, Nardi IK, Knippler CM, Foltz DR. Cell Rep. 2016 May 25. pii: S2211-1247(16)30557-5. doi: 10.1016/j.celrep.2016.05.004. PMID: 27239045

Classical Genetics with Saccharomyces cerevisiae. Amberg DC, Burke DJ. Cold Spring Harb Protoc. 2016 May 2;2016(5):pdb.top077628. doi: 10.1101/pdb.top077628. PMID: 27140921

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Singh R, Kuscu C, Quinlan A, Qi Y, Adli M. Nucleic Acids Res. 2015 Oct 15;43(18):e118. doi: 10.1093/nar/gkv575. Epub 2015 Jun 1. PMID: 26032770

Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling. Hospenthal MK, Redzej A, Dodson K, Ukleja M, Frenz B, Rodrigues C, Hultgren SJ, DiMaio F, Egelman EH, Waksman G. Cell. 2016 Jan 14;164(1-2):269-78. doi: 10.1016/j.cell.2015.11.049. Epub 2015 Dec 24. PMID: 26724865

Assembly-driven activation of the AIM2 foreign-dsDNA sensor provides a polymerization template for downstream ASC. Morrone SR, Matyszewski M, Yu X, Delannoy M, Egelman EH, Sohn J. Nat Commun. 2015 Jul 22;6:7827. doi: 10.1038/ncomms8827. PMID: 26197926

Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). Kumar P, Kuscu C, Dutta A. Trends Biochem Sci. 2016 Jun 1. pii: S0968-0004(16)30032-9. doi: 10.1016/j.tibs.2016.05.004. Review. PMID: 27263052

A Pro-metastatic tRNA Pathway. Kuscu C, Dutta A. Cell. 2016 Jun 2;165(6):1314-5. doi: 10.1016/j.cell.2016.05.066. PMID: 27259143

Tgif1 and Tgif2 Regulate Axial Patterning in Mouse. Melhuish TA, Taniguchi K, Wotton D. PLoS One. 2016 May 17;11(5):e0155837. doi: 10.1371/journal.pone.0155837. eCollection 2016. PMID: 27187787

A CREB1-TGFβ2 self-sustaining loop in glioblastoma. Wotton D. Cancer Discov. 2014 Oct;4(10):1123-5. doi: 10.1158/2159-8290.CD-14-0861. PMID: 25274684

The Mot1 ATPase and Spt16 Histone Chaperone Co-Regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization. True JD, Muldoon JJ, Carver MN, Poorey K, Shetty SJ, Bekiranov S, Auble DT. J Biol Chem. 2016 May 16. pii: jbc.M116.735134. PMID: 27226635

Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma. Capaldo BJ, Roller D, Axelrod MJ, Koeppel AF, Petricoin EF, Slingluff CL Jr, Weber MJ, Mackey AJ, Gioeli D, Bekiranov S. PLoS One. 2015 Sep 25;10(9):e0138210. doi: 10.1371/journal.pone.0138210. eCollection 2015. PMID: 26405815

MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex. Lee KY, Im JS, Shibata E, Park J, Handa N, Kowalczykowski SC, Dutta A. Nat Commun. 2015 Jul 28;6:7744. doi: 10.1038/ncomms8744. PMID: 26215093

RNA Polymerase I and Fob1 contributions to transcriptional silencing at the yeast rDNA locus. Buck SW, Maqani N, Matecic M, Hontz RD, Fine RD, Li M, Smith JS. Nucleic Acids Res. 2016 Apr 8. pii: gkw212. PMID: 27060141

Centromeres of a Different CAL-ibre. Zasadzińska E, Foltz DR. Dev Cell. 2016 Apr 18;37(2):105-6. doi: 10.1016/j.devcel.2016.04.006. PMID: 27093076

Ethanolamine Signaling Promotes Salmonella Niche Recognition and Adaptation during Infection. Anderson CJ, Clark DE, Adli M, Kendall MM. PLoS Pathog. 2015 Nov 13;11(11):e1005278. doi: 10.1371/journal.ppat.1005278. eCollection 2015 Nov. Erratum in: PLoS Pathog. 2015 Dec;11(12):e1005365. PMID: 26565973

Harbom LJ, Chronister WD, McConnell MJ. Single neuron transcriptome analysis can reveal more than cell type classification: Does it matter if every neuron is unique? Bioessays. 2016 Feb;38(2):157-61. doi: 10.1002/bies.201500097. Epub 2016 Jan 8. PubMed PMID: 26749010.

Lacar, B, Linker, S.B., Jaeger, B.N., Krishnaswami, S., Barron, J., Kelder, M.S., Parylak, S., Paquola, A., Venepally, P., Novotny, M., O’Connor, C., Fitzpatrick, C., Erwin, J., Hsu, J.Y., Husband, D. McConnell, M.J., Lasken, R. and F.H. Gage. (2016). Nuclear RNA-seq of Single Neurons Reveals Signatures of Activation. Nature Communications, in press.

Song S, Miranda CJ, Braun L, Meyer K, Frakes AE, Ferraiuolo L, Likhite S, Bevan AK, Foust KD, McConnell MJ, Walker CM, Kaspar BK. Major histocompatibility complex class I molecules protect motor neurons from astrocyte-induced toxicity in amyotrophic lateral sclerosis. Nat Med. 2016 Feb 29;PubMed PMID: 26928464.

Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc. 2016 Mar;11(3):499-524. PubMed PMID: 26890679.

Sharlow, E., Leimgruber, S., Lira, A., McConnell, MJ, Norambuena, A., Bloom, G., Epperly, M., Greenberger, J., Lazo, J.S. A small molecule screen exposes mTOR signaling pathway involvement in radiation-induced apoptosis. ACS Chem Biol. 2016. Mar 14 (Epub). PubMed PMID: 26938669

Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A. Cell Rep. 2015 Jun 23;11(11):1749-59. doi: 10.1016/j.celrep.2015.05.020. Epub 2015 Jun 4. PMID: 26051933

The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus. Sakurai K, Reon BJ, Anaya J, Dutta A. Mol Cancer Res. 2015 May;13(5):828-38. doi: 10.1158/1541-7786.MCR-15-0016-T. Epub 2015 Feb 20. PMID: 25700553

The Current Revolution in Cryo-EM. Egelman EH. Biophys J. 2016 Mar 8;110(5):1008-12. doi: 10.1016/j.bpj.2016.02.001. Review. No abstract available. PMID: 26958874

Finding Protein and Nucleotide Similarities with FASTA. Pearson WR. Curr Protoc Bioinformatics. 2016 Mar 24;53:3.9.1-3.9.25. doi: 10.1002/0471250953.bi0309s53. PMID: 27010337

Cytotoxic mechanisms of immunotherapy: Harnessing complement in the action of anti-tumor monoclonal antibodies. Taylor RP, Lindorfer MA. Semin Immunol. 2016 Mar 18. pii: S1044-5323(16)00010-5. doi: 10.1016/j.smim.2016.03.003. Review. PMID: 27009480

DNA Replication Dynamics of the GGGGCC Repeat of the C9orf72 Gene. Thys RG, Wang YH. J Biol Chem. 2015 Nov 27;290(48):28953-62. doi: 10.1074/jbc.M115.660324. Epub 2015 Oct 13. PMID: 26463209

Formaldehyde crosslinking: a tool for the study of chromatin complexes. Hoffman EA, Frey BL, Smith LM, Auble DT. J Biol Chem. 2015 Oct 30;290(44):26404-11. doi: 10.1074/jbc.R115.651679. Epub 2015 Sep 9. Review. PMID: 26354429

Degree of recruitment of DOT1L to MLL-AF9 defines level of H3K79 Di- and tri-methylation on target genes and transformation potential. Kuntimaddi A, Achille NJ, Thorpe J, Lokken AA, Singh R, Hemenway CS, Adli M, Zeleznik-Le NJ, Bushweller JH. Cell Rep. 2015 May 5;11(5):808-20. doi: 10.1016/j.celrep.2015.04.004. Epub 2015 Apr 23. PMID: 25921540

Biological Processes Discovered by High-Throughput Sequencing. Reon BJ, Dutta A. Am J Pathol. 2016 Jan 29. pii: S0002-9440(16)00006-7. doi: 10.1016/j.ajpath.2015.10.033. Review. PMID: 26828742

Biophysical Journal Special Issue: Focus on Cryo-EM. Egelman EH, Engel A. Biophys J. 2016 Feb 23;110(4):E01. doi: 10.1016/j.bpj.2016.01.025. No abstract available. PMID: 26910436

Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy. Sborgi L, Ravotti F, Dandey VP, Dick MS, Mazur A, Reckel S, Chami M, Scherer S, Huber M, Böckmann A, Egelman EH, Stahlberg H, Broz P, Meier BH, Hiller S. Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13237-42. doi: 10.1073/pnas.1507579112. Epub 2015 Oct 13. PMID: 26464513

Most partial domains in proteins are alignment and annotation artifacts. Triant DA, Pearson WR. Genome Biol. 2015 May 15;16:99. doi: 10.1186/s13059-015-0656-7. PMID: 25976240

Epigenetic States of nephron progenitors and epithelial differentiation. Adli M, Parlak M, Li Y, El-Dahr SS. J Cell Biochem. 2015 Jun;116(6):893-902. doi: 10.1002/jcb.25048. Review. PMID: 25560433

The distinct functions of CENP-C and CENP-T/W in centromere propagation and function in Xenopus egg extracts. Krizaic I, Williams SJ, Sánchez P, Rodríguez-Corsino M, Stukenberg PT, Losada A. Nucleus. 2015;6(2):133-43. doi: 10.1080/19491034.2014.1003509. Epub 2015 Jan 8. PMID: 25569378

2015

Real-time analysis of the detailed sequence of cellular events in mAb-mediated complement-dependent cytotoxicity of B-cell lines and of chronic lymphocytic leukemia B-cells. Lindorfer MA, Cook EM, Tupitza JC, Zent CS, Burack R, de Jong RN, Beurskens FJ, Schuurman J, Parren PW, Taylor RP. Mol Immunol. 2015 Dec 12;70:13-23. doi: 10.1016/j.molimm.2015.12.007. PMID: 26690706

The molecular basis for flexibility in the flexible filamentous plant viruses. DiMaio F, Chen CC, Yu X, Frenz B, Hsu YH, Lin NS, Egelman EH. Nat Struct Mol Biol. 2015 Aug;22(8):642-4. doi: 10.1038/nsmb.3054. Epub 2015 Jul 13. PMID: 26167882

Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas. Roller DG, Capaldo B, Bekiranov S, Mackey AJ, Conaway MR, Petricoin EF, Gioeli D, Weber MJ. Oncotarget. 2015 Dec 10. doi: 10.18632/oncotarget.6548. PMID: 26673621

Efficacy of Hybrid Tetrahydrobenzo[d]thiazole Based Aryl Piperazines D-264 and D-301 at D2 and D3 Receptors. Zhen J, Antonio T, Jacob JC, Grandy DK, Reith ME, Dutta AK, Selley DE. Neurochem Res. 2015 Dec 31. PMID: 26718829

