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Publications

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2008
The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse., Durfee, Tim, Nelson Richard, Baldwin Schuyler, Plunkett Guy, Burland Valerie, Mau Bob, Petrosino Joseph F., Qin Xiang, Muzny Donna M., Ayele Mulu, et al. , Journal of bacteriology, 2008 Apr, Volume 190, Issue 7, p.2597-606, (2008) Abstract
Pleiotropic patterns of quantitative trait loci for 70 murine skeletal traits., Kenney-Hunt, Jane P., Wang Bing, Norgard Elizabeth A., Fawcett Gloria, Falk Doug, Pletscher Susan L., Jarvis Joseph P., Roseman Charles, Wolf Jason, and Cheverud James M. , Genetics, 2008 Apr, Volume 178, Issue 4, p.2275-88, (2008) Abstract
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays., Matejková, Petra, Strouhal Michal, Smajs David, Norris Steven J., Palzkill Timothy, Petrosino Joseph F., Sodergren Erica, Norton Jason E., Singh Jaz, Richmond Todd A., et al. , BMC microbiology, 2008, Volume 8, p.76, (2008) Abstract
Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF., Bourgogne, Agathe, Garsin Danielle A., Qin Xiang, Singh Kavindra V., Sillanpaa Jouko, Yerrapragada Shailaja, Ding Yan, Dugan-Rocha Shannon, Buhay Christian, Shen Hua, et al. , Genome biology, 2008, Volume 9, Issue 7, p.R110, (2008) Abstract
Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells., Gu, Peili, Reid Jeffrey G., Gao Xiaolian, Shaw Chad A., Creighton Chad, Tran Peter L., Zhou Xiaochuan, Drabek Rafal B., Steffen David L., Hoang David M., et al. , PloS one, 2008, Volume 3, Issue 7, p.e2548, (2008) Abstract
2007
Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes., Dunning Hotopp, Julie C., Clark Michael E., Oliveira Deodoro C. S. G., Foster Jeremy M., Fischer Peter, Muñoz Torres Mónica C., Giebel Jonathan D., Kumar Nikhil, Ishmael Nadeeza, Wang Shiliang, et al. , Science (New York, N.Y.), 2007 Sep 21, Volume 317, Issue 5845, p.1753-6, (2007) Abstract
Genome-wide detection and characterization of positive selection in human populations., Sabeti, Pardis C., Varilly Patrick, Fry Ben, Lohmueller Jason, Hostetter Elizabeth, Cotsapas Chris, Xie Xiaohui, Byrne Elizabeth H., McCarroll Steven A., Gaudet Rachelle, et al. , Nature, 2007 Oct 18, Volume 449, Issue 7164, p.913-8, (2007) Abstract
A second generation human haplotype map of over 3.1 million SNPs., Frazer, Kelly A., Ballinger Dennis G., Cox David R., Hinds David A., Stuve Laura L., Gibbs Richard A., Belmont John W., Boudreau Andrew, Hardenbol Paul, Leal Suzanne M., et al. , Nature, 2007 Oct 18, Volume 449, Issue 7164, p.851-61, (2007) Abstract
Sequence variation in DOCK9 and heterogeneity in bipolar disorder., Detera-Wadleigh, Sevilla D., Liu Chun-yu, Maheshwari Manjula, Cardona Imer, Corona Winston, Akula Nirmala, Steele C. J. M., Badner Judith A., Kundu Mukta, Kassem Layla, et al. , Psychiatric genetics, 2007 Oct, Volume 17, Issue 5, p.274-86, (2007) Abstract
Direct selection of human genomic loci by microarray hybridization., Albert, Thomas J., Molla Michael N., Muzny Donna M., Nazareth Lynne, Wheeler David, Song Xingzhi, Richmond Todd A., Middle Chris M., Rodesch Matthew J., Packard Charles J., et al. , Nature methods, 2007 Nov, Volume 4, Issue 11, p.903-5, (2007) Abstract
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project., Birney, Ewan, Stamatoyannopoulos John A., Dutta Anindya, Guigó Roderic, Gingeras Thomas R., Margulies Elliott H., Weng Zhiping, Snyder Michael, Dermitzakis Emmanouil T., Thurman Robert E., et al. , Nature, 2007 Jun 14, Volume 447, Issue 7146, p.799-816, (2007) Abstract
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project., Birney, Ewan, Stamatoyannopoulos John A., Dutta Anindya, Guigó Roderic, Gingeras Thomas R., Margulies Elliott H., Weng Zhiping, Snyder Michael, Dermitzakis Emmanouil T., Thurman Robert E., et al. , Nature, 2007 Jun 14, Volume 447, Issue 7146, p.799-816, (2007) Abstract
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project., Birney, Ewan, Stamatoyannopoulos John A., Dutta Anindya, Guigó Roderic, Gingeras Thomas R., Margulies Elliott H., Weng Zhiping, Snyder Michael, Dermitzakis Emmanouil T., Thurman Robert E., et al. , Nature, 2007 Jun 14, Volume 447, Issue 7146, p.799-816, (2007) Abstract
