Myers Lab Publications

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2012


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.  (2012).  Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res.  Feb 2. [Epub ahead of print].  PMID: 22300769.  See Research Highlight in Nature Reviews Genetics. doi:10.1038/nrg3219.

Gertz, J., Varley, K. E., Davis, N. S., Baas, B. J., Goryshin, I. Y., Vaidyanathan, R., Kuersten, S. and Myers, R. M.  (2012).  Transposon-based construction of strand-specific RNA-seq libraries.  Genome Res. 22: 134-41.  PMID: 22128135.  PMCID: PMC3246200.

Sequeira, A., Morgan, L., Walsh, D. M., Cartagena, P. M., Choudary, P., Li, J., Schatzberg, A. F., Watson, S. J., Akil, H., Myers, R. M., Jones, E. G., Bunney, W. E. and Vawter, M. P.  (2012).  Gene expression changes in the prefrontal cortex, anterior cingulate cortex and nucleus accumbens of mood disorders subjects that committed suicide.  PLoS One. 2012;7(4):e35367. Epub 2012 Apr 30.  PMID: 22558144 [PubMed - in process].

Monahan, K., Rudnick, N. D., Kehayova, P. D., Pauli, F., Newberry, K. N., Myers, R. M. and Maniatis, T.  (2012).  The role of CTCF and cohesin in the generation of single cell diversity of protocadherin-α gene expression.  Proc. Natl. Acad. Sci.  USA.  May 1. [Epub ahead of print].  PMID: 22550178.  [PubMed - as supplied by publisher].

Chen, Y., Negre, N., Li, Q., Mieczkowska, J. O., Slattery, M., Liu, T., Zhang, Y., Kim, T., He, H., Zieba, J., Ruan, Y., Bickel, P. J., Myers, R. M., Wold, B. J., White, K. P., Lieb, J. D. and Liu, S.  (2012).  Systematic evaluation of factors influencing ChIP-seq fidelity.  Nat. Methods.  Apr 22.  PMID: 22522655 [PubMed - as supplied by publisher].

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P, Mauceli, E., Zody, M. C., Pirun, M., Johnson, J., White, S., Birney, E., Searle, S., Schmutz, J., Grimwood, J., Dickson, M. C., Myers, R. M., Miller, C. T., Summers, B. R., Knecht, A. K., Brady, S. D., Zhang, H., Pollen, A. A., Howes, T., Amemiya, C., Broad Whole Genome Sequencing Platform and Whole Genome Assembly Team, Lander, E. S., DiPalma, F., Lindblad-Toh, K. and Kingsley, D. M.  (2012).  The genomic basis of adaptive evolution in threespine sticklebacks.  Nature 484: 55-61.  PMID: 22481358 [PubMed - in process].  PMCID: PMC3322419.  Comment in Nature 484: 46-47.

Kirigin, F. F., Lindstedt, K., Sellars, M., Ciofani, M., Low, S. L., Jones, L., Bell, F., Pauli, F., Bonneau, R., Myers, R. M., Littman, D. R. and Chong, M. M. W. (2012). Dynamic microRNA gene transcription and processing during T cell development. J. Immunol.  188: 3257-3267.  PMID: 22379031.  [PubMed - as supplied by publisher].

Zimmerman J. W., Pennison, M. J., Brezovich I., Yi, N., Yang, C. T., Ramaker, R., Absher, D., Myers, R. M., Kuster, N., Costa, F. P., Barbault, A. and Pasche, B.  (2012).  Cancer cell proliferation is inhibited by specific modulation frequencies.  Br. J. Cancer.  106: 307-313.  PMID: 22134506.  PMCID: PMC3261663.

Jones, F. C., Chan, Y. F., Schmutz, J., Grimwood, J., Brady, S., Southwick, A., Absher, D., Myers,  R. M., Schluter, D. and Kingsley, D. M.  (2012).  A genome-wide SNP genotyping array reveals patterns of global and species pair divergence in sticklebacks.  Curr Biol. 22: 83-90.  PMID: 22197244.  [PubMed - as supplied by publisher].

 

2011


ENCODE Project Consortium.  (2011).  A user’s guide to the Encyclopedia of DNA Elements (ENCODE).  PLoS Biol.  9: e1001046.  PMID: 21526222.  PMCID: PMC3079585.

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.  PLoS Genetics.  7: e1002228. Epub Aug 11.  PMID: 21852959.  PMCID: PMC3154961.

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. 21: 1017-1027.  PMID: 21521786.  PMCID: PMC3129245.

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.  Nov 10.  [Epub ahead of print].  PMID: 22074947.  [PMC Journal - In Process].

Ng, S-L., Friedman, B.A., Schmid, S., Gertz, J., Myers, R. M., tenOever, B. R. and Maniatis, T.  (2011).  IKKe regulates the balance between the type I and type II interferon responses.  Proc. Natl. Acad. Sci. USA.  108: 21170-21175.  PMID: 22171011.  PMCID: PMC3248534.

Sklar, P., Ripke, S., Scott, L. J., Andreassen, O. A., Cichon, S., Craddock, N., Edenberg, H. J., Nurnberger Jr, J. I., Rietschel, M., Blackwood, D., Corvin, A., Flickinger, M., Guan, W., Mattingsdal, M., McQuillin, A., Kwan, P., Wienker, T. F., Daly, M., Dudbridge, F., Holmans, P. A., Lin, D., Burmeister, M., Greenwood, T. A., Hamshere, M. L., Muglia, P., Smith, E. N., Zandi, P. P., Nievergelt, C. M., McKinney, R., Shilling, P. D., Schork, N. J., Bloss, C. S., Foroud, T., Koller, D. L., Gershon, E. S., Liu, C., Badner, J. A., Scheftner, W. A., Lawson, W. B., Nwulia, E. A., Hipolito, M., Coryell, W., Rice, J., Byerley, W., McMahon, F. J., Schulze, T. G., Berrettini, W., Lohoff, F. W., Potash, J. B., Mahon, P. B., McInnis, M. G., Zöllner, S., Zhang, P., Craig, D. W., Szelinger, S., Barrett, T. B., Breuer, R., Meier, S., Strohmaier, J., Witt, S. H., Tozzi, F., Farmer, A., McGuffin, P., Strauss, J., Xu, W., Kennedy, J. L., Vincent, J. B., Matthews, K., Day, R., Ferreira, M. A., O’Dushlaine, C., Perlis, R., Raychaudhuri, S., Ruderfer, D., Hyoun, P. L., Smoller, J. W., Li, J., Absher, D., Thompson, R. C., Meng, F. G., Schatzberg, A. F., Bunney, W. E. , Barchas, J. D., Jones, E. G., Watson, S. J., Myers, R. M., Akil, H., Boehnke, M., Chambert, K., Moran, J., Scolnick, E., Djurovic, S., Melle, I., Morken, G., Gill, M., Morris, D., Quinn, E., Mühleisen, T. W., Degenhardt, F. A., Mattheisen, M., Schumacher, J., Maier, W., Steffens, M., Propping, P., Nöthen, M. M., Anjorin, A., Bass, N., Gurling, H., Kandaswamy, R., Lawrence, J., McGhee, K., McIntosh, A., McLean, A. W., Muir, W., J., Pickard, B. S., Breen, G., St. Clair, D., Caesar, S., Gordon-Smith, K., Jones, L., Fraser, C., Green, E. K., Grozeva, D., Jones, I. R., Kirov, G., Moskvina, V., Nikolov, I., O’Donovan, M. C., Owen, M. J., Collier, D. A., Elkin, A., Williamson, R., Young, A. H., Ferrier, I. N., Stefansson, K., Stefansson, H., Steinberg, S., Gustafsson, O., Bergen, S. E, Nimgaonkar, V., Hultman, C., Landén, M., Lichtenstein, P., Sullivan, P., Schalling, M., Osby, U., Backlund, L., Frisén, L., Langstrom, N., Jamain, S., Leboyer, M., Etain, B., Bellivier, F., Petursson, H., Sigurosson, E., Müller-Mysok, B., Lucae, S., Schwarz, M., Schofield, P. R., Martin, N., Montgomery, G. W., Lathrop, M., Óskarsson, H., Bauer, M., Wright, A., Mitchell, P. B., Hautzinger, M., Reif, A., Kelsoe, J. R. and Purcell, S. M.  (2011).  Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.  Nat. Genet. 43: 977-983.  PMID: 21926972.  [PubMed - in process].

Kucera, K. S., Reddy, T. E., Pauli, F., Gertz, J., Logan, J. E., Myers, R. M., and Willard, H. F. (2011).  Allele-specific distribution of RNA polymerase II on female X chromosomes.  Hum. Molec. Genet.  20: 3964-3673.  PMID: 21791549.  PMCID: PMC3177651.

Moon, E., Rollins, B., Mesén, A., Sequeira, A., Myers, R. M., Akil, H., Watson, S. J., Barchas, J., Jones, E. G., Schatzberg, A., Bunney, W. E., Delisi, L. E., Byerley, W., and Vawter, M. P.  (2011).  Lack of association to a NRG1 missense polymorphism in schizophrenia or bipolar disorder in a Costa Rican population.  Schizophr. Res.  131: 52-57.  PMID: 21745728.  PMCID: PMC3159824.

McGuire, V., Van Den Eeden, S. K., Tanner, C. M., 
Kamel, F., Umbach, D. M., Marder, K., M.P.H., Mayeux, R., Ritz, B., Ross, G. W., Petrovitch, H., Topol, B., Popat, R. A., Costello, S., Manthripragada, A. D., Southwick, A., Myers, R. M., and Nelson, L. M.  (2011).  Association of DRD2 and DRD3 polymorphisms with Parkinson’s disease in a multiethnic consortium.  J. Neurol. Sci.  307: 22-29.  PMID: 21663922.  PMCID: PMC3155471.

The Cancer Genome Atlas Research Network  (2011).  Integrated genomic analyses of ovarian carcinoma.  Nature.  474: 609-615.  PMID: 21720365.  PMCID: PMC3163504.

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.  107: 155-166.  PMID: 21304547.  PMCID: PMC3136628.

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.  PMID: 21281405.  [PubMed - in process].

 

2010


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.  20: 890-898.  PMID: 20501695.  PMCID: PMC2892090.

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. 80: 265-272.  PMID: 21443745.  PMCID: PMC3084526.

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.   PMCID: PMC3084526.  Erratum in J. Am. Coll. Cardiol.  (2011).  57: 520.

