BrainGrab: Capturing Curator Expertise as Reusable Annotation Rules (2009)
Daniel H. Haft, Malay K. Basu, Roland A. Richter
Experienced biocurators can outperform automated systems on specific genes once they determine which pieces of evidence should drive annotation, and which annotations should be spread. The annotation...
Abstract Bacteriocins are peptide antibiotics from ribosomally translated precursors, produced by bacteria often through extensive post-translational modification. Minimal sequence conservation,...
Orphan SelD proteins and selenium-dependent molybdenum hydroxylases (2008)
Haft, Daniel H, Self, William T
Abstract Bacterial and Archaeal cells use selenium structurally in selenouridine-modified tRNAs, in proteins translated with selenocysteine, and in the selenium-dependent molybdenum hydroxylases...
Daniel H Haft, Daniel H Haft, William T Self
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Bacterial and Archaeal cells use selenium structurally in...
Selengut, Jeremy D., Haft, Daniel H., Davidsen, Tanja, Ganapathy, Anurhada, Gwinn-Giglio, Michelle, Nelson, William C., ...
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan A. Eisen, ...
Haft, Daniel H, Paulsen, Ian T, Ward, Naomi, Selengut, Jeremy D
Abstract Background Protein translocation to the proper cellular destination may be guided by various classes of sorting signals recognizable in the primary sequence. Detection in some genomes, but...
Comparative Genomics of Emerging Human Ehrlichiosis Agents (2006)
Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan Eisen, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
TIGRFAMs and Genome Properties: tools for the (2006)
Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle Gwinn-giglio, William C. Nelson, ...
assignment of molecular function and biological process in prokaryotic genomes
Daniel H Haft, Ian T Paulsen, Naomi Ward, Jeremy D Selengut
Research article Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic
Selengut, Jeremy D., Haft, Daniel H., Davidsen, Tanja, Ganapathy, Anurhada, Gwinn-Giglio, Michelle, Nelson, William C., ...
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff...
Myers, Garry S.A., Rasko, David A., Cheung, Jackie K., Ravel, Jacques, Seshadri, Rekha, DeBoy, Robert T., ...
Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide...
Myers, Garry S.A., Rasko, David A., Cheung, Jackie K., Ravel, Jacques, Seshadri, Rekha, DeBoy, Robert T., ...
Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide...
Selengut, Jeremy D., Haft, Daniel H., Davidsen, Tanja, Ganapathy, Anurhada, Gwinn-Giglio, Michelle, Nelson, William C., ...
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff...
Daniel H. Haft, Jeremy Selengut, Emmanuel F. Mongodin, Karen E. Nelson
Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. Repeats of 21–37 bp typically show weak dyad symmetry and...
Haft, Daniel H., Selengut, Jeremy D., Brinkac, Lauren M., Zafar, Nikhat, White, Owen
Motivation: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes...
Haft, Daniel H., Selengut, Jeremy D., Brinkac, Lauren M., Zafar, Nikhat, White, Owen
Motivation: The presence or absence of metabolic pathways, and structures provides context that makes protein annotation far more reliable. Compiling such information across microbial genomes...
Nelson, Karen E., Fouts, Derrick E., Mongodin, Emmanuel F., Ravel, Jacques, DeBoy, Robert T., Kolonay, James F., ...
The genomes of three strains of Listeria monocytogenes that have been associated with food‐borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69...
Haft, Daniel H., Selengut, Jeremy D., Brinkac, Lauren M., Zafar, Nikhat, White, Owen
Motivation: The presence or absence of metabolic pathways, and structures provides context that makes protein annotation far more reliable. Compiling such information across microbial genomes...
The TIGRFAMs database of protein families (2003)
Haft, Daniel H., Selengut, Jeremy D., White, Owen
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature...
DOI: 10.1093/nar/gkg128 The TIGRFAMs database of protein families (2002)
Daniel H. Haft, Jeremy D. Selengut, Owen White
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature...
HMM-based databases in InterPro (2002)
Bateman, Alex, Haft, Daniel H.
Protein family databases are an important resource for protein annotation and understanding protein evolution and function. In recent years hidden Markov models (HMMs) have become one of the key...
Conserved protein domains are maintained in an average ratio to proteome size (2001)
Abstract Background Conserved domains (CD) in proteins play a crucial role in protein interactions, DNA binding, enzyme activity, and other important cellular processes. We proposed to study ratios...
TIGRFAMs: a protein family resource for the functional identification of proteins (2001)
Haft, Daniel H., Loftus, Brendan J., Richardson, Delwood L., Yang, Fan, Eisen, Jonathan A., Paulsen, Ian T., ...
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional...