Initiation of replication in Xenopus egg extracts at a spatially defined origin. Lee KY, Dutta A. Cell Cycle. 2015 Aug 3;14(15):2391. doi: 10.1080/15384101.2015.1063306. Epub 2015 Jun 19. No abstract available. PMID: 26091433

Environmental and chemotherapeutic agents induce breakage at genes involved in leukemia-causing gene rearrangements in human hematopoietic stem/progenitor cells. Thys RG, Lehman CE, Pierce LC, Wang YH. Mutat Res. 2015 Sep;779:86-95. doi: 10.1016/j.mrfmmm.2015.06.011. Epub 2015 Jun 27. PMID: 26163765

A Centromere-Signaling Network Underlies the Coordination among Mitotic Events. Trivedi P, Stukenberg PT. Trends Biochem Sci. 2015 Dec 16. pii: S0968-0004(15)00210-8. doi: 10.1016/j.tibs.2015.11.002. PMID: 26705896

Identification of the posttranslational modifications present in centromeric chromatin. Bailey AO, Panchenko T, Shabanowitz J, Lehman SM, Bai DL, Hunt DF, Black BE, Foltz DR. Mol Cell Proteomics. 2015 Dec 18. pii: mcp.M115.053710. PMID: 26685127

GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. PLoS Genet. 2015 Mar 27;11(3):e1005108. doi: 10.1371/journal.pgen.1005108. eCollection 2015 Mar. PMID: 25815464

Genome-wide predictors of NF-κB recruitment and transcriptional activity. Cieślik M, Bekiranov S. BioData Min. 2015 Nov 26;8:37. eCollection 2015. PMID: 26617673

Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. Brennand KJ, Marchetto MC, Benvenisty N, Brüstle O, Ebert A, Izpisua Belmonte JC, Kaykas A, Lancaster MA, Livesey FJ, McConnell MJ, McKay RD, Morrow EM, Muotri AR, Panchision DM, Rubin LL, Sawa A, Soldner F, Song H, Studer L, Temple S, Vaccarino FM, Wu J, Vanderhaeghen P, Gage FH, Jaenisch R. Stem Cell Reports. 2015 Nov 20. pii: S2213-6711(15)00308-2. doi: 10.1016/j.stemcr.2015.10.011. PMID: 26610635

Actin Polymerization is Stimulated by Actin Crosslinking Protein Palladin. Gurung R, Yadav R, Brungardt JG, Orlova A, Egelman EH, Beck MR. Biochem J. 2015 Nov 25. pii: BJ20151050. PMID: 26607837

Sequential replication-coupled destruction at G1/S ensures genome stability. Coleman KE, Grant GD, Haggerty RA, Brantley K, Shibata E, Workman BD, Dutta A, Varma D, Purvis JE, Cook JG. Genes Dev. 2015 Aug 15;29(16):1734-46. doi: 10.1101/gad.263731.115. Epub 2015 Aug 13. PMID: 26272819

Targeted H3R26 deimination specifically facilitates estrogen receptor binding by modifying nucleosome structure. Guertin MJ, Zhang X, Anguish L, Kim S, Varticovski L, Lis JT, Hager GL, Coonrod SA. PLoS Genet. 2014 Sep 11;10(9):e1004613. doi: 10.1371/journal.pgen.1004613. eCollection 2014 Sep.PMID: 25211228

DNA replication dynamics of the GGGGCC repeat of C9orf72.Thys RG, Wang YH. J Biol Chem. 2015 Oct 13. pii: jbc.M115.660324.PMID: 26463209

Ibrutinib interferes with the cell-mediated anti-tumor activities of therapeutic CD20 antibodies: implications for combination therapy. Da Roit F, Engelberts PJ, Taylor RP, Breij EC, Gritti G, Rambaldi A, Introna M, Parren PW, Beurskens FJ, Golay J. Haematologica. 2015 Jan;100(1):77-86. doi: 10.3324/haematol.2014.107011. Epub 2014 Oct 24. PMID: 25344523

Kif2a depletion generates chromosome segregation and pole coalescence defects in animal caps and inhibits gastrulation of the Xenopus embryo. Eagleson G, Pfister K, Knowlton AL, Skoglund P, Keller R, Stukenberg PT. Mol Biol Cell. 2015 Mar 1;26(5):924-37. doi: 10.1091/mbc.E13-12-0721. Epub 2015 Jan 7. PMID: 25568341

Rad51 Paralogs Remodel Pre-synaptic Rad51 Filaments to Stimulate Homologous Recombination. Taylor MR, Špírek M, Chaurasiya KR, Ward JD, Carzaniga R, Yu X, Egelman EH, Collinson LM, Rueda D, Krejci L, Boulton SJ. Cell. 2015 Jul 16;162(2):271-86. doi: 10.1016/j.cell.2015.06.015. PMID: 26186187

Archaeal actin from a hyperthermophile forms a single-stranded filament. Braun T, Orlova A, Valegård K, Lindås AC, Schröder GF, Egelman EH. Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):9340-5. doi: 10.1073/pnas.1509069112. Epub 2015 Jun 29. PMID: 26124094

Three-dimensional reconstruction of helical polymers. Egelman EH. Arch Biochem Biophys. 2015 Sep 1;581:54-8. doi: 10.1016/j.abb.2015.04.004. Epub 2015 Apr 22. Review. PMID: 25912526

Structural plasticity of helical nanotubes based on coiled-coil assemblies. Egelman EH, Xu C, DiMaio F, Magnotti E, Modlin C, Yu X, Wright E, Baker D, Conticello VP. Structure. 2015 Feb 3;23(2):280-9. doi: 10.1016/j.str.2014.12.008. Epub 2015 Jan 22. PMID: 25620001

The Xenopus ORFeome: A resource that enables functional genomics. Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ. Dev Biol. 2015 Sep 24. pii: S0012-1606(15)30172-X. doi: 10.1016/j.ydbio.2015.09.004. PMID: 26391338

Formaldehyde crosslinking: a tool for the study of chromatin complexes. Hoffman EA, Frey BL, Smith LM, Auble DT. J Biol Chem. 2015 Sep 9. pii: jbc.R115.651679. PMID: 26354429

Virology. A virus that infects a hyperthermophile encapsidates A-form DNA. DiMaio F, Yu X, Rensen E, Krupovic M, Prangishvili D, Egelman EH. Science. 2015 May 22;348(6237):914-7. doi: 10.1126/science.aaa4181. PMID: 25999507

Protein Function Prediction: Problems and Pitfalls. Pearson WR. Curr Protoc Bioinformatics. 2015 Sep 3;51:4.12.1-8. doi: 10.1002/0471250953.bi0412s51.PMID: 26334923

A complex of p190RhoGAP-A and anillin modulates RhoA-GTP and the cytokinetic furrow in human cells. Manukyan A, Ludwig K, Sanchez-Manchinelly S, Parsons SJ, Stukenberg PT. J Cell Sci. 2015 Jan 1;128(1):50-60. doi: 10.1242/jcs.151647. Epub 2014 Oct 29. PMID: 25359885

Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations. Wierman MB, Matecic M, Valsakumar V, Li M, Smith DL Jr, Bekiranov S, Smith JS. Aging (Albany NY). 2015 Mar;7(3):177-94. PMID: 25769345

Environmental and chemotherapeutic agents induce breakage at genes involved in leukemia-causing gene rearrangements in human hematopoietic stem/progenitor cells. Thys RG, Lehman CE, Pierce LC, Wang YH. Mutat Res. 2015 Jun 27;779:86-95. doi: 10.1016/j.mrfmmm.2015.06.011. PMID: 26163765

Poly(Q) Expansions in ATXN7 Affect Solubility but Not Activity of the SAGA Deubiquitinating Module. Lan X, Koutelou E, Schibler AC, Chen YC, Grant PA, Dent SY. Mol Cell Biol. 2015 May;35(10):1777-87. doi: 10.1128/MCB.01454-14. Epub 2015 Mar 9. PMID: 25755283

Discovery of CTCF-sensitive Cis-spliced fusion RNAs between adjacent genes in human prostate cells. Qin F, Song Z, Babiceanu M, Song Y, Facemire L, Singh R, Adli M, Li H. PLoS Genet. 2015 Feb 6;11(2):e1005001. doi: 10.1371/journal.pgen.1005001. eCollection 2015 Feb. PMID: 25658338

The molecular basis for flexibility in the flexible filamentous plant viruses. DiMaio F, Chen CC, Yu X, Frenz B, Hsu YH, Lin NS, Egelman EH. Nat Struct Mol Biol. 2015 Jul 13. doi: 10.1038/nsmb.3054. PMID: 26167882

Archaeal actin from a hyperthermophile forms a single-stranded filament. Braun T, Orlova A, Valegård K, Lindås AC, Schröder GF, Egelman EH. Proc Natl Acad Sci U S A. 2015 Jun 29. pii: 201509069. PMID: 26124094

De novo protein structure determination from near-atomic-resolution cryo-EM maps. Wang RY, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F. Nat Methods. 2015 Apr;12(4):335-8. doi: 10.1038/nmeth.3287. Epub 2015 Feb 23. PMID: 25707029

Initiation of replication in Xenopus egg extracts at a spatially defined origin. Lee KY, Dutta A. Cell Cycle. 2015 Jun 19:0. No abstract available. PMID: 26091433

tRFdb: a database for transfer RNA fragments. Kumar P, Mudunuri SB, Anaya J, Dutta A. Nucleic Acids Res. 2015 Jan;43(Database issue):D141-5. doi: 10.1093/nar/gku1138. Epub 2014 Nov 11. PMID: 25392422

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Singh R, Kuscu C, Quinlan A, Qi Y, Adli M. Nucleic Acids Res. 2015 Jun 1. pii: gkv575. PMID: 26032770

Most partial domains in proteins are alignment and annotation artifacts. Triant DA, Pearson WR. Genome Biol. 2015 May 15;16(1):99. doi: 10.1186/s13059-015-0656-7.PMID: 25976240

De novo mutations in SIK1 cause a spectrum of developmental epilepsies. Hansen J, Snow C, Tuttle E, Ghoneim DH, Yang CS, Spencer A, Gunter SA, Smyser CD, Gurnett CA, Shinawi M, Dobyns WB, Wheless J, Halterman MW, Jansen LA, Paschal BM, Paciorkowski AR. Am J Hum Genet. 2015 Apr 2;96(4):682-90. doi: 10.1016/j.ajhg.2015.02.013. PMID: 25839329

DNA secondary structure at chromosomal fragile sites in human disease. Thys RG, Lehman CE, Pierce LC, Wang YH. Curr Genomics. 2015 Feb;16(1):60-70. doi: 10.2174/1389202916666150114223205. PMID: 25937814

The acetyltransferase Tip60 is a critical regulator of the differentiation-dependent amplification of human papillomaviruses. Hong S, Dutta A, Laimins LA. J Virol. 2015 Apr;89(8):4668-75. doi: 10.1128/JVI.03455-14. Epub 2015 Feb 11. PMID: 25673709

The AAA+ proteins Pontin and Reptin enter adult age: from understanding their basic biology to the identification of selective inhibitors. Matias PM, Baek SH, Bandeiras TM, Dutta A, Houry WA, Llorca O, Rosenbaum J. Front Mol Biosci. 2015 May 5;2:17. doi: 10.3389/fmolb.2015.00017. eCollection 2015. PMID: 25988184

Disruption of the ran system by cysteine oxidation of the nucleotide exchange factor RCC1. Chatterjee M, Paschal BM. Mol Cell Biol. 2015 Feb;35(3):566-81. doi: 10.1128/MCB.01133-14. Epub 2014 Dec 1. PMID: 25452301

MUNC, a long noncoding RNA that facilitates the function of MyoD in skeletal myogenesis. Mueller AC, Cichewicz MA, Dey BK, Layer R, Reon BJ, Gagan JR, Dutta A. Mol Cell Biol. 2015 Feb;35(3):498-513. doi: 10.1128/MCB.01079-14. Epub 2014 Nov 17. PMID: 25403490

Structure of the type VI secretion system contractile sheath. Kudryashev M, Wang RY, Brackmann M, Scherer S, Maier T, Baker D, DiMaio F, Stahlberg H, Egelman EH, Basler M. Cell. 2015 Feb 26;160(5):952-62. doi: 10.1016/j.cell.2015.01.037. PMID: 25723169

PolyQ expansions in ATXN7 affect solubility but not activity of the SAGA deubiquitinating module. Lan X, Koutelou E, Schibler AC, Chen YC, Grant PA, Dent SY. Mol Cell Biol. 2015 Mar 9. pii: MCB.01454-14. PMID: 25755283.

