Affiliation: Lawrence Berkeley National Laboratory
- A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaDongying Wu
DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Nature 462:1056-60. 2009....
- A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitansMircea Podar
Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
Genome Biol 9:R158. 2008..Little is known about the mechanisms that enable this relationship...
- The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degraderAthanasios Lykidis
Department of Energy DOE Joint Genome Institute, Walnut Creek, California, United States of America
PLoS ONE 5:e9729. 2010..Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source...
- Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YXAthanasios Lykidis
Department of Energy, Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598, USA
J Bacteriol 189:2477-86. 2007..In addition to providing an overview of the physiology of a soil actinomycete, this study presents insights on the transcriptional regulation and secretion of cellulases which may facilitate the industrial exploitation of these systems...
- Comparative genomics and evolution of eukaryotic phospholipid biosynthesisAthanasios Lykidis
Genome Biology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
Prog Lipid Res 46:171-99. 2007..Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase...
- Genomic characterization of methanomicrobiales reveals three classes of methanogensIain Anderson
Joint Genome Institute, Walnut Creek, California, USA
PLoS ONE 4:e5797. 2009..While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens...
- Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix oreniiKonstantinos Mavromatis
DOE Joint Genome Institute, Walnut Creek, California, United States of America
PLoS ONE 4:e4192. 2009....
- Genomics of aerobic cellulose utilization systems in actinobacteriaIain Anderson
U S Department of Energy Joint Genome Institute, Walnut Creek, California, USA
PLoS ONE 7:e39331. 2012..Mining of genome data for cellulose degradative enzymes followed by experimental verification successfully identified several actinobacteria species which were not previously known to degrade cellulose as cellulolytic organisms...
- GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomesAmrita Pati
Genome Biology Program, Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
Nat Methods 7:455-7. 2010....
- The integrated microbial genomes system: an expanding comparative analysis resourceVictor M Markowitz
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, USA
Nucleic Acids Res 38:D382-90. 2010..Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at http://img.jgi.doe.gov...
- An experimental metagenome data management and analysis systemVictor M Markowitz
Biological Data Management and Technology Center, Lawrence Berkeley National Lab, USA
Bioinformatics 22:e359-67. 2006..IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context. IMG/M is available at http://img.jgi.doe.gov/m...
- Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortiumAthanasios Lykidis
Joint Genome Institute, Lawrence National Berkeley Laboratory, Walnut Creek, CA, USA
ISME J 5:122-30. 2011..These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H(2)-producing syntroph-methanogen partnership that may serve to improve community stability...
- Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reductionIain Anderson
Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598, USA
J Bacteriol 190:2957-65. 2008....
- IMG/M: a data management and analysis system for metagenomesVictor M Markowitz
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
Nucleic Acids Res 36:D534-8. 2008..IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m...
- The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensionsVictor M Markowitz
Biological Data Management and Technology Center, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
Nucleic Acids Res 36:D528-33. 2008..IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov...
- The integrated microbial genomes (IMG) systemVictor M Markowitz
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
Nucleic Acids Res 34:D344-8. 2006..IMG allows users to focus their analysis on subsets of genes and genomes of interest and to save the results of their analysis. IMG is available at http://img.jgi.doe.gov...
- Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000Helene Feil
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 102:11064-9. 2005..The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to the epiphytic fitness and stress tolerance of this organism...
- Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insightsAnamitra Bhattacharyya
Integrated Genomics, Inc, Chicago, Illinois 60612, USA
Genome Res 12:1556-63. 2002..We also predicted and developed a new defined growth medium for Xylella...
- The genome sequence of the facultative intracellular pathogen Brucella melitensisVito G DelVecchio
Institute of Molecular Biology and Medicine, University of Scranton, Scranton, PA 18510, USA
Proc Natl Acad Sci U S A 99:443-8. 2002..Several features of the B. melitensis genome are similar to those of the symbiotic Sinorhizobium meliloti...
- Neutral-lipid analysis reveals elevation of acylglycerols and lack of cholesterol esters in Plasmodium falciparum-infected erythrocytesParwez Nawabi
Departments of Pathology and Microbiology Immunology, Northwestern University Medical School, Chicago, Illinois 60611, USA
Eukaryot Cell 2:1128-31. 2003..Evidence for P. falciparum and T. gondii homologues of acyl coenzyme A:diacylglycerol acyltransferase suggests that acylglycerols may be the conserved neutral lipids in apicomplexans...
- Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strainsAnamitra Bhattacharyya
Integrated Genomics, Inc, 2201 West Campbell Park Drive, Chicago, IL 60612, USA
Proc Natl Acad Sci U S A 99:12403-8. 2002..This study demonstrates the effectiveness of comparative analysis strategies in the interpretation of genomes that are closely related...
- The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaeaUwe Deppenmeier
Department of General Microbiology, Institute of Microbiology and Genetics, Georg August University, Goettingen, Germany
J Mol Microbiol Biotechnol 4:453-61. 2002..These findings might indicate that lateral gene transfer has played an important evolutionary role in forging the physiology of this metabolically versatile methanogen...
- Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomicsMatthew Daugherty
Integrated Genomics, Incorporated, Chicago, Illinois 60612 and the Scripps Research Institute, La Jolla, California 92037, USA
J Biol Chem 277:21431-9. 2002..This enzyme was previously suggested as a point of CoA biosynthesis regulation, and we have observed significant differences in mRNA levels of the corresponding human gene in normal and tumor cells by Northern blot analysis...
- Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586Vinayak Kapatral
Integrated Genomics, Chicago, Illinois 60612, USA
J Bacteriol 184:2005-18. 2002..The metabolic capabilities of F. nucleatum revealed by its genome are therefore consistent with its specialized niche in the mouth...