Publications

2012

Orozco LD, Bennett BJ, Farber CR, Ghazalpour A, Pan C, Che N, Wen P, Qi HX, Mutukulu A, Siemers N, Neuhaus I, Yordanova R, Gargalovic P, Pellegrini M, Kirchgessner T, Lusis AJ. (2012). Unraveling Inflammatory Responses using Systems Genetics and Gene-Environment Interactions in Macrophages. Cell, 151(3):658-70.  doi: 10.1016/j.cell.2012.08.043. PMID: 23101632

Ghazalpour A, Rau CD, Farber CR, Bennett BJ, Orozco LD, van Nas A, Pan C, Allayee H, Beaven SW, Civelek M, Davis RC, Drake TA, Friedman RA, Furlotte N, Hui ST, Jentsch JD, Kostem E, Kang HM, Kang EY, Joo JW, Korshunov VA, Laughlin RE, Martin LJ, Ohmen JD, Parks BW, Pellegrini M, Reue K, Smith DJ, Tetradis S, Wang J, Wang Y, Weiss JN, Kirchgessner T, Gargalovic PS, Eskin E, Lusis AJ, LeBoeuf RC. Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. Mamm Genome. 2012 Oct;23(9-10):680-92. doi: 10.1007/s00335-012-9411-5.

Farber CR. Systems genetics: a novel approach to dissect the genetic basis of osteoporosis. Curr Osteoporos Rep. 2012 Sep;10(3):228-35. doi: 10.1007/s11914-012-0112-5.

Furlotte NA, Kang EY, Van Nas A, Farber CR, Lusis AJ, Eskin E. Increasing association mapping power and resolution in mouse genetic studies through the use of meta-analysis for structured populations. Genetics. 2012 Jul;191(3):959-67. doi: 10.1534/genetics.112.140277.

Casellas J, Gularte RJ, Farber CR, Varona L, Mehrabian M, Schadt EE, Lusis AJ, Attie AD, Yandell BS, Medrano JF. Genome scans for transmission ratio distortion regions in mice. Genetics. 2012 May;191(1):247-59. doi: 10.1534/genetics.111.135988.

2011

Ghazalpour, A., Bennett, B., Petyuk, V.A., Orozco, L., Hagopian, R., Mungrue, I.N.,Farber, C.R., Sinsheimer, J., Kang, H.M., Furlotte, N., Park, C.C., Wen, P.Z., Brewer, H., Weitz, K., Camp, D.G. 2nd, Pan, C., Yordanova, R., Neuhaus, I., Tilford, C., Siemers, N., Gargalovic, P., Eskin, E., Kirchgessner, T., Smith, D.J., Smith, R.D., Lusis, A.J. (2011). Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genetics, 7(6), e1001393. PMID: 21695224

de Jong, S., Kas, M.J., Kiernan, J., de Mooij-van Malsen, A.G., Oppelaar, H., Janson, E., Vukobradovic, I., Farber, C.R., Stanford, W.L., Ophoff, R.A. (2011). Hippocampal gene expression analysis highlights ly6a/sca-1 as candidate gene for previously mapped novelty induced behaviors in mice. PLoS One, 6(6), e20716. PMID: 21673958

Farber, C.R., Kelly, S.A., Baruch, E., Yu, D., Hua, K., Nehrenberg, D.L., de Villena, F.P.,Buus, R.J., Garland, T. Jr., Pomp, D. (2011). Identification of quantitative trait loci influencing skeletal architecture in mice: emergence of Cdh1 as a primary candidate gene regulating femoral morphology. Journal of Bone and Mineral Research. doi: 10.1002/jbmr.436. PMID: 21638317

Farber, C.R., Bennett, B.J., Orozco, L., Zou, W., Lira, A., Kostem, E., Kang, H.M.,Furlotte, N., Berberyan, A., Ghazalpour, A., Suwanwela, J., Drake, T.A., Eskin, E., Wang, Q.T., Teitelbaum, S.L., Lusis, A.J. (2011). Mouse genome-wide association and systems genetics identify Asxl2 as a regulator of bone mineral density and osteoclastogenesis. PLoS Genetics., 7(4), e1002038. PMID:21490954

