Aakrosh Ratan

Murray, C. S., Karram, M., Bass, D. J., Doceti, M., Becker, D., Nunez, J. C. B., . . . Bergland, A. O. (2024). Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species.. bioRxiv. doi:10.1101/2024.04.16.589693

Santen, R. J., Karaguzel, G., Livaoglu, M., Yue, W., Cline, J. M., Ratan, A., & Sasano, H. (2024). Role of ERα and Aromatase in Juvenile Gigantomastia. JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 109(7), 1765-1772. doi:10.1210/clinem/dgae019

Eljilany, I., Saghand, P. G., Chen, J., Ratan, A., McCarter, M., Carpten, J., . . . Tarhini, A. A. (2023). The T Cell Immunoscore as a Reference for Biomarker Development Utilizing Real-World Data from Patients with Advanced Malignancies Treated with Immune Checkpoint Inhibitors. CANCERS, 15(20). doi:10.3390/cancers15204913

Yang, C., Wierbilowicz, K., Dworak, N. M., Bae, S. Y., Tengse, S. B., Abianeh, N., . . . Paschal, B. M. (2023). Induction of PARP7 Creates a Vulnerability for Growth Inhibition by RBN2397 in Prostate Cancer Cells. CANCER RESEARCH COMMUNICATIONS, 3(4), 592-606. doi:10.1158/2767-9764.CRC-23-0086

Kim, H. L., Li, T., Kalsi, N., Nguyen, H. T. T., Shaw, T. A. A., Ang, K. C. C., . . . Horton, B. P. P. (2023). Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise. COMMUNICATIONS BIOLOGY, 6(1). doi:10.1038/s42003-023-04510-0

Jun, G., English, A. C., Metcalf, G. A., Yang, J., Chaisson, M. J., Pankratz, N., . . . Sedlazeck, F. J. (2023). Structural variation across 138,134 samples in the TOPMed consortium.. Res Sq. doi:10.21203/rs.3.rs-2515453/v1

Jun, G., English, A. C., Metcalf, G. A., Yang, J., Chaisson, M. J., Pankratz, N., . . . Sedlazeck, F. J. (2023). Structural variation across 138,134 samples in the TOPMed consortium.. bioRxiv. doi:10.1101/2023.01.25.525428

Wheeler, M. M., Stilp, A. M., Rao, S., Halldorsson, B. V., Beyter, D., Wen, J., . . . Reiner, A. P. (2022). Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-35354-7

Barnard-Kubow, K. B., Becker, D., Murray, C. S., Porter, R., Gutierrez, G., Erickson, P., . . . Bergland, A. O. (2022). Genetic Variation in Reproductive Investment Across an Ephemerality Gradient in Daphnia pulex. MOLECULAR BIOLOGY AND EVOLUTION, 39(6). doi:10.1093/molbev/msac121

Cheon, H., Xing, J. C., Moosic, K. B., Ung, J., Chan, V. W., Chung, D. S., . . . Loughran Jr, T. P. (2022). Genomic landscape of TCRαβ and TCRγδ T-large granular lymphocyte leukemia. BLOOD, 139(20), 3058-3072. doi:10.1182/blood.2021013164

Baer, C., Kimura, S., Rana, M. S., Kleist, A. B., Flerlage, T., Feith, D. J., . . . Mullighan, C. G. (2022). CCL22 mutations drive natural killer cell lymphoproliferative disease by deregulating microenvironmental crosstalk. NATURE GENETICS, 54(5), 637-+. doi:10.1038/s41588-022-01059-2

Sahu, D., Chatrath, A., Ratan, A., & Dutta, A. (2022). Integrated bioinformatic pipeline using whole-exome and RNAseq data to identify germline variants correlated with cancer. STAR PROTOCOLS, 3(2). doi:10.1016/j.xpro.2022.101273

Torn, C., Liu, X., Onengut-Gumuscu, S., Counts, K. M., Moreno, J. L., Remedios, C. L., . . . Parikh, H. M. (2022). Telomere length is not a main factor for the development of islet autoimmunity and type 1 diabetes in the TEDDY study. SCIENTIFIC REPORTS, 12(1). doi:10.1038/s41598-022-08058-7

