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Publications

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SOS Response (Genetics)
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
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
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
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
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
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
Atlas2 Cloud: a framework for personal genome analysis in the cloud., Evani, Uday S., Challis Danny, Yu Jin, Jackson Andrew R., Paithankar Sameer, Bainbridge Matthew N., Jakkamsetti Adinarayana, Pham Peter, Coarfa Cristian, Milosavljevic Aleksandar, et al. , BMC genomics, 2012, Volume 13 Suppl 6, p.S19, (2012) Abstract
Identification of mutations leading to the Lesch-Nyhan syndrome by automated direct DNA sequencing of in vitro amplified cDNA., Gibbs, R. A., Nguyen P. N., McBride L. J., Koepf S. M., and Caskey C. T. , Proceedings of the National Academy of Sciences of the United States of America, 1989 Mar, Volume 86, Issue 6, p.1919-23, (1989) 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
Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project., Chen, Rui, Sodergren Erica, Weinstock George M., and Gibbs Richard A. , Genome research, 2004 Apr, Volume 14, Issue 4, p.679-84, (2004) Abstract
The MEDLINE Retriever., Fowler, J., Barber S., Gilson H., Long K. B., and Gorry G. A. , Proceedings / the ... Annual Symposium on Computer Application [sic] in Medical Care. Symposium on Computer Applications in Medical Care, 1992, p.473-7, (1992) Abstract
Pash: efficient genome-scale sequence anchoring by Positional Hashing., Kalafus, Ken J., Jackson Andrew R., and Milosavljevic Aleksandar , Genome research, 2004 Apr, Volume 14, Issue 4, p.672-8, (2004) 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
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
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
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
Hares and tortoises in the race to sequence the human genome: expectations and realities., Gibbs, R. A. , Trends in genetics : TIG, 1997 Oct, Volume 13, Issue 10, p.381-3, (1997)
PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features., Hamosh, Ada, Sobreira Nara, Hoover-Fong Julie, Sutton Reid V., Boehm Corinne, Schiettecatte François, and Valle David , Human mutation, 2013 Apr, Volume 34, Issue 4, p.566-71, (2013) 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
Collaborative Social and Medical Service System., Petermann, C. A., Bobroff R. B., Moore D. M., Gilson H. S., Li Y., Dargahi R., Classen D. W., Fowler J., Moreau D. R., and Beck J. R. , Proceedings / the ... Annual Symposium on Computer Application [sic] in Medical Care. Symposium on Computer Applications in Medical Care, 1994, p.614-8, (1994) Abstract
An integrative variant analysis suite for whole exome next-generation sequencing data., Challis, Danny, Yu Jin, Evani Uday S., Jackson Andrew R., Paithankar Sameer, Coarfa Cristian, Milosavljevic Aleksandar, Gibbs Richard A., and Yu Fuli , BMC bioinformatics, 2012, Volume 13, p.8, (2012) Abstract


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