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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/

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

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	26.	Research Digital expression profiling of novel diatom transcripts provides insight into their biological functions Uma Maheswari, Kamel Jabbari, Jean-Louis Petit, Betina M Porcel, Andrew E Allen, Jean-Paul Cadoret, Alessandra De Martino, Marc Heijde, Raymond Kaas, Julie La Roche, Pascal J Lopez, Véronique Martin-Jézéquel, Agnès Meichenin, Thomas Mock, Micaela Schnitzler Parker, Assaf Vardi, E Virginia Armbrust, Jean Weissenbach, Michaël Katinka, Chris Bowler Genome Biology 2010, 11:R85 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Digital expression profiling of the diatom transcriptome under varying environmental conditions provides insights into the roles of novel diatom genes.
	27.	Research Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing Qi Zhao, Ewen F Kirkness, Otavia L Caballero, Pedro A Galante, Raphael B Parmigiani, Lee Edsall, Samantha Kuan, Zhen Ye, Samuel Levy, Ana Tereza R Vasconcelos, Bing Ren, Sandro J de Souza, Anamaria A Camargo, Andrew JG Simpson, Robert L Strausberg Genome Biology 2010, 11:R114 (25 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Sequencing of the exome and transcriptome of a breast cancer cell line allows discovery of potentially tumorigenic loss of heterozygosity events.
	28.	Research Mimivirus relatives in the Sargasso sea Elodie Ghedin, Jean-Michel Claverie Virology Journal 2005, 2:62 (16 August 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	29.	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
	30.	Methodology A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula Klementina Kakar, Maren Wandrey, Tomasz Czechowski, Tanja Gaertner, Wolf-Rüdiger Scheible, Mark Stitt, Ivone Torres-Jerez, Yongli Xiao, Julia C Redman, Hank C Wu, Foo Cheung, Christopher D Town, Michael K Udvardi Plant Methods 2008, 4:18 (8 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	31.	Research Using comparative genomics to reorder the human genome sequence into a virtual sheep genome Brian P Dalrymple, Ewen F Kirkness, Mikhail Nefedov, Sean McWilliam, Abhirami Ratnakumar, Wes Barris, Shaying Zhao, Jyoti Shetty, Jillian F Maddox, Margaret O'Grady, Frank Nicholas, Allan M Crawford, Tim Smith, Pieter J de Jong, John McEwan, V Hutton Oddy, Noelle E Cockett, Genome Biology 2007, 8:R152 (30 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using BAC-end sequences, a sparse marker map and the sequences of the human, dog and cow genomes, an accurate and detailed sub-gene level map of the sheep genome has been constructed.
	32.	Research article *The Escherichia coli* K-12 ORFeome: a resource for comparative molecular microbiology** Seesandra V Rajagopala, Natsuko Yamamoto, Adrienne E Zweifel, Tomoko Nakamichi, Hsi-Kuang Huang, Jorge Mendez-Rios, Jonathan Franca-Koh, Meher Boorgula, Kazutoshi Fujita, Ken-ichirou Suzuki, James C Hu, Barry L Wanner, Hirotada Mori, Peter Uetz BMC Genomics 2010, 11:470 (11 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	33.	Software SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services Damian DG Gessler, Gary S Schiltz, Greg D May, Shulamit Avraham, Christopher D Town, David Grant, Rex T Nelson BMC Bioinformatics 2009, 10:309 (23 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	34.	Research article Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes Valerie W Hu, Bryan C Frank, Shannon Heine, Norman H Lee, John Quackenbush BMC Genomics 2006, 7:118 (18 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	35.	Research article *Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus* spp.)** Abhishek Bohra, Anuja Dubey, Rachit K Saxena, R Varma Penmetsa, KN Poornima, Naresh Kumar, Andrew D Farmer, Gudipati Srivani, Hari D Upadhyaya, Ragini Gothalwal, S Ramesh, Dhiraj Singh, Kulbhushan Saxena, PB Kavi Kishor, Nagendra K Singh, Christopher D Town, Gregory D May, Douglas R Cook, Rajeev K Varshney BMC Plant Biology 2011, 11:56 (29 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	36.	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
	37.	Research article *The Alveolate Perkinsus marinus: Biological Insights from EST Gene Discovery* Sandeep J Joseph, José A Fernández-Robledo, Malcolm J Gardner, Najib M El-Sayed, Chih-Horng Kuo, Eric J Schott, Haiming Wang, Jessica C Kissinger, Gerardo R Vasta BMC Genomics 2010, 11:228 (7 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	38.	Research article Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens Carla Risso, Jun Sun, Kai Zhuang, Radhakrishnan Mahadevan, Robert DeBoy, Wael Ismail, Susmita Shrivastava, Heather Huot, Sagar Kothari, Sean Daugherty, Olivia Bui, Christophe H Schilling, Derek R Lovley, Barbara A Methé BMC Genomics 2009, 10:447 (22 September 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome-scale metabolic modeling of Rhodoferax ferrireducens reveals that while key enzymes for growth via photosynthesis or sugar fermentation are missing, growth of this Fe(III)-reducing bacterium on many different substrates in nutrient-depleted environments is possible.
