The Genome of the Natural Genetic Engineer Agrobacterium (2009)
Tumefaciens C, Derek W. Wood, Joao C. Setubal, Rajinder Kaul, Dave E. Monks, Joao P. Kitajima, ...
The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity...
Mavrodi, Dmitri V, Loper, Joyce E, Paulsen, Ian T, Thomashow, Linda S
Abstract Background Pseudomonas fluorescens Pf-5 is a plant-associated bacterium that inhabits the rhizosphere of a wide variety of plant species and and produces secondary metabolites suppressive of...
EcoCyc: A comprehensive view of Escherichia coli biology (2009)
Keseler, Ingrid M., Bonavides-Martínez, César, Collado-Vides, Julio, Gama-Castro, Socorro, Gunsalus, Robert P., Johnson, D. Aaron, ...
EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the...
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria (2008)
Dufresne, Alexis, Ostrowski, Martin, Scanlan, David J, Garczarek, Laurence, Mazard, Sophie, Palenik, Brian P, ...
Abstract Background The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the...
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria (2008)
Dufresne, Alexis, Ostrowski, Martin, Scanlan, David J., Garczarek, Laurence, Mazard, Sophie, Palenik, Brian P., ...
Background: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different...
Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans (2007)
Sievert, Stefan M., Scott, Kathleen M., Klotz, Martin G., Chain, Patrick S. G., Hauser, Loren J., Hemp, James, ...
Author Posting. © American Society for Microbiology, 2008. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive...
Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa (2007)
Kelly A. Brayton, David R. Herndon, Linda Hannick, Lowell S. Kappmeyer, Shawn J. Berens, ...
Babesia bovis is an apicomplexan tick-transmitted pathogen of cattle imposing a global risk and severe constraints to livestock health and economic development. The complete genome sequence was...
The Chlamydomonas genome reveals the evolution of key animal and plant functions. (2007)
Merchant, Sabeeha S., Prochnik, Simon E., Vallon, Olivier, Harris, Elizabeth H., Karpowicz, Steven J., Witman, George B., ...
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as...
Ren, Qinghu, Chen, Kaixi, Paulsen, Ian T.
TransportDB (http://www.membranetransport.org/) is a comprehensive database resource of information on cytoplasmic membrane transporters and outer membrane channels in organisms whose complete genome...
The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2 (2006)
Kathleen M. Scott, Stefan M. Sievert, Fereniki N. Abril, Lois A. Ball, Chantell J. Barrett, Rodrigo A. Blake, ...
Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal...
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2 (2006)
Scott, Kathleen M., Sievert, Stefan M., Abril, Fereniki N., Ball, Lois A., Barrett, Chantell J., Blake, Rodrigo A., ...
© 2006 Scott et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any...
The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2 (2006)
Scott, Kathleen M., Sievert, Stefan M., Abril, Fereniki N., Ball, Lois A., Barrett, Chantell J., Blake, Rodrigo A., ...
Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal...
falciparum antigens by antigenic analysis of genomic and proteomic (2006)
Z. Bozdech, M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu, Z. Bozdech, ...
plasmodium
Daniel H Haft, Ian T Paulsen, Naomi Ward, Jeremy D Selengut
Research article Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic
Su, Zhengchang, Mao, Fenglou, Dam, Phuongan, Wu, Hongwei, Olman, Victor, Paulsen, Ian T., ...
Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem,...
Myers, Garry S.A., Rasko, David A., Cheung, Jackie K., Ravel, Jacques, Seshadri, Rekha, DeBoy, Robert T., ...
Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide...
Myers, Garry S.A., Rasko, David A., Cheung, Jackie K., Ravel, Jacques, Seshadri, Rekha, DeBoy, Robert T., ...
Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide...
Whole-genome transporter analyses have been conducted on 141 organisms whose complete genome sequences are available. For each organism, the complete set of membrane transport systems was identified...
Computational inference and experimental validation (2005)
Zhengchang Su, Fenglou Mao, Phuongan Dam, Hongwei Wu, Victor Olman, Ian T. Paulsen, ...
of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
EcoCyc: a comprehensive database resource for Escherichia coli (2005)
Keseler, Ingrid M., Collado-Vides, Julio, Gama-Castro, Socorro, Ingraham, John, Paley, Suzanne, Paulsen, Ian T., ...
The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both...
Khan, Asis, Taylor, Sonya, Su, Chunlei, Mackey, Aaron J., Boyle, Jon, Cole, Robert, ...
Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and...
Naomi Ward, Øivind Larsen, James Sakwa, Live Bruseth, Hoda Khouri, A. Scott Durkin, ...
