Publications


		Publications from the SHGC Scientific Journal Publications Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, 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 EA, 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 SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK. (2005). Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434:724-31. Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G Jr, Dickson M, Grimwood J, Schmutz J, Myers RM, Schluter D, Kingsley DM. (2005). Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science 307:1928-33. Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, Branscomb E, Brown NC, Bruno WJ, Buckingham JM, Callen DF, Campbell CS, Campbell ML, Campbell EW, Caoile C, Challacombe JF, Chasteen LA, Chertkov O, Chi HC, Christensen M, Clark LM, Cohn JD, Denys M, Detter JC, Dickson M, Dimitrijevic-Bussod M, Escobar J, Fawcett JJ, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Goodwin LA, Grady DL, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Hildebrand CE, Huang W, Israni S, Jett J, Jewett PB, Kadner K, Kimball H, Kobayashi A, Krawczyk MC, Leyba T, Longmire JL, Lopez F, Lou Y, Lowry S, Ludeman T, Manohar CF, Mark GA, McMurray KL, Meincke LJ, Morgan J, Moyzis RK, Mundt MO, Munk AC, Nandkeshwar RD, Pitluck S, Pollard M, Predki P, Parson-Quintana B, Ramirez L, Rash S, Retterer J, Ricke DO, Robinson DL, Rodriguez A, Salamov A, Saunders EH, Scott D, Shough T, Stallings RL, Stalvey M, Sutherland RD, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Torney DC, Tran-Gyamfi M, Tsai M, Ulanovsky LE, Ustaszewska A, Vo N, White PS, Williams AL, Wills PL, Wu JR, Wu K, Yang J, Dejong P, Bruce D, Doggett NA, Deaven L, Schmutz J, Grimwood J, Richardson P, Rokhsar DS, Eichler EE, Gilna P, Lucas SM, Myers RM, Rubin EM, Pennacchio LA. (2004). The sequence and analysis of duplication-rich human chromosome 16. Nature 432:988-94. Noonan JP, Grimwood J, Danke J, Schmutz J, Dickson M, Amemiya CT, Myers RM. (2004). Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Research 14:2397-405. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, 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 Research 14:2121-7. International Human Genome Sequencing Consortium. (2004). Finishing the euchromatic sequence of the human genome. Nature 431:931-45. ENCODE Project Consortium. (2004). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306:636-40. Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, Aerts A, Altherr M, Bajorek E, Black S, Branscomb E, Caoile C, Challacombe JF, Chan YM, Denys M, Detter JC, 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 JP, Pitluck S, Pollard M, Predki P, Priest J, Ramirez L, 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 JF, Eichler EE, Olsen A, Pennacchio LA, Rokhsar DS, Richardson P, Lucas SM, Myers RM, Rubin EM. The DNA sequence and comparative analysis of human chromosome 5. Nature 431:268-74. Peichel CL, Ross JA, Matson CK, Dickson M, Grimwood J, Schmutz J, Myers RM, Mori S, Schluter D, Kingsley DM. (2004). The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome. Curr Biol. 14:1416-24. Schmutz J, Wheeler J, Grimwood J, Dickson M, Yang J, Caoile C, Bajorek E, Black S, Chan YM, 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, Myers RM. (2004). Quality assessment of the human genome sequence. Nature 429:365-8. Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Garcia C, Georgescu AM, Glavina T, Gomez M, Gonzales E, Groza M, Hammon N, Hawkins T, Haydu L, Ho I, Huang W, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Larionov V, Leem SH, Lopez F, Lou Y, Lowry S, Malfatti S, Martinez D, McCready P, Medina C, Morgan J, Nelson K, Nolan M, Ovcharenko I, Pitluck S, Pollard M, Popkie AP, Predki P, Quan G, Ramirez L, Rash S, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, She X, Smith D, Slezak T, 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 TS, DeJong P, Dickson M, Gordon D, Eichler EE, Pennacchio LA, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM. (2004). The DNA sequence and biology of human chromosome 19. Nature 428:529-535. Li JZ, Vawter MP, Walsh DM, Tomita H, Evans SJ, Choudary PV, Lopez JF, Avelar A, Shokoohi V, Chung T, Mesarwi O, Jones EG, Watson SJ, Akil H, Bunney WE Jr, Myers RM. (2004). Abstract Systematic changes in gene expression in postmortem human brains associated with tissue pH and terminal medical conditions. Human Mol Genetics 13:609-616. Tomita H, Vawter MP, Walsh DM, Evans SJ, Choudary PV, Li J, Overman KM, Atz ME, Myers RM, Jones EG, Watson SJ, Akil H, Bunney WE Jr. (2004) Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol Psychiatry. 55(4):346-52. Noonan JP, Grimwood J, Schmutz J, Dickson M, Myers RM. (2004). Gene conversion and the evolution of protocadherin gene cluster diversity. Genome Research 14:354-366. Vawter MP, Evans S, Choudary P, Tomita H, Meador-Woodruff J, Molnar M, Li J, Lopez JF, Myers R, Cox D, Watson SJ, Akil H, Jones EG, Bunney WE.(2004) Gender-specific gene expression in post-mortem human brain: localization to sex chromosomes. Neuropsychopharmacology. 29(2):373-84. Murphy E, Yu D, Grimwood J, Schmutz J, Dickson M, Jarvis MA, Hahn G, Nelson JA, Myers RM, Shenk TE. (2003). Coding potential of laboratory and clinical strains of human cytomegalovirus. PNAS 100:14976-14981. Noonan JP, Li J, Nguyen L, Caoile C, Dickson M, Grimwood J, Schmutz J, Feldman MW, Myers RM. (2003). Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster. Am J Hum Genet. 72:621-635. Strausberg et al. (2003). Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. PNAS 99:16899-16903. Evans SJ, Choudary PV, Vawter MP, Li J, Meador-Woodruff JH, Lopez JF, Burke SM, Thompson RC, Myers RM, Jones EG, Bunney WE, Watson SJ, Akil H. (2003) DNA microarray analysis of functionally discrete human brain regions reveals divergent transcriptional profiles. Neurobiol Dis. 14(2):240-50. Yang WS, Hsiung CA, Ho LT, Chen YT, He CT, Curb JD, Grove J, Quertermous T, Chen YD, Kuo SS, Chuang LM; Sapphire Study Group. (2003) Genetic epistasis of adiponectin and PPARgamma2 genotypes in modulation of insulin sensitivity: a family-based association study. Diabetologia. 46(7):977-83. Olivier M, Chuang LM, Chang MS, Chen YT, Pei D, Ranade K, de Witte A, Allen J, Tran N, Curb D, Pratt R, Neefs H, de Arruda Indig M, Law S, Neri B, Wang L, Cox DR. (2002) High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology. Nucleic Acids Res. 30(12):e53. Ranade K, Shue WH, Hung YJ, Hsuing CA, Chiang FT, Pesich R, Hebert J, Olivier M, Chen YD, Pratt R, Olshen R, Curb D, Botstein D, Risch N, Cox DR. (2001) The glycine allele of a glycine/arginine polymorphism in the beta2-adrenergic receptor gene is associated with essential hypertension in a population of Chinese origin. Am J Hypertens. 14(12):1196-200. Olivier M, Bustos VI, Levy MR, Smick GA, Moreno I, Bushard JM, Almendras AA, Sheppard K, Zierten DL, Aggarwal A, Carlson CS, Foster BD, Vo N, Kelly L, Liu X, Cox DR. (2001) Complex high-resolution linkage disequilibrium and haplotype patterns of single-nucleotide polymorphisms in 2.5 Mb of sequence on human chromosome 21. Genomics. 78(1-2):64-72. Wu Q, Zhang T, Cheng JF, Kim Y, Grimwood J, Schmutz J, Dickson M, Noonan JP, Zhang MQ, Myers RM, Maniatis T. (2001). Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Research 11:389-404. Olivier M, Aggarwal A, Allen J, Almendras AA, Bajorek ES, Beasley EM, Brady SD, Bushard JM, Bustos VI, Chu A, Chung TR, De Witte A, Denys ME, Dominguez R, Fang NY, Foster BD, Freudenberg RW, Hadley D, Hamilton LR, Jeffrey TJ, Kelly L, Lazzeroni L, Levy MR, Lewis SC, Liu X, Lopez FJ, Louie B, Marquis JP, Martinez RA, Matsuura MK, Misherghi NS, Norton JA, Olshen A, Perkins SM, Perou AJ, Piercy C, Piercy M, Qin F, Reif T, Sheppard K, Shokoohi V, Smick GA, Sun WL, Stewart EA, Fernando J, Tejeda, Tran NM, Trejo T, Vo NT, Yan SC, Zierten DL, Zhao S, Sachidanandam R, Trask BJ, Myers RM, Cox DR. (2001) A high-resolution radiation hybrid map of the human genome draft sequence. Science. 