Liu Y, Mayo MW, Xiao A, Hall EH, Amin EB, Kadota K, Adusumilli PS, Jones DR. Loss of BRMS1 promotes a mesenchymal phenotype through NF-κB-dependent regulation of Twist1. Mol Cell Biol. 2015 Jan;35(1):303-17. doi: 10.1128/MCB.00869-14. Epub 2014 Nov 3.PMID: 25368381.

Kudryashev M, Wang RY, Brackmann M, Scherer S, Maier T, Baker D, DiMaio F, Stahlberg H, Egelman EH, Basler M. Structure of the Type VI Secretion System Contractile Sheath. Cell. 2015 Feb 26;160(5):952-62. doi: 10.1016/j.cell.2015.01.037. PMID: 25723169

Wang RY, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F. De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nat Methods. 2015 Feb 23. doi: 10.1038/nmeth.3287. PMID: 25707029

Regulation of the mitogen-activated protein kinase kinase (MEK)-1 by NAD(+)-dependent deacetylases. Yeung F, Ramsey CS, Popko-Scibor AE, Allison DF, Gray LG, Shin M, Kumar M, Li D, McCubrey JA, Mayo MW. Oncogene. 2015 Feb 5;34(6):798-804. doi: 10.1038/onc.2014.39. Epub 2014 Mar 31. PMID: 24681949

Three-Dimensional Reconstruction of Helical Polymers. Egelman EH. Arch Biochem Biophys. 2015 Apr 22. pii: S0003-9861(15)00197-6. doi: 10.1016/j.abb.2015.04.004. PMID: 25912526

Degree of Recruitment of DOT1L to MLL-AF9 Defines Level of H3K79 Di- and Tri-methylation on Target Genes and Transformation Potential. Kuntimaddi A, Achille NJ, Thorpe J, Lokken AA, Singh R, Hemenway CS, Adli M, Zeleznik-Le NJ, Bushweller JH. Cell Rep. 2015 Apr 21. pii: S2211-1247(15)00379-4. doi: 10.1016/j.celrep.2015.04.004. PMID: 25921540

Connecting the microtubule attachment status of each kinetochore to cell cycle arrest through the spindle assembly checkpoint. Stukenberg PT, Burke DJ. Chromosoma. 2015 Apr 28. PMID: 25917595

Fcγ-receptor-mediated trogocytosis impacts mAb-based therapies: historical precedence and recent developments. Taylor RP, Lindorfer MA. Blood. 2015 Jan 29;125(5):762-6. doi: 10.1182/blood-2014-10-569244. Epub 2014 Dec 10. PMID: 25498911

Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations. Weirman MB, Matecic M, Valsakumar V, Li M, Smith DL Jr, Bekiranov S, Smith JS. Aging (Albany NY). 2015 Mar 7. MID: 25769345

De Novo Mutations in SIK1 Cause a Spectrum of Developmental Epilepsies. Hansen J, Snow C, Tuttle E, Ghoneim DH, Yang CS, Spencer A, Gunter SA, Smyser CD, Gurnett CA, Shinawi M, Dobyns WB, Wheless J, Halterman MW, Jansen LA, Paschal BM, Paciorkowski AR. Am J Hum Genet. 2015 Apr 2;96(4):682-90. doi: 10.1016/j.ajhg.2015.02.013. PMID: 25839329

Activin upregulation by NF-κB is required to maintain mesenchymal features of cancer stem-like cells in non-small cell lung cancer. Wamsley JJ, Kumar M, Allison DF, Clift SH, Holzknecht CM, Szymura SJ, Hoang SA, Xu X, Moskaluk CA, Jones DR, Bekiranov S, Mayo MW. Cancer Res. 2015 Jan 15;75(2):426-35. doi: 10.1158/0008-5472.CAN-13-2702. Epub 2014 Nov 28. PMID: 25432175

Qin F, Song Z, Babiceanu M, Song Y, Facemire L, Singh R, Adli M, Li H. Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells. PLoS Genet. 2015 Feb 6;11(2):e1005001. doi: 10.1371/journal.pgen.1005001. eCollection 2015 Feb. PMID: 25658338

Sakurai K, Reon BJ, Anaya J, Dutta A. The lncRNA DRAIC/PCAT29 locus constitutes a tumor suppressive nexus. Mol Cancer Res. 2015 Feb 20. pii: molcanres.0016.2015. PMID: 25700553

Hong S, Dutta A, Laimins LA. The acetyltransferase Tip60 is a critical regulator of the differentiation-dependent amplification of human papillomaviruses. J Virol. 2015 Feb 11. pii: JVI.03455-14. PMID: 25673709

Yeung F, Ramsey CS, Popko-Scibor AE, Allison DF, Gray LG, Shin M, Kumar M, Li D, McCubrey JA, Mayo MW. Regulation of the mitogen-activated protein kinase kinase (MEK)-1 by NAD(+)-dependent deacetylases. Oncogene. 2015 Feb 5;34(6):798-804. doi: 10.1038/onc.2014.39. Epub 2014 Mar 31. PubMed PMID:24681949; PubMed Central PMCID: PMC4182313.

Chatterjee M, Paschal BM. Disruption of the Ran System by Cysteine Oxidation of the Nucleotide Exchange Factor RCC1. Mol Cell Biol. 2015 Feb 1;35(3):566-81. doi: 10.1128/MCB.01133-14. Epub 2014 Dec 1. PubMed PMID: 25452301; PubMed Central PMCID: PMC4285427.

Mueller AC, Cichewicz MA, Dey BK, Layer R, Reon BJ, Gagan JR, Dutta A. MUNC, a Long Noncoding RNA That Facilitates the Function of MyoD in Skeletal Myogenesis. Mol Cell Biol. 2015 Feb 1;35(3):498-513. doi: 10.1128/MCB.01079-14. Epub 2014 Nov 17. PubMed PMID: 25403490; PubMed Central PMCID: PMC4285423.

Taylor RP, Lindorfer MA. FcŒ≥-receptor-mediated trogocytosis impacts mAb-based therapies: historical precedence and recent developments. Blood. 2015 Jan 29;125(5):762-766. Epub 2014 Dec 10. Review. PubMed PMID: 25498911.

Kumar P, Mudunuri SB, Anaya J, Dutta A. tRFdb: a database for transfer RNA fragments. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D141-5. doi:10.1093/nar/gku1138. Epub 2014 Nov 11. PubMed PMID: 25392422.

Wamsley JJ, Kumar M, Allison DF, Clift SH, Holzknecht CM, Szymura SJ, Hoang SA, Xu X, Moskaluk CA, Jones DR, Bekiranov S, Mayo MW. Activin Upregulation by NF-Œ∫B Is Required to Maintain Mesenchymal Features of Cancer Stem-like Cells in Non-Small Cell Lung Cancer. Cancer Res. 2015 Jan 15;75(2):426-35. doi: 10.1158/0008-5472.CAN-13-2702. Epub 2014 Nov 28. PubMed PMID: 25432175; PubMed Central PMCID: PMC4297542.

Galkin VE, Orlova A, Vos MR, Schr√∂der GF, Egelman EH. Near-atomic resolution for one state of f-actin. Structure. 2015 Jan 6;23(1):173-82. doi: 10.1016/j.str.2014.11.006. Epub 2014 Dec 18. PubMed PMID: 25533486; PubMed Central PMCID: PMC4286464.

Roit FD, Engelberts PJ, Taylor RP, Breij EC, Gritti G, Rambaldi A, Introna M, Parren PW, Beurskens FJ, Golay J. Ibrutinib interferes with the cell-mediated anti-tumor activities of therapeutic CD20 antibodies: implications for combination therapy. Haematologica. 2015 Jan;100(1):77-86. doi: 10.3324/haematol.2014.107011. Epub 2014 Oct 24. PubMed PMID: 25344523; PubMed Central PMCID: PMC4281316.

Manukyan A, Ludwig K, Sanchez-Manchinelly S, Parsons SJ, Stukenberg PT. A complex of p190RhoGAP-A and anillin modulates RhoA-GTP and the cytokinetic furrow in human cells. J Cell Sci. 2015 Jan 1;128(1):50-60. doi: 10.1242/jcs.151647. Epub 2014 Oct 29. PubMed PMID: 25359885; PubMed Central PMCID: PMC4282047.

Liu Y, Mayo MW, Xiao A, Hall EH, Amin EB, Kadota K, Adusumilli PS, Jones DR. Loss of BRMS1 promotes a mesenchymal phenotype through NF-Œ∫B-dependent regulation of Twist1. Mol Cell Biol. 2015 Jan;35(1):303-17. doi: 10.1128/MCB.00869-14. Epub 2014 Nov 3. PubMed PMID: 25368381; PubMed Central PMCID: PMC4295387.

Cox KH, Quinnies KM, Eschendroeder A, Didrick PM, Eugster EA, Rissman EF. Number of X-chromosome genes influences social behavior and vasopressin gene expression in mice. Psychoneuroendocrinology. 2015 Jan;51:271-81. doi: 10.1016/j.psyneuen.2014.10.010. Epub 2014 Oct 23. PubMed PMID: 25462900.

