Publications

Simpson, N. E., Gertz, J., Imberg, K., Myers, R. M. and Garabedian, M. J.  (2011).  Enhanced genome-wide occupancy of estrogen receptor alpha by the co-chaperone p23 in breast cancer cells.  Molec. Endocrin.  Submitted.

Reddy, T. E., Gertz, J., Pauli, F., Kucera, K. S., Newberry, K. M., Marinov, G. K., Mortazavi, A., Williams, B. A., Wold, B., Willard, H. F. and Myers, R. M.  (2011).  Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Submitted.

McGuire, V., Van Den Eeden, S. K., Tanner, C. M., Kamel, F., Umbach, D. M., Marder, K., Mayeux, R., Ritz, B., Webster Ross, G., Petrovitch, H., Topol, B., Popat, R. A., Southwick, A., Myers, R. M. and Nelson, L. M.  (2011).  Association of DRD2 and DRD3 Polymorphisms with Parkinson’s Disease in a Multiethnic Consortium. Submitted.

Gertz, J., Varley, K., Reddy, T., Bowling, K., Pauli, F., Parker, S., Kucera, K., Willard, H. and Myers, R. M.  (2011).  Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.  Submitted.

The Cancer Genome Atlas Research Network  (2011).  Integrated genomic analyses of ovarian carcinoma.  Nature.  In press.

Kobayashi, Y., Absher, D. M., Gulzar, Z. G., Young, S., McKenney, J. K., Peehl, D., Brooks, J. D., Myers, R. M., and Sherlock, G.  (2011). DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res. Apr 26. [Epub ahead of print]. doi:10.1101/gr.119487.110.  PMID: 21521786.

Greenwood, A. K., Jones, F. C., Chan, Y. F., Brady, S. D., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., Kingsley, D. M., and Peichel, C. L.  (2011).  The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks.  Heredity.  Feb 9. [Epub ahead of print].  PMID: 21304547.  

The ENCODE Project Consortium.  (2011).  A user's guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol.  Volume 9, Issue 4.  e1001046.  doi:10.1371/journal.pbio.1001046.

Popat, R. A., Van Den Eeden, S. K., Tanner, C. M., Kamel, F., Umbach, D. M., Marder, K., Mayeux, R., Ritz, B., Webster Ross, G., Petrovitch, H., Topol, B., McGuire, V., Costello, S., Manthripragada, A. D., Southwick, A., Myers, R. M. and Nelson, L. M.  (2011).  Coffee, ADORA2A, and CYP1A2: the caffeine connection in Parkinson’s disease. Eur. J. Neurol. 18: 756-765.  doi: 10.1111/j.1468-1331.2011.03353.x.  PMID: 21281405.

Krolewski, D. M., Medina, A., Kerman, I. A., Bernard, R., Burke, S., Thompson, R. C., Bunney, W. E. Jr., Schatzberg, A. F., Myers, R. M., Akil, H., Jones, E. G. and Watson, S. J.  (2010).  Expression patterns of corticotropin-releasing factor, arginine vasopressin, histidine decarboxylase, melanin-concentrating hormone, and orexin genes in the human hypothalamus.  J. Comp. Neurol.  15: 4591-4611.  PMID: 20886624.  PMCID: PMC2965642.

Mendoza-Fandino, G. A., Gee, J. M., Ben-Dor, S., Gonzalez-Quevedo, C., Lee, K., Kobayashi, Y., Hartiala, J., Myers, R. M., Leal, S. M., Allayee, H. and Patel, P. I.  (2010).  A Novel g.-1258G>A Mutation in a Conserved Putative Regulatory Element of PAX9 is Associated with Autosomal Dominant Molar Hypodontia. Clin. Gen. Aug 12. doi: 10.1111/j.1399-0004.2010.01529.x. [Epub ahead of print].  PMID: 21443745.