Casto, A. M., Li, J. Z., Absher, D., Myers, R., Ramachandran, S. and Feldman, M. W.  (2010). Characterization of X-linked SNP genotypic variation in globally distributed human populations.  Genome Biol. 11: R10.  PMID: 20109212.  PMCID: PMC2847713.

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.  5: e9402.  PMID: 20195375.  PMCID: PMC2827556.

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.  16: 634-646.  PMID: 20386568.  PMCID: PMC2927798.

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. 20: 301-310.  PMID: 20067941. PMCID: PMC2840986.

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. 107: 3622-3627.  PMID: 20139301.  PMCID: PMC2840454.

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.  PMCID: PMC2824416.

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.  (2010).  Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.  Science 327: 302-305.  PMID: 20007865.  PMCID: PMC3109066.

 

2009


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.  PMID: 20025784.  PMCID: PMC2812948.

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. 19: 2163-2171.  PMID: 19801529.  PMCID: PMC2792167.

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. 19: 2324-2333.  PMID: 19767417. PMCID: PMC2792178.

Lamb, N. E., Myers, R. M. and Gunter, C.  (2009).  Education and personalized genomics: deciphering the public’s genetic health report.  (Perspective).  Personalized Med. 6: 681-690.  PMID: 20161675.  PMCID: PMC2821046.

Pasche, B. and Myers, R. M.  (2009).  One step forward toward identification of the genetic signature of glioblastomas.  (Review).  JAMA.  302: 325-326.  PMID: 19602695.  [PubMed - in process].

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: PMC2752811.

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 461: 1079-1083.  PMID: 19783981.  PMCID: PMC2776091.

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 and W. E., Vawter, M. P.  (2009).  Exon expression in lymphoblastoid cell lines from subjects with schizophrenia before and after glucose deprivation.  BMC Med. Genomics 2: 62.  PMID: 19772658.  PMCID: PMC2760574.

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.  PMCID: PMC2735003.

Coop, G., Pickrell, J. K., Novembre, J., Kudaravalli, S., Li, J., Absher, J., 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.

Brunner, A. L.,Johnson, D. S., Kim, S. W., Valouev, A., Reddy, T. E., Neff, N. F., Anton, E., Medina, C., Nguyen. L., Chiao, E., Oyolu, C. B., Schroth, G. P., Absher, D., Baker, J. C. and Myers, R. M.  (2009).  Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.  Genome Res. 19: 1044-1056. PMID: 19273619.  PMCID: PMC2694474.

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.  PMID: 19416921.  PMCID: PMC2678639.

Pickrell, J. K., Coop, G., Novembre, J., Kudaravalli, S. Li, J., Absher, D., Srinivasan, B. S., Barsh, G. S., Myers, R. M., Feldman, M. W. and Pritchard, J. K.  (2009).  Signals of recent positive selection in a worldwide sample of human populations.  Genome Res. 19: 826-837. PMID: 19307593. PMCID: PMC2675971.

Rollins, B., Martin, M. V., Sequeira, P. A., Moon, E. A., Morgan, L. Z., Watson, S. J., Schatzberg, A., Akil, H., Myers, R. M., Jones, E. G., Wallace, D. C., Bunney, W. E. and Vawter, M. P.  (2009).  Mitochondrial variants in schizophrenia, bipolar disorder, and major depressive disorder.  PLoS ONE.  4: e4913.  [Epub 2009 Mar 17].  PMID: 19290059.  PMCID: PMC2654519.

 

Stanford Work


Itsara, A., Cooper, G. M., Baker, C., Girirajan, S., Li, J., Absher, D.,  Krauss, R., Myers, R. M., Mefford, H., Cann, H. S., Singleton, A. A.,  Nickerson, D. A. and Eichler, E. E.  (2008).  Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease.  Am. J. Hum. Genet. 4: 148-161. PMID: 19166990.  PMCID: PMC2667981.

Shao, L., Martin, M. V., Watson, S. J., Schatzberg, A., Akil, H., Myers, R. M., Jones, E. G., Bunney W. E. and Vawter, M. P.  (2008).  Mitochondrial involvement in psychiatric disorders.  Ann. Med.  40: 281-295.  PMID: 18428021.  PMCID: PMC3098560.

Akil, H., Evans, S. J., Turner, C. A., Perez, J., Myers, R. M., Bunney, W. E., Jones, E. G., Watson, S. J. and the Pritzker Consortium.  (2008).  The fibroblast growth factor family and mood disorders.  Novartis Found. Symp.  289: 94-96; discussion 97-100, 193-195.  PMID: 18497097.

Ji, H., Jiang, H., Ma, W., Johnson, D. S., Myers, R. M., and Wong, W. H.  (2008).  An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data.  Nat. Biotechnol. 26: 1293-1300.  PMID: 18978777.  PMCID: PMC2596672.

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nussbaum, C., Myers, R. M., Brown, M., Li, W. and Liu, X. S.  (2008).  Model-based analysis of ChIP-Seq (MACS). Genome Biol.  9: R137.  PMID: 18798982.  PMCID: PMC2592715.

The Cancer Genome Atlas (TCGA) Research Network  (2008).  Comprehensive genomic characterization defines novel cancer genes and core pathways in human glioblastomas.  Nature.  455: 1061-1068.  PMID: 18772890.  PMCID: PMC2671642.

Valouev, A., Johnson, D. S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R. M. and Sidow, A.  (2008). Genome-wide analysis of transcription factor binding sites based on ChIP-seq data.  Nat. Methods.  5: 829-834.  PMID: 19160518.  PMCID: PMC2917543.

Assimes, T. L., Knowles, J. W., Basu, A., Iribarren, C., Southwick, A., Tang, H., Absher, D., Li, J., Fair, J. M., Rubin, G. D., Sidney, S., Fortmann, S. P., Go, A. S., Hlatky, M. A., Myers, R. M., Risch, N. and Quertermous, T.  (2008).  Susceptibility locus for clinical and subclinical coronary artery disease at chromosome 9p21 in the multi-ethnic ADVANCE Study.  Hum. Mol. Genet.  17: 2320-2328. PMID: 18443000.  PMCID: PMC2733811.

McGowan, K. A., Li, J. Z., Park, C. Y., Beaudry, V., Tabor, H. K., Sabnis, A. J., Zhang, W., Fuchs, H., Hrabe de Angelis, M., Myers, R. M., Attardi, L. D. and Barsh. G. S.  (2008).  Genetics of dark skin: ribosomal protein mutations act through p53.  Nat. Genet. 40: 963-970.  PMID: 18641651.  [PubMed - indexed for MEDLINE].

Schroeder, D. I. and Myers, R. M.  (2008).  Multiple transcription start sites for FOXP2 with varying cellular specificities.  Gene.  413: 42-28.  PMID: 18316164.  [PubMed - indexed for MEDLINE].

Sequeira, A., Meng, F., Rollins, B., Myers, R. M., Jones, E. G., Watson, S. J., Akil, H., Schatzberg, A. F., Barchas, J., Bunney, W. E. and Vawter, M. P.  (2008).  Coding SNPs included in exon arrays for the study of psychiatric disorders.  Molec. Psych. 13: 363-365.  PMID: 18347597.  PMCID: PMC3098557.

Johnson, D. S., Li, W., Gordon, D. B., Bhattacharjee, A., Curry, B., Ghosh, J., Brizuela, L., Carroll, J. S., Brown, M., Flicek, P., Koch, C., Dunham, I., Bieda, M., Xu, X., Farnham, P., Kapranov, P., Nix, D. A., Gingeras, T., Zhang, X., Holster, H., Jing, N., Green, R., Song, J., McCuine, S. A., Anton, E., Nguyen, L., Trinklein, N. D., Ye, Z., Ching, K., Hawkins, D., Ren, B., Scacheri1, P. C., Rozowsky, J., Karpikov, A., Euskirchen, G., Weissman, S., Gerstein, M., Snyder, M., Yang, A., Moqtaderi, Z., Hirsch, H., Shulha, H. P., Fu, Y., Weng, Z., Struhl, K., Myers, R. M., Lieb, J. D., and Liu, X. S. (2008).  Systematic evaluation of variability in simulated ChIP-chip experiments.  Genome Res.  18: 393-403. PMID: 18258921.  PMCID: PMC2259103.

Li, J. Z., Absher, D. M., Tang, H. Southwick, A. M., Casto, A. M., Ramachandran, S., Cann, H. M., Barsh, G. S., Feldman, M., Cavalli-Sforza, L. L. and Myers, R. M.  (2008).  Worldwide human relationships inferred from genome-wide patterns of variation.  Science.  319: 1100-1104.  (*co-first authors).  PMID: 18292342.  [PubMed - indexed for MEDLINE].

Wold, B. and Myers, R. M. (2008).  Sequence census methods for functional genomics.  Nature Meth.  5: 19-21.  PMID: 18165803.  [PubMed - indexed for MEDLINE].

*Johnson, D. S., *Mortazavi, A., Myers, R. M. and Wold, B.  (2007).  Genome-wide mapping of in vivo protein DNA interactions.  Science. 316:  1497-1502. (*co-first authors).  PMID: 17540862.  [PubMed - indexed for MEDLINE].  See also: Perspective by Stanley Fields.  Science.  316: 1441-1442.

Strehlow, A. T., Li, J. Z. and Myers, R. M.  (2007).  Wild-type huntingtin participates in protein trafficking between the Golgi and the extracellular space.  Hum. Molec. Genet.  16: 391-409.  PMID: 17189290.  [PubMed - indexed for MEDLINE].

Cooper, S. J., Trinklein, N. D., Nguyen, L. and Myers, R. M.  (2007).  Serum Response Factor binding sites differ in three human cell types.  Genome Res.  17: 136-144.  PMID: 17200232.  PMCID: PMC1781345.

Collins, P. J., Kobayashi, Y., Nguyen, L., Trinklein, N. D. and Myers, R. M.  (2007).  The ets-related transcription factor GABP directs bidirectional transcription.  PLoS Genet.  3: e208.  PMID: 18020712.  PMCID: PMC2077898.

Trinklein, N. D., Karaöz, U., Wu, J., Halees, A., Force Aldred, S., Collins, P. J., Zheng, D., Zhang, Z., Gerstein, M., Snyder, M., Myers, R. M. and Weng, Z.  (2007).  Integrated analysis of experimental datasets reveals many novel promoters in 1% of the human genome.  Genome Res.  17: 720-731.   PMID: 17567992.  PMCID: PMC3098557.

ENCODE Project Consortium. (2007).  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.  Nature.  447:  799-816.  See also:  News and Views by John M. Greally.  Nature.  447: 782-783.  PMID: 17571346.  PMCID: PMC2212820.