Sienkiewicz, K., & Ratan, A. (2022). Protocol for integrative subtyping of lower-grade gliomas using the SUMO pipeline. STAR PROTOCOLS, 3(1). doi:10.1016/j.xpro.2021.101110

Sienkiewicz, K., Chen, J., Chatrath, A., Lawson, J. T., Sheffield, N. C., Zhang, L., & Ratan, A. (2022). Detecting molecular subtypes from multi-omics datasets using SUMO. CELL REPORTS METHODS, 2(1). doi:10.1016/j.crmeth.2021.100152

Sienkiewicz, K., Yang, C., Paschal, B. M., & Ratan, A. (2022). Genomic analyses of the metastasis-derived prostate cancer cell lines LNCaP, VCaP, and PC3-AR. PROSTATE, 82(4), 442-451. doi:10.1002/pros.24290

Siren, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., . . . Paten, B. (2021). Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. SCIENCE, 374(6574), 1461-+. doi:10.1126/science.abg8871

Suryamohan, K., Diwanji, D., Stawiski, E. W., Gupta, R., Miersch, S., Liu, J., . . . Seshagiri, S. (2021). Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2. COMMUNICATIONS BIOLOGY, 4(1). doi:10.1038/s42003-021-02030-3

Natarajan, P., Pampana, A., Graham, S. E., Ruotsalainen, S. E., Perry, J. A., de Vries, P. S., . . . Kuopio, T. (2021). Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-22339-1

Olson, T. L., Cheon, H., Xing, J. C., Olson, K. C., Paila, U., Hamele, C. E., . . . Loughran, T. P. J. (2021). Frequent somatic TET2 mutations in chronic NK-LGL leukemia with distinct patterns of cytopenias. BLOOD, 138(8), 662-673. doi:10.1182/blood.2020005831

Chatrath, A., Ratan, A., & Dutta, A. (2021). Germline variants predictive of tumor mutational burden and immune checkpoint inhibitor efficacy. ISCIENCE, 24(3). doi:10.1016/j.isci.2021.102248

Chatrath, A., Ratan, A., & Dutta, A. (2021). Germline Variants That Affect Tumor Progression. TRENDS IN GENETICS, 37(5), 433-443. doi:10.1016/j.tig.2020.10.005

Onengut-Gumuscu, S., Paila, U., Chen, W. -M., Ratan, A., Zhu, Z., Steck, A. K., . . . Rich, S. S. (2020). Novel genetic risk factors influence progression of islet autoimmunity to type 1 diabetes. SCIENTIFIC REPORTS, 10(1). doi:10.1038/s41598-020-75690-6

Bick, A. G., Weinstock, J. S., Nandakumar, S. K., Fulco, C. P., Bao, E. L., Zekavat, S. M., . . . Natarajan, P. (2021). Inherited causes of clonal haematopoiesis in 97,691 whole genomes (vol 586, pg 763, 2020). NATURE, 591(7849), E27. doi:10.1038/s41586-021-03280-1

Fang, C., Wang, Z., Han, C., Safgren, S. L., Helmin, K. A., Adelman, E. R., . . . Zang, C. (2020). Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation. GENOME BIOLOGY, 21(1). doi:10.1186/s13059-020-02152-7

Li, X., Li, Z., Zhou, H., Gaynor, S. M., Liu, Y., Chen, H., . . . Lin, X. (2020). Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. NATURE GENETICS, 52(9), 969-+. doi:10.1038/s41588-020-0676-4

Grabski, D. F., Ratan, A., Gray, L. R., Bekiranov, S., Rekosh, D., Hammarskjold, M. -L., & Rasmussen, S. K. (2021). Upregulation of human endogenous retrovirus-K (HML-2) mRNAs in hepatoblastoma: Identification of potential new immunotherapeutic targets and biomarkers. JOURNAL OF PEDIATRIC SURGERY, 56(2), 286-292. doi:10.1016/j.jpedsurg.2020.05.022

Kathuria, K., & Ratan, A. (2020). SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures. PLOS COMPUTATIONAL BIOLOGY, 16(3). doi:10.1371/journal.pcbi.1007737

Chatrath, A., Przanowska, R., Kiran, S., Su, Z., Saha, S., Wilson, B., . . . Dutta, A. (2020). The pan-cancer landscape of prognostic germline variants in 10,582 patients. GENOME MEDICINE, 12(1). doi:10.1186/s13073-020-0718-7

