Daniel H Haft

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. pmc A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
    Daniel H Haft
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Comput Biol 1:e60. 2005
  2. 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
  3. 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
  4. pmc Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species
    Karen E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:2386-95. 2004
  5. pmc Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain
    Steven R Gill
    Microbial Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:2426-38. 2005
  6. pmc Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Genet 1:e65. 2005
  7. 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
  8. pmc Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
    Karen E Nelson
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 185:5591-601. 2003
  9. ncbi request reprint The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 423:81-6. 2003
  10. 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

Detail Information

Publications33

  1. pmc A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
    Daniel H Haft
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Comput Biol 1:e60. 2005
    ..It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated...
  2. 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...
  3. 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...
  4. pmc Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species
    Karen E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:2386-95. 2004
    ..Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs...
  5. pmc Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain
    Steven R Gill
    Microbial Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:2426-38. 2005
    ..Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis...
  6. pmc Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Genet 1:e65. 2005
    ....
  7. 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
    ....
  8. pmc Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
    Karen E Nelson
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 185:5591-601. 2003
    ..gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease...
  9. ncbi request reprint The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 423:81-6. 2003
    ..The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis...
  10. 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...
  11. 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...
  12. pmc Structural flexibility in the Burkholderia mallei genome
    William C Nierman
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:14246-51. 2004
    ..Variation in simple sequence repeats in key genes can provide a mechanism for generating antigenic variation that may account for the mammalian host's inability to mount a durable adaptive immune response to a B. mallei infection...
  13. pmc Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"
    Herve Tettelin
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 102:13950-5. 2005
    ..Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes...
  14. ncbi request reprint Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nat Biotechnol 20:1118-23. 2002
    ....
  15. pmc Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family
    Daniel H Haft
    The J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Biol 8:70. 2010
    ..TOMM peptides are small and highly variable, frequently missed by gene-finders and occasionally situated far from the thiazole/oxazole forming genes. Thus, locating a substrate for a particular TOMM pathway can be a challenging endeavor...
  16. ncbi request reprint The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Biotechnol 22:554-9. 2004
    ....
  17. 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...
  18. pmc Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners
    Daniel H Haft
    J Craig Venter Institute, 9704 Rockville, MD 20850, USA
    BMC Genomics 12:21. 2011
    ..Evolutionary pressures and relationships to other cellular constituents impose recognizable grammars on each class of rSAM-containing system, shaping patterns in results obtained through various comparative genomics analyses...
  19. pmc Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens
    Garry S A Myers
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 16:1031-40. 2006
    ....
  20. pmc GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease
    Daniel H Haft
    Department of Bioinformatics, J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS ONE 6:e28886. 2011
    ....
  21. 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...
  22. pmc The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
    C Robin Buell
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 100:10181-6. 2003
    ..Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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...
  28. pmc A strain-variable bacteriocin in Bacillus anthracis and Bacillus cereus with repeated Cys-Xaa-Xaa motifs
    Daniel H Haft
    The J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Biol Direct 4:15. 2009
    ..cereus, but has gone unrecognized because it is always encoded far from its maturation protein operon. Patterns of insertions and deletions among twenty-four variants suggest a repeating functional unit of Cys-Xaa-Xaa...
  29. pmc Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification
    Daniel H Haft
    J Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 193:2745-55. 2011
    ..Interpretation of comparative genomics evidence suggests unexpected (nonbacteriocin) roles for natural products from several of these systems...
  30. pmc The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium
    Jonathan A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:9509-14. 2002
    ..tepidum and many Archaeal species...
  31. pmc Orphan SelD proteins and selenium-dependent molybdenum hydroxylases
    Daniel H Haft
    Department of Bioinformatics, J, Craig Venter Institute, Rockville, MD 20850, USA
    Biol Direct 3:4. 2008
    ..We propose that certain accessory proteins, and orphan selD itself, are markers through which new selenium-dependent molybdenum hydroxylases can be found...
  32. ncbi request reprint Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
    Mary Ann Moran
    Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA
    Nature 432:910-3. 2004
    ..This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean...
  33. ncbi request reprint HMM-based databases in InterPro
    Alex Bateman
    Pfam Group, The Wellcome Trust Sanger Institute, Hinxton, UK
    Brief Bioinform 3:236-45. 2002
    ..This paper reviews the Pfam, TIGRFAMs and SMART databases that use the profile-HMMs provided by the HMMER package...