Knowles, J. W., Wang, H., Itakura, H., Southwick, A., Myers, R. M., Iribarren, C., Fortmann, S. P., Go, A. S., Quertermous, T. and Hlatky, M. A.  (2007).  Association of polymorphisms in platelet and hemostasis system genes with acute myocardial infarction.  Am. Heart J.  154: 1052-1058. PMID: 18035074.  [PubMed - indexed for MEDLINE].

Hlatky, M. A., Ashley, E., Quertermous, T., Boothroyd, D. B., Ridker, P., Southwick, A., Myers, R. M., Iribarren, C., Fortmann, S. P. and Go, A. S.; for the Atherosclerotic Disease, Vascular Function and Genetic Epidemiology (ADVANCE) Study.  (2007).  Matrix metalloproteinase circulating levels, genetic polymorphisms, and susceptibility to acute myocardial infarction among patients with coronary artery disease.  Am. Heart J.  154: 1043-1051.  PMID: 18035073.  [PubMed - indexed for MEDLINE].

Hlatky, M. A., Quertermous, T., Boothroyd, D. B., Priest, J. R., Glassford, A. J., Myers, R. M., Fortmann, S. P., Iribarren, C., Tabor, H. K., Assimes, T. L., Tibshirani, R. J. and Go, A. S.  (2007).  Polymorphisms in hypoxia inducible factor 1 and the initial clinical presentation of coronary disease.  Am. Heart J.  154: 1035-1042.  PMID: 18035072.  [PubMed - indexed for MEDLINE].

Karssen, A. M., Her, S., Li, J. Z., Patel, P. D., Meng, F., Bunney, Jr., W. E., Jones, E. G., Watson, S. J., Akil, H., Myers, R. M., Schatzberg, A. F. and Lyons, D. M.  (2007).  Stress-induced changes in primate prefrontal profiles of gene expression.  Mol. Psychiatry.  12: 1089-1102.  PMID: 17893703.  [PubMed - indexed for MEDLINE].

Atz, M., Walsh, D., Cartagena. P., Li, J., Evans, S., Choudary, P., Overman, K., Stein, R., Tomita, H., Potkin, S., Myers, R., Watson, S. J., Jones, E. G., Akil, H., Bunney, W. E. Jr., Vawter, M. P. and Members of National Institute of Mental Health Conte Center and Pritzker Neuropsychiatric Disorders Research Consortium.  (2007).  Methodological considerations for gene expression profiling of human brain.  J. Neurosci. Methods.  163: 295-309.  PMID: 1751205.  [PubMed - indexed for MEDLINE].

Li, J. Z., Meng, F., Tsavaler, L., Evans, S. J., Choudary, P. V., Tomita, H., Vawter, M. P., Walsh, D., Shokoohi, V., Chung, T., Bunney, W. E., Jones, E. G., Akil, H., Watson, S. J. and Myers, R. M.  (2007).  Sample matching by inferred agonal stress in gene expression analyses of the brain.  BMC Genomics.  8: 336.  PMID: 17892578.   PMCID: PMC2213675.

Lin, J. M., Collins, P. J., Trinklein N. D., Fu, Y., Xi, H., Myers, R. M. and Weng, Z.  (2007).  Transcription factor binding and histone modifications in human bidirectional promoters.  Genome Res. 17: 818-827.  PMID: 17568000.  PMCID: PMC1891341.

Denoeud, F., Kapranov, P., Ucla, C., Frankish, A., Castelo, R., Drenkow, J., Lagarde, J., Alioto, T., Manzano, C., Chrast, J., Dike, S., Wyss, C., Henrichsen, C. N., Holroyd, N., Dickson, M. C., Taylor, R., Hance, Z., Foissac, S., Myers, R. M., Rogers, J., Hubbard, T., Harrow, J., Guigo, R., Gingeras, T. R., Antonarakis, S. E. and Reymond, A.  (2007).  Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions.  Genome Res.  17: 746-759.  PMID: 17567994.  PMCID: PMC1891335.

Assimes, T. L., Knowles, J. W., Priest, J. R., Basu A., Borchert, A., Volcik, K. A., Grove, M. L., Tabor, H. K., Southwick, A., Tabibiazar, R., Sidney, S., Boerwinkle, E., Go, A. S., Iribarren, C., Hlatky, M. A., Fortmann, S. P., Myers, R. M., Kuhn, H., Risch, N. and Quertermous, T.  (2007).  A near null variant of 12/15-LOX encoded by a novel SNP in ALOX15 and the risk of coronary artery disease.  Atherosclerosis.  198: 136-144.  PMID: 17959182.  PMCID: PMC2440699.

Watson, J. D., Caudy, A. A., Myers, R. M. and Witkowski, J. A.  (2007).  Recombinant DNA: Genes and Genomes, 3rd Edition.  W. H. Freeman Press.  ISBN 0-7167-2866-4.

Elbaz, A., Nelson, L. M., Payami, H., Ioannidis, J. P. A., Fiske, B. K., Annesi, G., Carmine, A., Factor, S. A., Ferrarese, C., Hadjigeorgiou, G. M., Higgins, D., Kawakami, H., Krueger, R., Marder, K., Mayeux, R., Mellick, G., Nutt, J., Ritz, B., Samii, A., Tanner,C. M., Van Broeckhoven, C., Van Den Eeden, S. K., Wirdefeldt, K., Zabetian, C. P., Dehem, M., Montimurro, J.S., Southwick, A., Myers, R. M., and Trikalinos, T. A.  (2006).  Lack of replication of thirteen single-nucleotide polymorphisms implicated in Parkinson’s disease: a large-scale international study.  Lancet Neurol. 5: 917-923.  PMID: 17052658.  [PubMed - indexed for MEDLINE].

Morin, R. D., Chang, E., Petrescu, A., Liao, N., Kirkpatrick, R., Griffith, M., Butterfield, Y. S.,  Stott, S., Barber, S., Babakaiff, R., Matsuo, C., Wong, D., Yang, G. S., Smailus, D. E., Brown-John, M., Mayo, M., Beland, J., Gibson, S., Olson, T., Tsai, M., Featherstone, R., Chand, S., Siddiqui, A. S., Jang, W., Lee, E., Klein, S. L., Prange, C., Myers, R. M., Green, E. D., Wagner, L., Gerhard, D. S., Marra, M. A., Jones, S. J. M., Holt, R. A.  (2006). Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis.  Genome Res.  16: 796-803.  PMID: 16672307.  PMCID: PMC1479861.

Mortazavi, A., Leeper Thompson, E. C., Garcia. S. T., Myers, R. M. and Wold, B.  (2006).  Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire.  Genome Res.  16: 1208-1221.  PMID: 16963704.  PMCID: PMC1581430.

Vawter, M. P., Tomita, H., Meng, F., Bolstad, B., Li, J., Evans, S., Choudary, P., Atz, M., Shao, L., Neal, C., Walsh, D., Burmeister, M., Speed, T., Myers, R., Jones, E. G., Watson, S. J., Akil, H. and Bunney, W. E.  (2006).  Mitochondrial related gene expression changes are sensitive to agonal-pH state: Implications for brain disorders.  Mol. Psychiatry.  11: 615, 663-679.  PMID: 16636682.

Karssen*, A. M., Li*, J. Z., Her, S., Patel, P. D., Meng, F., Evans, S. J., Vawter, M. P., Tomita, H., Choudary, P. V., Bunney, Jr., W. E., Jones, E. G., Watson, S. J., Akil, H., Myers, R. M., Schatzberg, A. F. and Lyons, D. M.  (2006).  Application of microarray technology in primate behavioral neuroscience research.  Methods.  38: 227-234.  (*co-first authors).  PMID: 16469505.

Cooper, S. J., Trinklein, N. D., Anton, E. D., Nguyen, L. and Myers, R. M.  (2006).  Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome.  Genome Res. 16: 1-10.  PMID: 16344566.   PMCID: PMC1781345.

Dai, M., Wang, P., Boyd, A. D., Kostov, G., Athey, B., Jones, E. G., Bunney, W. E., Myers, R. M., Speed, T. P., Akil, H., Watson, S. J. and Meng, F.  (2005). Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.  Nucleic Acids Res.  33: e175.  PMID: 16284200.  PMCID: PMC1283542.

Choudary, P.V., Molnar, M., Evans, S. J., Tomita, H., Li, J.Z., Vawter, M.P., Myers, R. M., Bunney Jr., W. E., Akil, H., Watson, S. J. and Jones, E. G.  (2005).  Altered cortical glutamatergic and GABAergic signal transmission with glial involvement in depression.  Proc. Nat. Acad. Sci. USA.  102: 15653-15658.  PMID: 16230605.  PMCID: PMC1257393.

Kopitar-Jerala, N., Schweiger, A., Myers, R. M., Turk, V., Turk, B.  (2005).  Sensitization of stefin B-deficient thymocytes towards staurosporin-induced apoptosis is independent of cysteine cathepsins.  FEBS Lett. 579: 2149-2155.  PMID: 15811333.  [PubMed - indexed for MEDLINE].

Carlson, C. S., Force Aldred, S., Tracy, R. P., Schwartz, S. M., Rieder, M., Liu, K., Williams, O. D., Irribarren, C., Lewis, E. C., Fornage, M., Boerwinkle, E., Gross, M., Nickerson, D. A., Myers, R. M., Siscovick, D. S., and Reiner, A. P.  (2005).  Polymorphisms within the C Reactive Protein promoter region are associated with plasma CRP levels.  Am. J. Hum. Genet.  77: 64-77.  Erratum in: Am J Hum Genet. 2008 Jan;82(1):251.  PMID: 15897982.  PMCID.: PMC1226195.

Kim, T. H., Barrera, L. O., Qu, C., Van Calcar, S., Trinklein, N. D., Cooper, S. J., Luna, R., Glass, C. K., Rosenfeld, M. G., Myers, R. M., and Ren, B.  (2005). Direct isolation and identification of promoters in the human genome.  Genome Res.  15: 830-839.  PMID: 15899964.  PMCID: PMC1142473.