Fry, E., Kim, S. K., Chigurapti, S., Mika, K. M., Ratan, A., Dammermann, A., . . . Lynch, V. J. (2020). Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth. GENOME BIOLOGY AND EVOLUTION, 12(3), 48-58. doi:10.1093/gbe/evz279

Wang, T. T., Yang, J., Dighe, S., Schmachtenberg, M. W., Leigh, N. T., Farber, E., . . . Olson, T. L. (2020). Whole Genome Sequencing of Spontaneously Occurring Rat Natural Killer Large Granular Lymphocyte Leukemia Identifies JAK1 Somatic Activating Mutation. CANCERS, 12(1). doi:10.3390/cancers12010126

Sienkiewicz, K., Chen, J., Chatrath, A., Lawson, J., Sheffield, N., Zhang, L., & Ratan, A. (2020). Data Integration with SUMO Detects Latent Relationships Between Patients in Lower-Grade Gliomas. doi:10.1101/2020.08.10.244343

Suryamohan, K., Krishnankutty, S. P., Guillory, J., Jevit, M., Schroeder, M. S., Wu, M., . . . Seshagiri, S. (2020). The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. NATURE GENETICS, 52(1), 106-+. doi:10.1038/s41588-019-0559-8

Kathuria, K., Ratan, A., McConnell, M., & Bekiranov, S. (2020). Implementation of a Hamming distance-like genomic quantum classifier using inner products on ibmqx2 and ibmq_16_melbourne. QUANTUM MACHINE INTELLIGENCE, 2(1). doi:10.1007/s42484-020-00017-7

Wall, J. D., Ratan, A., & Stawiski, E. (2019). Identification of African-Specific Admixture between Modern and Archaic Humans. AMERICAN JOURNAL OF HUMAN GENETICS, 105(6), 1254-1261. doi:10.1016/j.ajhg.2019.11.005

Wall, J. D., Stawiski, E. W., Ratan, A., Kim, H. L., Kim, C., Gupta, R., . . . Peterson, A. S. (2019). The GenomeAsia 100K Project enables genetic discoveries across Asia. NATURE, 576(7785), 106-+. doi:10.1038/s41586-019-1793-z

Kachroo, P., Hecker, J., Chawes, B. L., Ahluwalia, T. S., Cho, M. H., Qiao, D., . . . Zoellner, S. (2019). Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma. CHEST, 156(6), 1068-1079. doi:10.1016/j.chest.2019.08.2202

Moosic, K. B., Paila, U., Olson, K. C., Dziewulska, K., Wang, T. T., Xing, J. C., . . . Olson, T. L. (2019). Genomics of LGL leukemia and select other rare leukemia/lymphomas. BEST PRACTICE & RESEARCH CLINICAL HAEMATOLOGY, 32(3), 196-206. doi:10.1016/j.beha.2019.06.003

Feng, J., Ratan, A., & Sheffield, N. C. (2019). Augmented Interval List: a novel data structure for efficient genomic interval search. BIOINFORMATICS, 35(23), 4907-4911. doi:10.1093/bioinformatics/btz407

Kitchen, S. A., Ratan, A., Bedoya-Reina, O. C., Burhans, R., Fogarty, N. D., Miller, W., & Baums, I. B. (2019). Genomic Variants Among Threatened Acropora Corals. G3-GENES GENOMES GENETICS, 9(5), 1633-1646. doi:10.1534/g3.119.400125

Chatrath, A., Kiran, M., Kumar, P., Ratan, A., & Dutta, A. (2019). The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients. MOLECULAR CANCER RESEARCH, 17(5), 1075-1086. doi:10.1158/1541-7786.MCR-18-0996

Chatrath, A., Przanowska, R., Kiran, S., Su, Z., Saha, S., Wilson, B., . . . Dutta, A. (2019). The Pan-Cancer Landscape of Prognostic Germline Variants in 10,582 Patients. doi:10.1101/19010264

Chatrath, A., Kiran, M., Kumar, P., Ratan, A., & Dutta, A. (2018). The Germline Variants rs61757955 and rs34988193 are Predictive of Survival in Low Grade Glioma Patients. doi:10.1101/497354