2014

Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties. Thompson PM, Tolbert CE, Shen K, Kota P, Palmer SM, Plevock KM, Orlova A, Galkin VE, Burridge K, Egelman EH, Dokholyan NV, Superfine R, Campbell SL. Structure. 2014 May 6;22(5):697-706. doi: 10.1016/j.str.2014.03.002. Epub 2014 Mar 27. PMID: 24685146

Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers. Nivaskumar M, Bouvier G, Campos M, Nadeau N, Yu X, Egelman EH, Nilges M, Francetic O. Structure. 2014 May 6;22(5):685-96. doi: 10.1016/j.str.2014.03.001. Epub 2014 Mar 27. PMID: 24685147

A user’s guide to the ribosomal DNA in Saccharomyces cerevisiae. Johnson JM, Smith JS, Schneider DA. Methods Mol Biol. 2014;1205:303-28. doi: 10.1007/978-1-4939-1363-3_18. PMID: 25213252

Centromere licensing: Mis18 is required to Polo-ver. Barnhart-Dailey MC, Foltz DR. Curr Biol. 2014 Sep 8;24(17):R808-10. doi: 10.1016/j.cub.2014.07.026. PMID: 25202874

Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17, and LPIN2 genes. Malhotra A, Shibata Y, Hall IM, Dutta A. Cancer Biol Ther. 2013 Sep;14(9):840-52. doi: 10.4161/cbt.25329. Epub 2013 Jul 26. PMID: 23792589

Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. Kumar P, Anaya J, Mudunuri SB, Dutta A. BMC Biol. 2014 Oct 1;12:78. doi: 10.1186/s12915-014-0078-0. PMID: 25270025

Yan C, Liu D, Li L, Wempe MF, Guin S, Khanna M, Meier J, Hoffman B, Owens C, Wysoczynski CL, Nitz MD, Knabe WE, Ahmed M, Brautigan DL, Paschal BM, Schwartz MA, Jones DN, Ross D, Meroueh SO, Theodorescu D. Discovery and characterization of small molecules that target the GTPase Ral. Nature. 2014 Nov 20;515(7527):443-7. doi: 10.1038/nature13713. Epub 2014 Sep 14. PubMed PMID: 25219851.

Pang X, Fan J, Zhang Y, Zhang K, Gao B, Ma J, Li J, Deng Y, Zhou Q, Egelman EH, Hsu VW, Sun F. A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature. Dev Cell. 2014 Oct 13;31(1):73-86. doi: 10.1016/j.devcel.2014.08.020. Epub 2014 Oct 2. PubMed PMID: 25284369; PubMed Central PMCID: PMC4198613.

Wu B, Peisley A, Tetrault D, Li Z, Egelman EH, Magor KE, Walz T, Penczek PA, Hur S. Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I. Mol Cell. 2014 Aug 21;55(4):511-23. doi: 10.1016/j.molcel.2014.06.010. Epub 2014 Jul 10. PubMed PMID: 25018021; PubMed Central PMCID: PMC4142144.

Kuscu C, Arslan S, Singh R, Thorpe J, Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol. 2014 Jul;32(7):677-83. doi: 10.1038/nbt.2916. Epub 2014 May 18. PubMed PMID: 24837660.

Nivaskumar M, Bouvier G, Campos M, Nadeau N, Yu X, Egelman EH, Nilges M, Francetic O. Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers. Structure. 2014 May 6;22(5):685-96. doi: 10.1016/j.str.2014.03.001. Epub 2014 Mar 27. PubMed PMID: 24685147; PubMed Central PMCID: PMC4016124.

Thompson PM, Tolbert CE, Shen K, Kota P, Palmer SM, Plevock KM, Orlova A, Galkin VE, Burridge K, Egelman EH, Dokholyan NV, Superfine R, Campbell SL. Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties. Structure. 2014 May 6;22(5):697-706. doi: 10.1016/j.str.2014.03.002. Epub 2014 Mar 27. PubMed PMID: 24685146; PubMed Central PMCID: PMC4039106.

Im JS, Keaton M, Lee KY, Kumar P, Park J, Dutta A. ATR checkpoint kinase and CRL1Œ≤TRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks. Genes Dev. 2014 Apr 15;28(8):875-87. doi: 10.1101/gad.239194.114. Epub 2014 Apr 3. PubMed PMID: 24700029; PubMed Central PMCID: PMC4003279.

Lu A, Magupalli VG, Ruan J, Yin Q, Atianand MK, Vos MR, Schr√∂der GF, Fitzgerald KA, Wu H, Egelman EH. Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes. Cell. 2014 Mar 13;156(6):1193-206. doi: 10.1016/j.cell.2014.02.008. PubMed PMID: 24630722; PubMed Central PMCID: PMC4000066.

Dey BK, Pfeifer K, Dutta A. The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration. Genes Dev. 2014 Mar 1;28(5):491-501. doi: 10.1101/gad.234419.113. Epub 2014 Feb 14. PubMed PMID: 24532688; PubMed Central PMCID: PMC3950346.

Egelman EH. Ambiguities in helical reconstruction. Elife. 2014 Dec 8;3. doi: 10.7554/eLife.04969. PubMed PMID: 25486515.

Lindberg MR, Hall IM, Quinlan AR. Population-based structural variation discovery with Hydra-Multi. Bioinformatics. 2014 Dec 2. pii: btu771. [Epub ahead of print] PubMed PMID: 25527832.

Viswanathan R, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT. Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method. Methods. 2014 Dec;70(2-3):97-107. doi: 10.1016/j.ymeth.2014.10.029. Epub 2014 Nov 1. PubMed PMID: 25448301; PubMed Central PMCID: PMC4267959.

Kostan J, Salzer U, Orlova A, T√∂r√∂ I, Hodnik V, Senju Y, Zou J, Schreiner C, Steiner J, Meril√§inen J, Nikki M, Virtanen I, Carugo O, Rappsilber J, Lappalainen P, Lehto VP, Anderluh G, Egelman EH, Djinoviƒá-Carugo K. Direct interaction of actin filaments with F-BAR protein pacsin2. EMBO Rep. 2014 Nov;15(11):1154-62. doi: 10.15252/embr.201439267. Epub 2014 Sep 12. PubMed PMID: 25216944; PubMed Central PMCID: PMC4253489.

Dar A, Wu D, Lee N, Shibata E, Dutta A. 14-3-3 proteins play a role in the cell cycle by shielding cdt2 from ubiquitin-mediated degradation. Mol Cell Biol. 2014 Nov;34(21):4049-61. doi: 10.1128/MCB.00838-14. Epub 2014 Aug 25. PubMed PMID: 25154416.

Taylor RP, Lindorfer MA. Analyses of CD20 monoclonal antibody-mediated tumor cell killing mechanisms: rational design of dosing strategies. Mol Pharmacol. 2014 Nov;86(5):485-91. doi: 10.1124/mol.114.092684. Epub 2014 Jun 18. Review. PubMed PMID: 24944188; PubMed Central PMCID: PMC4201137.

Kumar P, Anaya J, Mudunuri SB, Dutta A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 2014 Oct 1;12:78. doi: 10.1186/s12915-014-0078-0. PubMed PMID: 25270025; PubMed Central PMCID: PMC4203973.

Wotton D. A CREB1-TGFŒ≤2 self-sustaining loop in glioblastoma. Cancer Discov. 2014 Oct;4(10):1123-5. doi: 10.1158/2159-8290.CD-14-0861. PubMed PMID: 25274684.

Cox KH, Bonthuis PJ, Rissman EF. Mouse model systems to study sex chromosome genes and behavior: relevance to humans. Front Neuroendocrinol. 2014 Oct;35(4):405-19. doi: 10.1016/j.yfrne.2013.12.004. Epub 2014 Jan 2. PubMed PMID: 24388960; PubMed Central PMCID: PMC4079771.

Barnhart-Dailey MC, Foltz DR. Centromere licensing: Mis18 is required to Polo-ver. Curr Biol. 2014 Sep 8;24(17):R808-10. doi: 10.1016/j.cub.2014.07.026.PubMed PMID: 25202874.

Faust GG, Hall IM. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics. 2014 Sep 1;30(17):2503-5. doi: 10.1093/bioinformatics/btu314. Epub 2014 May 7. PubMed PMID: 24812344; PubMed Central PMCID: PMC4147885.

Stolzenberg DS, Stevens JS, Rissman EF. Histone deacetylase inhibition induces long-lasting changes in maternal behavior and gene expression in female mice. Endocrinology. 2014 Sep;155(9):3674-83. doi: 10.1210/en.2013-1946. Epub 2014 Jun 16. PubMed PMID: 24932804; PubMed Central PMCID: PMC4138561.

Goodman WA, Garg RR, Reuter BK, Mattioli B, Rissman EF, Pizarro TT. Loss of estrogen-mediated immunoprotection underlies female gender bias in experimental Crohn’s-like ileitis. Mucosal Immunol. 2014 Sep;7(5):1255-65. doi: 10.1038/mi.2014.15. Epub 2014 Mar 12. PubMed PMID: 24621993; PubMed Central PMCID: PMC4139459.

Shibata E, Dar A, Dutta A. CRL4Cdt2 E3 ubiquitin ligase and proliferating cell nuclear antigen (PCNA) cooperate to degrade thymine DNA glycosylase in S phase. J Biol Chem. 2014 Aug 15;289(33):23056-64. doi: 10.1074/jbc.M114.574210. Epub 2014 Jun 24. PubMed PMID: 24962565; PubMed Central PMCID: PMC4132804.

Rissman EF, Adli M. Minireview: transgenerational epigenetic inheritance: focus on endocrine disrupting compounds. Endocrinology. 2014 Aug;155(8):2770-80. doi: 10.1210/en.2014-1123. Epub 2014 Jun 2. Review. PubMed PMID: 24885575; PubMed Central PMCID: PMC4098001.

Bjerke GA, Yang CS, Frierson HF, Paschal BM, Wotton D. Activation of Akt signaling in prostate induces a TGFŒ≤-mediated restraint on cancer progression and metastasis. Oncogene. 2014 Jul 10;33(28):3660-7. doi: 10.1038/onc.2013.342. Epub 2013 Sep 2. PubMed PMID: 23995785; PubMed Central PMCID: PMC3939071.

Matson DR, Stukenberg PT. CENP-I and Aurora B act as a molecular switch that ties RZZ/Mad1 recruitment to kinetochore attachment status. J Cell Biol. 2014 May 26;205(4):541-54. doi: 10.1083/jcb.201307137. PubMed PMID: 24862574; PubMed Central PMCID: PMC4033774.

Nivaskumar M, Bouvier G, Campos M, Nadeau N, Yu X, Egelman EH, Nilges M, Francetic O. Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers. Structure. 2014 May 6;22(5):685-96. doi: 10. 1016/j.str.2014.03.001. Epub 2014 Mar 27. PubMed PMID: 24685147; PubMed Central PMCID: PMC4016124.

Zhang Y, Kim J, Mueller AC, Dey B, Yang Y, Lee DH, Hachmann J, Finderle S, Park DM, Christensen J, Schiff D, Purow B, Dutta A, Abounader R. Multiple receptor tyrosine kinases converge on microRNA-134 to control KRAS, STAT5B, and glioblastoma. Cell Death Differ. 2014 May;21(5):720-34. doi: 10.1038/cdd.2013.196. Epub 2014 Jan 17. PubMed PMID: 24440911; PubMed Central PMCID: PMC3978301.

Paciorkowski AR, Weisenberg J, Kelley JB, Spencer A, Tuttle E, Ghoneim D, Thio LL, Christian SL, Dobyns WB, Paschal BM. Autosomal recessive mutations in nuclear transport factor KPNA7 are associated with infantile spasms and cerebellar malformation. Eur J Hum Genet. 2014 May;22(5):587-93. doi: 10.1038/ejhg.2013.196. Epub 2013 Sep 18. PubMed PMID: 24045845; PubMed Central PMCID: PMC3992559.