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular,...
Ward, Naomi, Larsen, Øivind, Sakwa, James, Bruseth, Live, Khouri, Hoda, Durkin, A. Scott, ...
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular,...
Ward, Naomi, Larsen, Øivind, Sakwa, James, Bruseth, Live, Khouri, Hoda, Durkin, A. Scott, ...
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular,...
Wu, Martin, Sun, Ling V., Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C., ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Wu, Martin, Sun, Ling V., Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C., ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Wu, Martin, Sun, Ling V., Vamathevan, Jessica, Riegler, Markus, Deboy, Robert, Brownlie, Jeremy C., ...
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a...
Nelson, Karen E., Fouts, Derrick E., Mongodin, Emmanuel F., Ravel, Jacques, DeBoy, Robert T., Kolonay, James F., ...
The genomes of three strains of Listeria monocytogenes that have been associated with food‐borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69...
TransportDB: a relational database of cellular membrane transport systems (2004)
Ren, Qinghu, Kang, Katherine H., Paulsen, Ian T.
TransportDB (http://www.membranetransport.org) is a relational database designed for describing the predicted cellular membrane transport proteins in organisms whose complete genome sequences are...
ToxoDB: accessing the Toxoplasma gondii genome (2003)
Jessica C. Kissinger, Bindu Gajria, Li Li, Ian T. Paulsen, David S. Roos
ToxoDB
ToxoDB: accessing the Toxoplasma gondii genome (2003)
Kissinger, Jessica C., Gajria, Bindu, Li, Li, Paulsen, Ian T., Roos, David S.
ToxoDB (http://ToxoDB.org) provides a genome resource for the protozoan parasite Toxoplasma gondii. Several sequencing projects devoted to T. gondii have been completed or are in progress: an EST...
Peter D. Karp, Monica Riley, Milton Saier, Ian T. Paulsen, Suzanne M. Paley, Alida Pellegrini-toole
EcoCyc is an organism-speci c Pathway/Genome Database that describes the metabolic and signal-transduction pathways of E. coli, its enzymes, and | a new addition | its transport proteins. MetaCyc is...
Karp, Peter D., Riley, Monica, Saier, Milton, Paulsen, Ian T., Collado-Vides, Julio, Paley, Suzanne M., ...
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of...
The EcoCyc and MetaCyc databases (2000)
Karp, Peter D., Riley, Monica, Saier, Milton, Paulsen, Ian T., Paley, Suzanne M., Pellegrini-Toole, Alida
EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and—a new addition—its transport...
Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas denitrificans▿ †
Sievert, Stefan M., Scott, Kathleen M., Klotz, Martin G., Chain, Patrick S. G., Hauser, Loren J., Hemp, James, ...
Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to...
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria
Dufresne, Alexis, Ostrowski, Martin, Scanlan, David J, Garczarek, Laurence, Mazard, Sophie, Palenik, Brian P, ...
Local niche occupancy of marine Synechococcus lineages is facilitated by lateral gene transfers. Genomic islands act as repositories for these transferred genes.
High-Throughput Phenotypic Characterization of Pseudomonas aeruginosa Membrane Transport Genes
Johnson, Daniel A., Tetu, Sasha G., Phillippy, Katherine, Chen, Joan, Ren, Qinghu, Paulsen, Ian T.
The deluge of data generated by genome sequencing has led to an increasing reliance on bioinformatic predictions, since the traditional experimental approach of characterizing gene function one at a...
Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5
Mavrodi, Dmitri V, Loper, Joyce E, Paulsen, Ian T, Thomashow, Linda S
Bailey, Andrew M., Paulsen, Ian T., Piddock, Laura J. V.
Salmonella enterica serovar Typhimurium SL1344, in which efflux pump genes (acrB, acrD, acrF, tolC) or regulatory genes thereof (marA, soxS, ramA) were inactivated, was grown in the presence of 240...
Genome Degradation in Brucella ovis Corresponds with Narrowing of Its Host Range and Tissue Tropism
Tsolis, Renee M., Seshadri, Rekha, Santos, Renato L., Sangari, Felix J., Lobo, Juan M. García, De Jong, Maarten F., ...
Brucella ovis is a veterinary pathogen associated with epididymitis in sheep. Despite its genetic similarity to the zoonotic pathogens B. abortus, B. melitensis and B. suis, B. ovis does not cause...
EcoCyc: A comprehensive view of Escherichia coli biology
Keseler, Ingrid M., Bonavides-Martínez, César, Collado-Vides, Julio, Gama-Castro, Socorro, Gunsalus, Robert P., Johnson, D. Aaron, ...
EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the...