Jividen, K., Kedzierska, K. Z., Yang, C. -S., Szlachta, K., Ratan, A., & Paschal, B. M. (2018). Genomic analysis of DNA repair genes and androgen signaling in prostate cancer. BMC CANCER, 18. doi:10.1186/s12885-018-4848-x

Burbulis, I. E., Wierman, M. B., Wolpert, M., Haakenson, M., Lopes, M. -B., Schiff, D., . . . McConnell, M. J. (2018). Improved molecular karyotyping in glioblastoma. MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS, 811, 16-26. doi:10.1016/j.mrfmmm.2018.06.002

Kedzierska, K. Z., Gerber, L., Cagnazzi, D., Krutzen, M., Ratan, A., & Kistler, L. (2018). SONiCS: PCR stutter noise correction in genome-scale microsatellites. BIOINFORMATICS, 34(23), 4115-4117. doi:10.1093/bioinformatics/bty485

Kathuria, K., & Ratan, A. (2018). SVXplorer: Identification of structural variants through overlap of discordant clusters. doi:10.1101/469981

Junqueira, A. C. M., Ratan, A., Acerbi, E., Drautz-Moses, D. I., Premkrishnan, B. N. V., Costea, P. I., . . . Schuster, S. C. (2017). The microbiomes of blowflies and houseflies as bacterial transmission reservoirs. SCIENTIFIC REPORTS, 7. doi:10.1038/s41598-017-16353-x

Kistler, L., Johnson, S. M., Irwin, M. T., Louis, E. E., Ratan, A., & Perry, G. H. (2017). A massively parallel strategy for STR marker development, capture, and genotyping. NUCLEIC ACIDS RESEARCH, 45(15). doi:10.1093/nar/gkx574

Fry, E., Kim, S., Chigurapti, S., Mika, K., Ratan, A., Dammermann, A., . . . Lynch, V. (2017). Functional architecture of deleterious genetic variants in the Wrangel Island mammoth genome. doi:10.1101/137455

Agaba, M., Ishengoma, E., Miller, W. C., McGrath, B. C., Hudson, C. N., Reina, O. C. B., . . . Cavener, D. R. (2016). Giraffe genome sequence reveals clues to its unique morphology and physiology. NATURE COMMUNICATIONS, 7. doi:10.1038/ncomms11519

Carpi, G., Kitchen, A., Kim, H. L., Ratan, A., Drautz-Moses, D. I., McGraw, J. J., . . . Schuster, S. C. (2016). Mitogenomes reveal diversity of the European Lyme borreliosis vector Ixodes ricinus in Italy. MOLECULAR PHYLOGENETICS AND EVOLUTION, 101, 194-202. doi:10.1016/j.ympev.2016.05.009

Welch, A. J., Collins, K., Ratan, A., Drautz-Moses, D. I., Schuster, S. C., & Lindqvist, C. (2016). Data characterizing the chloroplast genomes of extinct and endangered Hawaiian endemic mints (Lamiaceae) and their close relatives. DATA IN BRIEF, 7, 900-922. doi:10.1016/j.dib.2016.03.037

Welch, A. J., Collins, K., Ratan, A., Drautz-Moses, D. I., Schuster, S. C., & Lindqvist, C. (2016). The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). MOLECULAR PHYLOGENETICS AND EVOLUTION, 99, 16-33. doi:10.1016/j.ympev.2016.02.024

Junqueira, A. C. M., Azeredo-Espin, A. M. L., Paulo, D. F., Marinho, M. A. T., Tomsho, L. P., Drautz-Moses, D. I., . . . Schuster, S. C. (2016). Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity. SCIENTIFIC REPORTS, 6. doi:10.1038/srep21762

Lan, T., Cheng, J., Ratan, A., Miller, W., Schuster, S., Farley, S., . . . Lindqvist, C. (2016). Genome-wide evidence for a hybrid origin of modern polar bears. doi:10.1101/047498

Fuller, Z. L., Niño, E. L., Patch, H. M., Bedoya-Reina, O. C., Baumgarten, T., Muli, E., . . . Miller, W. (2015). Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.. BMC genomics, 16, 518. doi:10.1186/s12864-015-1712-0

