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Publications

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Species Specificity
Characterization of cryptic flagellin genes in Shigella boydii and Shigella dysenteriae., Tominaga, A., Mahmoud M. A., Al Mamun A. A., and Mukaihara T. , Genes & genetic systems, 2001 Apr, Volume 76, Issue 2, p.111-20, (2001) Abstract
The genome sequence of taurine cattle: a window to ruminant biology and evolution., Elsik, Christine G., Tellam Ross L., Worley Kim C., Gibbs Richard A., Muzny Donna M., Weinstock George M., Adelson David L., Eichler Evan E., Elnitski Laura, Guigó Roderic, et al. , Science (New York, N.Y.), 2009 Apr 24, Volume 324, Issue 5926, p.522-8, (2009) Abstract
Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa., Doddapaneni, Harshavardhan, Yao Jiqiang, Lin Hong, Walker Andrew M., and Civerolo Edwin L. , BMC genomics, 2006, Volume 7, p.225, (2006) Abstract
Initial sequencing and analysis of the human genome., Lander, E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al. , Nature, 2001 Feb 15, Volume 409, Issue 6822, p.860-921, (2001) Abstract
Spatial Behavior
A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel., Levenson, Jonathan M., Choi Sangdun, Lee Sun-Young, Cao Yun Anna, Ahn Hyung Jin, Worley Kim C., Pizzi Marina, Liou Hsiou-Chi, and Sweatt David J. , The Journal of neuroscience : the official journal of the Society for Neuroscience, 2004 Apr 21, Volume 24, Issue 16, p.3933-43, (2004) Abstract
Genetic disruption of cortical interneuron development causes region- and GABA cell type-specific deficits, epilepsy, and behavioral dysfunction., Powell, Elizabeth M., Campbell Daniel B., Stanwood Gregg D., Davis Caleb F., Noebels Jeffrey L., and Levitt Pat , The Journal of neuroscience : the official journal of the Society for Neuroscience, 2003 Jan 15, Volume 23, Issue 2, p.622-31, (2003) Abstract
Spasm
[Results of treatment of flexion spasms in children]., Popielarska, A., Gregorczuk J., Suffczyńska-Kotowska M., and Mazurowa M. , Neurologia i neurochirurgia polska, 1971, Volume 5, Issue 3, p.387-91, (1971)
Sp1 Transcription Factor
Characterization of the rat GRIK5 kainate receptor subunit gene promoter and its intragenic regions involved in neural cell specificity., Chew, L. J., Yuan X., Scherer S. E., Qie L., Huang F., Hayes W. P., and Gallo V. , The Journal of biological chemistry, 2001 Nov 9, Volume 276, Issue 45, p.42162-71, (2001) Abstract
SOXB1 Transcription Factors
Orphan nuclear receptor GCNF is required for the repression of pluripotency genes during retinoic acid-induced embryonic stem cell differentiation., Gu, Peili, LeMenuet Damien, Chung Arthur C. - K., Mancini Michael, Wheeler David A., and Cooney Austin J. , Molecular and cellular biology, 2005 Oct, Volume 25, Issue 19, p.8507-19, (2005) Abstract
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)
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
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
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
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
European admixture on the Micronesian island of Kosrae: lessons from complete genetic information., Bonnen, Penelope E., Lowe Jennifer K., Altshuler David M., Breslow Jan L., Stoffel Markus, Friedman Jeffrey M., and Pe'er Itsik , European journal of human genetics : EJHG, 2010 Mar, Volume 18, Issue 3, p.309-16, (2010) Abstract
A SNP discovery method to assess variant allele probability from next-generation resequencing data., Shen, Yufeng, Wan Zhengzheng, Coarfa Cristian, Drabek Rafal, Chen Lei, Ostrowski Elizabeth A., Liu Yue, Weinstock George M., Wheeler David A., Gibbs Richard A., et al. , Genome research, 2010 Feb, Volume 20, Issue 2, p.273-80, (2010) Abstract
PBHoney: identifying genomic variants via long-read discordance and interrupted mapping., English, Adam C., Salerno William J., and Reid Jeffrey G. , BMC bioinformatics, 2014, Volume 15, p.180, (2014) Abstract


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