Lu G, Su G, Zhao Y, Johnston WF, Sherman NE, Rissman EF, Lau C, Ailawadi G, Upchurch GR Jr. Dietary phytoestrogens inhibit experimental aneurysm formation in male mice. J Surg Res. 2014 May 1;188(1):326-38. doi: 10.1016/j.jss.2013.11.1108. Epub 2013 Dec 3. PubMed PMID: 24388399; PubMed Central PMCID: PMC3972298.

Datta S, Snow CJ, Paschal BM. A pathway linking oxidative stress and the Ran GTPase system in progeria. Mol Biol Cell. 2014 Apr;25(8):1202-15. doi: 10.1091/mbc.E13-07-0430. Epub 2014 Feb 12. PubMed PMID: 24523287; PubMed Central PMCID: PMC3982987.

Banerjee B, Kestner CA, Stukenberg PT. EB1 enables spindle microtubules to regulate centromeric recruitment of Aurora B. J Cell Biol. 2014 Mar 17;204(6):947-63. doi: 10.1083/jcb.201307119. Epub 2014 Mar 10. PubMed PMID: 24616220; PubMed Central PMCID: PMC3998792.

Sun D, Layer R, Mueller AC, Cichewicz MA, Negishi M, Paschal BM, Dutta A. Regulation of several androgen-induced genes through the repression of the miR-99a/let-7c/miR-125b-2 miRNA cluster in prostate cancer cells. Oncogene. 2014 Mar 13;33(11):1448-57. doi: 10.1038/onc.2013.77. Epub 2013 Mar 18. PubMed PMID: 23503464; PubMed Central PMCID: PMC3915043.

Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Reprint of: policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. Horm Behav. 2014 Feb;65(2):190-3. doi: 10.1016/j.yhbeh.2013.09.001. Epub 2013 Nov 28. PubMed PMID: 24289987.

Cie≈õlik M, Bekiranov S. Combinatorial epigenetic patterns as quantitative predictors of chromatin biology. BMC Genomics. 2014 Jan 28;15:76. doi: 10.1186/1471-2164-15-76. PubMed PMID: 24472558; PubMed Central PMCID: PMC3922690.

Snow CJ, Paschal BM. Roles of the nucleoporin Tpr in cancer and aging. Adv Exp Med Biol. 2014;773:309-22. doi: 10.1007/978-1-4899-8032-8_14. Review. PubMed PMID: 24563354.

Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Reprint of: policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich, et al. Front Neuroendocrinol. 2014 Jan;35(1):2-5. doi: 10.1016/j.yfrne.2013.09.003. Epub 2013 Nov 21. PubMed PMID: 24268499.

Taylor RP, Lindorfer MA. The role of complement in mAb-based therapies of cancer. Methods. 2014 Jan 1;65(1):18-27. doi: 10.1016/j.ymeth.2013.07.027. Epub 2013 Jul 22. Review. PubMed PMID: 23886909.

Johnson JM, Smith JS, Schneider DA. A user’s guide to the ribosomal DNA in Saccharomyces cerevisiae. Methods Mol Biol. 2014;1205:303-28. doi: 10.1007/978-1-4939-1363-3_18. PubMed PMID: 25213252.

Zy≈Çkiewicz E, Stukenberg PT. Xenopus egg extracts as a simplified model system for structure-function studies of dynein regulators. Methods Mol Biol.2014;1136:117-33. doi: 10.1007/978-1-4939-0329-0_8. PubMed PMID: 24633797.

Pearson WR. BLAST and FASTA similarity searching for multiple sequence alignment. Methods Mol Biol. 2014;1079:75-101. doi: 10.1007/978-1-62703-646-7_5. PubMed PMID: 24170396.

Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res. 2014 Jan;42(Database issue):D485-9. doi: 10.1093/nar/gkt1243. Epub 2013 Dec 6. PubMed PMID: 24319146; PubMed Central PMCID: PMC3964973.

Floyd DH, Zhang Y, Dey BK, Kefas B, Breit H, Marks K, Dutta A, Herold-Mende C, Synowitz M, Glass R, Abounader R, Purow BW. Novel anti-apoptotic microRNAs 582-5p and 363 promote human glioblastoma stem cell survival via direct inhibition of caspase 3, caspase 9, and Bim. PLoS One. 2014 May 7;9(5):e96239. doi: 10.1371/journal.pone.0096239. eCollection 2014. PubMed PMID: 24805821; PubMed Central PMCID: PMC4013090.

Hall EH, Liu Y, Xiao A, Shock L, Brautigan DL, Mayo MW, Adusumilli PS, Jones Inhibition of breast cancer metastasis suppressor 1 promotes a mesenchymal phenotype in lung epithelial cells that express oncogenic K-RasV12 and loss of p53. PLoS One. 2014 Apr 24;9(4):e95869. doi: 10.1371/journal.pone.0095869. eCollection 2014. PubMed PMID: 24763730; PubMed Central PMCID: PMC3999110.

Negishi M, Wongpalee SP, Sarkar S, Park J, Lee KY, Shibata Y, Reon BJ, Abounader R, Suzuki Y, Sugano S, Dutta A. A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins. PLoS One. 2014 Apr 18;9(4):e95216. doi: 10.1371/journal.pone.0095216. eCollection 2014. PubMed PMID: 24748121; PubMed Central PMCID: PMC3991591.

Bjerke GA, Pietrzak K, Melhuish TA, Frierson HF Jr, Paschal BM, Wotton D. Prostate cancer induced by loss of Apc is restrained by TGFŒ≤ signaling. PLoS One. 2014 Mar 20;9(3):e92800. doi: 10.1371/journal.pone.0092800. eCollection 2014. PubMed PMID: 24651496; PubMed Central PMCID: PMC3961420.

Cohen JN, Tewalt EF, Rouhani SJ, Buonomo EL, Bruce AN, Xu X, Bekiranov S, Fu YX, Engelhard VH. Tolerogenic properties of lymphatic endothelial cells are controlled by the lymph node microenvironment. PLoS One. 2014 Feb 4;9(2):e87740. doi: 10.1371/journal.pone.0087740. eCollection 2014. PubMed PMID: 24503860; PubMed Central PMCID: PMC3913631.

Dey BK, Mueller AC, Dutta A. Long non-coding RNAs as emerging regulators of differentiation, development, and disease. Transcription. 2014;5(4):e944014. doi: 10.4161/21541272.2014.944014. Epub 2014 Oct 30. PubMed PMID: 25483404.

Near-atomic resolution for one state of F-actin. Galkin VE, Orlova A, Vos MR, Schröder GF, Egelman EH. Structure. 2015 Jan 6;23(1):173-82. doi: 10.1016/j.str.2014.11.006. Epub 2014 Dec 18. PMID: 25533486

Direct interaction of actin filaments with F-BAR protein pacsin2. Kostan J, Salzer U, Orlova A, Törö I, Hodnik V, Senju Y, Zou J, Schreiner C, Steiner J, Meriläinen J, Nikki M, Virtanen I, Carugo O, Rappsilber J, Lappalainen P, Lehto VP, Anderluh G, Egelman EH, Djinović-Carugo K. EMBO Rep. 2014 Nov;15(11):1154-62. doi: 10.15252/embr.201439267. Epub 2014 Sep 12. PMID: 25216944

2013

1: Bjerke GA, Yang CS, Frierson HF, Paschal BM, Wotton D. Activation of Akt signaling in prostate induces a TGFŒ≤-mediated restraint on cancer progression and metastasis. Oncogene. 2014 Jul 10;33(28):3660-7. doi: 10.1038/onc.2013.342. Epub 2013 Sep 2. PubMed PMID: 23995785; PubMed Central PMCID: PMC3939071.

2: Paciorkowski AR, Weisenberg J, Kelley JB, Spencer A, Tuttle E, Ghoneim D, Thio LL, Christian SL, Dobyns WB, Paschal BM. Autosomal recessive mutations in nuclear transport factor KPNA7 are associated with infantile spasms and cerebellar malformation. Eur J Hum Genet. 2014 May;22(5):587-93. doi: 10.1038/ejhg.2013.196. Epub 2013 Sep 18. PubMed PMID: 24045845; PubMed Central PMCID: PMC3992559.

3: Lu G, Su G, Zhao Y, Johnston WF, Sherman NE, Rissman EF, Lau C, Ailawadi G, Upchurch GR Jr. Dietary phytoestrogens inhibit experimental aneurysm formation in male mice. J Surg Res. 2014 May 1;188(1):326-38. doi: 10.1016/j.jss.2013.11.1108. Epub 2013 Dec 3. PubMed PMID: 24388399; PubMed Central PMCID: PMC3972298.

4: Sun D, Layer R, Mueller AC, Cichewicz MA, Negishi M, Paschal BM, Dutta A. Regulation of several androgen-induced genes through the repression of the miR-99a/let-7c/miR-125b-2 miRNA cluster in prostate cancer cells. Oncogene. 2014 Mar 13;33(11):1448-57. doi: 10.1038/onc.2013.77. Epub 2013 Mar 18. PubMed PMID: 23503464; PubMed Central PMCID: PMC3915043.

5: Wierman MB, Smith JS. Yeast sirtuins and the regulation of aging. FEMS Yeast Res. 2014 Feb;14(1):73-88. doi: 10.1111/1567-1364.12115. Epub 2013 Nov 14. PubMed PMID: 24164855.

6: Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Reprint of: policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. Horm Behav. 2014 Feb;65(2):190-3. doi: 10.1016/j.yhbeh.2013.09.001. Epub 2013 Nov 28. PubMed PMID: 24289987.

7: Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Reprint of: policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich, et al. Front Neuroendocrinol. 2014 Jan;35(1):2-5. doi: 10.1016/j.yfrne.2013.09.003. Epub 2013 Nov 21. PubMed PMID: 24268499.

8: Taylor RP, Lindorfer MA. The role of complement in mAb-based therapies of cancer. Methods. 2014 Jan 1;65(1):18-27. doi: 10.1016/j.ymeth.2013.07.027. Epub 2013 Jul 22. Review. PubMed PMID: 23886909.

9: Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res. 2014 Jan;42(Database issue):D485-9. doi: 10.1093/nar/gkt1243. Epub 2013 Dec 6. PubMed PMID: 24319146; PubMed Central PMCID: PMC3964973.

10: Mills LJ, Pearson WR. Adjusting scoring matrices to correct overextended alignments. Bioinformatics. 2013 Dec 1;29(23):3007-13. doi: 10.1093/bioinformatics/btt517. Epub 2013 Aug 31. PubMed PMID: 23995390; PubMed Central PMCID: PMC3834790.

11: Im JS, Lee KY, Dillon LW, Dutta A. Human Primpol1: a novel guardian of stalled replication forks. EMBO Rep. 2013 Dec;14(12):1032-3. doi: 10.1038/embor.2013.171. Epub 2013 Nov 5. PubMed PMID: 24189099; PubMed Central PMCID: PMC3981087.

