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...
Worden, Alexandra Z., Lee, Jea-Hyeok, Mock, Thomas, Rouzé, Pierre, Simmons, Melinda P., Aerts, Andrea L., ...
Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from...
González, José M., Fernández-Gómez, Beatriz, Fernàndez-Guerra, Antoni, Gómez-Consarnau, Laura, Sánchez, Olga, Coll-Lladó, Montserrat, ...
6 pages, 4 figures, 1 table.-- PMID: 18552178 [PubMed].-- Printed version published Jun 24, 2008.-- Supporting information available at: http://www.pnas.org/content/105/25/8724/suppl/DCSupplemental
Environmental Genome Shotgun Sequencing of the Sargasso Sea (2008)
Sargasso Sea, J. Craig Venter, Et Al, J. Craig Venter, Karin Remington, John F. Heidelberg, ...
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Annotation-based inference of transporter function (2008)
Lee, Thomas J., Paulsen, Ian, Karp, Peter
Motivation: We present a method for inferring and constructing transport reactions for transporter proteins based primarily on the analysis of the names of individual proteins in the genome...
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...
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...
Multidimensional annotation of the Escherichia coli K-12 genome (2007)
Karp, Peter D., Keseler, Ingrid M., Shearer, Alexander, Latendresse, Mario, Krummenacker, Markus, Paley, Suzanne M., ...
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns...
Multidimensional annotation of the Escherichia coli K-12 genome (2007)
Karp, Peter D, Keseler, Ingrid M, Santos-Zavaleta, Alberto, Peñaloza-Spínola, Mónica I, Bonavides-Martinez, Cesar, Ingraham, John, ...
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns...
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii (2006)
Khan, Asis, Böhme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, ...
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has...
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii (2006)
Khan, Asis, Böhme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, ...
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Borkovich, Katherine A., Alex, Lisa A., Yarden, Oded, Freitag, Michael, Turner, Gloria E., Read, Nick D., ...
We present an analysis of over 1,100 of the ∼10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and...
Brodhagen, Marion, Paulsen, Ian, Loper, Joyce E.
Pyoluteorin is a chlorinated polyketide antibiotic secreted by the rhizosphere bacterium Pseudomonas fluorescens Pf-5. Genes encoding enzymes and transcriptional regulators involved in pyoluteorin...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Borkovich, Katherine A., Alex, Lisa A., Yarden, Oded, Freitag, Michael, Turner, Gloria E., Read, Nick D., ...
We present an analysis of over 1,100 of the ∼10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and...
Brodhagen, Marion, Paulsen, Ian, Loper, Joyce E.
Pyoluteorin is a chlorinated polyketide antibiotic secreted by the rhizosphere bacterium Pseudomonas fluorescens Pf-5. Genes encoding enzymes and transcriptional regulators involved in pyoluteorin...
Boyle, Jon P., Rajasekar, Badri, Saeij, Jeroen P. J., Ajioka, James W., Berriman, Matthew, Paulsen, Ian, ...
Toxoplasma gondii, an obligate intracellular protozoan of the phylum Apicomplexa, is estimated to infect over a billion people worldwide as well as a great many other mammalian and avian hosts....
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii
Khan, Asis, Böhme, Ulrike, Kelly, Krystyna A., Adlem, Ellen, Brooks, Karen, Simmonds, Mark, ...
Toxoplasma gondii is a globally distributed protozoan parasite that can infect virtually all warm-blooded animals and humans. Despite the existence of a sexual phase in the life cycle, T. gondii has...
Chen, Sheng, Cui, Shenghui, McDermott, Patrick F., Zhao, Shaohua, White, David G., Paulsen, Ian, ...
The mechanisms involved in fluoroquinolone resistance in Salmonella enterica include target alterations and overexpression of efflux pumps. The present study evaluated the role of known and putative...
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...
Multidimensional annotation of the Escherichia coli K-12 genome
Karp, Peter D., Keseler, Ingrid M., Shearer, Alexander, Latendresse, Mario, Krummenacker, Markus, Paley, Suzanne M., ...
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns...
González, José M., Fernández-Gómez, Beatriz, Fernàndez-Guerra, Antoni, Gómez-Consarnau, Laura, Sánchez, Olga, Coll-Lladó, Montserrat, ...
Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However,...
Slater, Steven C., Goldman, Barry S., Goodner, Brad, Setubal, João C., Farrand, Stephen K., Nester, Eugene W., ...
The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant...
Annotation-based inference of transporter function
Lee, Thomas J., Paulsen, Ian, Karp, Peter
Motivation: We present a method for inferring and constructing transport reactions for transporter proteins based primarily on the analysis of the names of individual proteins in the genome...
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,...