Park, C.C., Gale, G.D., de Jong, S., Ghazalpour, A., Bennett, B.J., Farber, C.R., Langfelder, P., Lin, A., Khan, A.H., Eskin, E., Horvath, S., Lusis, A.J., Ophoff, R.A., Smith, D.J. (2011). Gene networks associated with conditional fear in mice identified using a systems genetics approach.  BMC Systems Biology., 5,43. PMID: 21410935

Suwanwela, J., Farber, C.R., Haung, B.L., Song, B., Pan, C., Lyons, K.M., Lusis, A.J. (2011). Systems genetics analysis of mouse chondrocyte differentiation. Journal of Bone and Mineral Research, 26(4), 747-60. PMID: 20954177

2010

Verdugo, R.A., Farber,C.R., Warden, C.H., & Medrano, J.F. (2010). Serious limitations of the QTL/microarray approach for QTL gene discovery. BMC Biology., 8,96. PMID: 20624276

Hsu, Y.H.*, Zillikens, M.C.*, Wilson, S.G.*, Farber, C.R.*, Demissie, S., Soranzo, E.N.,Bianchi, E., Grundberg, L., Liang, L., Richards, J.B., Estrada, K., Zhou, Y., van Nas, A., Moffatt, M.F., Zhai, G., Hofman, A., van Meurs, J.B., Pols, H.A., Price, R.I., Nilsson, O., Pastinen, T., Cupples, L.A., Lusis, A.J., Schadt, E.E., Ferrari, S., Uitterlinden, A.G., Rivadeneira, F., Spector, T.D., Karasik, D., & Kiel, D.P. (2010). An integration of genome-wide association study and gene expression  profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits. PLoS Genetics, 6(6), e1000977. PMID: 20548944. (*Co-First Authors)

Farber, C.R. (2010). Identification of a gene module associated with BMD through the integration of network analysis and genome-wide association data. Journal of Bone and Mineral Research, 25(11), 2359-67. PMID: 20499364

Bennett, B.J.*, Farber, C.R.*, Orozco, L.*, Kang, H.M.*, Ghazalpour, A., Siemers, N.,Neubauer, M., Neuhaus, I., Yordanova, R., Guan, B., Truong, A., Yang, W.P., He, A., Kayne, P., Gargalovic, P., Kirchgessner, T., Pan, C., Castellani, L.W., Kostem, E., Furlotte, N., Drake, T.A., Eskin, E., & Lusis A.J. (2010). A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Research, 20(2), 281-90. PMID: 20054062. (*Co-First Authors)

Casellas, J., Farber, C.R., Verdugo, R.A., & Medrano, J.F. (2010). Segregation analysis of a sex ratio distortion locus in congenic mice. Journal of Heredity, 101(3), 351-9. PMID: 20032064

Farber, C.R., & Rosen, C.J. (2010) Genetics of Osteoporosis. Translational Endocrinology and Metabolism, 1(1), 87-116.

2009

Rincon, G., Farber, E.A., Farber, C.R., Nkrumah, J.D., & Medrano, J.F. (2009). Polymorphisms in the STAT6 gene and their association with carcass traits in feedlot cattle. Animal Genetics, 40(6):878-82.

Farber, C.R. & Lusis, A.J. (2009). Future of osteoporosis genetics: enhancing genome-wide association studies. Journal of Bone and Mineral Research, 24(12), 1937-42. PMID:19888896

Casellas, J., Farber, C.R., Gularte, R.J., Haus, K.A., Warden, C.H., & Medrano, J.F. (2009). Evidence of maternal QTL affecting growth and obesity in adult mice. Mammalian Genome, 20(5), 269-80. PMID: 19399551

Farber, C.R., Aten, J.E., Farber, E.A., de Vera,V., Gularte, R., Islas-Trejo, A., Wen, P., Horvath, S., Lucero, M., Lusis, A.J., & Medrano, J.F. (2009). Genetic dissection of a major mouse obesity QTL (Carfhg2): integration of gene expression and causality modeling. Physiological Genomics, 37(3), 294-302. PMID: 19336533

