Charles R. Farber

Abood, A., Mesner, L. D., Jeffery, E. D., Murali, M., Lehe, M. D., Saquing, J., . . . Sheynkman, G. M. (2024). Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease.. American journal of human genetics, S0002-9297(24)00227-1. doi:10.1016/j.ajhg.2024.07.003

Allayee, H., Farber, C. R., Seldin, M. M., Williams, E. G., James, D. E., & Lusis, A. J. (2023). Systems genetics approaches for understanding complex traits with relevance for human disease. ELIFE, 12. doi:10.7554/eLife.91004

Dillard, L. J., Rosenow, W. T., Calabrese, G. M., Mesner, L. D., Al-Barghouthi, B. M., Abood, A., . . . Farber, C. R. (2023). Single-Cell Transcriptomics of Bone Marrow Stromal Cells in Diversity Outbred Mice: A Model for Population-Level scRNA-Seq Studies. JOURNAL OF BONE AND MINERAL RESEARCH, 38(9), 1350-1363. doi:10.1002/jbmr.4882

Friedman, M. A., Buettmann, E. G., Zeineddine, Y., Abraham, L. B., Hoppock, G. A., Meas, S. J., . . . Donahue, H. J. (2024). Genetic variation influences the skeletal response to hindlimb unloading in the eight founder strains of the diversity outbred mouse population. JOURNAL OF ORTHOPAEDIC RESEARCH, 42(1), 134-140. doi:10.1002/jor.25646

Migotsky, N., Surabhi Kumar., Shuster, J., Coulombe, J., Senwar, B., Gestos, A., . . . Silva, M. (2023). Multi-Scale Cortical Bone Traits Vary in Two Mouse Models of Genetic Diversity. doi:10.1101/2023.06.02.543484

Abood, A., Mesner, L., Jeffery, E., Murali, M., Lehe, M., Saquing, J., . . . Sheynkman, G. (2023). Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease. doi:10.1101/2023.03.17.531557

Gonzalez, T. L., Schaub, A. M., Lee, B., Cui, J., Taylor, K. D., Dorfman, A. E., . . . Pisarska, M. D. (2023). Infertility and treatments used have minimal effects on first-trimester placental DNA methylation and gene expression. FERTILITY AND STERILITY, 119(2), 301-312. doi:10.1016/j.fertnstert.2022.11.010

Moran, M. M., Ko, F. C., Mesner, L. D., Calabrese, G. M., Al-Barghouthi, B. M., Farber, C. R., & Sumner, D. R. (2022). Intramembranous bone regeneration in diversity outbred mice is heritable. BONE, 164. doi:10.1016/j.bone.2022.116524

Castaldi, P. J., Abood, A., Farber, C. R., & Sheynkman, G. M. (2022). Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease. HUMAN MOLECULAR GENETICS, 31(R1), R123-R136. doi:10.1093/hmg/ddac196

Abood, A., Mesner, L., Rosenow, W., Al-Barghouthi, B. M., Horowitz, N., Morgan, E. F., . . . Farber, C. R. (2022). Identification of Known and Novel Long Noncoding RNAs Potentially Responsible for the Effects of Bone Mineral Density (BMD) Genomewide Association Study (GWAS) Loci. JOURNAL OF BONE AND MINERAL RESEARCH, 37(8), 1500-1510. doi:10.1002/jbmr.4622

Logan, J. G., Yun, S., Teachman, B. A., Bao, Y., Farber, E., & Farber, C. R. (2022). Genome-Wide mRNA Expression Analysis of Acute Psychological Stress Responses. MEDICC REVIEW, 24(2), 35-42. doi:10.37757/MR2022.V24.N2.6

Wang, T., Yang, L., Yuan, M., Farber, C. R., Spolski, R., Leonard, W. J., . . . Annex, B. H. (2022). MicroRNA-30b Is Both Necessary and Sufficient for Interleukin-21 Receptor-Mediated Angiogenesis in Experimental Peripheral Arterial Disease. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 23(1). doi:10.3390/ijms23010271

