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Member - J. Craig Venter Institute

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

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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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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

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