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Member - J. Craig Venter Institute

Founded in 1992,J. Craig Venter Institute is a not-for-profit research institute whose primary research interests are in structural, functional and comparative analysis of genomes and gene products from a wide variety of organisms

http://www.tigr.org/

Research staff and students at J. Craig Venter Institute:

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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at J. Craig Venter Institute

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	1.	Research Analysis of whole genome sequences of 16 strains of rubella virus from the United States, 1961–2009 Emily Abernathy, Min-hsin Chen, Jayati Bera, Susmita Shrivastava, Ewen Kirkness, Qi Zheng, William Bellini, Joseph Icenogle Virology Journal 2013, 10:32 (25 January 2013) Abstract \| Full text \| PDF \| PubMed
	2.	Research article *Sequencing of mitochondrial genomes of nine Aspergillus* and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability** Vinita Joardar, Natalie F Abrams, Jessica Hostetler, Paul J Paukstelis, Suchitra Pakala, Suman B Pakala, Nikhat Zafar, Olukemi O Abolude, Gary Payne, Alex Andrianopoulos, David W Denning, William C Nierman BMC Genomics 2012, 13:698 (12 December 2012) Abstract \| Full text \| PDF \| PubMed
	3.	Research article Comparative genomic analysis and phylogenetic position of Theileria equi Lowell S Kappmeyer, Mathangi Thiagarajan, David R Herndon, Joshua D Ramsay, Elisabet Caler, Appolinaire Djikeng, Joseph J Gillespie, Audrey OT Lau, Eric H Roalson, Joana C Silva, Marta G Silva, Carlos E Suarez, Massaro W Ueti, Vishvanath M Nene, Robert H Mealey, Donald P Knowles, Kelly A Brayton BMC Genomics 2012, 13:603 (9 November 2012) Abstract \| Full text \| PDF \| PubMed
	4.	Methodology Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing Kelvin Li, Susmita Shrivastava, Anushka Brownley, Dan Katzel, Jayati Bera, Anh Thu Nguyen, Vishal Thovarai, Rebecca Halpin, Timothy B Stockwell Virology Journal 2012, 9:261 (6 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	5.	Research article Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana Roshan Shrestha, Benoit Tesson, Trina Norden-Krichmar, Stephen Federowicz, Mark Hildebrand, Andrew E Allen BMC Genomics 2012, 13:499 (20 September 2012) Abstract \| Full text \| PDF \| PubMed
	6.	Research Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury Derrick E Fouts, Rembert Pieper, Sebastian Szpakowski, Hans Pohl, Susan Knoblach, Moo-Jin Suh, Shih-Ting Huang, Inger Ljungberg, Bruce M Sprague, Sarah K Lucas, Manolito Torralba, Karen E Nelson, Suzanne L Groah Journal of Translational Medicine 2012, 10:174 (28 August 2012) Abstract \| Full text \| PDF \| PubMed
	7.	Research article *A Multilocus Sequence Typing System (MLST) reveals a high level of diversity and a genetic component to Entamoeba histolytica* virulence** Carol A Gilchrist, Ibne Karim M Ali, Mamun Kabir, Faisal Alam, Sana Scherbakova, Eric Ferlanti, Gareth D Weedall, Neil Hall, Rashidul Haque, William A Petri, Elisabet Caler BMC Microbiology 2012, 12:151 (27 July 2012) Abstract \| Full text \| PDF \| PubMed
	8.	Research How do alignment programs perform on sequencing data with varying qualities and from repetitive regions? Xiaoqing Yu, Kishore Guda, Joseph Willis, Martina Veigl, Zhenghe Wang, Sanford Markowitz, Mark D Adams, Shuying Sun BioData Mining 2012, 5:6 (18 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Study of popular genetic alignment tools including Novoalign finds programmes perform similarly when analyzing high quality sequence data, and recommends trimming low quality base reads to improve alignment.
	9.	Research article Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications Jianguo Lu, Eric Peatman, Haibao Tang, Joshua Lewis, Zhanjiang Liu BMC Genomics 2012, 13:246 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology
	10.	Research article *Comparative genome analysis of 19 Ureaplasma urealyticum* and Ureaplasma parvum strains** Vanya Paralanov, Jin Lu, Lynn B Duffy, Donna M Crabb, Susmita Shrivastava, Barbara A Methé, Jason Inman, Shibu Yooseph, Li Xiao, Gail H Cassell, Ken B Waites, John I Glass BMC Microbiology 2012, 12:88 (30 May 2012) Abstract \| Full text \| PDF \| PubMed
	11.	Research article Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat Sunish K Sehgal, Wanlong Li, Pablo D Rabinowicz, Agnes Chan, Hana Šimková, Jaroslav Doležel, Bikram S Gill BMC Plant Biology 2012, 12:64 (4 May 2012) Abstract \| Full text \| PDF \| PubMed
