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1. Full Text The Phaeodactylum genome reveals the evolutionary history of diatom genomes
by Wyrwicz, Lucjan S and Mangogna, Manuela and Rayko, Edda and Green, Beverley R and Lommer, Markus and Van de Peer, Yves and Lucas, Susan and Valentin, Klaus and Kaplan, Aaron and Martin-Jézéquel, Véronique and Medlin, Linda K and Montsant, Anton and Grigoriev, Igor V and Secq, Marie-Pierre Oudot-Le and Allen, Andrew E and Stanley, Michele and Jorgensen, Richard E and Huysman, Marie J. J and Brownlee, Colin and Napoli, Carolyn and von Dassow, Peter and Maumus, Florian and Mock, Thomas and Jenkins, Bethany D and Shapiro, Harris and Fournet, Jérome and Badger, Jonathan H and Lopez, Pascal J and Heijde, Marc and Detter, J. Chris and Joubert, Yolaine and Beszteri, Bank and Chiovitti, Anthony and Jabbari, Kamel and Petit, Jean-Louis and Sussman, Michael R and Berges, John A and Haruta, Miyoshi and Lindquist, Erica and Willis, Anusuya and Vandepoele, Klaas and Kroth, Peter G and Otillar, Robert P and Rynearson, Tatiana A and De Martino, Alessandra and Coesel, Sacha and Cadoret, Jean-Paul and Jiroutova, Katerina and Grimwood, Jane and Rychlewski, Leszek and Salamov, Asaf and Kuo, Alan and Durkin, Colleen and McGinnis, Karen and La Roche, Julie and Siaut, Magali and Porcel, Betina M and Choi, Chang Jae and Vyverman, Wim and Taylor, Alison R and Martens, Cindy and Rokhsar, Daniel S and Armbrust, E. Virginia and Kröger, Nils and Gruber, Ansgar and Poulsen, Nicole and Bowler, Chris and Katinka, Michael and Obornik, Miroslav and Weissenbach, Jean and Verret, Fréderic and Vardi, Assaf and Maheswari, Uma and Falciatore, Angela and Robison, Matthew and Parker, Micaela Schnitzler and Schmutz, Jeremy and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 11/2008, Volume 456, Issue 7219, pp. 239 - 244
Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth... 
BACTERIA | METABOLISM | MULTIDISCIPLINARY SCIENCES | RECIPROCAL GENE LOSS | YEASTS | COMPONENTS | THALASSIOSIRA-PSEUDONANA | MECHANISMS | BACILLARIOPHYCEAE | Protein Structure, Tertiary | Sequence Homology, Amino Acid | Genes, Bacterial - genetics | Signal Transduction | Diatoms - genetics | Genome - genetics | Molecular Sequence Data | DNA, Algal - analysis | Evolution, Molecular | Diatoms | Genetic aspects | Natural history | Genetics | Bacteria | Evolution | Genes | Genomics | Life Sciences | Populations and Evolution | Vegetal Biology | Biodiversity
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2. Full Text Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils
by Naomi L. Ward and Jean F. Challacombe and Peter H. Janssen and Bernard Henrissat and Pedro M. Coutinho and Martin Wu and Gary Xie and Daniel H. Haft and Michelle Sait and Jonathan Badger and Ravi D. Barabote and Brent Bradley and Thomas S. Brettin and Lauren M. Brinkac and David Bruce and Todd Creasy and Sean C. Daugherty and Tanja M. Davidsen and Robert T. DeBoy and J. Chris Detter and Robert J. Dodson and A. Scott Durkin and Anuradha Ganapathy and Michelle Gwinn-Giglio and Cliff S. Han and Hoda Khouri and Hajnalka Kiss and Sagar P. Kothari and Ramana Madupu and Karen E. Nelson and William C. Nelson and Ian Paulsen and Kevin Penn and Qinghu Ren and M. J. Rosovitz and Jeremy D. Selengut and Susmita Shrivastava and Steven A. Sullivan and Roxanne Tapia and L. Sue Thompson and Kisha L. Watkins and Qi Yang and Chunhui Yu and Nikhat Zafar and Liwei Zhou and Cheryl R. Kuske and Joint Genome Institute (JGI)
Applied and Environmental Microbiology, ISSN 0099-2240, 04/2009, Volume 75, Issue 7, pp. 2046 - 2056
Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit... 
