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Publications

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South Africa
Complete Khoisan and Bantu genomes from southern Africa., Schuster, Stephan C., Miller Webb, Ratan Aakrosh, Tomsho Lynn P., Giardine Belinda, Kasson Lindsay R., Harris Robert S., Petersen Desiree C., Zhao Fangqing, Qi Ji, et al. , Nature, 2010 Feb 18, Volume 463, Issue 7283, p.943-7, (2010) Abstract
SOS Response (Genetics)
The mutA mistranslator tRNA-induced mutator phenotype requires recA and recB genes, but not the derepression of lexA-regulated functions., Ren, L., Al Mamun A. A., and Humayun M. Z. , Molecular microbiology, 1999 May, Volume 32, Issue 3, p.607-15, (1999) Abstract
Hypermutagenesis in mutA cells is mediated by mistranslational corruption of polymerase, and is accompanied by replication fork collapse., Al Mamun, Abu Amar M., Gautam Satyendra, and Humayun Zafri M. , Molecular microbiology, 2006 Dec, Volume 62, Issue 6, p.1752-63, (2006) Abstract
Identity and function of a large gene network underlying mutagenic repair of DNA breaks., Al Mamun, Abu Amar M., Lombardo Mary-Jane, Shee Chandan, Lisewski Andreas M., Gonzalez Caleb, Lin Dongxu, Nehring Ralf B., Saint-Ruf Claude, Gibson Janet L., Frisch Ryan L., et al. , Science (New York, N.Y.), 2012 Dec 7, Volume 338, Issue 6112, p.1344-8, (2012) Abstract
The Escherichia coli UVM response is accompanied by an SOS-independent error-prone DNA replication activity demonstrable in vitro., Al Mamun, A. A., Yadava R. S., Ren L., and Humayun M. Z. , Molecular microbiology, 2000 Oct, Volume 38, Issue 2, p.368-80, (2000) Abstract
Somatostatin
Association between somatostatin receptor 5 gene polymorphisms and pancreatic cancer risk and survival., Li, Donghui, Tanaka Motofumi, Brunicardi Charles F., Fisher William E., Gibbs Richard A., and Gingras Marie-Claude , Cancer, 2011 Jul 1, Volume 117, Issue 13, p.2863-72, (2011) Abstract
Solutions
Whole exome capture in solution with 3 Gbp of data., Bainbridge, Matthew N., Wang Min, Burgess Daniel L., Kovar Christie, Rodesch Matthew J., D'Ascenzo Mark, Kitzman Jacob, Wu Yuan-Qing, Newsham Irene, Richmond Todd A., et al. , Genome biology, 2010, Volume 11, Issue 6, p.R62, (2010) Abstract
Solubility
Sequence variation in the soluble epoxide hydrolase gene and subclinical coronary atherosclerosis: interaction with cigarette smoking., Wei, Qi, Doris Peter A., Pollizotto Martin V., Boerwinkle Eric, Jacobs David R., Siscovick David S., and Fornage Myriam , Atherosclerosis, 2007 Jan, Volume 190, Issue 1, p.26-34, (2007) Abstract
Deep sequencing of systematic combinatorial libraries reveals β-lactamase sequence constraints at high resolution., Deng, Zhifeng, Huang Wanzhi, Bakkalbasi Erol, Brown Nicholas G., Adamski Carolyn J., Rice Kacie, Muzny Donna, Gibbs Richard A., and Palzkill Timothy , Journal of molecular biology, 2012 Dec 7, Volume 424, Issue 3-4, p.150-67, (2012) Abstract
Solanum tuberosum
The complete genome sequence of 'Candidatus Liberibacter solanacearum', the bacterium associated with potato zebra chip disease., Lin, Hong, Lou Binghai, Glynn Jonathan M., Doddapaneni Harshavardhan, Civerolo Edwin L., Chen Chuanwu, Duan Yongping, Zhou Lijuan, and Vahling Cheryl M. , PloS one, 2011, Volume 6, Issue 4, p.e19135, (2011) Abstract
Software Design
Large-scale sequencing library production: an adaptor-based strategy., Povinelli, C. M., and Gibbs R. A. , Analytical biochemistry, 1993 Apr, Volume 210, Issue 1, p.16-26, (1993) Abstract
Software