Hillier, L. W., Graves, T. A., Fulton, R. S., Fulton, L. A., Pepin, K. H., Minx, P., Wagner-McPherson, C., Layman, D., Wylie, K., Sekhon, M., Becker, M. C., Fewell, G. A., Delehaunty, K. D., Miner, T. L., Nash, W. E., Kremitzki, C., Oddy, L., Du, H., Sun, H., Bradshaw-Cordum, H., Ali, J., Carter, J., Cordes, M., Harris, A., Isak, A., van Brunt, A., Nguyen, C., Du, F., Courtney, L., Kalicki, J., Ozersky, P., Abbott, S., Armstrong, J., Belter, E. A., Caruso, L., Cedroni, M., Cotton, M., Davidson, T., Desai, A., Elliott, G., Erb, T., Fronick, C., Gaige, T., Haakenson, W., Haglund, K., Holmes, A., Harkins, R., Kim, K., Kruchowski, S. S., Strong, C. M., Grewal, N., Goyea, E., Hou, S., Levy, A., Martinka, S., Mead, K., McLellan, M. D., Meyer, R., Randall-Maher, J., Tomlinson, C., Dauphin-Kohlberg, S., Kozlowicz-Reilly, A., Shah, N., Swearengen-Shahid, S., Snider, J., Strong, J. T. , Thompson, J., Yoakum, M., Leonard, S., Pearman, C., Trani, L., Radionenko, M., Waligorski, J. E., Wang, C., Rock, S. M., Tin-Wollam, A-M., Maupin, R., Latreille, P., Wendl, M. C., Yang, S-P., Pohl, C., Wallis, J. W., Spieth, J., Bieri, T. A., Berkowicz, N., Osborne, J., Ding, L., Meyer, R., Sabo, A., Shotland, Y., Sinha, P., Wohldmann, P. E., Cook, L. L., Hickenbotham, M. T., Eldred, J., Williams, D., Jones, T. A., She, X., Ciccarelli, F. D., Izaurralde, E., Taylor, J., Schmutz, J., Myers, R. M., Cox, D. R., McPherson, J. D., Mardis, E. R.,  Clifton, S. W., Warren, W. C., Chinwalla, A. T., Eddy, S. R., Marra, M. A., Ovcharenko, I., Furey, T. S., Miller, W., Eichler, E. E., Bork, P., Suyama, M., Torrents, D., Waterston, R. H. and Wilson, R. K.  (2005).  Generation and annotation of the DNA sequences of human chromosomes 2 and 4.  Nature.  434: 724-731.  PMID: 15815621.  [PubMed - indexed for MEDLINE].

Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villareal, G., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D. and Kingsley, D. M.  (2005).  Widespread parallel evolution of stickleback armor plates determined by ancestral genetic variation in Ectodysplasin.  Science.  307: 1928-1933.  PMID: 15790847.

Martin, J., Han, C., Gordon, L. A., Terry, A., Prabhakar, S., She, X., Xie, G., Hellsten, U., Man Chan, Y-M., Altherr, M., Couronne, O., Aerts, A., Bajorek, E., Black, S., Blumer, H., Branscomb, E., Brown, N. C., Bruno, W. J., Buckingham, J. M., Callen, D. F., Campbell, C. S., Campbell, M. L., Campbell, E. W., Caoile, C., Challacombe, J. F., Chasteen, L. A., Chertkov, O., Chi, H. C., Christensen, M., Clark, L. M., Cohn, J. D., Denys, M., Detter, J. C.,  Dickson, M., Dimitrijevic-Bussod, M., Escobar, J., Fawcett, J. J., Flowers, D., Fotopulos, D., Glavina, T., Gomez, M., Gonzales, E., Goodstein, D., Goodwin, L. A., Grady, D. L., Grigoriev, I., Groza, M., Hammon, N., Hawkins. T., Haydu, L., Hildebrand, C. E., Huang, W., Israni, S., Jett, J., Jewett, P. E., Kadner, K., Kimball, H., Kobayashi, A., Krawczyk, M-C., Leyba, T., Longmire, J. L., Lopez, F., Lou, Y., Lowry, S., Ludeman, T., Mark, G. A., McMurray, K. L., Meincke, L. J., Morgan, J., Moyzis. R. K., Mundt, M. O., A. Munk, A. C., Nandkeshwar, R. D., Pitluck, S., Pollard, M., Predki, P., Parson-Quintana, B., Ramirez, L., Rash, S., Retterer, J., Ricke, D. O., Robinson, D. L., Rodriguez, A., Salamov, A., Saunders, E. H., Scott, D., Shough, T., Stallings, R. L., Stalvey, M., Sutherland, R. D., Tapia, R., Tesmer, J. G., Thayer, N., Thompson, L. S., Tice, H., Torney, D. C., Tran-Gyamfi, M., Tsai, M., Ulanovsky, L. E.,  Ustaszewska, A., Vo, N., White, P. S., Williams, A. L., Wills, P. L., Wu, J-R., Wu, K., Yang, J., DeJong, P., Bruce, D., Doggett, N., Deaven, L., Schmutz, J., Grimwood, J., Richardson, P., Rokhsar, D. S., Eichler, E. E., Gilna, P., Lucas, S. M., Myers, R. M., Rubin, E. M., and Pennacchio, L. A.  (2005). The sequence and analysis of duplication-rich human chromosome 16.  Nature.  432: 988-994.  PMID: 15616553.  [PubMed - in.dexed for MEDLINE].

Noonan, J. P., Grimwood, J., Danke, J., Schmutz, J., Dickson, M., Amemiya, C. T. and Myers, R. M.  (2004).  Coelacanth genome sequence reveals the evolutionary history of vertebrate genes.  Genome Res.  12: 2397-2405.  PMID: 15545497.  .PMCID: PMC534663.

Evans, S. J., Choudary, P. V., Neal, C. R., Li, J. Z., Vawter, M. P., Tomita, H., Lopez, J. F., Thompson, R. C., Meng, F., Stead, J. D., Walsh, D. M., Myers, R. M., Bunney, W. E., Watson, S. J., Jones, E. G. and Akil, H.  (2004).  Dysregulation of the fibroblast growth factor system in major depression.  Proc. Natl. Acad. Sci. USA. 101: 15506-15511.  PMID: 15483108.

Schmutz, J., Grimwood, J. and Myers, R. M.  (2004).  Assembly of DNA sequencing data.  In:  Methods in Molecular Biology, “Bacterial Artificial Chromosomes: Methods and Protocols”, eds. S. Zhao and M. Stodolsky.  Humana Press. 255: 319-332.  PMID: 15020835.

Schmutz, J., Grimwood, J. and Myers, R. M.  (2004).  Sequence finishing.  In:  Methods in Molecular Biology, “Bacterial Artificial Chromosomes: Methods and Protocols”, eds. S. Zhao and M. Stodolsky.  Humana Press. 255: 333-342.  PMID: 15020836.

Kingsley, D., Zhu, B., Osoegawa, K., de Jong, P. J., Schein, J., Marra, M., Peichel, C., Amemiya, C., Schluter, D., Balabhadra, S., Friedlander, B., Chan, Y. M., Dickson, M., Grimwood, J., Schmutz, J., Talbot, W. and Myers, R. M.  (2004).  New genomic tools for molecular studies of evolutionary change in sticklebacks.  Behavior.  141: 1331-1344.

Vawter, M. P., Evans, S., Choudary, P., Tomita, H., Meador-Woodruff, J., Molnar, M., Li, J., Lopez, J. F., Myers, R., Cox, D., Watson, S. J., Akil, H., Jones, E. G., Bunney, W. E.  (2004).  Gender-specific gene expression in post-mortem human brain: Localization to sex chromosomes.  Neuropsychopharmacology.  29: 373-384.

Schmutz, J., Wheeler, J., Grimwood, J., Dickson, M., Yang, J., Caoile, C., Bajorek, E., Black, S., Chan, Y. M., Denys, M., Escobar, J., Flowers, D., Fotopulos, D., Garcia, C., Gomez, M., Gonzales, E., Haydu, L., Lopez, F., Ramirez, L., Retterer, J., Rodriguez, A., Rogers, S., Salazar, A., Tsai, M., and Myers, R. M.  (2004). Quality assessment of the human genome sequence.  Nature. 429: 365-368.  PMID: 15164052.  [PubMed - indexed for MEDLINE].

Gerhard, D.S., Wagner, L., Feingold, E.A., Shenmen, C.M., Grouse, L.H., Schuler, G., Klein, S.L., Old, S., Rasooly, R., Good, P., Guyer, M., Peck, A.M., Derge, J.G., Lipman, D., Collins, F.S., Jang, W., Sherry, S., Feolo, M., Misquitta, L., Lee, E., Rotmistrovsky, K., Greenhut, S.F., Schaefer, C.F., Buetow, K., Bonner, T.I., Haussler, D., Kent, J., Kiekhaus, M., Furey, T., Brent, M., Prange, C., Schreiber, K., Shapiro, N., Bhat, N.K., Hopkins, R.F., Hsie, F., Driscoll, T., Soares, M.B., Casavant, T.L., Scheetz, T.E., Brown-stein, M.J., Usdin, T.B., Toshiyuki, S., Carninci, P., Piao, Y., Dudekula, D.B., Ko, M.S., Kawakami, K., Suzuki, Y., Sugano, S., Gruber, C.E., Smith, M.R., Simmons, B., Moore, T., Waterman, R., Johnson, S.L., Ruan, Y., Wei, C.L., Mathavan, S., Gunaratne, P.H., Wu, J., Garcia, A.M., Hulyk, S.W., Fuh, E., Yuan, Y., Sneed, A., Kowis, C., Hodgson, A., Muzny, D.M., McPherson, J., Gibbs, R.A., Fahey, J., Helton, E., Ketteman, M., Madan, A., Rodrigues, S., Sanchez, A., Whiting, M., Madari, A., Young, A.C., Wetherby, K.D., Granite, S.J., Kwong, P.N., Brinkley, C.P., Pearson, R.L., Bouffard, G.G., Blakesly, R.W., Green, E.D., Dickson, M.C., Rodriguez, A.C., Grimwood, J., Schmutz, J., Myers, R.M., Butterfield, Y.S., Griffith, M., Griffith, O.L., Krzywinski, M.I., Liao, N., Morin, R., Palmquist, D., Petrescu, A.S., Skalska, U., Smailus, D.E., Stott, J.M., Schnerch, A., Schein, J.E., Jones, S.J., Holt, R.A., Baross, A., Marra, M.A., Clifton, S., Makowski, K.A., Bosak, S., Malek, J.; MGC Project Team.  (2004).  The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).  Genome Res.  10B: 2121-2127. Erratum in: Genome Res. 6: 804. Morrin, Ryan [corrected to Morin, Ryan].  PMID: 15489334.  PMCID: PMC528928.