IRON UPTAKE | MICROBIAL COMMUNITIES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BACTERIAL DIVERSITY | PSEUDOMONAS-AERUGINOSA | ESCHERICHIA-COLI | COPY NUMBER | MICROBIOLOGY | SP-NOV | SIDEROPHORE BIOSYNTHESIS | ACIDIC SPHAGNUM-PEAT | 16S RIBOSOMAL-RNA | Cyanobacteria - genetics | Genome, Bacterial | Nitrogen - metabolism | Soil Microbiology | Carbohydrate Metabolism | Molecular Sequence Data | DNA, Bacterial - chemistry | Macrolides - metabolism | Phylogeny | Bacteria - genetics | Fungi - genetics | Proteobacteria - genetics | Sequence Analysis, DNA | Sequence Homology | Bacteria - isolation & purification | DNA, Bacterial - genetics | Biological Transport | Anti-Bacterial Agents - biosynthesis | Analysis | Cyanobacteria | Physiological aspects | Genetic aspects | Research | Bacterial genetics | Hydration (Chemistry) | Soil microbiology | ABC transporter | Evolutionary and Genomic Microbiology
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3. Full Text Comparative Genomics Reveals Mechanism for Short-Term and Long-Term Clonal Transitions in Pandemic Vibrio Cholerae
by Jongsik Chun and Christopher J. Grim and Nur A. Hasan and Je Hee Lee and Seon Young Choi and Bradd J. Haley and Elisa Taviani and Yoon-Seong Jeon and Dong Wook Kim and Jae-Hak Lee and Thomas S. Brettin and David C. Bruce and Jean F. Challacombe and J. Chris Detter and Cliff S. Han and A. Christine Munk and Olga Chertkov and Linda Meincke and Elizabeth Saunders and Ronald A. Walters and Anwar Huq and G. Balakrish Nair and Rita R. Colwell and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 9/2009, Volume 106, Issue 36, pp. 15442 - 15447
Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment and a serious public health threat. V. cholerae... 
Pandemics | Vibrio cholerae | Genomics | Genes | Evolution | Multigene family | Genomes | Cholera | Prophages | Horizontal gene transfer | Cholera toxin prophage | Lateral gene transfer | Genomic islands | SEROGROUP CONVERSION | EL-TOR STRAINS | genomic islands | MULTIDISCIPLINARY SCIENCES | BANGLADESH | COMPETENCE | lateral gene transfer | PHAGE | BIOTYPE | CLASSICAL CTX PROPHAGE | DNA | GENES | cholera toxin prophage | Genomic Islands - genetics | Species Specificity | Molecular Sequence Data | Phylogeny | Sequence Analysis, DNA | Genetic Variation | Cholera Toxin - genetics | Base Sequence | Vibrio cholerae O1 - genetics | Gene Transfer, Horizontal - genetics | Cluster Analysis | Evolution, Molecular | Genetic aspects | Research | Identification and classification | Index Medicus | PUBLIC HEALTH | BACTERIA | BASIC BIOLOGICAL SCIENCES | GENETICS | CLONING | CHOLERA | Biological Sciences
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4. Full Text Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7
by Garret Suen and David M. Stevenson and David C. Bruce and Olga Chertkov and Alex Copeland and Jan-Feng Cheng and Chris Detter and John C. Detter and Lynne A. Goodwin and Cliff S. Han and Loren J. Hauser and Natalia N. Ivanova and Nikos C. Kyrpides and Miriam L. Land and Alla Lapidus and Susan Lucas and Galina Ovchinnikova and Sam Pitluck and Roxanne Tapia and Tanja Woyke and Julie Boyum and David Mead and Paul J. Weimer and Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Journal of Bacteriology, ISSN 0021-9193, 10/2011, Volume 193, Issue 19, pp. 5574 - 5575
Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley... 
MICROBIOLOGY | SEQUENCE | Genome, Bacterial - genetics | Ruminococcus - genetics | Deinococcus | Genetic aspects | Research | Bacterial genetics | Identification and classification | BIOFUELS | RUMINANTS | BASIC BIOLOGICAL SCIENCES | BIOLOGY | FERMENTATION | ETHANOL | 60 APPLIED LIFE SCIENCES | STOMACH | PRODUCTION | Genome Announcements
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5. Full Text The Genome of the Diatom Thalassiosira pseudonana: Ecology, Evolution, and Metabolism
by E. Virginia Armbrust and John A. Berges and Chris Bowler and Beverley R. Green and Diego Martinez and Nicholas H. Putnam and Shiguo Zhou and Andrew E. Allen and Kirk E. Apt and Michael Bechner and Mark A. Brzezinski and Balbir K. Chaal and Anthony Chiovitti and Aubrey K. Davis and Mark S. Demarest and J. Chris Detter and Tijana Glavina and David Goodstein and Masood Z. Hadi and Uffe Hellsten and Mark Hildebrand and Bethany D. Jenkins and Jerzy Jurka and Vladimir V. Kapitonov and Nils Kröger and Winnie W. Y. Lau and Todd W. Lane and Frank W. Larimer and J. Casey Lippmeier and Susan Lucas and Mónica Medina and Anton Montsant and Miroslav Obornik and Micaela Schnitzler Parker and Brian Palenik and Gregory J. Pazour and Paul M. Richardson and Tatiana A. Rynearson and Mak A. Saito and David C. Schwartz and Kimberlee Thamatrakoln and Klaus Valentin and Assaf Vardi and Frances P. Wilkerson and Daniel S. Rokhsar and Joint Genome Institute (JGI)
Science, ISSN 0036-8075, 10/2004, Volume 306, Issue 5693, pp. 79 - 86
Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for ~20% of global carbon fixation. We report the 34... 