Assimes, T. L., Holm, H., Kathiresan, S., Reilly, M. P., Thorleifsson, G., Voight, B. F., Erdmann, J., Willenborg, C., Vaidya, D., Xie, C., Patterson, C. C., Morgan, T. M., Burnett, M. S., Li, M., Hlatky, M. A., Knowles, J. W., Thompson, J. R., Absher, D., Iribarren, C., Go, A., Fortmann, S. P., Sidney, S., Risch, N., Tang, H., Myers, R. M., Berger, K., Stoll, M., Shah, S. H., Thorgeirsson, G., Andersen, K., Herrera, J. E., Faraday, N., Kim, Y., Kral, B. G., Mathias, R., Ruczinski, I., Suktitipat, B., Wilson, W. F., Yanek, L. R., Becker, L. C., Linsel-Nitschke, P., Lieb, W., König, I. R., Hengstenberg, C., Fischer, M., Stark, K., Reinhard, W., Winogradow, J.,  Grassl, M., Grosshennig, A., Preuss, M., Schreiber, S., Wichmann, H-E., Meisinger, C., Yee, J., Friedlander, Y., Do, R., Meigs, J. B., Williams, G., Nathan, D. M., MacRae, C. A., Qu, L., Wilensky, R. L., Matthai J. R., W. H., Qasim, A. N., Hakonarson, H., Pichard, A. D., Kent, K. M., Satler, L., Lindsay, J. M., Waksman, R., Knouff, C. W., Waterworth, D. M., Walker, M. C., Mooser, V. E., Marrugat, J., Lucas, G., Subirana, I., Sala, J., Ramos, R., Martinelli, N., Olivieri, O., Trabetti, E. Malerba, G., Pignatti, P. F., C., Mirel, D., Parkin, M., Hirschhorn, J. N., Asselta, R., Duga, S., Musunuru, K., Daly, M. J., Purcell, S., Eifert, S., Braund, P. S., Wright, B. J., Balmforth, A. J.,. Ball, S. G., Myocardial Infarction Genetics Consortium, Wellcome Trust Case Control Consortium, Cardiogenics, Ouwehand, W. H., Deloukas, P., Scholz, M., Cambien, F., Huge, A., Scheffold, T., Salomaa, V., Girelli, D., Granger, C. B., Peltonen, L., McKeown, P. P., Altshuler, D., Melander, O., Devaney, J. M.,  Epstein, S. E., Rader, D. J., Elosua, R., Engert, J. C., Anand, S. S., Hall, A. S., Ziegler, A., O’Donnell, C. J., Spertus, J. A., Siscovick, D., Schwartz, S. M., Becker, D., Thorsteinsdottir, U., Stefansson, K., Schunkert, H., Samani, N. J., Quertermous, T.  (2010).  Lack of Association Between the Trp719Arg Polymorphism in Kinesin-Like Protein-6 and Coronary Artery Disease in 19 Case-Control Studies. J. Amer. Coll. Cardiol.  56: 1552-1563. PMID: 20933357.  

Bernard, R., Kerman, I. A., Thompson, R. C., Jones, E. G., Bunney, W. E., Barchas, J. D., Schatzberg, A. F., Myers, R. M., Akil, H. and Watson. S. J.  (2010).  Altered expression of glutamate signaling, growth factor, and glia genes in the locus coeruleus of patients with major depression. Mol. Psychiatry.  Apr. 13. [Epub ahead of print]. PMID: 20386568.  PMCID: PMC2927798.

Landolin, J. M., Johnson, D. S., Trinklein, N. D., Aldred, S. F., Medina, C., Shulha, H., Weng, Z., Myers, R. M.  (2010).  Sequence features that drive human promoter function and tissue specificity.   Genome Res.  In press.  

Ding, F., Li, H. H., Li, J., Myers, R. M. and Francke, U.  (2010). Neonatal starvation response and developmental changes in gene expression revealed by hypothalamic gene expression profiling in mice.   PLoS ONE. Feb 24; 5: e9402.  PMID: 20195375.  PMCID: PMC2827556.