Braenne, I., Onengut-Gumuscu, S., Chen, R., Manichaikul, A. W., Rich, S. S., Chen, W. -M., & Farber, C. R. (2021). Dynamic changes in immune gene co-expression networks predict development of type 1 diabetes. SCIENTIFIC REPORTS, 11(1). doi:10.1038/s41598-021-01840-z

Harp, S. J., Martini, M., Rosenow, W., Mesner, L. D., Johnson, H., Farber, C. R., & Rissman, E. F. (2022). Fentanyl-induced acute and conditioned behaviors in two inbred mouse lines: Potential role for Glyoxalase. PHYSIOLOGY & BEHAVIOR, 243. doi:10.1016/j.physbeh.2021.113630

Friedman, M. A., Abood, A., Senwar, B., Zhang, Y., Maroni, C. R., Ferguson, V. L., . . . Donahue, H. J. (2021). Genetic variability affects the skeletal response to immobilization in founder strains of the diversity outbred mouse population. BONE REPORTS, 15. doi:10.1016/j.bonr.2021.101140

Le, Q., Madhu, V., Hart, J. M., Farber, C. R., Zunder, E. R., Dighe, A. S., & Cui, Q. (2021). Current evidence on potential of adipose derived stem cells to enhance bone regeneration and future projection. WORLD JOURNAL OF STEM CELLS, 13(9). doi:10.4252/wjsc.v13.i9.1248

Maroni, C. R., Friedmann, M. A., Zhang, Y., McClure, M. J., Fulle, S., Farber, C. R., & Donahue, H. J. (2021). Genetic variability affects the response of skeletal muscle to disuse. JOURNAL OF MUSCULOSKELETAL & NEURONAL INTERACTIONS, 21(3), 387-396. Retrieved from https://www.webofscience.com/

Sabik, O. L., Ackert-Bicknell, C. L., & Farber, C. R. (2021). A computational approach for identification of core modules from a co-expression network and GWAS data. STAR PROTOCOLS, 2(3). doi:10.1016/j.xpro.2021.100768

Abood, A., & Farber, C. R. (2021). Using "-omics" Data to Inform Genome-wide Association Studies (GWASs) in the Osteoporosis Field. CURRENT OSTEOPOROSIS REPORTS, 19(4), 369-380. doi:10.1007/s11914-021-00684-w

Al-Barghouthi, B. M., Mesner, L. D., Calabrese, G. M., Brooks, D., Tommasini, S. M., Bouxsein, M. L., . . . Farber, C. R. (2021). Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-23649-0

Moon, H. H., Clines, K. L., O'Day, P. J., Al-Barghouthi, B. M., Farber, E. A., Farber, C. R., . . . Clines, G. A. (2021). Osteoblasts Generate Testosterone From DHEA and Activate Androgen Signaling in Prostate Cancer Cells. JOURNAL OF BONE AND MINERAL RESEARCH, 36(8), 1566-1579. doi:10.1002/jbmr.4313

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

Zhang, Q., Mesner, L. D., Calabrese, G. M., Dirckx, N., Li, Z., Verardo, A., . . . Clemens, T. L. (2021). Genomic variants within chromosome 14q32.32 regulate bone mass through MARK3 signaling in osteoblasts. JOURNAL OF CLINICAL INVESTIGATION, 131(7). doi:10.1172/JCI142580

Laker, R. C., Altintas, A., Lillard, T. S., Zhang, M., Connelly, J. J., Sabik, O. L., . . . Yan, Z. (2021). Exercise during pregnancy mitigates negative effects of parental obesity on metabolic function in adult mouse offspring. JOURNAL OF APPLIED PHYSIOLOGY, 130(3), 605-616. doi:10.1152/japplphysiol.00641.2020