Proteins | Electrodes | Enzymes | Genes | Genomes | Plants | Diatoms | Eukaryotic cells | Plastids | Chromosomes | Research Article | WORLD OCEAN | POLYAMINES | PLASMODIUM-FALCIPARUM | NUCLEUS | MULTIDISCIPLINARY SCIENCES | MARINE DIATOMS | GENE-TRANSFER | SILICA | PROTEINS | PHYTOPLANKTON | FAMILY | Adaptation, Physiological | Light-Harvesting Protein Complexes - genetics | Silicic Acid - metabolism | Diatoms - genetics | Light-Harvesting Protein Complexes - metabolism | Algal Proteins - physiology | Molecular Sequence Data | Restriction Mapping | Diatoms - metabolism | Mitochondria - genetics | Ecosystem | Light | Algal Proteins - genetics | Plastids - genetics | Urea - metabolism | Diatoms - chemistry | Light-Harvesting Protein Complexes - chemistry | Symbiosis | Nitrogen - metabolism | Algal Proteins - chemistry | Iron - metabolism | Sequence Analysis, DNA | Diatoms - cytology | Biological Evolution | DNA - genetics | Sequence Alignment | Animals | Cell Nucleus - genetics | Energy Metabolism | Genome | Photosynthesis | Genetic aspects | Research | Evolution | Marine ecology | Metabolism | Algae | Genomics
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6. Full Text Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
by Berka, Randy and Huang, Katherine and Detter, J Chris and Coutinho, Pedro M and Martinez, Diego and Putnam, Nik and Helfenbein, Kevin G and Rokhsar, Daniel and Ramaiya, Preethi and Larimer, Frank and Gelpke, Maarten D Sollewijn and Chapman, Jarrod and Larrondo, Luis F and Cullen, Dan and Henrissat, Bernard and Joint Genome Institute (JGI)
Nature Biotechnology, ISSN 1087-0156, 06/2004, Volume 22, Issue 6, pp. 695 - 700
White rot fungi efficiently degrade lignin, a complex aromatic polymer in wood that is among the most abundant natural materials on earth. These fungi use... 
COPRINUS-CINEREUS | ORGANIZATION | GLYOXAL OXIDASE | ELEMENTS | PHANEROCHAETE-CHRYSOSPORIUM | FILAMENTOUS FUNGUS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DEGRADATION | LIGNIN PEROXIDASE GENES | IDENTIFICATION | NEUROSPORA-CRASSA | DNA, Fungal - genetics | Genomics | Glycoside Hydrolases - genetics | DNA, Fungal - chemistry | DNA, Fungal - isolation & purification | Retroelements - genetics | Phanerochaete - genetics | Lignin - metabolism | Genome, Fungal | Transposases - genetics | Classification | Peroxidases - metabolism | Base Composition - genetics | Glycosyltransferases - genetics | Genes, Fungal - genetics | Biodegradation, Environmental | Introns - genetics | Gene Library | Oxidoreductases - metabolism | Oxidoreductases - genetics | Exons - genetics | Fungal Proteins - genetics | Fungal Proteins - classification | Sequence Analysis, DNA | Laccase - genetics | Laccase - metabolism | Polysaccharides - metabolism | Glycosyltransferases - metabolism | Cytochrome P-450 Enzyme System - genetics | Glycoside Hydrolases - metabolism | Peroxidases - genetics | Phanerochaete - metabolism | Cellulose - metabolism | Fungal Proteins - metabolism
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7. Full Text Genome Sequence of Nitrosomonas sp. Strain AL212, an Ammonia-Oxidizing Bacterium Sensitive to High Levels of Ammonia
by Suwa Yuichi and Jeanette M. Norton and Annette Bollmann and Martin G. Klotz and Lisa Y. Stein and Hendrikus J. Laanbroek and Daniel J. Arp and Lynne A. Goodwin and Olga Chertkov and Brittany Held and David Bruce and J. Chris Detter and Janine C. Detter and Roxanne Tapia and Cliff S. Han and Joint Genome Institute (JGI)
Journal of Bacteriology, ISSN 0021-9193, 09/2011, Volume 193, Issue 18, pp. 5047 - 5048
Errata ( vol. 193 , p. 6112 ) Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg... 