	39.	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
	40.	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
	41.	Research Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura Benjamin P Berman, Barret D Pfeiffer, Todd R Laverty, Steven L Salzberg, Gerald M Rubin, Michael B Eisen, Susan E Celniker Genome Biology 2004, 5:R61 (20 August 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 27 predicted gene-regulatory regions in the Drosophila melanogaster genome were analyzed in vivo, confirming 15 active enhancer regions. A comparison with Drosophila pseudoobscura sequences revealed that conservation of binding-site clusters accurately discriminates functional regions from non-functional ones.
	42.	Software The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results John C Braisted, Srilatha Kuntumalla, Christine Vogel, Edward M Marcotte, Alan R Rodrigues, Rong Wang, Shih-Ting Huang, Erik S Ferlanti, Alexander I Saeed, Robert D Fleischmann, Scott N Peterson, Rembert Pieper BMC Bioinformatics 2008, 9:529 (9 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	43.	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
	44.	Research A novel strategy for the identification of antigens that are recognised by bovine MHC class I restricted cytotoxic T cells in a protozoan infection using reverse vaccinology Simon P Graham, Yoshikazu Honda, Roger Pellé, Duncan M Mwangi, E Jane Glew, Etienne P de Villiers, Trushar Shah, Richard Bishop, Pierre van der Bruggen, Vishvanath Nene, Evans LN Taracha Immunome Research 2007, 3:2 (9 February 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	45.	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
	46.	Research Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites Tobias J Sargeant, Matthias Marti, Elisabet Caler, Jane M Carlton, Ken Simpson, Terence P Speed, Alan F Cowman Genome Biology 2006, 7:R12 (20 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A new software was used to predict exported proteins that are conserved between malaria parasites infecting rodents and those infecting humans, revealing a lineage-specific expansion of exported proteins.
	47.	Research *Integral and peripheral association of proteins and protein complexes with Yersinia pestis* inner and outer membranes** Rembert Pieper, Shih-Ting Huang, David J Clark, Jeffrey M Robinson, Hamid Alami, Prashanth P Parmar, Moo-Jin Suh, Srilatha Kuntumalla, Christine L Bunai, Robert D Perry, Robert D Fleischmann, Scott N Peterson Proteome Science 2009, 7:5 (19 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	48.	Method A vertebrate case study of the quality of assemblies derived from next-generation sequences Liang Ye, LaDeana W Hillier, Patrick Minx, Nay Thane, Devin P Locke, John C Martin, Lei Chen, Makedonka Mitreva, Jason R Miller, Kevin V Haub, David J Dooling, Elaine R Mardis, Richard K Wilson, George M Weinstock, Wesley C Warren Genome Biology 2011, 12:R31 (31 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In a comparative analysis, the chicken genome is assembled using Sanger, Illumina or 454 reads from the same biological sample
	49.	Research article Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data Anita Grigoriadis, Alan Mackay, Jorge S Reis-Filho, Dawn Steele, Christian Iseli, Brian J Stevenson, C Victor Jongeneel, Haukur Valgeirsson, Kerry Fenwick, Marjan Iravani, Maria Leao, Andrew JG Simpson, Robert L Strausberg, Parmjit S Jat, Alan Ashworth, A Munro Neville, Michael J O'Hare Breast Cancer Research 2006, 8:R56 (2 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	50.	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