Schmutz, J., Martin, J., Terry, A., Couronne, O., Grimwood, J., Lowry, S., Gordon, L. A., Scott, D., Xie, G., Huang, W., Hellsten, U., Tran-Gyam, M., She, X., Prabhakar, S.,  Aerts, A., Altherr, M., Bajorek, E., Black, S., Branscomb, E., Caoile, C., Challacombe, J. F., Chan, Y. M., Denys, M., Detter, C., Escobar, J., Flowers, D., Fotopulos, D., Glavina, T., Gomez, M., Gonzales, E., Goodstein, D., Grigoriev, I., Groza, M., Hammon, N., Hawkins, T., Haydu, L., Israni, S., Jett, J., Kadner, K., Kimball, H., Kobayashi, A., Lopez, F., Lou, Y., Martinez, D., Medina, C., Morgan, J., Nandkeshwar, R., Noonan, J. P., Pitluck, S., Pollard, M., Predki, P., Priest, J., Ramirez, L., Rash, S., Retterer, J., Rodriguez, A., Rogers, S., Salamov, A., Salazar, A., Thayer, N., Tice, H., Tsai, M., Ustaszewska, A.,  Vo, N., Wheeler, J., Wu, K., Yang, J., Dickson, M., Cheng, J.-F., Eichler, E. E., Olsen, A., Pennacchio, L. A., Rokhsar, D. S., Richardson, P., Lucas, S. M., Myers, R. M. and Rubin, E. M.  (2004).  The DNA sequence and comparative analysis of human chromosome 5.  Nature.  431: 268-274.  PMID: 15372022.  [PubMed - indexed for MEDLINE].

Peichel, C. L., Ross, J. A., Matson, C. K., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Mori, S., Schluter, D. and Kingsley, D. M.  (2004).  The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome.  Current Biol. 14: 1416-1424.  PMID: 15324658.

International Human Genome Sequencing Consortium.  (2004).  Finishing the euchromatic sequence of the human genome.  Nature.  431: 931-945.  PMID: 15496913.

ENCODE Project Consortium.  (2004).  The ENCODE (ENCyclopedia Of DNA Elements) Project.  Science.  306: 636-640.  PMID: 15499007.

Murray, J. I., Whitfield, M. L., Trinklein, N. D., Myers, R. M., Brown, P. O. and Botstein, D.  (2004).  Diverse and specific gene expression responses to stresses in cultured human cells.  Molec. Biol. Cell. 5: 2361-2374.  PMID: 15004229.  PMCID: PMC404029.

Li, J., Nguyen, L., Gleason, C. Lotspeich, L., Spiker, D., Risch, N. and Myers, R. M.  (2004).  Lack of evidence for an association between WNT2 and RELN polymorphisms and autism.  Amer. J. Med. Genet.: Neuropsych. Genet. 126B: 51-57.  PMID: 15048648.

Grimwood, J., Gordon, L.A., Terry, A., Olsen, A., Schmutz, J., Hellsten, U., Goodstein, D., Couronne, O., Tran-Gyam, M., Aerts, A., Altherr, M., Bajorek, E., Black, S., Caenepeel, S., Caoile, C., Chan, Y. M., Christensen, M., Cleland, C. A., Copeland, A.,  Dalin, E., Dehal, P., Denys, M., Detter, J. C., Escobar, J., Flowers, D., Fotopulos, D.,  Garcia, C., Glavina, T., Gomez, M., Gonzales, E., Hammon, N., Haydu, L., Ho. I., Huang, W., Israni, S., Jett, J., Kadner, K., Kimball, H., Kobayashi, A., Lopez, F., Lou, Y., Lowry, S., Martinez, D., Medina, C., Morgan, J., Nelson, K., Nolan, M., Ovcharenko, I., Pitluck, S., Pollard, M., Popkie, A. P., Ramirez, L., Rash, S., Retterer, J., Rodriguez, A., Rogers, S., Salamov, A., Salazar, A., She, X., Smith, D., Solovyev, V.,  Thayer, N., Tice, H., Tsai, M., Ustaszewska, A., Vo, N., Wagner, M., Wheeler, J., Wu, K., Xie, G., Yang, J., Dubchak, I., Furey, T. S., DeJong, P., Dickson, M., Gordon, D., Eichler, E. E., Pennacchio, L. A., Richardson, P., Stubbs, L., Branscomb, E., Rokhsar, D. S., Myers, R. M., Rubin, E. M., and Lucas, S. M. (2004).  The DNA sequence and biology of human chromosome 19.  Nature.  428: 529-535.  PMID: 15057824.  [PubMed - indexed for MEDLINE].

Trinklein, N., Chen, W. C., Kingston, R. E. and Myers, R. M.  (2004). Transcriptional regulation and binding of HSF1 and HSF2 to 32 human heat shock genes during thermal stress and differentiation.  Cell Stress and Chaparones.  9: 21-28.  PMID: 15270074.  PMCID: PMC1065302.

Li, J., Vawter, M. P., Walsh, D. M., Tomita, H., Evans, S. J., Choudary, P. V., Lopez, J. F., Avelar, A., Shokoohi, V., Chung, T., Mesarwi, O., Jones, E. G., Watson, S. J., Akil, H., Bunney, W. E. and Myers, R. M.  (2004).  Systematic changes in gene expression in postmortem human brains associated with tissue pH and terminal medical conditions.  Hum. Molec. Genet.  13: 609-616.  PMID: 14734628.

Noonan, J. P., Grimwood, J., Schmutz, J., Dickson, M., and Myers, R. M.  (2004).  Gene conversion and the evolution of protocadherin gene cluster diversity.   Genome Res. 14: 354-366.  PMID: 14993203.  PMCID: PMC353213.

Trinklein, N. D., Murray, J. I., Hartman, S. J., Botstein, D., and Myers, R. M. (2004).  The role of heat shock transcription factor 1 in the regulation of the mammalian heat shock response.  Molec. Biol. Cell.  15: 1254-1261.  PMID: 14668476.  PMCID: PMC363119.

Tomita, H., Vawter, M. P., Walsh, D. M., Evan, S., Choudary, P. V., Li, J., Overman,  K., Atz, M., Myers, R. M., Jones, E. G., Watson, S. J., Akil, H. and Bunney, W. E.  (2004).  Effect of agonal and postmortem factors on microarray expression profile: quality control methods in microarray analyses of postmortem human brain.  Biol. Psychiatry. 55: 346-352.  PMID: 14960286.

Cirman, T., Oresic, K., Droga Mazovec, G., Turk, V., Reed, J. C., Myers, R. M., Salvesen, G. S., and Turk, B. (2004).  Selective disruption of lysosomes in HeLa cells triggers apoptosis, mediated by cleavage of Bid by multiple papain-like lysosomal cathepsins.  J. Biol. Chem. 279: 3578-3587.

Trinklein, N. D., Force Aldred, S., Hartman, S. J., Schroeder, D. I., Otillar, R. and Myers, R. M. (2004).   An abundance of bidirectional promoters in the human genome.  Genome Res.  14: 62-66.  PMID: 14707170.  PMCID: PMC314279.

Bunney, W. E., Bunney, B. G., Vawter, M. P., Tomita, H., Li, J., Evans, S. J., Choudary, P. V., Myers, R. M., Jones, E. G., Watson, S. J., Akil, H.  (2003). Microarray technology: a review of new strategies to discover candidate vulnerability genes in psychiatric disorders.  Am. J. Psychiatry.  160: 657-666.

Evans S. J., Choudary, P. V., Vawter, M. P., Li, J., Meador-Woodruff, J. H., Lopez, J. F., Burke, S. M., Thompson, R. C., Myers, R. M., Jones, E. G., Bunney, W. E., Watson, S. J., and Akil, H.  (2003).  DNA microarray analysis of functionally discrete human brain regions reveals divergent transcriptional profiles.  Neurobiol. Dis. 14: 240-250.

Murphy, E., Yu, D., Grimwood, J., Schmutz, J., Dickson, M., Jarvis, M., Hahn, G., Nelson, J. A., Myers, R. M. and Shenk, T.  (2003).  Coding potential of laboratory and clinical strains of human cytomegalovirus.  Proc. Natl. Acad. Sci. USA.  100: 14976-14981.

Houseweart, M. K., Pennacchio, L. A., Vilaythong, A., Peters, C., Noebels, J. L. and Myers, R. M.  (2003).  Cathepsin B but not cathepsin L or S contributes to the pathogenesis of Unverricht-Lundborg progressive myoclonus epilepsy (EPM1).  J. Neurobiology 56: 315-327.  PMID: 12918016.

Houseweart, M. K., Vilaythong, A., Yin, X.-M., Noebels, J. L. and Myers, R. M.  (2003).  Apoptosis caused by cathepsins does not require Bid signaling in an in vivo model of progressive myoclonus epilepsy (EPM1).  Cell Death and Diff.  10: 1329-1335.

Khambata Ford, S., Liu, Y., Gleason, C., Dickson, M., Altman, R. B., Batzoglou, S., and Myers, R. M.  (2003).  Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay.  Genome  Res.  13: 1765-1774.

Noonan, J. P., Li, J., Nguyen, L., Caoile, C., Dickson, M., Grimwood, J., Schmutz, J., Feldman, M. W. and Myers, R. M.  (2003).  Extensive linkage disequilibrium, a common 16.7 kb deletion and evidence of balancing selection in the human protocadherin alpha cluster.  Amer. J. Hum. Genet. 72: 621-635.   PMID: 12577201.  PMCID: PMC1180238.

Trinklein, N., Force Aldred, S., Saldanha, A. and Myers, R. M.  (2003).   Identification and functional analysis of human transcriptional promoters. Genome  Res.  13:  308-312.  PMID: 12566409.  PMCID: PMC420378.

Schmutz, J., Wheeler, J., Grimwood, J., Dickson, M., and Myers, R. M.  (2003). Assessing the quality of finished genomic sequence. Cold Spring Harb. Symp. Quant. Biol.  68: 31-37.  PMID: 15338600.

Shannon, P., Pennacchio, L. A., Houseweart, M. K., Minassian, B. A., and Myers, R. M.  (2002). Neuropathological changes in a murine model of Progressive Myoclonus Epilepsy: Cystatin B deficiency and Unverricht-Lundborg disease.  J. Neuropath. Exp. Neurol. 61: 1085-1091.  PMID: 12484571.

Stickney, H. L., Schmutz J., Woods, I. G., Holtzer C. C., Dickson, M. C., Kelly, P. D., Myers, R. M. and Talbot, W. S.  (2002).  Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays.  Genome Res. 12: 1929-1934.