MICROBIOLOGY | DIVERSITY | Genome, Bacterial | DNA, Bacterial - genetics | Nitrosomonas - metabolism | Oxidation-Reduction | Ammonia - metabolism | Plasmids | Nitrosomonas - isolation & purification | Molecular Sequence Data | DNA, Bacterial - chemistry | Nitrosomonas - genetics | Chemoautotrophic Growth | Sequence Analysis, DNA | Ammonia | Research | Bacterial genetics | Properties | Genomics | Genome Announcements
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8. Full Text Genome Sequence of Hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. cholerae
by Christopher J. Grim and Nur A. Hasan and Elisa Taviani and Bradd Haley and Jongsik Chun and Thomas S. Brettin and David C. Bruce and J. Chris Detter and Cliff S. Han and Olga Chertkov and Jean Challacombe and Anwar Huq and G. Balakrish Nair and Rita R. Colwell
Journal of Bacteriology, ISSN 0021-9193, 07/2010, Volume 192, Issue 13, pp. 3524 - 3533
Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley... 
ISLAND | EL-TOR STRAINS | ASIA | DISEASE | MICROBIOLOGY | BANGLADESH | MOZAMBIQUE | VARIANT | Genome, Bacterial - genetics | Models, Genetic | Vibrio cholerae - genetics | Vibrio cholerae O1 - genetics | Genetic aspects | Genomes | Research | Bacterial genetics | Vibrio cholerae | Genomics and Proteomics
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9. Full Text Capturing single cell genomes of active polysaccharide degraders: An unexpected contribution of verrucomicrobia
by Martinez-Garcia, Manuel and Brazel, David M and Swan, Brandon K and Arnosti, Carol and Chain, Patrick S. G and Reitenga, Krista G and Xie, Gary and Poulton, Nicole J and Gomez, Monica Lluesma and Masland, Dashiell E. D and Thompson, Brian and Bellows, Wendy K and Ziervogel, Kai and Lo, Chien-Chi and Ahmed, Sanaa and Gleasner, Cheryl D and Detter, Chris J and Stepanauskas, Ramunas and Joint Genome Institute (JGI)
PLoS ONE, ISSN 1932-6203, 04/2012, Volume 7, Issue 4, p. e35314
Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel... 
GEN. NOV | AMPLIFICATION | HYDROLYSIS RATES | METABOLISM | MULTIDISCIPLINARY SCIENCES | SEQUENCE | MARINE-BACTERIA | ASSEMBLAGES | DEGRADATION | RIBOSOMAL-RNA | IDENTIFICATION | Cellulases - genetics | Amino Acid Sequence | Fresh Water - microbiology | Genome, Bacterial | Seawater - microbiology | Xylans - metabolism | Bacterial Proteins - genetics | Fluorescent Dyes - metabolism | Molecular Sequence Data | Verrucomicrobia - enzymology | Verrucomicrobia - isolation & purification | Phylogeny | Sequence Analysis, DNA | Polysaccharides - metabolism | Hydrolysis | Verrucomicrobia - metabolism | Cellulases - metabolism | Glucans | Conserved Sequence | Bacterial Proteins - metabolism | Verrucomicrobia - genetics | Single-Cell Analysis | Water Microbiology | Polysaccharides | Proteases | Biomass energy | Ecosystems | Analysis | Genes | Genomics | Fluorescence | Genomes | Bioremediation | Enrichment | Flow cytometry | Laboratories | Science | Xylan | Esterases | Hybridization | Biopolymers | Data bases | Degradation | Taxa | Bacterioplankton | Microorganisms | Annotations | Phylogenetics | Deoxyribonucleic acid--DNA | Saccharides | Biodegradation | Carbohydrates | Enzymes | Laminarin | Cultivation | Prokaryotes | Bioprospecting | Biofuels | Substrates | Peptidases | Algorithms | Glycoside hydrolase | Deoxyribonucleic acid | DNA
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10. Full Text Artificial polyploidy improves bacterial single cell genome recovery
by Dichosa, Armand E. K and Fitzsimons, Michael S and Lo, Chien-Chi and Weston, Lea L and Preteska, Lara G and Snook, Jeremy P and Zhang, Xiaojing and Gu, Wei and McMurry, Kim and Green, Lance D and Chain, Patrick S and Detter, J. Chris and Han, Cliff S and Joint Genome Institute (JGI)
PLoS ONE, ISSN 1932-6203, 05/2012, Volume 7, Issue 5, p. e37387
Background: Single cell genomics (SCG) is a combination of methods whose goal is to decipher the complete genomic sequence from a single cell and has been... 