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome., Margulies, Elliott H., Cooper Gregory M., Asimenos George, Thomas Daryl J., Dewey Colin N., Siepel Adam, Birney Ewan, Keefe Damian, Schwartz Ariel S., Hou Minmei, et al. , Genome research, 2007 Jun, Volume 17, Issue 6, p.760-74, (2007) Abstract
A genomewide admixture map for Latino populations., Price, Alkes L., Patterson Nick, Yu Fuli, Cox David R., Waliszewska Alicja, McDonald Gavin J., Tandon Arti, Schirmer Christine, Neubauer Julie, Bedoya Gabriel, et al. , American journal of human genetics, 2007 Jun, Volume 80, Issue 6, p.1024-36, (2007) Abstract
Characterizing the cancer genome in lung adenocarcinoma., Weir, Barbara A., Woo Michele S., Getz Gad, Perner Sven, Ding Li, Beroukhim Rameen, Lin William M., Province Michael A., Kraja Aldi, Johnson Laura A., et al. , Nature, 2007 Dec 6, Volume 450, Issue 7171, p.893-8, (2007) Abstract
28-way vertebrate alignment and conservation track in the UCSC Genome Browser., Miller, Webb, Rosenbloom Kate, Hardison Ross C., Hou Minmei, Taylor James, Raney Brian, Burhans Richard, King David C., Baertsch Robert, Blankenberg Daniel, et al. , Genome research, 2007 Dec, Volume 17, Issue 12, p.1797-808, (2007) Abstract
Corticotropin releasing hormone (CRH) gene variation: comprehensive resequencing for variant and molecular haplotype discovery in monosomic hybrid cell lines., Shimmin, Lawrence C., Natarajan Sivamani, Ibarguen Heladio, Montasser May, Kim Do-Kyun, Hanis Craig L., Boerwinkle Eric, Wadhwa Pathik D., and Hixson James E. , DNA sequence : the journal of DNA sequencing and mapping, 2007 Dec, Volume 18, Issue 6, p.434-44, (2007) Abstract
Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques., Hernandez, Ryan D., Hubisz Melissa J., Wheeler David A., Smith David G., Ferguson Betsy, Rogers Jeffrey, Nazareth Lynne, Indap Amit, Bourquin Traci, McPherson John, et al. , Science (New York, N.Y.), 2007 Apr 13, Volume 316, Issue 5822, p.240-3, (2007) Abstract
Evolutionary and biomedical insights from the rhesus macaque genome., Gibbs, Richard A., Rogers Jeffrey, Katze Michael G., Bumgarner Roger, Weinstock George M., Mardis Elaine R., Remington Karin A., Strausberg Robert L., Venter Craig J., Wilson Richard K., et al. , Science (New York, N.Y.), 2007 Apr 13, Volume 316, Issue 5822, p.222-34, (2007) Abstract
Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032., Gioia, Jason, Yerrapragada Shailaja, Qin Xiang, Jiang Huaiyang, Igboeli Okezie C., Muzny Donna, Dugan-Rocha Shannon, Ding Yan, Hawes Alicia, Liu Wen, et al. , PloS one, 2007, Volume 2, Issue 9, p.e928, (2007) Abstract
Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032., Gioia, Jason, Yerrapragada Shailaja, Qin Xiang, Jiang Huaiyang, Igboeli Okezie C., Muzny Donna, Dugan-Rocha Shannon, Ding Yan, Hawes Alicia, Liu Wen, et al. , PloS one, 2007, Volume 2, Issue 9, p.e928, (2007) Abstract
Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus., Highlander, Sarah K., Hultén Kristina G., Qin Xiang, Jiang Huaiyang, Yerrapragada Shailaja, Mason Edward O., Shang Yue, Williams Tiffany M., Fortunov Régine M., Liu Yamei, et al. , BMC microbiology, 2007, Volume 7, p.99, (2007) Abstract
2006
Desmosomal dysfunction due to mutations in desmoplakin causes arrhythmogenic right ventricular dysplasia/cardiomyopathy., Yang, Zhao, Bowles Neil E., Scherer Steven E., Taylor Michael D., Kearney Debra L., Ge Shuping, Nadvoretskiy Vyacheslav V., DeFreitas Gilberto, Carabello Blasé, Brandon Lois I., et al. , Circulation research, 2006 Sep 15, Volume 99, Issue 6, p.646-55, (2006) Abstract
Recurrent duplication-driven transposition of DNA during hominoid evolution., Johnson, Matthew E., Cheng Ze, Morrison Anne V., Scherer Steven, Ventura Mario, Gibbs Richard A., Green Eric D., and Eichler Evan E. , Proceedings of the National Academy of Sciences of the United States of America, 2006 Nov 21, Volume 103, Issue 47, p.17626-31, (2006) Abstract


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