Tabor, H. K., Risch, N. J. and Myers, R. M.  (2002). OPINION:  Candidate gene approaches for studying complex genetic traits: practical considerations.  Nat. Rev. Genet.  3: 391-397.  PMID: 11988764.

Spiker, D., Lotspeich, L. J., Dimiceli, S., Myers, R. M. and Risch, N.  (2002).  Behavioral variation in autism multiplex families: Evidence for a continuous severity gradient.  Amer. J. Med. Genet.: Neuropsychiatric Genet. 114: 129-136.  PMID: 11857572.

Li, J., Tabor, H., Gleason, C., Nguyen, L., Lotspeich, L., Spiker, D., Risch, N. and Myers, R. M.  (2002).  Lack of association between HoxA1 and HoxB1 gene variants and autism in 110 multiplex families.  Amer. J. Med. Genet.: Neuropsychiatric Genet.  114: 24-30.

 Spiker, D., Lotspeich, L. J., Dimiceli, S., Szatmari, P., Myers, R. M. and Risch, N.  (2001).  Birth order effects on nonverbal IQ scores in autism multiplex families.  J. Autism Devel. Disord. 31: 449-460.  PMID: 11794410.

Lieuallen, K., Pennacchio, L. A., Park, M., Myers, R. M., Lennon, G. G.  (2001).  Cystatin B-deficient mice have increased expression of apoptosis and glial activation genes.  Hum. Molec. Genet. 10: 1867-1871.  PMID: 11555622.

Wu, Q., Zhang, T., Chen, J.-C., Kim, Y., Grimwood, J., Schmutz, J., Dickson, M., Noonan, J., Zhang, M. Q., Myers, R. M. and Maniatis, T.  (2001).  Comparative DNA sequence analysis of mouse and human protocadherin gene clusters.  Genome  Res. 11: 389-404.  PMID: 11230163.  PMCID: PMC311048.

Olivier, M., et al.  (2001).  A high resolution radiation hybrid map of the human genome.  Science 298: 1298-1302.

International Human Genome Sequencing Consortium.  (2001).  Initial sequencing and analysis of the human genome.  Nature 409: 860-921.

The International Human Genome Mapping Consortium.  (2001).  A physical map of the human genome.  Nature 409: 934-941.

Salmon, B., Hallmayer, J., Rogers, T., Kalaydijieva, L., Peterson, P. B., Nicholas, P., Pingree, C., McMahon, W., Spiker, D., Lotspeich, L., Kraemer, H., McCague, P., Dimiceli,S., Nouri, N., Pitts, T., Yang, J., Hinds, D., Myers, R. M. and Risch, N. (1999).  Absence of linkage and linkage disequilibrium to chromosome 15q11-q13 markers in 139 multiplex families with autism.  Amer. J. Med. Genet. 88: 551-556.

Li, Z., Karlovich, C. A., Fish, M., Scott, M. P. and Myers, R. M. (1999).  A putative Drosophila homolog of the Huntington disease gene.  Hum. Molec. Genet. 8: 1807-1815.

Risch, N., Spiker, D., Lotspeich, L., Nouri, N., Hinds, D., Hallmayer, J., et al. and Myers, R. M.  (1999).  A genomic screen for autism: Evidence for a multi-locus etiology.  Am. J. Hum. Genet. 65: 493-507.

Rogers, T., Kalaydijieva, L., Hallmayer, J., et al., Risch, N. and Myers, R. M.  (1999).  Exclusion of linkage to the HLA region in ninety multiplex families with autism.  J. Autism and Develop. Disorders 29: 195-201.

Shelbourne, P. F., Killeen, N., Hevner, R. F., Johnston, H. M., Tecott, L., Lewandoski, M., Ennis, M., Ramirez, L., Li, A., Iannicola, C., Littman, D. R. and Myers, R. M. (1999).  A Huntington’s disease CAG expansion at the muring Hdh locus is unstable and associated with behavioural abnormalities in mice. Hum. Molec. Genet. 8: 763-774.

Usdin, M., Shelbourne, P. F., Myers, R. M. and Madison, D. V. (1999).  Impaired synaptic plasticity in mice carrying the Huntington’s disease mutation.  Hum. Molec. Genet. 8: 839-846.

Beasley, E. M., Myers, R. M., Cox, D. R. and Lazzeroni, L. C.  (1999).  Statistical refinement of primer design parameters.  In: PCR Applications: Protocols for Functional Genomics.  (eds. Michael Innis, David Gelfand & John Sninsky, Academic Press). pp. 55-71.

Birren, B., Green, E. D., Hieter, P., Klapholz, S., Myers, R. M. Riethman, H. and Roskams, J., eds.  (1999).  Genome Analysis: A Laboratory Manual.  Cold Spring Harbor Laboratory Press.  Vol. 4: Mapping Genomes.

Birren, B., Green, E. D., Klapholz, S., Myers, R. M., Riethman, H. and Roskams, J., eds.  (1999).  Genome Analysis: A Laboratory Manual.  Cold Spring Harbor Laboratory Press.  Vol. 3: Cloning Systems.

Serratosa, J. M., Gardiner, R. M., Lehesjoki, A. E., Pennacchio, L. A., Myers, R. M. (1999). The Molecular Genetic bases of the Progressive Myoclonus Epilepsies; Lippincot-Raven Publisher; Delgado-Escueta, A.V., Wilson, W., Olsen, R., and Porter, R. Eds. Basic Mechanisms of the Epilepsies, Second Edition.  Advances in Neurology 79: 383-398.  PMID: 10514828.

Pennacchio, L. A., Bouley, D. M., Higgins, K. M., Scott, M. P., Noebels, J. L., and Myers, R. M.  (1998).  Progressive ataxia, myoclonic epilepsy, and cerebellar apoptosis in cystatin B-deficient mice.  Nature Genet. 20: 251-258.

Deloukas, P., Schuler, G. D., Gyapay, G., Beasley, E. M., et al., Myers, R. M., Cox, D. R., Weissenbach, J., Boguski, M. S. and Bentley, D. R.  (1998).  A physical map of 30,000 human genes.  Science 282: 744-746.

Karlovich, C. A., John, R. M., Ramirez, L., Stainier, D. Y. R. and Myers, R. M. (1998).  Characterization of the Huntington disease (HD) gene homolog in the zebrafish Danio rerio.  Gene 217: 117-125.

Birren, B., Green, E. D., Klapholz, S., Myers, R. M. and Roskams, J., eds.  (1998).  Genome Analysis: A Laboratory Manual.  Cold Spring Harbor Laboratory Press.  Vol. 2: Detecting Genes.

Myers, R. M., Hedrick, L. and Hayashi, K. (1998).  Detection of DNA Variation, in Genome Analysis: A Laboratory Manual. Vol. 4. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.  pp. 287-384.

Eisen, J. A., Kaiser, D. and Myers, R. M.  (1997).  Gastrogenomic delights: a movable feast.  Nature Med.  3: 1076-1078.

Green, E. D., Birren, B., Klapholz, S., Myers, R. M. and Hieter, P., eds.  (1997).  Genome Analysis: A Laboratory Manual.  Cold Spring Harbor Laboratory Press.  Vol. 1: Analyzing DNA.

Goodman, L., Boguski, M., Chakravarti, A., Gibbs, R., Green, E., and Myers, R. M. (1997).  Genome horizons [editorial].  Genome Res. 7: 567-568.

Bell, S. M., Shaw, M. Jou, Y.-S., Myers, R. M. and Knowles, M. A. (1997).  Identification and characterisation of the human homologue of SH3BP2, an SH3 binding domain protein within a common region of deletion at 4p16.3 involved in bladder cancer.  Genomics 44: 163-170.

Aaltonen, J., Horelli-Kuitunen, N., Fan, J.-B., Bjorses, P., Perheentupa, J., Myers, R., Palotie, A. and Peltonen, L. (1997).  High-resolution physical and transcriptional mapping of the autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy locus on chromosome 21q22.3 by FISH. Genome Res. 7: 820-829.

Stewart, E. A., McKusick, K. B., Aggarwal, A., Bajorek, E., Brady, S., Chu, A., Fang, N., Hadley, D., Harris, M., Hussain, S., Lee, R., Maratukulam, A., O’Connor, K., Perkins, S., Piercy, M., Qin, F., Reif, T., Sanders, C, She, X., Sun, W-L, Tabar, P., Voyticky, S., Cowles, S., Fan, J-B., Mader, C, Quackenbush, J., Myers, R. M. and Cox, D. R. (1997). An STS-based radiation hybrid map of the human genome.  Genome Res. 7: 422-433.

Virtaneva, K., D’Amato, E., Miao, J., Koskiniemi, M., Norio, R., Avanzini, G., Franceschetti, S., Michelucci, R., Tassinari, C. A., Omer, S., Pennacchio, L. A., Myers, R. M. Dieguez-Lucena, J. L., Krahe, R., de la Chapelle, A. and Lehesjoki, A.-E. (1997).  Unstable minisatellite expansion causing recessively inherited myoclonus epilepsy, EPM1.  Nature Genet. 15: 393-396.

Boguski, M. S., Cox, D. R. and Myers, R. M., editors.  (1996).  Genomes and Evolution.  Current Opinion in Genetics & Development 6 (6).

Mastrianni, J. A., Iannicola, C., Myers, R. M., DeArmond, S. and Prusiner, S. B.  (1996).  Mutation of the prion protein gene at codon 208 in familial Creutzfeldt-Jakob disease.  Neurology.  47: 1305-1312.

Pennacchio, L.A. and Myers, R.M. (1996).  Isolation and characterization of the mouse cystatin B gene.  Genome Res. 6: 1103-1109.  PMID: 8938434.

Schuler, G. D., Boguski,  M. S., Stewart, E. A., Stein, L. D., Gyapay, G., et al., Myers, R. M., Cox, D. R., James, M. R., Bentley, D., Deloukas, P., Lander E. S. and Hudson, T. J. (1996).  A gene map of the human genome.  Science 274: 540-546.

Bell, S. M., Zuo, J., Myers, R. M. and Knowles, M. A. (1996). Fluorescence in situ hybridization deletion mapping at 4p16.3 in bladder cancer cell lines refines the localisation of the critical interval to 30 kb.  Genes, Chromosomes and Cancer 17: 108-117.

Boguski, M., Chakravarti, A., Gibbs, R., Green, E., and Myers, R. M. (1996).  The end of the beginning: the race to begin human genome sequencing [editorial].  Genome Res. 6: 771-772.