12: Pokrass MJ, Liu MF, Lindorfer MA, Taylor RP. Activation of complement by monoclonal antibodies that target cell-associated Œ≤‚ÇÇ-microglobulin: implications for cancer immunotherapy. Mol Immunol. 2013 Dec;56(4):549-60. doi: 10.1016/j.molimm.2013.05.242. Epub 2013 Aug 1. PubMed PMID: 23911412.

13: Burke TL, Miller JL, Grant PA. Direct inhibition of Gcn5 protein catalytic activity by polyglutamine-expanded ataxin-7. J Biol Chem. 2013 Nov 22;288(47):34266-75. doi: 10.1074/jbc.M113.487538. Epub 2013 Oct 15. PubMed PMID: 24129567; PubMed Central PMCID: PMC3837167.

14: Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et¬†al. Andrology. 2013 Nov;1(6):802-5. doi: 10.1111/j.2047-2927.2013.00151.x. PubMed PMID: 24166945.

15: Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. Endocrinology. 2013 Nov;154(11):3957-60. doi: 10.1210/en.2013-1854. Epub 2013 Sep 18. PubMed PMID: 24048095.

16: Mesner LD, Valsakumar V, Cieslik M, Pickin R, Hamlin JL, Bekiranov S. Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins. Genome Res. 2013 Nov;23(11):1774-88. doi: 10.1101/gr.155218.113. Epub 2013 Jul 16. PubMed PMID: 23861383; PubMed Central PMCID: PMC3814878.

17: Wolstenholme JT, Goldsby JA, Rissman EF. Transgenerational effects of prenatal bisphenol A on social recognition. Horm Behav. 2013 Nov;64(5):833-9. doi: 10.1016/j.yhbeh.2013.09.007. Epub 2013 Oct 5. PubMed PMID: 24100195; PubMed Central PMCID: PMC3955720.

18: Taylor RP. Gnawing at Metchnikoff’s paradigm. Blood. 2013 Oct 24;122(17):2922-4. doi: 10.1182/blood-2013-07-514083. PubMed PMID: 24159161.

19: Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. Eur J Endocrinol. 2013 Oct 21;169(6):E1-4. doi: 10.1530/EJE-13-0763. Print 2013 Dec. PubMed PMID: 24057478.

20: Terai K, Shibata E, Abbas T, Dutta A. Degradation of p12 subunit by CRL4Cdt2 E3 ligase inhibits fork progression after DNA damage. J Biol Chem. 2013 Oct 18;288(42):30509-14. doi: 10.1074/jbc.C113.505586. Epub 2013 Sep 10. PubMed PMID: 24022480; PubMed Central PMCID: PMC3798521.

21: Poorey K, Viswanathan R, Carver MN, Karpova TS, Cirimotich SM, McNally JG, Bekiranov S, Auble DT. Measuring chromatin interaction dynamics on the second time scale at single-copy genes. Science. 2013 Oct 18;342(6156):369-72. doi: 10.1126/science.1242369. Epub 2013 Oct 3. PubMed PMID: 24091704; PubMed Central PMCID: PMC3997053.

22: Gupta A, Jha S, Engel DA, Ornelles DA, Dutta A. Tip60 degradation by adenovirus relieves transcriptional repression of viral transcriptional activator EIA. Oncogene. 2013 Oct 17;32(42):5017-25. doi: 10.1038/onc.2012.534. Epub 2012 Nov 26. PubMed PMID: 23178490; PubMed Central PMCID: PMC3955737.

23: Bonthuis PJ, Rissman EF. Neural growth hormone implicated in body weight sex differences. Endocrinology. 2013 Oct;154(10):3826-35. doi: 10.1210/en.2013-1234. Epub 2013 Jul 16. PubMed PMID: 23861378; PubMed Central PMCID: PMC3776866.

24: Abel JL, Rissman EF. Running-induced epigenetic and gene expression changes in the adolescent brain. Int J Dev Neurosci. 2013 Oct;31(6):382-90. doi: 10.1016/j.ijdevneu.2012.11.002. Epub 2012 Nov 23. PubMed PMID: 23178748; PubMed Central PMCID: PMC3686974.

25: Jazaeri AA, Shibata E, Park J, Bryant JL, Conaway MR, Modesitt SC, Smith PG, Milhollen MA, Berger AJ, Dutta A. Overcoming platinum resistance in preclinical models of ovarian cancer using the neddylation inhibitor MLN4924. Mol Cancer Ther. 2013 Oct;12(10):1958-67. doi: 10.1158/1535-7163.MCT-12-1028. Epub 2013 Aug 12 PubMed PMID: 23939375; PubMed Central PMCID: PMC3795967.

26: Wagenseller AG, Shada A, D’Auria KM, Murphy C, Sun D, Molhoek KR, Papin JA, Dutta A, Slingluff CL Jr. MicroRNAs induced in melanoma treated with combination targeted therapy of Temsirolimus and Bevacizumab. J Transl Med. 2013 Sep 18;11:218. doi: 10.1186/1479-5876-11-218. PubMed PMID: 24047116; PubMed Central PMCID: PMC3853033.

27: Cie≈õlik M, Hoang SA, Baranova N, Chodaparambil S, Kumar M, Allison DF, Xu X, Wamsley JJ, Gray L, Jones DR, Mayo MW, Bekiranov S. Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition. Epigenetics Chromatin. 2013 Sep 2;6(1):28. doi: 10.1186/1756-8935-6-28. PubMed PMID: 24004852; PubMed Central PMCID: PMC3847279.

28: Malhotra A, Shibata Y, Hall IM, Dutta A. Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17, and LPIN2 genes. Cancer Biol Ther. 2013 Sep;14(9):840-52. doi: 10.4161/cbt.25329. Epub 2013 Jul 26. PubMed PMID: 23792589; PubMed Central PMCID: PMC3909553.

29: Dar A, Shibata E, Dutta A. Deubiquitination of Tip60 by USP7 determines the activity of the p53-dependent apoptotic pathway. Mol Cell Biol. 2013 Aug;33(16):3309-20. doi: 10.1128/MCB.00358-13. Epub 2013 Jun 17. PubMed PMID: 23775119; PubMed Central PMCID: PMC3753911.

30: Zasadzi≈Ñska E, Barnhart-Dailey MC, Kuich PH, Foltz DR. Dimerization of the CENP-A assembly factor HJURP is required for centromeric nucleosome deposition. EMBO J. 2013 Jul 31;32(15):2113-24. doi: 10.1038/emboj.2013.142. Epub 2013 Jun 14 PubMed PMID: 23771058; PubMed Central PMCID: PMC3730228.

31: Kumar M, Allison DF, Baranova NN, Wamsley JJ, Katz AJ, Bekiranov S, Jones DR, Mayo MW. NF-Œ∫B regulates mesenchymal transition for the induction of non-small cell lung cancer initiating cells. PLoS One. 2013 Jul 30;8(7):e68597. doi: 10.1371/journal.pone.0068597. Print 2013. PubMed PMID: 23935876; PubMed Central PMCID: PMC3728367.

32: Bharadwaj P, McInnis C, Madden AM, Bonthuis PJ, Zup S, Rissman EF, Park JH. Increased dendritic spine density and tau expression are associated with individual differences in steroidal regulation of male sexual behavior. PLoS One. 2013 Jul 16;8(7):e69672. doi: 10.1371/journal.pone.0069672. Print 2013. PubMed PMID: 23874981; PubMed Central PMCID: PMC3713039.

33: Bailey AO, Panchenko T, Sathyan KM, Petkowski JJ, Pai PJ, Bai DL, Russell DH, Macara IG, Shabanowitz J, Hunt DF, Black BE, Foltz DR. Posttranslational modification of CENP-A influences the conformation of centromeric chromatin. Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11827-32. doi: 10.1073/pnas.1300325110. Epub 2013 Jul 1. PubMed PMID: 23818633; PubMed Central PMCID: PMC3718089.

34: Abbas T, Keaton M, Dutta A. Regulation of TGF-Œ≤ signaling, exit from the cell cycle, and cellular migration through cullin cross-regulation: SCF-FBXO11 turns off CRL4-Cdt2. Cell Cycle. 2013 Jul 15;12(14):2175-82. doi: 10.4161/cc.25314. PubMed PMID: 23892434; PubMed Central PMCID: PMC3755067.

35: Johnson JM, French SL, Osheim YN, Li M, Hall L, Beyer AL, Smith JS. Rpd3- and spt16-mediated nucleosome assembly and transcriptional regulation on yeast ribosomal DNA genes. Mol Cell Biol. 2013 Jul;33(14):2748-59. doi: 10.1128/MCB.00112-13. Epub 2013 May 20. PubMed PMID: 23689130; PubMed Central PMCID: PMC3700123.

36: Pearson WR. An introduction to sequence similarity (“homology”) searching. Curr Protoc Bioinformatics. 2013 Jun;Chapter 3:Unit3.1. doi: 10.1002/0471250953.bi0301s42. Review. PubMed PMID: 23749753; PubMed Central PMCID: PMC3820096.

37: Li M, Valsakumar V, Poorey K, Bekiranov S, Smith JS. Genome-wide analysis of functional sirtuin chromatin targets in yeast. Genome Biol. 2013 May 27;14(5):R48. doi: 10.1186/gb-2013-14-5-r48. PubMed PMID: 23710766; PubMed Central PMCID: PMC4053722.

38: Snow CJ, Dar A, Dutta A, Kehlenbach RH, Paschal BM. Defective nuclear import of Tpr in Progeria reflects the Ran sensitivity of large cargo transport. J Cell Biol. 2013 May 13;201(4):541-57. doi: 10.1083/jcb.201212117. Epub 2013 May 6. PubMed PMID: 23649804; PubMed Central PMCID: PMC3653351.

39: Burke DJ. Unbiased segregation of yeast chromatids in Saccharomyces cerevisiae. Chromosome Res. 2013 May;21(3):193-202. doi: 10.1007/s10577-013-9348-x. Review. PubMed PMID: 23681653.

40: Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res. 2013 May;23(5):762-76. doi: 10.1101/gr.143677.112. Epub 2013 Feb 14. PubMed PMID: 23410887; PubMed Central PMCID: PMC3638133.

41: Galkin VE, Kolappan S, Ng D, Zong Z, Li J, Yu X, Egelman EH, Craig L. The structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism. J Bacteriol. 2013 Apr;195(7):1360-70. doi: 10.1128/JB.01989-12. Epub 2012 Nov 21. PubMed PMID: 23175654; PubMed Central PMCID: PMC3624524.

42: Park J, Long DT, Lee KY, Abbas T, Shibata E, Negishi M, Luo Y, Schimenti JC, Gambus A, Walter JC, Dutta A. The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination. Mol Cell Biol. 2013 Apr;33(8):1632-44. doi: 10.1128/MCB.01503-12. Epub 2013 Feb 11. PubMed PMID: 23401855; PubMed Central PMCID: PMC3624244.

43: Abbas T, Mueller AC, Shibata E, Keaton M, Rossi M, Dutta A. CRL1-FBXO11 promotes Cdt2 ubiquitylation and degradation and regulates Pr-Set7/Set8-mediated cellular migration. Mol Cell. 2013 Mar 28;49(6):1147-58. doi: 10.1016/j.molcel.2013.02.003. Epub 2013 Mar 7. PubMed PMID: 23478445; PubMed Central PMCID: PMC3615078.

