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...
Campbell, Barbara J., Smith, Julie L., Hanson, Thomas E., Klotz, Martin G., Stein, Lisa Y., Lee, Charles K., ...
Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are...
Campbell, Barbara J., Smith, Julie L., Hanson, Thomas E., Klotz, Martin G., Stein, Lisa Y., Lee, Charles K., ...
Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are...
Acidithiobacillus ferrooxidansmetabolism: from genome sequence to industrial applications (2008)
Valdés, Jorge, Pedroso, Inti, Quatrini, Raquel, Dodson, Robert J, Tettelin, Herve, Blake, Robert, ...
Abstract Background Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a...
Coyne, Robert S, Thiagarajan, Mathangi, Jones, Kristie M, Wortman, Jennifer R, Tallon, Luke J, Haas, Brian J, ...
Abstract Background Tetrahymena thermophila , a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic...
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans (2008)
Podar, Mircea, Anderson, Iain, Makarova, Kira S, Elkins, James G, Ivanova, Natalia, Wall, Mark A, ...
Abstract Background The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea....
A simple, fast, and accurate method of phylogenomic inference (2008)
Abstract The explosive growth of genomic data provides an opportunity to make increased use of protein markers for phylogenetic inference. We have developed an automated pipeline for phylogenomic...
Since their discovery in the 1670s
Environmental Genome Shotgun Sequencing of the Sargasso Sea (2008)
Sargasso Sea, J. Craig Venter, Et Al, J. Craig Venter, Karin Remington, John F. Heidelberg, ...
The following resources related to this article are available online at
Jonathan A Eisen, John F Heidelberg, Owen White, Steven L Salzberg
for symmetric chromosomal inversions around the
Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii (2007)
Cédric Norais, Michelle Hawkins, Amber L. Hartman, Jonathan A. Eisen, Hannu Myllykallio, Thorsten Allers
The halophilic archaeon Haloferax volcanii has a multireplicon genome, consisting of a main chromosome, three secondary chromosomes, and a plasmid. Genes for the initiator protein Cdc6/Orc1, which...
Genetic and physical mapping of DNA replication origins in Haloferax volcanii (2007)
Cédric Norais, Michelle Hawkins, Amber L Hartman, Jonathan A. Eisen, Hannu Myllykallio, Thorsten Allers
The halophilic archaeon Haloferax volcanii has a multi-replicon genome, consisting of a main chromosome, three secondary chromosomes, and a plasmid. Genes for the initiator protein Cdc6/Orc1, which...
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007)
Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron L. Halpern, Shannon J. Williamson, Karin Remington, ...
Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a...
Douglas B. Rusch, Aaron L. Halpern, Granger Sutton, Karla B. Heidelberg, Shannon Williamson, Shibu Yooseph, ...
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine...
The Sorcerer II global ocean sampling expedition: expanding the universe of protein families (2007)
Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron L. Halpern, Shannon J. Williamson, Karin Remington, ...
Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan A. Eisen, ...
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...
Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters (2006)
Wu, Dongying, Daugherty, Sean C, Van Aken, Susan E, Pai, Grace H, Watkins, Kisha L, Khouri, Hoda, ...
Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking...
Leebens-Mack, Jim, Vision, Todd, Brenner, Eric, Bowers, John E., Cannon, Steven, Clement, Mark J., ...
In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal...
Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters (2006)
Dongying Wu, Sean C. Daugherty, Grace H. Pai, Kisha L. Watkins, Hoda Khouri, ...
Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking...
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2006)
Yooseph, Shibu, Sutton, Granger, Rusch, Douglas B., Halpern, Aaron L., Williamson, Shannon J., Remington, Karin, ...
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...
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
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...
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...
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...
TIGRFAMs: a protein family resource for the functional identification of proteins (2001)
Haft, Daniel H., Loftus, Brendan J., Richardson, Delwood L., Yang, Fan, Eisen, Jonathan A., Paulsen, Ian T., ...
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional...
Evidence for symmetric chromosomal inversions around the replication origin in bacteria (2000)
Eisen, Jonathan A., Heidelberg, John F., White, Owen, Salzberg, Steven L.
Background: Whole-genome comparisons can provide great insight into many aspects of biology. Until recently, however, comparisons were mainly possible only between distantly related species. Complete...
A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity (2000)
Pollock, David D., Eisen, Jonathan A., Doggett, Norman A., Cummings, Michael P.
Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic...
Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions (1995)
Eisen, Jonathan A., Sweder, Kevin S., Hanawalt, Philip C.
The SNF2 family of proteins includes representatives from a variety of species with roles In cellular processes such as transcrlptional regulation (e.g. M0T1, SNF2 and BRM), maintenance of chromosome...
Eisen, Jonathan A., Benito, Maria-Ines, Walbot, Virginia
The Mutator transposable element system of maize is the most active transposable element system characterized in higher plants. While Mutator has been used to generate and tag thousands of new maize...
Hazen, Tracy H., Wu, Dongying, Eisen, Jonathan A., Sobecky, Patricia A.
The horizontal transfer of genes by mobile genetic elements such as plasmids and phages can accelerate genome diversification of Vibrio spp., affecting their physiology, pathogenicity, and ecological...
An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)
Wu, Dongying, Hartman, Amber, Ward, Naomi, Eisen, Jonathan A.
Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for much of what we know about the phylogenetic diversity of both cultured and uncultured microorganisms....
Coyne, Robert S, Thiagarajan, Mathangi, Jones, Kristie M, Wortman, Jennifer R, Tallon, Luke J, Haas, Brian J, ...
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
Podar, Mircea, Anderson, Iain, Makarova, Kira S, Elkins, James G, Ivanova, Natalia, Wall, Mark A, ...
Sequencing of the complete genome of Ignicoccus hospitalis gives insight into its association with another species of Archaea, Nanoarchaeum equitans.
Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications
Valdés, Jorge, Pedroso, Inti, Quatrini, Raquel, Dodson, Robert J, Tettelin, Herve, Blake, Robert, ...
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...
Campbell, Barbara J., Smith, Julie L., Hanson, Thomas E., Klotz, Martin G., Stein, Lisa Y., Lee, Charles K., ...
Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are...
Assembling the Marine Metagenome, One Cell at a Time
Woyke, Tanja, Xie, Gary, Copeland, Alex, González, José M., Han, Cliff, Kiss, Hajnalka, ...
The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of...
Yang, Joyce C., Madupu, Ramana, Durkin, A. Scott, Ekborg, Nathan A., Pedamallu, Chandra S., Hostetler, Jessica B., ...
Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring...
Human gut microbiome adopts an alternative state following small bowel transplantation
Hartman, Amber L., Lough, Denver M., Barupal, Dinesh K., Fiehn, Oliver, Fishbein, Thomas, Zasloff, Michael, ...
Small bowel transplants provide an exceptional opportunity for long-term study of the microbial ecology of the human small bowel. The ileostomy created at time of transplant for ongoing monitoring of...
A simple, fast, and accurate method of phylogenomic inference
An automated pipeline for phylogenomic analysis (AMPHORA) is presented that overcomes existing limits to large-scale protein phylogenetic inference.