Yang, X., Deignan, J.L., Qi, H., Zhu, J., Qian, S., Zhong, J., Torosyan, G., Majid, S., Falkard, B., Kleinhanz, R.R., Karlsson, J., Castellani, L.W., Mumick, S., Wang, K., Xie, T., Coon, M., Zhang, C., Estrada-Smith, D., Farber, C.R., Wang, S.S., van Nas, A., Ghazalpour, A., Zhang, B., Macneil, D.J., Lamb J.R., Dipple, K.M., Reitman, M.L., Mehrabian, M., Lum, P.Y., Schadt, E.E., Lusis, A.J., & Drake, T.A. (2009). Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nature Genetics,  41(4), 415-23. PMID: 19270708

Farber, C.R., van Nas, A., Ghazalpour, A., Aten, J.E., Doss, S., Sos, B., Schadt, E.E., Ingram-Drake, L., Davis, R.C., Horvath, S., Smith, D.J., Drake, T.A., & Lusis, A.J. (2009). An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association. Journal of Bone and Mineral Research, 24(1), 105-16. PMID: 1876792

2008

Ghazalpour, A., Doss, S., Kang, H., Farber, C., Wen, P.Z., Brozell, A., Castellanos, R., Eskin, E., Smith, D.J., Drake, T.A., Lusis, A.J. (2008). High-resolution mapping of gene expression using association in an outbred mouse stock. PLoS Genet., 4(8), e1000149. PMID:18688273

Farber, C.R., Chitwood, J., Lee, S.N., Verdugo, R.A., Islas-Trejo, A., Rincon, G., Lindberg, I., & Medrano, J.F. (2008). Overexpression of Scg5 increases enzymatic activity of PCSK2 and is inversely correlated with body weight in congenic mice. BMC Genetics, 9,34. PMID: 18439298

Farber, C.R., & Lusis, A.J. (2008). Integrating global gene expression analysis and genetics. Advances in Genetics, 60, 571-601. PMID: 18358333

2007

Farber, C.R. & Medrano, J.F. (2007). Dissection of a genetically complex cluster of growth and obesity QTLs on mouse chromosome 2 using subcongenic intercrosses. Mammalian Genome, 18(9), 635-45. PMID: 17694346

Farber, C.R., & Medrano, J.F. (2007). Fine mapping reveals sex bias in quantitative trait loci affecting growth, skeletal size and obesity-related traits on mouse chromosomes 2 and 11. Genetics, 175(1), 349-60. PMID: 17110492

2006

Farber, C.R., Corva, P.M, & Medrano, J.F. (2006). Genome-wide isolation of growth and obesity QTL using mouse speed congenic strains. BMC Genomics, 7, 102. PMID: 16670015