PipMaker--a web server for aligning two genomic DNA sequences., Schwartz, S., Zhang Z., Frazer K. A., Smit A., Riemer C., Bouck J., Gibbs R., Hardison R., and Miller W. , Genome research, 2000 Apr, Volume 10, Issue 4, p.577-86, (2000) Abstract
BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results., Worley, K. C., Wiese B. A., and Smith R. F. , Genome research, 1995 Sep, Volume 5, Issue 2, p.173-84, (1995) Abstract
Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing., Wu, Jiaqian, Shteynberg David, Arumugam Manimozhiyan, Gibbs Richard A., and Brent Michael R. , Genome research, 2004 Apr, Volume 14, Issue 4, p.665-71, (2004) Abstract
PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences., Yao, Jiqiang, Lin Hong, Van Deynze Allen, Doddapaneni Harshavardhan, Francis Martha, Lemos Eliana Gertrudes Macedo, and Civerolo Edwin L. , BMC microbiology, 2008, Volume 8, p.185, (2008) Abstract
The Atlas genome assembly system., Havlak, Paul, Chen Rui, Durbin James K., Egan Amy, Ren Yanru, Song Xing-Zhi, Weinstock George M., and Gibbs Richard A. , Genome research, 2004 Apr, Volume 14, Issue 4, p.721-32, (2004) Abstract
Software for automated analysis of DNA fingerprinting gels., Fuhrmann, Daniel R., Krzywinski Martin I., Chiu Readman, Saeedi Parvaneh, Schein Jacqueline E., Bosdet Ian E., Chinwalla Asif, Hillier Ladeana W., Waterston Robert H., McPherson John D., et al. , Genome research, 2003 May, Volume 13, Issue 5, p.940-53, (2003) Abstract
Fine mapping and identification of candidate pulmonary adenoma susceptibility 1 genes using advanced intercross lines., Wang, Min, Lemon William J., Liu Gongjie, Wang Yian, Iraqi Fuad A., Malkinson Alvin M., and You Ming , Cancer research, 2003 Jun 15, Volume 63, Issue 12, p.3317-24, (2003) Abstract
Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies., Coarfa, Cristian, and Milosavljevic Aleksandar , Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2008, p.102-13, (2008) Abstract
Analysis of rare, exonic variation amongst subjects with autism spectrum disorders and population controls., Liu, Li, Sabo Aniko, Neale Benjamin M., Nagaswamy Uma, Stevens Christine, Lim Elaine, Bodea Corneliu A., Muzny Donna, Reid Jeffrey G., Banks Eric, et al. , PLoS genetics, 2013 Apr, Volume 9, Issue 4, p.e1003443, (2013) Abstract
BEAUTY-X: enhanced BLAST searches for DNA queries., Worley, K. C., Culpepper P., Wiese B. A., and Smith R. F. , Bioinformatics (Oxford, England), 1998, Volume 14, Issue 10, p.890-1, (1998) Abstract
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads., Miller, Christopher A., Hampton Oliver, Coarfa Cristian, and Milosavljevic Aleksandar , PloS one, 2011, Volume 6, Issue 1, p.e16327, (2011) Abstract
Large-scale concatenation cDNA sequencing., Yu, W., Andersson B., Worley K. C., Muzny D. M., Ding Y., Liu W., Ricafrente J. Y., Wentland M. A., Lennon G., and Gibbs R. A. , Genome research, 1997 Apr, Volume 7, Issue 4, p.353-8, (1997) Abstract
SNPdetector: a software tool for sensitive and accurate SNP detection., Zhang, Jinghui, Wheeler David A., Yakub Imtiaz, Wei Sharon, Sood Raman, Rowe William, Liu Paul P., Gibbs Richard A., and Buetow Kenneth H. , PLoS computational biology, 2005 Oct, Volume 1, Issue 5, p.e53, (2005) Abstract
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications., Yilmaz, Pelin, Kottmann Renzo, Field Dawn, Knight Rob, Cole James R., Amaral-Zettler Linda, Gilbert Jack A., Karsch-Mizrachi Ilene, Johnston Anjanette, Cochrane Guy, et al. , Nature biotechnology, 2011 May, Volume 29, Issue 5, p.415-20, (2011) Abstract


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