Wang, C., Sanders, C. M., Yang, Q., Schroeder, Jr., H. W., Wang, E., Babrzadeh, F., Gharizadeh, B., Myers, R. M., Hudson, Jr., J. R., Davis, R. W. and Han, J.  (2010).  High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets.  Proc Natl Acad Sci USA. 107: 1518-1523.  PMID: 20080641. [PubMed - as supplied by publisher].

Amemiya, C. T., Powers, T. P., Prohaska, S. J., Grimwood, J. Schmutz, J., Dickson, M., Miyake, T., Schoenborn, M. A., Myers, R. M., Ruddle, F. H. and Stadler, P. F.  (2010).  Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome.  Proc. Natl. Acad. Sci. USA. Published online before print February 5, 2010, doi:10.1073/pnas.0914312107.

Goode, D. L., Cooper, G. M., Schmutz, J., Dickson, M., Gonzales, E., Tsai, M., Karra, K., Davydov, E., Batzoglou, S., Myers, R. M. and Sidow, A.  (2010).  Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes.  Genome Res.  Jan 12. [Epub ahead of print].  PMID: 20067941.  [PubMed - as supplied by publisher].

Zakharia, F., Basu, A., Absher, D., Assimes, T. L., Go, A. S., Hlatky, M. A., Iribarren, C., Knowles, J. W., Li, J., Narasimhan, B., Sidney, S., Southwick, A., Myers, R. M., Quertermous, T., Risch, N., and Tang, H. (2009).  Characterizing the admixed African ancestry of African Americans.  Genome Biol.  10: R141.  [Epub ahead of print]. PMID: 20025784.  [PubMed - as supplied by publisher].

Chan, Y. F., Marks, M. E., Jones, F. C., Villarreal Jr., G., Shapiro, M. D., Fisher, S., Southwick, A. M., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., Petrov, D., Jónsson, B., Schluter, D., Bell, M. A. and Kingsley, D. M.  (2009).  Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.  Science 327: 302-305.  PMID: 20007865.  [PubMed - as supplied by publisher].

Wheeler, H. E., Metter, E. J., Tanaka, T., Absher, D., Higgins, J., Zahn, J. M., Wilhelmy, J., Davis, R. W., Singleton, A. W., Myers, R. M., Ferrucci, L. and Kim, S. K.  (2009).  Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging.  PLoS Genet. 5: e1000685.  doi:10.1371/journal.pgen.1000685.  PMID: 19834535.  PMCID - in process.

Martin, M. V., Rollins, B., Sequeira, P. A., Mesen, A., Byerley, W., Stein, R., Moon, E. A., Akil, H., Jones, E. G., Watson, S. J., Barchas, J., Delisi, L. E., Myers, R. M., Schatzberg, A., Bunney, W. E., and Vawter, M. P.  (2009).  Exon expression in lymphoblastoid cell lines from subjects with schizophrenia before and after glucose deprivation. MC Med. Genomics 2: 62. [Epub ahead of print].  PMID: 19772658. PMCID: PMC2760574.