44: Abbas T, Keaton MA, Dutta A. Genomic instability in cancer. Cold Spring Harb Perspect Biol. 2013 Mar 1;5(3):a012914. doi: 10.1101/cshperspect.a012914. Review. PubMed PMID: 23335075; PubMed Central PMCID: PMC3578360.

45: Wolstenholme JT, Rissman EF, Bekiranov S. Sexual differentiation in the developing mouse brain: contributions of sex chromosome genes. Genes Brain Behav. 2013 Mar;12(2):166-80. doi: 10.1111/gbb.12010. Epub 2013 Jan 10. PubMed PMID: 23210685; PubMed Central PMCID: PMC3581734.

46: Jha S, Gupta A, Dar A, Dutta A. RVBs are required for assembling a functional TIP60 complex. Mol Cell Biol. 2013 Mar;33(6):1164-74. doi: 10.1128/MCB.01567-12. Epub 2013 Jan 7. PubMed PMID: 23297341; PubMed Central PMCID: PMC3592018.

47: Mueller AC, Sun D, Dutta A. The miR-99 family regulates the DNA damage response through its target SNF2H. Oncogene. 2013 Feb 28;32(9):1164-72. doi: 10.1038/onc.2012.131. Epub 2012 Apr 23. PubMed PMID: 22525276; PubMed Central PMCID: PMC3407337.

48: Liu Y, Mayo MW, Nagji AS, Hall EH, Shock LS, Xiao A, Stelow EB, Jones DR. BRMS1 suppresses lung cancer metastases through an E3 ligase function on histone acetyltransferase p300. Cancer Res. 2013 Feb 15;73(4):1308-17. doi: 10.1158/0008-5472.CAN-12-2489. Epub 2012 Dec 26. PubMed PMID: 23269275; PubMed Central PMCID: PMC3578176.

49: Stellfox ME, Bailey AO, Foltz DR. Putting CENP-A in its place. Cell Mol Life Sci. 2013 Feb;70(3):387-406. doi: 10.1007/s00018-012-1048-8. Epub 2012 Jun 23. Review. PubMed PMID: 22729156; PubMed Central PMCID: PMC4084702.

50: Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR. Binary Interval Search: a scalable algorithm for counting interval intersections. Bioinformatics. 2013 Jan 1;29(1):1-7. doi: 10.1093/bioinformatics/bts652. Epub 2012 Nov 4. PubMed PMID: 23129298; PubMed Central PMCID: PMC3530906.

51: Pearson WR. Selecting the Right Similarity-Scoring Matrix. Curr Protoc Bioinformatics. 2013;43:3.5.1-3.5.9. PubMed PMID: 24509512; PubMed Central PMCID: PMC3848038.

52: Gore AC, Balthazart J, Bikle D, Carpenter DO, Crews D, Czernichow P, Diamanti-Kandarakis E, Dores RM, Grattan D, Hof PR, Hollenberg AN, Lange C, Lee AV, Levine JE, Millar RP, Nelson RJ, Porta M, Poth M, Power DM, Prins GS, Ridgway EC, Rissman EF, Romijn JA, Sawchenko PE, Sly PD, S√∂der O, Taylor HS, Tena-Sempere M, Vaudry H, Wallen K, Wang Z, Wartofsky L, Watson CS. Policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. Horm Res Paediatr. 2013;80(5):305-8. doi: 10.1159/000355668. Epub 2013 Oct 9. PubMed PMID: 24107550.

53: Hoang SA, Bekiranov S. The network architecture of the Saccharomyces cerevisiae genome. PLoS One. 2013 Dec 9;8(12):e81972. doi: 10.1371/journal.pone.0081972. eCollection 2013. PubMed PMID: 24349163; PubMed Central PMCID: PMC3857230.

54: Cox KH, So NL, Rissman EF. Foster dams rear fighters: strain-specific effects of within-strain fostering on aggressive behavior in male mice. PLoS One. 2013 Sep 10;8(9):e75037. doi: 10.1371/journal.pone.0075037. eCollection 2013. PubMed PMID: 24040381; PubMed Central PMCID: PMC3769275.

55: Miller JL, Grant PA. The role of DNA methylation and histone modifications in transcriptional regulation in humans. Subcell Biochem. 2013;61:289-317. doi: 10.1007/978-94-007-4525-4_13. Review. PubMed PMID: 23150256.

56: Human Primpol1: a novel guardian of stalled replication forks. Im JS, Lee KY, Dillon LW, Dutta A. EMBO Rep. 2013 Dec;14(12):1032-3. doi: 10.1038/embor.2013.171. Epub 2013 Nov 5. No abstract available. PMID: 24189099

2012

1: Gupta A, Jha S, Engel DA, Ornelles DA, Dutta A. Tip60 degradation by adenovirus relieves transcriptional repression of viral transcriptional activator EIA. Oncogene. 2013 Oct 17;32(42):5017-25. doi: 10.1038/onc.2012.534. Epub 2012 Nov 26. PubMed PMID: 23178490; PubMed Central PMCID: PMC3955737.

2: Abel JL, Rissman EF. Running-induced epigenetic and gene expression changes in the adolescent brain. Int J Dev Neurosci. 2013 Oct;31(6):382-90. doi: 10.1016/j.ijdevneu.2012.11.002. Epub 2012 Nov 23. PubMed PMID: 23178748; PubMed Central PMCID: PMC3686974.

3: Galkin VE, Kolappan S, Ng D, Zong Z, Li J, Yu X, Egelman EH, Craig L. The structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism. J Bacteriol. 2013 Apr;195(7):1360-70. doi: 10.1128/JB.01989-12. Epub 2012 Nov 21. PubMed PMID: 23175654; PubMed Central PMCID: PMC3624524.

4: Mueller AC, Sun D, Dutta A. The miR-99 family regulates the DNA damage response through its target SNF2H. Oncogene. 2013 Feb 28;32(9):1164-72. doi: 10.1038/onc.2012.131. Epub 2012 Apr 23. PubMed PMID: 22525276; PubMed Central PMCID: PMC3407337.

5: Liu Y, Mayo MW, Nagji AS, Hall EH, Shock LS, Xiao A, Stelow EB, Jones DR. BRMS1 suppresses lung cancer metastases through an E3 ligase function on histone acetyltransferase p300. Cancer Res. 2013 Feb 15;73(4):1308-17. doi: 10.1158/0008-5472.CAN-12-2489. Epub 2012 Dec 26. PubMed PMID: 23269275; PubMed Central PMCID: PMC3578176.

6: Stellfox ME, Bailey AO, Foltz DR. Putting CENP-A in its place. Cell Mol Life Sci. 2013 Feb;70(3):387-406. doi: 10.1007/s00018-012-1048-8. Epub 2012 Jun 23. Review. PubMed PMID: 22729156; PubMed Central PMCID: PMC4084702.

7: Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR. Binary Interval Search: a scalable algorithm for counting interval intersections. Bioinformatics. 2013 Jan 1;29(1):1-7. doi: 10.1093/bioinformatics/bts652. Epub 2012 Nov 4. PubMed PMID: 23129298; PubMed Central PMCID: PMC3530906.

8: McCullough SD, Xu X, Dent SY, Bekiranov S, Roeder RG, Grant PA. Reelin is a target of polyglutamine expanded ataxin-7 in human spinocerebellar ataxia type 7 (SCA7) astrocytes. Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21319-24. doi: 10.1073/pnas.1218331110. Epub 2012 Dec 10. PubMed PMID: 23236151; PubMed Central PMCID: PMC3535616.

9: Keyes BE, Sykes KD, Remington CE, Burke DJ. Sister chromatids segregate at mitosis without mother-daughter bias in Saccharomyces cerevisiae. Genetics. 2012 Dec;192(4):1553-7. doi: 10.1534/genetics.112.145680. Epub 2012 Oct 10. PubMed PMID: 23051643; PubMed Central PMCID: PMC3512160.

10: Dey BK, Mueller AC, Dutta A. Non-micro-short RNAs: the new kids on the block. Mol Biol Cell. 2012 Dec;23(24):4664-7. doi: 10.1091/mbc.E12-10-0716. PubMed PMID: 23239791; PubMed Central PMCID: PMC3521675.

11: Gagan J, Dey BK, Layer R, Yan Z, Dutta A. Notch3 and Mef2c proteins are mutually antagonistic via Mkp1 protein and miR-1/206 microRNAs in differentiating myoblasts. J Biol Chem. 2012 Nov 23;287(48):40360-70. doi: 10.1074/jbc.M112.378414. Epub 2012 Oct 10. PubMed PMID: 23055528; PubMed Central PMCID: PMC3504751.

12: Galkin VE, Orlova A, Egelman EH. Are ParM filaments polar or bipolar? J Mol Biol. 2012 Nov 2;423(4):482-5. doi: 10.1016/j.jmb.2012.08.006. Epub 2012 Aug 21. PubMed PMID: 22922064; PubMed Central PMCID: PMC3467344.

13: Locke LW, Mayo MW, Yoo AD, Williams MB, Berr SS. PET imaging of tumor associated macrophages using mannose coated 64Cu liposomes. Biomaterials. 2012 Nov;33(31):7785-93. doi: 10.1016/j.biomaterials.2012.07.022. Epub 2012 Jul 26. PubMed PMID: 22840225.

14: Allison DF, Wamsley JJ, Kumar M, Li D, Gray LG, Hart GW, Jones DR, Mayo MW. Modification of RelA by O-linked N-acetylglucosamine links glucose metabolism to NF-Œ∫B acetylation and transcription. Proc Natl Acad Sci U S A. 2012 Oct 16;109(42):16888-93. doi: 10.1073/pnas.1208468109. Epub 2012 Oct 1. PubMed PMID: 23027940; PubMed Central PMCID: PMC3479489.

15: Faust GG, Hall IM. YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics. 2012 Oct 1;28(19):2417-24. Epub 2012 Jul PubMed PMID: 22829624; PubMed Central PMCID: PMC3463118.

16: Dey BK, Gagan J, Yan Z, Dutta A. miR-26a is required for skeletal muscle differentiation and regeneration in mice. Genes Dev. 2012 Oct 1;26(19):2180-91. doi: 10.1101/gad.198085.112. PubMed PMID: 23028144; PubMed Central PMCID: PMC3465739.

17: Demirel PB, Keyes BE, Chaterjee M, Remington CE, Burke DJ. A redundant function for the N-terminal tail of Ndc80 in kinetochore-microtubule interaction in Saccharomyces cerevisiae. Genetics. 2012 Oct;192(2):753-6. doi: 10.1534/genetics.112.143818. Epub 2012 Jul 30. PubMed PMID: 22851650; PubMed Central PMCID: PMC3454895.

18: Yu X, Goforth C, Meyer C, Rachel R, Wirth R, Schr√∂der GF, Egelman EH. Filaments from Ignicoccus hospitalis show diversity of packing in proteins containing N-terminal type IV pilin helices. J Mol Biol. 2012 Sep 14;422(2):274-81. doi: 10.1016/j.jmb.2012.05.031. Epub 2012 May 30. PubMed PMID: 22659006; PubMed Central PMCID: PMC3599786.