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

Sabik, O. L., Calabrese, G. M., Taleghani, E., Ackert-Bicknell, C. L., & Farber, C. R. (2020). Identification of a Core Module for Bone Mineral Density through the Integration of a Co-expression Network and GWAS Data. CELL REPORTS, 32(11). doi:10.1016/j.celrep.2020.108145

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

Logan, J. G., Teachman, B. A., Liu, X., Farber, C. R., Liu, Z., & Annex, B. H. (2020). Acute psychological stress, autonomic function, and arterial stiffness among women. INTERNATIONAL JOURNAL OF PSYCHOPHYSIOLOGY, 155, 219-226. doi:10.1016/j.ijpsycho.2020.06.015

Doolittle, M. L., Calabrese, G. M., Mesner, L. D., Godfrey, D. A., Maynard, R. D., Ackert-Bicknell, C. L., & Farber, C. R. (2020). Genetic analysis of osteoblast activity identifies Zbtb40 as a regulator of osteoblast activity and bone mass. PLOS GENETICS, 16(6). doi:10.1371/journal.pgen.1008805

Chermside-Scabbo, C. J., Harris, T. L., Brodt, M. D., Braenne, I., Zhang, B., Farber, C. R., & Silva, M. J. (2020). Old Mice Have Less Transcriptional Activation But Similar Periosteal Cell Proliferation Compared to Young-Adult Mice in Response to in vivo Mechanical Loading. JOURNAL OF BONE AND MINERAL RESEARCH, 35(9), 1751-1764. doi:10.1002/jbmr.4031

Logan, J. G., Yun, S., Bao, Y., Farber, E., & Farber, C. R. (2020). RNA-sequencing analysis of differential gene expression associated with arterial stiffness. VASCULAR, 28(5), 655-663. doi:10.1177/1708538120922650

Cui, D., Drake, J. C., Wilson, R. J., Shute, R. J., Lewellen, B., Zhang, M., . . . Yan, Z. (2020). A novel voluntary weightlifting model in mice promotes muscle adaptation and insulin sensitivity with simultaneous enhancement of autophagy and mTOR pathway. FASEB JOURNAL, 34(6), 7330-7344. doi:10.1096/fj.201903055R

Friedman, M., Abood, A., Senwar, B., Zhang, Y., Maroni, C. R., Ferguson, V., . . . Donahue, H. (2020). Genetic Variability affects the Skeletal Response to Unloading. doi:10.1101/2020.06.26.174326

Maroni, C. R., Friedman, M., Zhang, Y., McClure, M., Fulle, S., Farber, C., & Donahue, H. (2020). Muscle Atrophy: Different Strains of Mice Respond Differently to Single Limb Immobilization. doi:10.1101/2020.11.03.367169

Lu, L., Huang, J., Xu, F., Xiao, Z., Wang, J., Zhang, B., . . . Williams, R. W. (2019). Genetic Dissection of Femoral and Tibial Microarchitecture. JBMR PLUS, 3(12). doi:10.1002/jbm4.10241

Doolittle, M., Calabrese, G., Mesner, L., Godfrey, D., Maynard, R., Ackert-Bicknell, C., & Farber, C. (2019). Genetic Analysis of Osteoblast Activity Identifies Zbtb40 as a Regulator of Osteoblast Activity and Bone Mass. doi:10.1101/828525

Sabik, O., Calabrese, G., Taleghani, E., Ackert-Bicknell, C., & Farber, C. (2019). Identification of a core module for bone mineral density through the integration of a co-expression network and GWAS data. doi:10.1101/803197

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

Zhang, Q., Riddle, R. C., Yang, Q., Rosen, C. R., Guttridge, D. C., Dirckx, N., . . . Clemens, T. L. (2019). The RNA demethylase FTO is required for maintenance of bone mass and functions to protect osteoblasts from genotoxic damage. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116(36), 17980-17989. doi:10.1073/pnas.1905489116

Mesner, L. D., Calabrese, G. M., Al-Barghouthi, B., Gatti, D. M., Sundberg, J. P., Churchill, G. A., . . . Farber, C. R. (2019). Mouse genome-wide association and systems genetics identifies Lhfp as a regulator of bone mass. PLOS GENETICS, 15(5). doi:10.1371/journal.pgen.1008123