	12.	Research *Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus* conidial proteome** Moo-Jin Suh, Natalie D Fedorova, Steven E Cagas, Susan Hastings, Robert D Fleischmann, Scott N Peterson, David S Perlin, William C Nierman, Rembert Pieper, Michelle Momany Proteome Science 2012, 10:30 (30 April 2012) Abstract \| Full text \| PDF \| PubMed
	13.	Proceedings A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters Youngik Yang, Kenneth Nephew, Sun Kim BMC Bioinformatics 2012, 13(Suppl 3):S15 (21 March 2012) Abstract \| Full text \| PDF \| PubMed
	14.	Software Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community Konstantinos Krampis, Tim Booth, Brad Chapman, Bela Tiwari, Mesude Bicak, Dawn Field, Karen E Nelson BMC Bioinformatics 2012, 13:42 (19 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cloud BioLinux includes over 135 pre-configured bioinformatics tools for sequence alignment, clustering, assembly, display and phylogeny, aimed at reducing costs to researchers of maintaining and configuring hardware, and encouraging sharing of codebase.
	15.	Original Differential Gene Expression to Investigate the Effects of Low-level Electrochemical Currents on Bacillus subtilis Robert Szkotak, Tagbo H R Niepa, Nikhil Jawrani, Jeremy L Gilbert, Marcus B Jones, Dacheng Ren AMB Express 2011, 1:39 (11 November 2011) Abstract \| Full text \| PDF \| PubMed
	16.	Software ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process Malay K Basu, Jeremy D Selengut, Daniel H Haft BMC Bioinformatics 2011, 12:434 (9 November 2011) Abstract \| Full text \| PDF \| PubMed
	17.	Research Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented
	18.	Research article The protein interaction map of bacteriophage lambda Seesandra V Rajagopala, Sherwood Casjens, Peter Uetz BMC Microbiology 2011, 11:213 (26 September 2011) Abstract \| Full text \| PDF \| PubMed
	19.	Invited speaker presentation Comparative analysis of the vaginal microbiome in health and disease Bryan A White, Andres M Gomez, Mengfei Ho, Margret Berg Miller, Susan M Thomas, Carl J Yeoman, Suleyman Yildirim, Douglas J Creedon, Tony L Goldberg, Steven R Leigh, Karen E Nelson, Rebecca M Stumpf, Brenda A Wilson Genome Biology 2011, 12(Suppl 1):I17 (19 September 2011) Full text \| PDF
	20.	Research article *Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella* Typhimurium** Charles Ansong, Nikola Tolić, Samuel O Purvine, Steffen Porwollik, Marcus Jones, Hyunjin Yoon, Samuel H Payne, Jessica L Martin, Meagan C Burnet, Matthew E Monroe, Pratap Venepally, Richard D Smith, Scott N Peterson, Fred Heffron, Michael McClelland, Joshua N Adkins BMC Genomics 2011, 12:433 (25 August 2011) Abstract \| Full text \| PDF \| PubMed
	21.	Research article Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis Yuanhong Han, Yun Kang, Ivone Torres-Jerez, Foo Cheung, Christopher D Town, Patrick X Zhao, Michael K Udvardi, Maria J Monteros BMC Genomics 2011, 12:350 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	22.	Research article In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism Srilatha Kuntumalla, Quanshun Zhang, John C Braisted, Robert D Fleischmann, Scott N Peterson, Arthur Donohue-Rolfe, Saul Tzipori, Rembert Pieper BMC Microbiology 2011, 11:147 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
	23.	Research article *Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence* Yuansha Chen, O Colin Stine, Jonathan H Badger, Ana I Gil, G Balakrish Nair, Mitsuaki Nishibuchi, Derrick E Fouts BMC Genomics 2011, 12:294 (6 June 2011) Abstract \| Full text \| PDF \| PubMed
	24.	Research article Recombinant expression and functional analysis of proteases from Streptococcus pneumoniae, Bacillus anthracis, and Yersinia pestis Keehwan Kwon, Jeremy Hasseman, Saeeda Latham, Carissa Grose, Yu Do, Robert D Fleischmann, Rembert Pieper, Scott N Peterson BMC Biochemistry 2011, 12:17 (5 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A modified pipeline for the high-throughput production of bacterial proteases is able to express and purify correctly 86.1% of protease genes identified through a bioinformatics screen, in a combination of five different expression vectors.
	25.	Research article Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems S Samuel Yang, Zheng Tu, Foo Cheung, Wayne Xu, JoAnn FS Lamb, Hans-Joachim G Jung, Carroll P Vance, John W Gronwald BMC Genomics 2011, 12:199 (19 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central