Johnson, R. L., Rothman, A. L., Xie, J., Goodrich, L. V., Bare, J. W., Bonifas, J. M., Quinn, A. G., Myers, R. M., Cox, D. R., Epstein, E. H. and Scott, M. P.  (1996).  Human homolog of patched, a candidate gene for the basal cell nevus syndrome.  Science 272: 1668-1671.

Virtaneva, K., Miao, J., Traskelin, A.-L., Stone, N., Warrington, J., Weissenbach, J., Myers, R. M., Cox, D.R., Sistonen, P., de la Chapelle and Lehesjoki, A-E. (1996). Progressive myoclonus epilepsy EPM1 locus maps to a 175 kb interval in distal 21q.  Am. J. Hum. Genet. 58: 1247-1253.

Pennacchio, L. A.,  Lehesjoki, A-E., Stone, N. E., Willour, V. L., Virtaneva, K., Miao, J., D’Amato, E., Ramirez, L., Faham, M., Koskiniemi, M., Warrington, J., Norio, R., de la Chapelle, A., Cox, D.R. and Myers, R. M.  (1996).  Mutations in the gene encoding cystatin B in Progressive Myoclonus Epilepsy (EPM1).  Science 271: 1731-1734.  PMID: 8596935.

Stone, N.E., Fan, J.B., Willour, V., Pennacchio, L.A., Warrington, J., Hu, A., de la Chapelle, A., Lehesjoki, A.E., Cox, D.R. and Myers, R.M.  (1996).  Construction of a 750 kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the Progressive Myoclonus Epilepsy (EPM1) gene.  Genome Res. 6: 218-225.

Burke, J., R., Enghild, J. J., Martin, M. E., Jou, Y.-S., Myers, R. M., Roses, A. D., Vance, J. M. and Strittmatter, W. J.  (1996).  Huntingtin and DRPLA proteins selectively interact with the enzyme GAPDH.  Nature Med. 2: 347-350.

Cox, D. R. and Myers, R. M.  (1996).  A map to the future.  Nature Genet. 12: 117-118.

 Green, E. D., Cox, D. R. and Myers, R. M. (1995).  The Human Genome Project and Its Impact on the Study of Human Disease.  In: The Metabolic Basis of Inherited Disease, Seventh Edition.  (eds. C.R. Scriver, A.L. Beaudet, W.S. Sly, and D. Valle; McGraw-Hill, Inc.) pp. 401-436.

Patil, N., Cox, D. R., Bhat, D., Faham, M., Myers, R. M. and Peterson, A. S.  (1995).  A potassium channel mutation in weaver mice implicates membrane excitability in granule cell differentiation.  Nature Genet.  11: 126-129.

Jou, Y.-S. and Myers, R. M. (1995).  Evidence from antibody studies that the CAG-repeat in the Huntington disease gene is expressed in the protein.  Hum. Mol. Genet.  4:  465-469.

Estabrooks, L. L., Breg, W. R., Hayden, M. R., Ledbetter, D. H., Myers, R. M., Wyandt, H. E., Yang-Feng, T. L., and Hirschhorn, K.  (1995).  Summary of the 1993 ancillary meeting “Recent research on chromosome 4p syndromes and genes”.  Amer. J. Hum. Genet. 55: 453-458.

Jou, Y.-S., Goold, R. D. and Myers, R. M. (1994).  Localization of the beta-2-macroglobulin receptor-associated protein 1 gene (LRPAP1) and other gene fragments to human chromosome 4p16.3 by direct cDNA selection.  Genomics 24: 410-413.

Patil, N., Peterson, A.,  Rothman, A., de Jong, P. J., Myers, R. M. and Cox, D. R.  (1994).  A high resolution physical map of 2.5 Mbp of the Down Syndrome region on human chromosome 21.  Hum. Molec. Genet.  3: 1811-1817.

Cox, D. R., Green, E. D., Cohen, D., Lander, E., and Myers, R. M.  (1994).  Assessing mapping progress in the Human Genome Project.  Science.  265: 2031-2032.

John, R. M., Robbins, C. A. and Myers, R. M. (1994).  Identification of genes within CpG-enriched DNA from human chromosome 4p16.3.  Hum. Molec. Genet. 3: 1611-1616.

Garcia, P. D. and Myers, R. M. (1994).  Pituitary cell line GH3 expresses two somatostatin receptor subtypes that inhibit adenylyl cyclase:  Molecular cloning and functional expression in HEK 293 cells of rat somatostatin receptor subtypes SSTR1 and SSTR2.  Molec. Pharmacol.  45: 402-409.

Fan, J.-B., DeYoung, J., Lagacé, R., Lina, R. A., Xu, Z., Murray, J. C., Buetow, K. H., Weissenbach, J., Goold, R. D., Cox, D. R. and Myers, R. M. (1994).  Isolation of yeast artificial chromosome clones from 54 polymorphic loci mapped with high odds on human chromosome 4.  Hum. Molec. Genet. 3: 243-246.

Myers, R. M., Goold, R. D. and van Ommen, G.-J. (1994).  Report of the Third International Workshop on Human Chromosome 4.  Cytogenetics and Cell Genetics 66:217-236.

 

UCSF Work


Richard III, C. W., Boehnke, M. Berg, D. J. Lichy, J. J., Meeker, T. C., Hauser, E., Myers, R. M. and Cox, D. R. (1993).  A radiation hybrid map of the distal short arm of human chromosome 11, containing the Beckwith-Weidemann and associated embryonal tumor disease loci.  Am. J. Hum. Genet. 52: 915-921.

Goold, R. D., diSibio, G. L., Xu, H., Lang, D. B., Dadgar, J., Magrane, G. G., Dugaiczyk, A., Smith, K. A., Cox, D. R., Masters, S.B. and Myers, R. M.  (1993).  The development of sequence-tagged sites for human chromosome 4.  Hum. Molec. Genet.  2: 1271-1288.

Zuo, J., Robbins, C., Baharloo, S., Cox, D. R., and Myers, R. M.  (1993).  Construction of cosmid contigs and high-resolution restriction mapping of the Huntington disease region of chromosome 4.  Hum. Molec. Genet.  2: 889-899.

Stuvé, L. L. and Myers, R. M. (1993).  Identification and characterization of a beta-globin promoter-binding factor from murine erythroleukemia cells.  Molec. Cell. Biol.  13: 4311-4322.

Bull, L. N., Hewitt, J. E., Cox, D. R. and Myers, R. M.  (1993).  Sensitivity of HincII to CpG methylation.  Nucleic Acids Res.  21:  2021.

Myers, R. M.  (1993).  The Pluses of Subtraction (Perspective).  Science 259: 942-943.

Neel, J. V., Satoh, C. and Myers, R. M.  (1993).  Report of a workshop on the application of molecular genetics to the study of mutation in the children of atomic bomb survivors.  Mut. Research 291: 1-20.

Pritchard, C. A., Zhu, N., Cox, D. R. and Myers, R. M.  (1993).  Molecular Genetics of Huntington Disease.  In: Advances in Genome Biology, Second Edition (ed. R. Verma; JAI Press).  pp. 157-205.

Hartzog, G. and Myers, R. M.  (1993).   Discrimination among potential activators of the beta-globin CACCC element by correlation of binding and transcriptional properties.  Molec. Cell. Biol.  13: 44-56.

Dugaiczyk, A., Goold, R., diSibio, G., and Myers, R. M.  (1992).  Improved sequencing of cosmids using new primers and linearized DNA.  Nucleic Acids Res.  20: 6421-6422.

Frazer, K. A., Boehnke, M., Budarf, M. L., Wolff, R. K., Emanuel, B. S., Myers, R. M., and Cox, D. R.  (1992).  A radiation hybrid map of the region on human chromosome 22 containing the neurofibromatosis type 2 locus.   Genomics 14: 574-584.

Rajpara, S. M., Garcia, P. D., Roberts, R., Eliassen, J. C., Owens, D. F., Maltby, D., Myers, R. M. and Mayeri, E.  (1992).  Identification and molecular cloning of a neuropeptide Y homolog that produces prolonged inhibition in Aplysia neurons.  Neuron  9: 505-513.

Pritchard, C., Zhu, N., Zuo, J., Bull, L., Pericak-Vance, M. A., Vance, J. M., Roses, A. D., Milatovich, A., Francke, U., Cox, D. R. and Myers, R. M. (1992).  Recombination of 4p16 DNA markers in an unusual family with Huntington disease.  Amer. J. Hum. Genet.  50: 1218-1230.

Zuo, J., Robbins, C., Taillon-Miller, P., Cox, D. R. and Myers, R. M.  (1992).  Cloning of the Huntington disease region in yeast artificial chromosomes.  Hum. Molec. Genet.  1 (3): 149-159.

Cox, D. R. and Myers, R. M.  (1992).  Bridging the gaps.  Current Biology.  2: 338-339.

Law,  A., Richard, C. W., Cottingham, R. W., Lathrop, G. M., Cox, D. R. and Myers, R. M.  (1992).  Genetic linkage analysis of bipolar affective disorder in an Old Order Amish pedigree.  Hum. Genet.  88: 562-568.

Sheffield, V. C., Beck, J. S., Stone, E. M. and Myers, R. M.  (1992).  A simple and efficient method for attachment of a 40-base pair, GC-rich sequence to PCR-amplified DNA.  BioTechniques  12: 386-387.

Pritchard, C., Cox, D. R. and Myers, R. M.  (1991).  Dinucleotide repeat polymorphism located at D4S169.  Nucleic Acids Res.  19: 6347.

Maricq, A. V., Peterson, A. S., Brake, A. J., Myers, R. M. and Julius, D.  (1991).  Primary structure and functional expression of a serotonin-gated ion channel.  Science 254: 432-437.

Gaensler, K. M. L., Burmeister, M., Brownstein, B. H., Taillon-Miller, P. and Myers, R. M.  (1991).  Physical mapping of yeast artificial chromosomes containing sequences from the human beta-globin gene region.  Genomics 10: 976-984.

Pritchard, C. A., Cox, D. R. and Myers, R. M. (1991).  Invited editorial: The end in sight for Huntington disease?  Amer. J. Hum. Genet. 49: 1-6.

Burmeister, M., Cox, D. R. and Myers, R. M.  (1991).  TaqI RFLP at D21S137.  Nucleic Acids Res.  19: 4020.

Burmeister, M., diSibio, G., Cox, D. R. and Myers, R. M.  (1991).  Identification of polymorphisms by genomic denaturing gradient gel electrophoresis:  application to the proximal region of human chromosome 21.  Nucleic Acids Res. 19: 1475-1481.