Hsu, Y. -H., Estrada, K., Evangelou, E., Ackert-Bicknell, C., Akesson, K., Beck, T., . . . Karasik, D. (2019). Meta-Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry. JOURNAL OF BONE AND MINERAL RESEARCH, 34(7), 1284-1296. doi:10.1002/jbmr.3698

Ganta, V. C., Choi, M., Farber, C. R., & Annex, B. H. (2019). Antiangiogenic VEGF₁₆₅b Regulates Macrophage Polarization via S100A8/S100A9 in Peripheral Artery Disease. CIRCULATION, 139(2), 226-242. doi:10.1161/CIRCULATIONAHA.118.034165

Lee, B., Koeppel, A. F., Wang, E. T., Gonzalez, T. L., Sun, T., Kroener, L., . . . Pisarska, M. D. (2019). Differential gene expression during placentation in pregnancies conceived with different fertility treatments compared with spontaneous pregnancies. FERTILITY AND STERILITY, 111(3), 535-546. doi:10.1016/j.fertnstert.2018.11.005

Friedman, M. A., Zhang, Y., Wayne, J. S., Farber, C. R., & Donahue, H. J. (2019). Single limb immobilization model for bone loss from unloading. JOURNAL OF BIOMECHANICS, 83, 181-189. doi:10.1016/j.jbiomech.2018.11.049

Al-Barghouthi, B. M., & Farber, C. R. (2019). Dissecting the Genetics of Osteoporosis using Systems Approaches. TRENDS IN GENETICS, 35(1), 55-67. doi:10.1016/j.tig.2018.10.004

Sun, T., Lee, B., Kinchen, J., Wang, E. T., Gonzalez, T. L., Chan, J. L., . . . Pisarska, M. D. (2019). Differences in First-Trimester Maternal Metabolomic Profiles in Pregnancies Conceived From Fertility Treatments. JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 104(4), 1005-1019. doi:10.1210/jc.2018-01118

Gonzalez, T. L., Sun, T., Koeppel, A. F., Lee, B., Wang, E. T., Farber, C. R., . . . Pisarska, M. D. (2018). Sex differences in the late first trimester Mark human placenta transcriptome. BIOLOGY OF SEX DIFFERENCES, 9. doi:10.1186/s13293-018-0165-y

Mesner, L., Calabrese, G., Al-Barghouthi, B., Gatti, D., Sundberg, J., Churchill, G., . . . Farber, C. (2018). Mouse Genome-Wide Association and Systems Genetics IdentifiesLhfpas a Regulator of Bone Mass. doi:10.1101/454678

Sabik, O., & Farber, C. (2018). RACER: A data visualization strategy for exploring multiple genetic associations. doi:10.1101/495366

Ganta, V. C., Choi, M. H., Kutateladze, A., Fox, T. E., Farber, C. R., & Annex, B. H. (2017). A MicroRNA93-Interferon Regulatory Factor-9-Immunoresponsive Gene-1-Itaconic Acid Pathway Modulates M2-Like Macrophage Polarization to Revascularize Ischemic Muscle. CIRCULATION, 135(24), 2403-+. doi:10.1161/CIRCULATIONAHA.116.025490

Sabik, O. L., Medrano, J. F., & Farber, C. R. (2017). Genetic Dissection of a QTL Affecting Bone Geometry. G3-GENES GENOMES GENETICS, 7(3), 865-870. doi:10.1534/g3.116.037424

Baliga, N. S., Bjoerkegren, J. L. M., Boeke, J. D., Boutros, M., Crawford, N. P. S., Dudley, A. M., . . . Vonesch, S. C. (2017). The State of Systems Genetics in 2017 commentary. CELL SYSTEMS, 4(1), 7-15. doi:10.1016/j.cels.2017.01.005