291(5507):1298-302. The International Human Genome Sequencing Consortium. (2001). The Human Genome: Initial Sequencing and Analysis. Nature 409: 860-921. The International Human Genome Mapping Consortium. (2001). A BAC fingerprint map of the human genome. Nature 409: 934-941. Olivier, M., Brady, S., Cox, D. (2001). A high resolution radiation hybrid map of the human genome. Science. 298: 1298-1302. Deloukas, P., G. D. Schuler, G. Gyapay, E. M. Beasley, et al., R. M. Myers, D. R. Cox, J. Weissenbach, M. S. Boguski, D. R. Bentley. (1998). A physical map of 30,000 human genes. Science 282: 744-746. 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. 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. Fan, J.-B., DeYoung, J., Lagac�, 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. 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 (8): 1271-1288. 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. 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. 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 _-globin gene region. Genomics 10: 976-984. 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. 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. Editorials and Reviews Schmutz J, Grimwood J. (2004). Genomes: fowl sequence. Nature 432:679-80. Grimwood J, Schmutz J. (2003). Genomics: six is seventh. Nature 425:775-776. Bunney WE, Bunney BG, Vawter MP, Tomita H, Li J, Evans SJ, Choudary PV, Myers RM, Jones EG, Watson SJ, Akil H. (2003) Microarray technology: a review of new strategies to discover candidate vulnerability genes in psychiatric disorders. Am J Psychiatry. 160(4):657-66. Tabor, H. K., Risch, N. J., and Myers, R. M. (2002). Candidate-gene approaches for studying complex genetic traits: practical considerations. Nature Reviews 3:1-7. Eisen, J. A., Kaiser, D. and Myers, R. M. (1997). Gastrogenomic delights: a movable feast. Nature Med. 3: 1076-1078. Cox, D. R. and Myers, R. M. (1996). A map to the future. Nature Genet. 12: 117-118. Boguski, M. S., Cox, D. R. and Myers, R. M., editors. (1996). Genomes and Evolution. Current Opinion in Genetics & Development 6 (6). 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. 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. 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. 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. Cox, D. R. and Myers, R. M. (1992). Bridging the gaps. Current Biology. 2: 338-339. Book Chapters Schmutz J, Wheeler J, Grimwood J, Dickson M, Myers RM. (2003). Assessing the quality of finished genomic sequence. Cold Spring Harb Symp Quant Biol. 68:31-7. Schmutz, J., Grimwood, J. and Myers, R. M. (2002). Assembly of DNA sequencing data. In: Methods in Molecular Biology, "Bacterial Artificial Chromosomes: Methods and Protocols", ed. (2002). Shaying Zhao. Humana Press. In press. Schmutz, J., Grimwood, J. and Myers, R. M. (2002). Sequence finishing. In: Methods in Molecular Biology, "Bacterial Artificial Chromosomes: Methods and Protocols", ed. Shaying Zhao. Humana Press. In press. Schmutz, J., Grimwood, J. and Myers, R. M. (2002). Quality assessment of finished BAC sequences. In: Methods in Molecular Biology, "Bacterial Artificial Chromosomes: Methods and Protocols", ed. Shaying Zhao. Humana Press. In press. 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., 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. 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. Matise, T. C., Wasmuth, J. J., Myers, R. M., and McPherson, J. D. (1999). Somatic Cell Genetics and Radiation Hybrid Mapping, in Genome Analysis: A Laboratory Manual. Vol. 4. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. pp. 259-302. 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. 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.