19: Lindorfer MA, Wiestner A, Zent CS, Taylor RP. Monoclonal antibody (mAb)-based cancer therapy: Is it time to reevaluate dosing strategies? Oncoimmunology. 2012 Sep 1;1(6):959-961. PubMed PMID: 23162771; PubMed Central PMCID: PMC3489759.

20: Abel JL, Rissman EF. Location, location, location: genetic regulation of neural sex differences. Rev Endocr Metab Disord. 2012 Sep;13(3):151-61. doi: 10.1007/s11154-011-9186-0. Review. PubMed PMID: 21607612; PubMed Central PMCID: PMC3622700.

21: Utepbergenov D, Derewenda U, Olekhnovich N, Szukalska G, Banerjee B, Hilinski MK, Lannigan DA, Stukenberg PT, Derewenda ZS. Insights into the inhibition of the p90 ribosomal S6 kinase (RSK) by the flavonol glycoside SL0101 from the 1.5 √Ö crystal structure of the N-terminal domain of RSK2 with bound inhibitor. Biochemistry. 2012 Aug 21;51(33):6499-510. doi: 10.1021/bi300620c. Epub 2012 Aug 6 PubMed PMID: 22846040; PubMed Central PMCID: PMC3462495.

22: Wolstenholme JT, Edwards M, Shetty SR, Gatewood JD, Taylor JA, Rissman EF, Connelly JJ. Gestational exposure to bisphenol a produces transgenerational changes in behaviors and gene expression. Endocrinology. 2012 Aug;153(8):3828-38. doi: 10.1210/en.2012-1195. Epub 2012 Jun 15. PubMed PMID: 22707478; PubMed Central PMCID: PMC3404345.

23: Tejada LD, Rissman EF. Sex differences in social investigation: effects of androgen receptors, hormones and test partner. J Neuroendocrinol. 2012 Aug;24(8):1144-53. doi: 10.1111/j.1365-2826.2012.02322.x. PubMed PMID: 22487205; PubMed Central PMCID: PMC3615635.

24: Stolzenberg DS, Stevens JS, Rissman EF. Experience-facilitated improvements in pup retrieval; evidence for an epigenetic effect. Horm Behav. 2012 Jul;62(2):128-35. doi: 10.1016/j.yhbeh.2012.05.012. Epub 2012 Jun 8. PubMed PMID: 22687346; PubMed Central PMCID: PMC3474355.

25: Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR. PSI-Search: iterative HOE-reduced profile SSEARCH searching. Bioinformatics. 2012 Jun 15;28(12):1650-1. doi: 10.1093/bioinformatics/bts240. Epub 2012 Apr 25. PubMed PMID: 22539666; PubMed Central PMCID: PMC3371869.

26: McClure JM, Wierman MB, Maqani N, Smith JS. Isonicotinamide enhances Sir2 protein-mediated silencing and longevity in yeast by raising intracellular NAD+ concentration. J Biol Chem. 2012 Jun 15;287(25):20957-66. doi: 10.1074/jbc.M112.367524. Epub 2012 Apr 26. PubMed PMID: 22539348; PubMed Central PMCID: PMC3375519.

27: Wotton D. TGF-Œ≤ drives DNA demethylation. Mol Cell. 2012 Jun 8;46(5):556-7. doi: 10.1016/j.molcel.2012.05.031. PubMed PMID: 22681884.

28: Gagan J, Dey BK, Dutta A. MicroRNAs regulate and provide robustness to the myogenic transcriptional network. Curr Opin Pharmacol. 2012 Jun;12(3):383-8. doi: 10.1016/j.coph.2012.02.001. Epub 2012 Mar 2. Review. PubMed PMID: 22386695; PubMed Central PMCID: PMC3369106.

29: Bassett EA, DeNizio J, Barnhart-Dailey MC, Panchenko T, Sekulic N, Rogers DJ, Foltz DR, Black BE. HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/histone H4 for centromere assembly. Dev Cell. 2012 Apr 17;22(4):749-62. doi: 10.1016/j.devcel.2012.02.001. Epub 2012 Mar 8. PubMed PMID: 22406139; PubMed Central PMCID: PMC3353549.

30: Gioeli D, Paschal BM. Post-translational modification of the androgen receptor. Mol Cell Endocrinol. 2012 Apr 16;352(1-2):70-8. doi: 10.1016/j.mce.2011.07.004. Epub 2011 Jul 24. PubMed PMID: 21820033.

31: Shibata Y, Kumar P, Layer R, Willcox S, Gagan JR, Griffith JD, Dutta A. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science. 2012 Apr 6;336(6077):82-6. doi: 10.1126/science.1213307. Epub 2012 Mar 8. Erratum in: Science. 2012 Jun 22;336(6088):1506. PubMed PMID: 22403181; PubMed Central PMCID: PMC3703515.

32: Addison ML, Rissman EF. Sexual dimorphism of growth hormone in the hypothalamus: regulation by estradiol. Endocrinology. 2012 Apr;153(4):1898-907. doi: 10.1210/en.2011-1982. Epub 2012 Feb 7. PubMed PMID: 22315455; PubMed Central PMCID: PMC3320260.

33: Bonthuis PJ, Cox KH, Rissman EF. X-chromosome dosage affects male sexual behavior. Horm Behav. 2012 Apr;61(4):565-72. doi: 10.1016/j.yhbeh.2012.02.003. Epub 2012 Feb 10. PubMed PMID: 22349083; PubMed Central PMCID: PMC3319230.

34: Niedzialkowska E, Wang F, Porebski PJ, Minor W, Higgins JM, Stukenberg PT. Molecular basis for phosphospecific recognition of histone H3 tails by Survivin paralogues at inner centromeres. Mol Biol Cell. 2012 Apr;23(8):1457-66. doi: 10.1091/mbc.E11-11-0904. Epub 2012 Feb 22. PubMed PMID: 22357620; PubMed Central PMCID: PMC3327328.

35: Moyle-Heyrman G, Viswanathan R, Widom J, Auble DT. Two-step mechanism for modifier of transcription 1 (Mot1) enzyme-catalyzed displacement of TATA-binding protein (TBP) from DNA. J Biol Chem. 2012 Mar 16;287(12):9002-12. doi: 10.1074/jbc.M111.333484. Epub 2012 Feb 1. PubMed PMID: 22298788; PubMed Central PMCID: PMC3308732.

36: Matson DR, Demirel PB, Stukenberg PT, Burke DJ. A conserved role for COMA/CENP-H/I/N kinetochore proteins in the spindle checkpoint. Genes Dev. 2012 Mar 15;26(6):542-7. doi: 10.1101/gad.184184.111. PubMed PMID: 22426531; PubMed Central PMCID: PMC3315115.

37: Liu Y, Mayo MW, Nagji AS, Smith PW, Ramsey CS, Li D, Jones DR. Phosphorylation of RelA/p65 promotes DNMT-1 recruitment to chromatin and represses transcription of the tumor metastasis suppressor gene BRMS1. Oncogene. 2012 Mar 1;31(9):1143-54. doi: 10.1038/onc.2011.308. Epub 2011 Jul 18. PubMed PMID: 21765477; PubMed Central PMCID: PMC3219802.

38: Galkin VE, Orlova A, Egelman EH. Actin filaments as tension sensors. Curr Biol. 2012 Feb 7;22(3):R96-101. doi: 10.1016/j.cub.2011.12.010. Review. PubMed PMID: 22321312; PubMed Central PMCID: PMC3277726.

39: Foltz DR, Stukenberg PT. A new histone at the centromere? Cell. 2012 Feb 3;148(3):394-6. doi: 10.1016/j.cell.2012.01.023. PubMed PMID: 22304909; PubMed Central PMCID: PMC3404608.

40: Silva MC, Bodor DL, Stellfox ME, Martins NM, Hochegger H, Foltz DR, Jansen 1. Cdk activity couples epigenetic centromere inheritance to cell cycle progression. Dev Cell. 2012 Jan 17;22(1):52-63. doi: 10.1016/j.devcel.2011.10.014. Epub 2011 Dec 8. PubMed PMID: 22169070.

41: Glidden EJ, Gray LG, Vemuru S, Li D, Harris TE, Mayo MW. Multiple site acetylation of Rictor stimulates mammalian target of rapamycin complex 2 (mTORC2)-dependent phosphorylation of Akt protein. J Biol Chem. 2012 Jan 2;287(1):581-8. doi: 10.1074/jbc.M111.304337. Epub 2011 Nov 14. PubMed PMID: 22084251; PubMed Central PMCID: PMC3249112.

42: Zhang Y, Dutta A, Abounader R. The role of microRNAs in glioma initiation and progression. Front Biosci (Landmark Ed). 2012 Jan 1;17:700-12. Review. PubMed PMID: 22201769; PubMed Central PMCID: PMC3278211.

43: Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj JC, Onengut-Gumuscu S, Concannon P. Evidence for two independent associations with type 1 diabetes at the 12q13 locus. Genes Immun. 2012 Jan;13(1):66-70. doi: 10.1038/gene.2011.56. Epub 2011 Aug 18. PubMed PMID: 21850031; PubMed Central PMCID: PMC3285513.

44: Hall IM, Quinlan AR. Detection and interpretation of genomic structural variation in mammals. Methods Mol Biol. 2012;838:225-48. doi: 10.1007/978-1-61779-507-7_11. Review. PubMed PMID: 22228015.

45: Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR. MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9. doi: 10.1093/nar/gkr799. Epub 2011 Nov 3. PubMed PMID: 22058127; PubMed Central PMCID: PMC3244993.

46: Taniguchi K, Anderson AE, Sutherland AE, Wotton D. Loss of Tgif function causes holoprosencephaly by disrupting the SHH signaling pathway. PLoS Genet. 2012;8(2):e1002524. doi: 10.1371/journal.pgen.1002524. Epub 2012 Feb 23. PubMed PMID: 22383895; PubMed Central PMCID: PMC3285584.

47: Dutta P, Tanti GK, Sharma S, Goswami SK, Komath SS, Mayo MW, Hockensmith JW, Muthuswami R. Global epigenetic changes induced by SWI2/SNF2 inhibitors characterize neomycin-resistant mammalian cells. PLoS One. 2012;7(11):e49822. doi: 10.1371/journal.pone.0049822. Epub 2012 Nov 28. PubMed PMID: 23209606; PubMed Central PMCID: PMC3509132.

48: Zerlanko BJ, Bartholin L, Melhuish TA, Wotton D. Premature senescence and increased TGFŒ≤ signaling in the absence of Tgif1. PLoS One. 2012;7(4):e35460. doi: 10.1371/journal.pone.0035460. Epub 2012 Apr 13. PubMed PMID: 22514746; PubMed Central PMCID: PMC3325954.

49: Quinlan AR, Hall IM. Characterizing complex structural variation in germline and somatic genomes. Trends Genet. 2012 Jan;28(1):43-53. doi: 10.1016/j.tig.2011.10.002. Epub 2011 Nov 15. Review. PubMed PMID: 22094265; PubMed Central PMCID: PMC3249479.