Lynch, V. J., Bedoya-Reina, O. C., Ratan, A., Sulak, M., Drautz-Moses, D. I., Perry, G. H., . . . Schuster, S. C. (2015). Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic.. Cell reports, 12(2), 217-228. doi:10.1016/j.celrep.2015.06.027

Ratan, A., Olson, T. L., Loughran, T. P. J., & Miller, W. (2015). Identification of indels in next-generation sequencing data. BMC BIOINFORMATICS, 16. doi:10.1186/s12859-015-0483-6

Kistler, L., Ratan, A., Godfrey, L. R., Crowley, B. E., Hughes, C. E., Lei, R., . . . Perry, G. H. (2015). Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.. Journal of human evolution, 79, 45-54. doi:10.1016/j.jhevol.2014.06.016

Kim, H. L., Ratan, A., Perry, G. H., Montenegro, A., Miller, W., & Schuster, S. C. (2014). Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history. NATURE COMMUNICATIONS, 5. doi:10.1038/ncomms6692

Bedoya-Reina, O. C., Ratan, A., Burhans, R., Kim, H. L., Giardine, B., Riemer, C., . . . Miller, W. (2013). Galaxy tools to study genome diversity. GIGASCIENCE, 2. doi:10.1186/2047-217X-2-17

Perry, G. H., Louis, E. E., Ratan, A., Bedoya-Reina, O. C., Burhans, R. C., Lei, R., . . . Miller, W. (2013). Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar.. Proceedings of the National Academy of Sciences of the United States of America, 110(15), 5823-5828. doi:10.1073/pnas.1211990110

Ratan, A., Miller, W., Guillory, J., Stinson, J., Seshagiri, S., & Schuster, S. C. (2013). Comparison of sequencing platforms for single nucleotide variant calls in a human sample.. PloS one, 8(2), e55089. doi:10.1371/journal.pone.0055089

Giardine, B. M., Riemer, C., Burhans, R., Ratan, A., & Miller, W. (2012). Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome.. Current protocols in bioinformatics, Chapter 15, 15.2.1-15.2.27. doi:10.1002/0471250953.bi1502s39

Gupta, R., Ratan, A., Rajesh, C., Chen, R., Kim, H. L., Burhans, R., . . . Thomas, G. (2012). Sequencing and analysis of a South Asian-Indian personal genome.. BMC genomics, 13, 440. doi:10.1186/1471-2164-13-440

Miller, W., Schuster, S. C., Welch, A. J., Ratan, A., Bedoya-Reina, O. C., Zhao, F., . . . Lindqvist, C. (2012). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.. Proceedings of the National Academy of Sciences of the United States of America, 109(36), E2382-E2390. doi:10.1073/pnas.1210506109

Perry, G. H., Reeves, D., Melsted, P., Ratan, A., Miller, W., Michelini, K., . . . Gilad, Y. (2012). A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar.. Genome biology and evolution, 4(2), 126-135. doi:10.1093/gbe/evr132

Miller, W., Hayes, V. M., Ratan, A., Petersen, D. C., Wittekindt, N. E., Miller, J., . . . Schuster, S. C. (2011). Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).. Proceedings of the National Academy of Sciences of the United States of America, 108(30), 12348-12353. doi:10.1073/pnas.1102838108

Locke, D. P., Hillier, L. W., Warren, W. C., Worley, K. C., Nazareth, L. V., Muzny, D. M., . . . Wilson, R. K. (2011). Comparative and demographic analysis of orang-utan genomes.. Nature, 469(7331), 529-533. doi:10.1038/nature09687

Ratan, A., Zhang, Y., Hayes, V. M., Schuster, S. C., & Miller, W. (2010). Calling SNPs without a reference sequence.. BMC bioinformatics, 11, 130. doi:10.1186/1471-2105-11-130

Lindqvist, C., Schuster, S. C., Sun, Y., Talbot, S. L., Qi, J., Ratan, A., . . . Wiig, O. (2010). Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear.. Proceedings of the National Academy of Sciences of the United States of America, 107(11), 5053-5057. doi:10.1073/pnas.0914266107

Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B., Kasson, L. R., . . . Hayes, V. M. (2010). Complete Khoisan and Bantu genomes from southern Africa.. Nature, 463(7283), 943-947. doi:10.1038/nature08795