Athanasios Lykidis

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. ncbi A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
  2. ncbi A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Genome Biol 9:R158. 2008
  3. ncbi Comparative genomics and evolution of eukaryotic phospholipid biosynthesis
    Athanasios Lykidis
    Genome Biology Program, DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Prog Lipid Res 46:171-99. 2007
  4. ncbi Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX
    Athanasios Lykidis
    Department of Energy, Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598, USA
    J Bacteriol 189:2477-86. 2007
  5. ncbi The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader
    Athanasios Lykidis
    Department of Energy DOE Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 5:e9729. 2010
  6. ncbi Genomic characterization of methanomicrobiales reveals three classes of methanogens
    Iain Anderson
    Joint Genome Institute, Walnut Creek, California, USA
    PLoS ONE 4:e5797. 2009
  7. ncbi Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii
    Konstantinos Mavromatis
    DOE Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 4:e4192. 2009
  8. ncbi Genomics of aerobic cellulose utilization systems in actinobacteria
    Iain Anderson
    U S Department of Energy Joint Genome Institute, Walnut Creek, California, USA
    PLoS ONE 7:e39331. 2012
  9. ncbi The integrated microbial genomes system: an expanding comparative analysis resource
    Victor 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
  10. ncbi GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
    Amrita Pati
    Genome Biology Program, Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
    Nat Methods 7:455-7. 2010

Collaborators

Detail Information

Publications24

  1. ncbi A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    Dongying Wu
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 462:1056-60. 2009
    ....
  2. ncbi A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
    Mircea 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...
  3. ncbi Comparative genomics and evolution of eukaryotic phospholipid biosynthesis
    Athanasios 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...
  4. ncbi Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX
    Athanasios 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...
  5. ncbi The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader
    Athanasios 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...
  6. ncbi Genomic characterization of methanomicrobiales reveals three classes of methanogens
    Iain 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...
  7. ncbi Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii
    Konstantinos Mavromatis
    DOE Joint Genome Institute, Walnut Creek, California, United States of America
    PLoS ONE 4:e4192. 2009
    ....
  8. ncbi Genomics of aerobic cellulose utilization systems in actinobacteria
    Iain 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...
  9. ncbi The integrated microbial genomes system: an expanding comparative analysis resource
    Victor 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...
  10. ncbi GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
    Amrita Pati
    Genome Biology Program, Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
    Nat Methods 7:455-7. 2010
    ....
  11. ncbi An experimental metagenome data management and analysis system
    Victor 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...
  12. ncbi Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
    Athanasios 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...
  13. ncbi Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction
    Iain Anderson
    Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598, USA
    J Bacteriol 190:2957-65. 2008
    ....
  14. ncbi The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions
    Victor 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...
  15. ncbi IMG/M: a data management and analysis system for metagenomes
    Victor 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...
  16. ncbi The integrated microbial genomes (IMG) system
    Victor 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...
  17. ncbi Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000
    Helene 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...
  18. ncbi Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights
    Anamitra 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...
  19. ncbi Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586
    Vinayak 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...
  20. ncbi Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics
    Matthew 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...
  21. ncbi The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea
    Uwe 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...
  22. ncbi Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains
    Anamitra 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...
  23. ncbi Neutral-lipid analysis reveals elevation of acylglycerols and lack of cholesterol esters in Plasmodium falciparum-infected erythrocytes
    Parwez 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...
  24. ncbi The genome sequence of the facultative intracellular pathogen Brucella melitensis
    Vito 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...