Calabrese, G. M., Mesner, L. D., Stains, J. P., Tommasini, S. M., Horowitz, M. C., Rosen, C. J., & Farber, C. R. (2017). Integrating GWAS and Co-expression Network Data Identifies Bone Mineral Density Genes SPTBN1 and MARK3 and an Osteoblast Functional Module. CELL SYSTEMS, 4(1), 46-+. doi:10.1016/j.cels.2016.10.014

Pisarska, M. D., Akhlaghpour, M., Lee, B., Barlow, G. M., Xu, N., Wang, E. T., . . . Williams, J. I. I. I. (2016). Optimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling. PRENATAL DIAGNOSIS, 36(11), 1061-1070. doi:10.1002/pd.4936

Sabik, O. L., & Farber, C. R. (2017). Using GWAS to identify novel therapeutic targets for osteoporosis. TRANSLATIONAL RESEARCH, 181, 15-26. doi:10.1016/j.trsl.2016.10.009

Calabrese, G., Mesner, L. D., Foley, P. L., Rosen, C. J., & Farber, C. R. (2016). Network Analysis Implicates Alpha-Synuclein (Snca) in the Regulation of Ovariectomy-Induced Bone Loss. SCIENTIFIC REPORTS, 6. doi:10.1038/srep29475

Li, C., Zhen, G., Chai, Y., Xie, L., Crane, J. L., Farber, E., . . . Wan, M. (2016). RhoA determines lineage fate of mesenchymal stem cells by modulating CTGF-VEGF complex in extracellular matrix. NATURE COMMUNICATIONS, 7. doi:10.1038/ncomms11455

Lusis, A. J., Seldin, M. M., Allayee, H., Bennett, B. J., Civelek, M., Davis, R. C., . . . Wang, J. (2016). The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits. JOURNAL OF LIPID RESEARCH, 57(6), 925-942. doi:10.1194/jlr.R066944

Gillespie, A. L., Teoh, J., Lee, H., Prince, J., Stadnisky, M. D., Anderson, M., . . . Brown, M. G. (2016). Genomic Modifiers of Natural Killer Cells, Immune Responsiveness and Lymphoid Tissue Remodeling Together Increase Host Resistance to Viral Infection. PLOS PATHOGENS, 12(2). doi:10.1371/journal.ppat.1005419

Zheng, H. -F., Forgetta, V., Hsu, Y. -H., Estrada, K., Rosello-Diez, A., Leo, P. J., . . . Richards, J. B. (2015). Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture. NATURE, 526(7571), 112-+. doi:10.1038/nature14878

Dokun, A. O., Chen, L., Okutsu, M., Farber, C. R., Hazarika, S., Jones, W. S., . . . Annex, B. H. (2015). ADAM12: a genetic modifier of preclinical peripheral arterial disease. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY, 309(5), H790-H803. doi:10.1152/ajpheart.00803.2014

Orozco, L. D., Morselli, M., Rubbi, L., Guo, W., Go, J., Shi, H., . . . Pellegrini, M. (2015). Epigenome-Wide Association of Liver Methylation Patterns and Complex Metabolic Traits in Mice. CELL METABOLISM, 21(6), 905-917. doi:10.1016/j.cmet.2015.04.025

Frey, J. L., Li, Z., Ellis, J. M., Zhang, Q., Farber, C. R., Aja, S., . . . Riddle, R. C. (2015). Wnt-Lrp5 Signaling Regulates Fatty Acid Metabolism in the Osteoblast. MOLECULAR AND CELLULAR BIOLOGY, 35(11), 1979-1991. doi:10.1128/MCB.01343-14

Gularte-Merida, R., Farber, C. R., Verdugo, R. A., Islas-Trejo, A., Famula, T. R., Warden, C. H., & Medrano, J. F. (2015). Overlapping mouse subcongenic strains successfully separate two linked body fat QTL on distal MMU 2. BMC GENOMICS, 16. doi:10.1186/s12864-014-1191-8