The MGC Project Team, Temple, G., Jang, W., Wagner, L., Shenmen, C. M., Gerhard, D. S., Rasooly, R., Feingold, E. A., Good, P., Guyer, M., Robinson, C., Peck, A .M., Derge, J. G., Lewis, J., Shoaf, D., Collins, F. S., Misquitta, L., Schaefer, C. F., Buetow, K. H., Bonner, T. I., Yankie, L., Ward, M., Phan, L., Astashyn, A., Brown, G., Farrell, C., Hart, J., Landrum, M., Maidak, B., Murphy, M., Murphy, T., Rajput, B., Riddick, L., Webb, D., Weber, J., Wu, W., Pruitt, K. D., Maglott, D., Siepel, A., Brejova, B., Diekhans, M., Harte, R., Baertsch, R., Kent, J., Haussler, D., Brent, M., Langton, L., Comstock, C.L.G., Stevens, M., Wei, C., Salehi-Ashtiani, K., Murray, R. R., Ghamsari, L., Mello, E., Lin, C., Pennacchio, C., Schreiber, K., Shapiro, N., Marsh, A., Pardes, E., Moore, T., Lebeau, A., Muratet, M., Simmons, B., Kloske, D., Sieja, S., Hudson, J., Sethupathy, P., Brownstein, M., Bhat, N., Lazar, J., Gruber, C.E., Smith, M.R., McPherson, J., Garcia, A. M., Gunaratne, P. H., Wu, J., Muzny, D., Gibbs, R. A., Young, A. C., Bouffard, G. G., Blakesley, R. W., Mullikin, J., Green, E. D., Dickson, M. C., Rodriguez, A. C., Grimwood, J., Schmutz, J., Myers, R. M., Hirst, M., Zeng, T., Tse, K., Moksa, M., Deng, M., Ma, K., Mah, D., Pang, J., Taylor, G., Chuah, E., Deng, A., Fichter, K., Go, A., Lee, S., Wang, J., Griffith, M., Morin, R., Moore, R. A., Mayo, M., Munro, S., Wagner, S., Jones, S., Holt, R.A., Marra, M.A., Hartigan, J., Graf, M., Wagner, R., Letovsky, S., Pulido, J. C., Robison, K., Mulligan, J., Sheen, L., Esposito, D., Hartley, J. L., Wall, V. E., Hopkins, R. F., Ohara, O. and Wiemann, S.  (2009).  The completion of the Mammalian Gene Collection (MGC).  Genome Res. Sept. 18. [Epub ahead of print].  PMID: 19767417.  PMCID - in process.

Hesselson, S., Matsson, P., Shima, J., Fukushima, H., Yee, S. W., Kobayashi, Y., Gow, J., Ha, C., Ma, B., Poon, A., Johns, S., Stryke, D., Castro, D., Tahara, H., Choi, J. H., Chen, L., Picard, N., Sjödin, E., Roelofs, M., Ferrin, T., Myers, R. M., Kroetz, D., Kwok, P. Y., and Giacomini, K.  (2009).  Genetic variation in the proximal promoter of ABC and SLC superfamilies: Liver and kidney specific expression and promoter activity predict variation.  PLos One.  4: e6942.  PMID: 19742321 [PubMed - in process].

Kitano, J., Ross, J. A., Mori, S., Kume, M., Jones, F. C., Chan, Y. F., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., Kingsley, D. M. and Peichel, C. L.  (2009).  A role for a neo-sex chromosome in stickleback speciation.  Nature. Sep 27. [Epub ahead of print].  PMID: 19783981.  PMCID - in process.

Reddy, T. E., Pauli, F., Sprouse, R. O., Neff, N. F., Newberry, K. M., Garabedian, M. J. and Myers, R. M.  (2009).  Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation.  Genome Res. 9: 2163-2171.  PMID: 19801529. PMCID - in process.

Coop, G., Pickrell, J. K., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Myers, R. M., Cavalli-Sforza, L. L., Feldman, M. W. and Pritchard, J. K.  (2009).  The role of geography in human adaptation.  PLoS Genet. 5: e1000500.  PMID: 19503611.  PMCID: PMC2685456.

Scott, L. J., Muglia, P., Kong, X. Q., Guan, W., Flickinger, M., Upmanyu, R., Tozzi, F., Li, J. Z., Burmeister, M., Absher, D., Thompson, R. C., Francks, C., Meng, F., Antoniades, A., Southwick, A. M., Schatzberg, A. F., Bunney, W. E., Barchas, J. D., Jones, E. G., Day, R., Matthews, K., McGuffin, P., Strauss, J. S., Kennedy, J. L., Middleton, L., Roses, A.D., Watson, S. J., Vincent, J. B., Myers, R. M., Farmer, A. E., Akil, H., Burns, D. K., and Boehnke, M.  (2009). Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry.  Proc. Natl. Acad. Sci. U.S.A.  106: 7501-7506.  [Epub 2009 Apr 28].  PMID: 19416921.  PMCID - in process.

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