Burmeister, M., Kim, S., Price, E. P., de Lange, T., Tantravahi, U., Myers, R. M. and Cox, D. R.  (1991).  A map of the distal region of the long arm of human chromosome 21 constructed by radiation hybrid mapping and pulsed-field gel electrophoresis.  Genomics  9: 19-30.

Richard, C. W., Withers, D. A., Meeker, T. C., Maurer, S., Evans, G., Myers, R. M. and Cox, D. R.  (1991).  A radiation hybrid map of the proximal long arm of human chromosome 11 containing the MEN-1 and bcl-1 disease gene loci.  Amer. J. Hum. Genet.  49: 1189-1196.

Burmeister, M., Cox, D. R. and Myers, R. M. (1990).  Dinucleotide repeat polymorphism located at D21S120.  Nucleic Acids Res.  18: 4969.

Duyk, G. M., Kim, S., Myers, R. M. and Cox, D. R.  (1990).  Exon trapping: A genetic screen to identify transcribed sequences in cloned mammalian genomic DNA.  Proc. Natl. Acad. Sci. USA.  87: 8995-8999.

Pritchard, C. A., Casher, D., Bull, L., Cox, D. R. and Myers, R. M.  (1990).  A cloned DNA segment from the telomeric region of human chromosome 4p is not detectably rearranged in Huntington disease patients.  Proc. Natl. Acad. Sci. USA.  87: 7309-7313.

Lopez, C. D., Yost, C. S., Prusiner, S. B., Myers, R. M. and Lingappa, V. R.  (1990).  Unusual topogenic sequence directs prion protein biogenesis.  Science 248: 226-229.

Stuvé, L. L. and Myers, R. M.  (1990).  A directly repeated sequence in the beta-globin promoter regulates transcription in murine erythroleukemia cells.  Molec. Cell Biol. 10: 972-981.

deLange, T., Shiue, L., Myers, R. M., Cox, D. R., Naylor, S. L., Killery, A. M. and Varmus, H. E.  (1990).  Structure and variability of human chromosome ends.  Molec. Cell Biol. 10:  518-527.

Yost, C. S., Lopez, C. D., Prusiner, S. B., Myers, R. M. and Lingappa, V. R.  (1990).  Non-hydrophobic extracytoplasmic determinant of stop transfer in the prion protein.  Nature 343: 669-672.

Brodsky, M. H., Warton, M., Myers, R. M. and Littman, D. R.  (1990).  Analysis of the site in CD4 that binds to the HIV envelope glycoprotein.  J. Immunol.  144: 3078-3086.

Cox, D. R., Burmeister, M., Price, E. R., Kim, S. and Myers, R. M.  (1990).  Radiation hybrid mapping: A somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes.  Science 250: 245-250.

Sheffield, V. C., Cox, D. R. and Myers, R. M. (1990).  Strategies for identifying DNA polymorphisms in PCR-amplified genomic DNA by denaturing gradient gel electrophoresis.  In:  PCR-Protocols and Applications: A Laboratory Manual (eds. M. Innis, D. Gelfand, J. Sninsky and T. White; Academic Press, San Diego).  pp. 206-218.

Myers, R. M., Sheffield, V. C. and Cox, D. R. (1989).  PCR and denaturing gradient gel electrophoresis.  In: The Polymerase Chain Reaction (eds. H. Erlich, R. Gibbs, H. Kazazian Jr; Cold Spring Harbor Press, Cold Spring Harbor, NY). pp. 177-181.

Myers, R. M., Cowie, A., Stuvé, L., Hartzog, G. and Gaensler, K. (1989).  Genetic and biochemical analysis of the mouse beta-major globin promoter.  In: Hemoglobin Switching, Part A: Transcriptional Regulation (eds. G. Stamatoyanopolous and A. Nienhuis; A.R. Liss, Inc., New York). pp 117-127.

Myers, R. M., Sheffield, V. C. and Cox, D. R. (1989).  Mutation detection by PCR, GC-clamps and denaturing gradient gel electrophoresis.  In: PCR Technology: Principles and Applications for DNA Amplification (ed. H. Erlich; Stockton Press, New York). pp 71-88.

Pritchard, C. A., Cox, D. R. and Myers, R. M. (1989).  Methylation at the Huntington disease-linked D4S95 locus.  Amer. J. Hum. Genet. 45: 335-336.

Cox, D. R., Pritchard, C. A., Uglum, E., Casher, D., Kobori, J., and Myers, R. M.  (1989).  Segregation of the Huntington disease region of human chromosome 4 in a somatic cell hybrid.  Genomics 4: 397-407.

Pritchard, C. A., Casher, D., Uglum, E., Cox, D. R., and Myers, R. M.  (1989).  Isolation and field- inversion gel electrophoresis analysis of DNA markers located close to the Huntington disease gene.  Genomics 4: 408-418.

Sheffield, V. C., Cox, D. R., Lerman, L. S. and Myers, R. M.  (1989).  Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes.  Proc. Natl. Acad. Sci. USA 86: 232-236.

 Cowie, A. and Myers, R. M.  (1988).  DNA sequences involved in transcriptional regulation of the mouse beta-globin promoter in murine erythroleukemia cells.  Molec. Cell. Biol. 8: 3122-3128.

Myers, R. M., Sheffield, V., and Cox, D. R. (1988).  Detection of single base changes in DNA: Ribonuclease cleavage and denaturing gradient gel electrophoresis.  In: Genomic Analysis: A Practical Approach (ed. K. Davies; IRL Press Ltd, Oxford), pp. 95-139.

Collins, M. and Myers, R. M.  (1987).  Alterations in DNA helix stability due to base modifications can be evaluated using denaturing gradient gel electrophoresis.  J. Mol. Biol. 198: 737-744.

 

 Postdoctorate Work


Myers, R. M., Maniatis, T. and Lerman, L. S. (1987).  Detection and localization of single base changes by denaturing gradient gel electrophoresis.  Meth. Enzymol. 155: 501-527.

Myers, R. M., Tilly, K. and Maniatis, T.  (1986).  Fine structure genetic analysis of a beta-globin promoter.  Science 232: 613-618.

Myers, R. M. and Maniatis, T. (1986).  Recent advances in the development of methods for detecting single base substitutions associated with human genetic diseases.  Cold Spring Harbor Symp. Quant. Biol. 51: 275-284.

Myers, R. M. (1986).  Generation of single and double base substitutions in cloned DNA fragments.  In: Gene Transfer Vectors for Mammalian Cells.  Cold Spring Harbor Press (Cold Spring Harbor, NY), pp 46-56.

Myers, R. M., Larin, Z. and Maniatis, T.  (1985).  Detection of single base substitutions by ribonuclease cleavage of mismatches in RNA:DNA duplexes.  Science 230: 1242-1246.

Myers, R. M., Lerman, L. S. and Maniatis, T.  (1985).  A general method for saturation mutagenesis of cloned DNA fragments.  Science 229: 242-247.

Myers, R. M., Fischer, S. G., Maniatis, T. and Lerman, L.S.  (1985).  Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis.  Nucleic Acids Res. 13: 3111-3130.

Myers, R. M., Fischer, S. G., Lerman, L. S. and Maniatis, T.  (1985).  Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis.  Nucleic Acids Res. 13: 3131-3146.

Myers, R. M., Lumelsky, N., Lerman, L. S. and Maniatis, T.  (1985).  Detection of single base substitutions in total genomic DNA.  Nature 313: 495-498.

 

Graduate Work


Jones, K. A., Myers, R. M., and Tjian, R.  (1984).  Mutational analysis of simian virus 40 large T antigen binding sites.  EMBO J. 3: 3247-3255.

Fisher, E. F., Feist, P. L., Beaucage, S. L., Myers, R. M., Tjian, R. and Caruthers, M. H.  (1984).  Interaction of AD2+D2 protein and simian virus 40 large T antigen with the large tumor antigen binding site I.  Biochemistry 23: 5938-5944.

Myers, R. M. (1982).  Dissertation:  T antigen : DNA interactions involved in SV40 DNA replication and regulation of viral gene expression.  The University of California at Berkeley.  NRLF C 2 938 630.

Learned, R. M., Myers, R. M. and Tjian, R. (1981).  Replication in monkey cells of plasmid DNA containing the minimal SV40 Origin.  In: Structure and DNA-protein interactions of replication origins, ICN-UCLA Symposia on Molecular and Cellular Biology, Volume XX­I, (eds. Dan S. Ray and C. Fred Fox, Academic Press, New York) pp. 555-566.

Myers, R. M., Kligman, M. and Tjian, R.  (1981).  Does simian virus 40 T antigen unwind DNA?  J. Biol. Chem. 256: 10156-10160.

Myers, R. M., Rio, D.  C., Robbins, A. K., and Tjian, R.  (1981).  SV40 gene expression is modulated by the cooperative binding of T antigen to DNA.  Cell 25: 373-384.

Myers, R. M., Williams, R. C. and Tjian, R.  (1981).  Oligomeric structure of a simian virus 40 T antigen in free form and bound to DNA.  J. Mol. Biol. 148: 347-353.

Myers, R. M. and Tjian, R.  (1980).  Construction and analysis of simian virus 40 origins defective in tumor antigen binding and DNA replication.  Proc. Natl. Acad. Sci. USA 77: 6491-6495.

Rio, D., Robbins, A., Myers, R. and Tjian, R.  (1980).  Regulation of simian virus 40 early transcription in vitro by a purified tumor antigen.  Proc. Natl. Acad. Sci. USA 77: 5706-5710.

 

Undergraduate Work


Milton, D. L., Napier, M. L., Myers, R. M. and Hardman, J. K. (1986). In vitro mutagenesis and overexpression of the E. coli trpA gene and the partial characterization of the resultant tryptophan synthase mutant alpha-subunits.  J. Biol. Chem. 261: 16604-16615.

Brock, P. W., Myers, R., Baker, D. C. and Hardman, J. K.  (1983).  Photoaffinity labeling of the indole sites on the Escherichia coli tryptophan synthase a-subunit.  Arch. Biochem. Biophys. 220: 435-443.
Hodo, H. G., Murphy, J., Hardman, J. K. and Myers, R. M.  (1977).

Substrate interactions with the alpha-subunit of the Escherichia coli tryptophan synthase.  Arch. Biochem. Biophys. 181: 419-427.

Hand, C. W. and Myers, R. M.  (1976).  Arrhenius parameters for the reaction of oxygen atoms with dicyanoacetylene.  J. Physical Chemistry 80: 557-558.