CYTOKINESIS | TARGETING FTSZ | MICROBIAL COMMUNITIES | METABOLISM | SMALL-MOLECULE | ENVIRONMENT | BIOLOGY | DYNAMICS | POLYMERASE | DIVISION PROTEIN FTSZ | MULTIPLE DISPLACEMENT AMPLIFICATION | Cell Division - genetics | Genome, Bacterial - genetics | Polyploidy | Bacillus subtilis - cytology | DNA, Bacterial - metabolism | Single-Cell Analysis - methods | Pyridines - pharmacology | Thiazoles - pharmacology | Genomics - methods | Cell Division - drug effects | Bacillus subtilis - drug effects | Bacillus subtilis - genetics | Genetic research | Genomes | Bacterial genetics | Genomics | DNA | Nucleotide sequence | Laboratories | Ecosystems | Bias | DNA damage | Archaea | Cell division | Recovery | Ecosystem biology | Amplification | Microorganisms | Algorithms | E coli | Bacteria | Cytoskeleton | Inhibition | Cell size | Molecular biology | Bioinformatics | Deoxyribonucleic acid--DNA | Deoxyribonucleic acid
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11. Full Text Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2
by Ahmed, Sanaa A and Awosika, Joy and Baldwin, Carson and Bishop-Lilly, Kimberly A and Biswas, Biswajit and Broomall, Stacey and Chain, Patrick S. G and Chertkov, Olga and Chokoshvili, Otar and Coyne, Susan and Davenport, Karen and Detter, J. Chris and Dorman, William and Erkkila, Tracy H and Folster, Jason P and Frey, Kenneth G and George, Matroner and Gleasner, Cheryl and Henry, Matthew and Hill, Karen K and Hubbard, Kyle and Insalaco, Joseph and Johnson, Shannon and Kitzmiller, Aaron and Krepps, Michael and Lo, Chien-Chi and Luu, Truong and McNew, Lauren A and Minogue, Timothy and Munk, Christine A and Osborne, Brian and Patel, Mohit and Reitenga, Krista G and Rosenzweig, C. Nicole and Shea, April and Shen, Xiaohong and Strockbine, Nancy and Tarr, Cheryl and Teshima, Hazuki and van Gieson, Eric and Verratti, Kathleen and Wolcott, Mark and Xie, Gary and Sozhamannan, Shanmuga and Gibbons, Henry S and Threat Characterization Consortium
PLoS ONE, ISSN 1932-6203, 11/2012, Volume 7, Issue 11, p. e48228
In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga toxin 2-converting phage caused a large outbreak of bloody... 
AGGREGATIVE ADHERENCE | BACTERIOPHAGES | HEMOLYTIC-UREMIC SYNDROME | SEQUENCES | ALIGNMENT | MULTIDISCIPLINARY SCIENCES | SALMONELLA-TYPHIMURIUM | RESISTANCE | GADE YHIE | OUTBREAK | PATHOGENS | Georgia (Republic) | Area Under Curve | Genomics | Humans | Virulence | Escherichia coli Infections - microbiology | Genotype | DNA - metabolism | Shiga Toxin 2 - metabolism | Shiga-Toxigenic Escherichia coli - genetics | Plasmids - metabolism | Sequence Analysis, DNA | Prophages - genetics | Shiga Toxin 2 - genetics | Genetic Variation | Microbial Sensitivity Tests | Phenotype | Yersinia pestis - genetics | Disease Outbreaks | Escherichia coli - genetics | Polymorphism, Single Nucleotide | Drug resistance in microorganisms | Analysis | Diarrhea | Genomes | Virulence (Microbiology) | Phylogeny | Epidemics | Military medicine | Shiga toxin | Laboratories | Phages | Homology | Outbreaks | Epidemiology | Gene sequencing | Streptococcus infections | E coli | Antibiotic resistance | Strains (organisms) | Genotypes | Medical research | Hemolytic uremic syndrome | Electron microscopy | Disease control | Disease prevention | Medicine | Infectious diseases | Antibiotics | Shiga toxin 2
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