The 2008 update of the Aspergillus nidulans genome annotation: A community effort (2009)
Russo Wortman, Jennifer, Gilsenan, Jane Mabey, Joardar, Vinita, Deegan, Jennifer, Clutterbuck, John, Andersen, Mikael R., ...
The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene...
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...
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...
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...
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...
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis (2007)
Carlton, Jane M., Hirt, Robert P., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, ...
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the ~160-megabase genome,...
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis (2007)
Carlton, Jane M., Hirt, Robert ., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, ...
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase...
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...
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis (2007)
Carlton, Jane M., Hirt, Robert ., Silva, Joana C., Delcher, Arthur L., Schatz, Michael, Zhao, Qi, ...
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase...
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...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan A. Eisen, ...
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., ...
© 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...
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. (2006)
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Jonathan A. Eisen, Robert S. Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R. Wortman, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
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...
Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan Eisen, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
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...
Martin Wu, Qinghu Ren, A. Scott Durkin, Sean C. Daugherty, Lauren M. Brinkac, Robert J. Dodson, ...
We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are...
Martin Wu, Qinghu Ren, Anthony Scott Durkin, Sean C Daugherty, Lauren M Brinkac, Robert J Dodson, ...
We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are...
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...
Naomi Ward, Øivind Larsen, James Sakwa, Live Bruseth, Hoda Khouri, A. Scott Durkin, ...
Methanotrophs are bacteria that use methane as a sole carbon source. The genome sequence of Methylococcus capsulatus deepens our understanding of methanotroph biology and its relationship to global...
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,...
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...
Ren, Qinghu, Gorovsky, Martin A.
Tetrahymena thermophila cells contain three forms of H2A: major H2A.1 and H2A.2, which make up ∼80% of total H2A, and a conserved variant, H2A.Z. We showed previously that acetylation of H2A.Z was...
TransportDB: a relational database of cellular membrane transport systems
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...
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
Seshadri, Rekha, Myers, Garry S. A., Tettelin, Hervé, Eisen, Jonathan A., Heidelberg, John F., Dodson, Robert J., ...
We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors...
Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath)
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,...
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...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Ren, Qinghu, Gorovsky, Martin A.
Tetrahymena thermophila cells contain three forms of H2A: major H2A.1 and H2A.2, which make up ∼80% of total H2A, and a conserved variant, H2A.Z. We showed previously that acetylation of H2A.Z was...
TransportDB: a relational database of cellular membrane transport systems
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...
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
Seshadri, Rekha, Myers, Garry S. A., Tettelin, Hervé, Eisen, Jonathan A., Heidelberg, John F., Dodson, Robert J., ...
We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors...
Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath)
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,...
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...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2
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...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C, Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan A, ...
Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens
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...
Badger, Jonathan H., Hoover, Timothy R., Brun, Yves V., Weiner, Ronald M., Laub, Michael T., Alexandre, Gladys, ...
The dimorphic prosthecate bacteria (DPB) are α-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this...
Ren, Qinghu, Chen, Kaixi, Paulsen, Ian T.
TransportDB () is a comprehensive database resource of information on cytoplasmic membrane transporters and outer membrane channels in organisms whose complete genome sequences are available. The...
Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment
Palenik, Brian, Ren, Qinghu, Dupont, Chris L., Myers, Garry S., Heidelberg, John F., Badger, Jonathan H., ...
Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary...
Genome Sequence of Aeromonas hydrophila ATCC 7966T: Jack of All Trades▿
Seshadri, Rekha, Joseph, Sam W., Chopra, Ashok K., Sha, Jian, Shaw, Jonathan, Graf, Joerg, ...
The complete genome of Aeromonas hydrophila ATCC 7966T was sequenced. Aeromonas, a ubiquitous waterborne bacterium, has been placed by the Environmental Protection Agency on the Contaminant Candidate...
Song, Xiaoyuan, Gjoneska, Elizabeta, Ren, Qinghu, Taverna, Sean D., Allis, C. David, Gorovsky, Martin A.
Phosphorylation of the C terminus SQ motif that defines H2A.X variants is required for efficient DNA double-strand break (DSB) repair in diverse organisms but has not been studied in ciliated...
Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa
Brayton, Kelly A, Lau, Audrey O. T, Herndon, David R, Hannick, Linda, Kappmeyer, Lowell S, Berens, Shawn J, ...
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 tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation
Palenik, Brian, Grimwood, Jane, Aerts, Andrea, Rouzé, Pierre, Salamov, Asaf, Putnam, Nicholas, ...
The smallest known eukaryotes, at ≈1-μm diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with...
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...
Fouts, Derrick E., Tyler, Heather L., DeBoy, Robert T., Daugherty, Sean, Ren, Qinghu, Badger, Jonathan H., ...
We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a...
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...
Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum
Wu, Dongying, Raymond, Jason, Wu, Martin, Chatterji, Sourav, Ren, Qinghu, Graham, Joel E., ...
In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an “Assembling the Tree of Life” project, we determined the genome sequence...
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...
Ward, Naomi L., Challacombe, Jean F., Janssen, Peter H., Henrissat, Bernard, Coutinho, Pedro M., Wu, Martin, ...
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria,...