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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 *The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation* Gretchen M Ehrenkaufer, Gareth D Weedall, Daryl Williams, Hernan A Lorenzi, Elisabet Caler, Neil Hall, Upinder Singh Genome Biology 2013, 14:R77 (26 July 2013) Abstract \| Full text \| PDF \| PubMed \| f1000 \| Editor’s summary Genome and transcriptome analyses of Entamoeba invadens reveal insights into the process of encystation and its role in pathogenicity
	2.	Methodology GenePattern flow cytometry suite Josef Spidlen, Aaron Barsky, Karin Breuer, Peter Carr, Marc-Danie Nazaire, Barbara Hill, Yu Qian, Ted Liefeld, Michael Reich, Jill P Mesirov, Peter Wilkinson, Richard H Scheuermann, Rafick-Pierre Sekaly, Ryan R Brinkman Source Code for Biology and Medicine 2013, 8:14 (3 July 2013) Abstract \| Full text \| PDF \| PubMed
	3.	Research Dual organism design cycle reveals small subunit substitutions that improve [NiFe] hydrogenase hydrogen evolution Isaac T Yonemoto, Christopher W Matteri, Thao Amy Nguyen, Hamilton O Smith, Philip D Weyman Journal of Biological Engineering 2013, 7:17 (2 July 2013) Abstract \| Full text \| PDF \| PubMed
	4.	Research article Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates Zongxin Ling, Xia Liu, Yueqiu Luo, Li Yuan, Karen E Nelson, Yuezhu Wang, Charlie Xiang, Lanjuan Li BMC Genomics 2013, 14:390 (10 June 2013) Abstract \| Full text \| PDF \| PubMed
	5.	Methodology Sequencing viral genomes from a single isolated plaque Jessica DePew, Bin Zhou, Jamison M McCorrison, David E Wentworth, Janaki Purushe, Galina Koroleva, Derrick E Fouts Virology Journal 2013, 10:181 (6 June 2013) Abstract \| Full text \| PDF \| PubMed
	6.	Research Evolution of a reassortant North American gull influenza virus lineage: drift, shift and stability Jeffrey S Hall, Joshua L TeSlaa, Sean W Nashold, Rebecca A Halpin, Timothy Stockwell, David E Wentworth, Vivien Dugan, Hon S Ip Virology Journal 2013, 10:179 (6 June 2013) Abstract \| Full text \| PDF \| PubMed
	7.	Research *Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae* O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity** Derrick E Fouts, Jochen Klumpp, Kimberly A Bishop-Lilly, Mathumathi Rajavel, Kristin M Willner, Amy Butani, Matthew Henry, Biswajit Biswas, Manrong Li, M Albert, Martin J Loessner, Richard Calendar, Shanmuga Sozhamannan Virology Journal 2013, 10:165 (28 May 2013) Abstract \| Full text \| PDF \| PubMed
	8.	Research *Genome of the long-living sacred lotus (Nelumbo nucifera* Gaertn.)** Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
	9.	Short Report Rapid research response to the 2009 A(H1N1)pdm09 influenza pandemic (Revised) Wendy A Keitel, Pedro A Piedra, Robert L Atmar, Gail Demmler, Hana M El Sahly, Jill Barrett, Rebecca A Halpin, Rosanna Lagos, Susan Fisher-Hoch, Flor Munoz BMC Research Notes 2013, 6:177 (3 May 2013) Abstract \| Full text \| PDF \| PubMed
	10.	Research *Genome of Acanthamoeba castellanii* highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling** Michael Clarke, Amanda J Lohan, Bernard Liu, Ilias Lagkouvardos, Scott Roy, Nikhat Zafar, Claire Bertelli, Christina Schilde, Arash Kianianmomeni, Thomas R Bürglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Heng Tan, Andrew P Hutchins, Thomas Weinmeier, Thomas Rattei, Jeffery SC Chu, Gregory Gimenez, Manuel Irimia, Daniel J Rigden, David A Fitzpatrick, Jacob Lorenzo-Morales, Alex Bateman, Cheng-Hsun Chiu, Petrus Tang et al. Genome Biology 2013, 14:R11 (1 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
	11.	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
	12.	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
	13.	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
	14.	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
	15.	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 \| Cited on BioMed Central
	16.	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
	17.	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
	18.	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 \| Cited on BioMed Central \| 1 comment \| 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.
	19.	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 \| Cited on BioMed Central \| f1000
	20.	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
	21.	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
	22.	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
	23.	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
	24.	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.
	25.	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