Research Topics
| Daniel H HaftSummaryAffiliation: J. Craig Venter Institute Country: USA Publications
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Detail Information
Publications
TIGRFAMs and Genome Properties in 2013Daniel 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...- GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine proteaseDaniel H Haft
Department of Bioinformatics, J Craig Venter Institute, Rockville, Maryland, United States of America
PLoS ONE 6:e28886. 2011.... - Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partnersDaniel 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... - A strain-variable bacteriocin in Bacillus anthracis and Bacillus cereus with repeated Cys-Xaa-Xaa motifsDaniel 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... - Orphan SelD proteins and selenium-dependent molybdenum hydroxylasesDaniel 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... - Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modificationDaniel 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... - Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modificationDaniel 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... - TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomesJeremy 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... - A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomesDaniel 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... - 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 speciesKaren 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... - 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 strainSteven 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... - Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83Karen 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... - Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soilsNaomi L Ward
The Institute for Genomic Research, Rockville, Maryland 20850, USA
Appl Environ Microbiol 75:2046-56. 2009.... 
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensisJohn F Heidelberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nat Biotechnol 20:1118-23. 2002....- Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor familyDaniel 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... - Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901Martin Wu
The Institute for Genomic Research, Rockville, Maryland, United States of America
PLoS Genet 1:e65. 2005.... - Structural flexibility in the Burkholderia mallei genomeWilliam 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... - Comparative genomics of emerging human ehrlichiosis agentsJulie 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... - 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... - The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteriaTimothy 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... - ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological processMalay 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... - The TIGRFAMs database of protein familiesDaniel 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... - The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000C 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... - Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein functionJeremy 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... - Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteriaJeremy 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... - Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentusJonathan 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... - Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringensGarry S A Myers
The Institute for Genomic Research, Rockville, Maryland 20850, USA
Genome Res 16:1031-40. 2006.... - Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomicsDaniel 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... - The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris HildenboroughJohn F Heidelberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nat Biotechnol 22:554-9. 2004.... - The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacteriumJonathan 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...