Jeremy D Selengut

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. pmc TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
    Jeremy D Selengut
    TIGR, Bioinformatics Department, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D260-4. 2007
  2. pmc Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils
    Naomi L Ward
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Appl Environ Microbiol 75:2046-56. 2009
  3. pmc TIGRFAMs and Genome Properties in 2013
    Daniel H Haft
    Informatics, J Craig Venter Institute, Rockville, MD 20850, USA
    Nucleic Acids Res 41:D387-95. 2013
  4. pmc ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
    Malay K Basu
    J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Bioinformatics 12:434. 2011
  5. pmc Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic
    Daniel H Haft
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville MD 20850, USA
    BMC Biol 4:29. 2006
  6. ncbi request reprint Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
    Daniel H Haft
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Bioinformatics 21:293-306. 2005
  7. ncbi request reprint Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus
    Garry S A Myers
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Biotechnol 25:569-75. 2007
  8. pmc Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function
    Jeremy D Selengut
    J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Bioinformatics 11:52. 2010
  9. pmc Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria
    Jeremy D Selengut
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    J Bacteriol 192:5788-98. 2010
  10. ncbi request reprint Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
    Jane M Carlton
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:512-9. 2002

Detail Information

Publications18

  1. pmc TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
    Jeremy D Selengut
    TIGR, Bioinformatics Department, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D260-4. 2007
    ..The TIGRFAMs and Genome Properties systems can be accessed at http://www.tigr.org/TIGRFAMs and http://www.tigr.org/Genome_Properties...
  2. pmc Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils
    Naomi L Ward
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Appl Environ Microbiol 75:2046-56. 2009
    ....
  3. pmc TIGRFAMs and Genome Properties in 2013
    Daniel H Haft
    Informatics, J Craig Venter Institute, Rockville, MD 20850, USA
    Nucleic Acids Res 41:D387-95. 2013
    ..At present, 4284 models appear in TIGRFAMs, while 628 systems are described by Genome Properties. Content derives both from subsystem discovery work and from biocuration of the scientific literature...
  4. pmc ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
    Malay K Basu
    J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Bioinformatics 12:434. 2011
    ..To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies...
  5. pmc Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic
    Daniel H Haft
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville MD 20850, USA
    BMC Biol 4:29. 2006
    ..Detection in some genomes, but not others, may reveal sorting system components by comparison of the phylogenetic profile of the class of sorting signal to that of various protein families...
  6. ncbi request reprint Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
    Daniel H Haft
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Bioinformatics 21:293-306. 2005
    ..Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics...
  7. ncbi request reprint Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus
    Garry S A Myers
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Biotechnol 25:569-75. 2007
    ..Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine...
  8. pmc Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function
    Jeremy D Selengut
    J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Bioinformatics 11:52. 2010
    ..The approach is based on the basic scoring mechanism employed by PPP, namely the use of binomial distribution statistics to optimize sequence similarity cutoffs during searches of partitioned training sets...
  9. pmc Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria
    Jeremy D Selengut
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    J Bacteriol 192:5788-98. 2010
    ..These findings suggest that M. tuberculosis relies heavily on coenzyme F(420) for its redox reactions. This dependence and the cofactor's rarity may make F(420)-related proteins promising drug targets...
  10. ncbi request reprint Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
    Jane M Carlton
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:512-9. 2002
    ..This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease...
  11. pmc Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification
    Daniel H Haft
    J Craig Venter Institute, Rockville, Maryland, USA
    J Bacteriol 194:36-48. 2012
    ..Their target proteins are destined to transit cellular membranes during their biosynthesis, during which most undergo additional posttranslational modifications such as glycosylation...
  12. pmc The TIGRFAMs database of protein families
    Daniel H Haft
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:371-3. 2003
    ..The database currently contains over 1600 protein families. TIGRFAMs is available for searching or downloading at www.tigr.org/TIGRFAMs...
  13. pmc Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus
    Jonathan H Badger
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    J Bacteriol 188:6841-50. 2006
    ..neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging...
  14. pmc Comparative genomics of emerging human ehrlichiosis agents
    Julie C Dunning Hotopp
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Genet 2:e21. 2006
    ..These discoveries provide significant insights into the biology of these obligate intracellular pathogens...
  15. pmc The InterPro Database, 2003 brings increased coverage and new features
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 31:315-8. 2003
    ..The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  16. pmc New developments in the InterPro database
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute Hinxton, Cambridge, UK
    Nucleic Acids Res 35:D224-8. 2007
    ..ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html...
  17. ncbi request reprint X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily
    Ezra Peisach
    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118 2394, USA
    Biochemistry 43:12770-9. 2004
    ..This observation combined with the modeling studies suggests that the target of MDP-1 is most likely a phosphotyrosine in an unknown protein rather than a small sugar-based substrate...
  18. ncbi request reprint The transcription factor Eyes absent is a protein tyrosine phosphatase
    Tina L Tootle
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nature 426:299-302. 2003
    ....