2004

Churchill, G.A., Airey, D.C., Allayee, H., Angel, J.M., Attie, A.D., Beatty, J., Beavis, W.D., Belknap, J.K., Bennett, B., Berrettini, W., Bleich, A., Bogue, M., Broman, K.W., Buck, K.J., Buckler, E., Burmeister, M., Chesler, E.J., Cheverud, J.M., Clapcote, S., Cook, M.N., Cox, R.D., Crabbe, J.C., Crusio, W.E., Darvasi, A., Deschepper, C.F., Doerge, R.W., Farber, C.R., Forejt, J., Gaile, D., Garlow, S.J., Geiger, H., Gershenfeld, H., Gordon, T., Gu, J., Gu, W., de Haan, G., Hayes, N.L., Heller, C., Himmelbauer, H., Hitzemann, R., Hunter, K., Hsu, H.C., Iraqi, F.A., Ivandic, B., Jacob, H.J., Jansen, R.C., Jepsen, K.J., Johnson, D.K., Johnson, T.E., Kempermann, G., Kendziorski, C., Kotb, M., Kooy, R.F., Llamas, B., Lammert, F., Lassalle, J.M., Lowenstein, P.R., Lu, L., Lusis, A., Manly, K.F., Marcucio, R., Matthews, D., Medrano, J.F., Miller, D.R., Mittleman, G., Mock, B.A., Mogil, J.S., Montagutelli, X., Morahan, G., Morris, D.G., Mott, R., Nadeau, J.H., Nagase, H., Nowakowski, R.S., O’Hara, B.F., Osadchuk, A.V., Page, G.P., Paigen, B., Paigen, K., Palmer, A.A., Pan, H.J., Peltonen-Palotie, L., Peirce, J., Pomp, D., Pravenec, M., Prows, D.R., Qi, Z., Reeves, R.H., Roder, J., Rosen, G.D., Schadt, E.E., Schalkwyk, L.C., Seltzer, Z., Shimomura, K., Shou, S., Sillanpää, M.J., Siracusa, L.D., Snoeck, H.W., Spearow, J.L., Svenson, K., Tarantino, L.M., Threadgill, D., Toth, L.A., Valdar, W., de Villena, F.P., Warden, C., Whatley, S., Williams, R.W., Wiltshire, T., Yi, N., Zhang, D., Zhang, M., Zou, F. (2004). The Collaborative Cross, a community resource for the genetic analysis of complex traits, Complex Trait Consortium, Nat Genet., 36(11), 1133-7. PMID: 15514660

Farber, C.R. & Medrano, J.F. (2004). Identification of putative homology between horse microsatellite flanking sequences and cross-species ESTs, mRNAs and genomic sequences. Animal Genetics, 35(1), 28-33.

2003

Abiola, O., Angel, J.M., Avner, P., Bachmanov, A.A., Belknap, J.K., Bennett, B., Blankenhorn, E.P., Blizard, D.A., Bolivar, V., Brockmann, G.A., Buck, K.J., Bureau, J.F., Casley, W.L., Chesler, E.J., Cheverud, J.M., Churchill, G.A., Cook, M., Crabbe, J.C., Crusio, W.E., Darvasi, A., de Haan, G., Dermant, P., Doerge, R.W., Elliot, R.W., Farber, C.R., Flaherty, L., Flint, J., Gershenfeld, H., Gibson, J.P., Gu, J., Gu, W., Himmelbauer ,H., Hitzemann, R., Hsu, H.C., Hunter, K., Iraqi, F.F., Jansen, R.C., Johnson, T.E., Jones, B.C., Kempermann, G., Lammert, F., Lu, L., Manly, K.F., Matthews, D.B., Medrano, J.F., Mehrabian, M., Mittlemann, G., Mock, B.A., Mogil, J.S., Montagutelli, X., Morahan, G., Mountz, J.D., Nagase, H., Nowakowski, R.S., O’Hara, B.F., Osadchuk, A.V., Paigen, B., Palmer, A.A., Peirce, J.L., Pomp, D., Rosemann, M., Rosen, G.D., Schalkwyk, L.C., Seltzer, Z., Settle, S., Shimomura, K., Shou, S., Sikela, J.M., Siracusa, L.D., Spearow, J.L., Teuscher, C., Threadgill, D.W., Toth, L.A., Toye, A.A., Vadasz, C., Van Zant, G., Wakeland, E., Williams, R.W., Zhang, H.G., Zou, F., & Consortium, C.T. (2003). The nature and identification of quantitative trait loci: a community’s view. Nature Review Genetics, 4(11), 911-6. PMID: 14634638

Farber, C.R., Raney, N.E., Rilington, V.D., Venta, P.J., & Ernst, C.W. (2003). Comparative mapping of genes flanking the human chromosome 12 evolutionary breakpoint in the pig. Cytogenetics and Genome Research, 102(1-4),139-44.

Farber, C.R., Raney, N.E., Kuhlers, D.L., Nadarajah, K., & Ernst, C.W. (2003). Mapping of porcine genetic markers generated by representational difference analysis. Animal Biotechnology, 14(1), 87-102.

Farber, C.R. & Medrano, J.F. (2003). Putative in silico mapping of DNA sequences to livestock genome maps using SSLP flanking sequences. Animal Genetics, 34(1), 11-8.