The PIR-International Protein Sequence Database (1998)
Winona C. Barker, John S. Garavelli, Daniel H. Haft, Lois T. Hunt, Christopher R. Marzec, Bruce C. Orcutt, ...
From its origin the Protein Information Resource (http://www-nbrf.georgetown.edu/pir/ ) has supported research on evolution and computational biology by designing and compiling a comprehensive,...
The Protein Information Resource (PIR) and the PIR-international protein sequence database (1997)
David G. George, Robert J. Dodson, John S. Garavelli, Daniel H. Haft, Lois T. Hunt, Christopher R. Marzec, ...
From its origin, the PIR has aspired to support research in computational biology and genomics through the compilation of a comprehensive, quality controlled and well-organized protein sequence...
The PIR-International protein sequence database (1996)
Winona C. Barker, John S. Garavelli, Daniel H. Haft, Lois T. Hunt, Christopher R. Marzec, Bruce C. Orcutt, ...
From its origin the Protein Information Resource
TIGRFAMs: a protein family resource for the functional identification of proteins
Haft, Daniel H., Loftus, Brendan J., Richardson, Delwood L., Yang, Fan, Eisen, Jonathan A., Paulsen, Ian T., ...
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional...
Complete genome sequence of Caulobacter crescentus
Nierman, William C., Feldblyum, Tamara V., Laub, Michael T., Paulsen, Ian T., Nelson, Karen E., Eisen, Jonathan, ...
The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic...
Haft, Carol Renfrew, Barr, Valarie A., Haft, Daniel H., Taylor, Simeon I.
Sorting nexin 1 (SNX1) is a protein that binds to the epidermal growth factor (EGF) receptor and is proposed to play a role in directing EGF receptors to lysosomes for degradation (R. C. Kurten, D....
Eisen, Jonathan A., Nelson, Karen E., Paulsen, Ian T., Heidelberg, John F., Wu, Martin, Dodson, Robert J., ...
The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum...
The TIGRFAMs database of protein families
Haft, Daniel H., Selengut, Jeremy D., White, Owen
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature...
Buell, C. Robin, Joardar, Vinita, Lindeberg, Magdalen, Selengut, Jeremy, Paulsen, Ian T., Gwinn, Michelle L., ...
We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome...
Complete Genome Sequence of the Oral Pathogenic Bacterium Porphyromonas gingivalis Strain W83
Nelson, Karen E., Fleischmann, Robert D., DeBoy, Robert T., Paulsen, Ian T., Fouts, Derrick E., Eisen, Jonathan A., ...
The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium Porphyromonas gingivalis strain W83, a major contributor to periodontal disease, was determined. Whole-genome...
Complete Genome Sequence of the Oral Pathogenic Bacterium Porphyromonas gingivalis Strain W83
Nelson, Karen E., Fleischmann, Robert D., DeBoy, Robert T., Paulsen, Ian T., Fouts, Derrick E., Eisen, Jonathan A., ...
Nelson, Karen E., Fouts, Derrick E., Mongodin, Emmanuel F., Ravel, Jacques, DeBoy, Robert T., Kolonay, James F., ...
The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69...
Structural flexibility in the Burkholderia mallei genome
Nierman, William C., DeShazer, David, Kim, H. Stanley, Tettelin, Herve, Nelson, Karen E., Feldblyum, Tamara, ...
The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of...
Gill, Steven R., Fouts, Derrick E., Archer, Gordon L., Mongodin, Emmanuel F., DeBoy, Robert T., Ravel, Jacques, ...
Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent...
Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., ...
The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single...
Haft, Daniel H, Selengut, Jeremy, Mongodin, Emmanuel F, Nelson, Karen E
Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. Repeats of 21–37 bp typically show weak dyad symmetry and...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
TIGRFAMs: a protein family resource for the functional identification of proteins
Haft, Daniel H., Loftus, Brendan J., Richardson, Delwood L., Yang, Fan, Eisen, Jonathan A., Paulsen, Ian T., ...
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional...
Complete genome sequence of Caulobacter crescentus
Nierman, William C., Feldblyum, Tamara V., Laub, Michael T., Paulsen, Ian T., Nelson, Karen E., Eisen, Jonathan, ...
The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic...
Haft, Carol Renfrew, Barr, Valarie A., Haft, Daniel H., Taylor, Simeon I.
Sorting nexin 1 (SNX1) is a protein that binds to the epidermal growth factor (EGF) receptor and is proposed to play a role in directing EGF receptors to lysosomes for degradation (R. C. Kurten, D....
Eisen, Jonathan A., Nelson, Karen E., Paulsen, Ian T., Heidelberg, John F., Wu, Martin, Dodson, Robert J., ...
The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum...
The TIGRFAMs database of protein families
Haft, Daniel H., Selengut, Jeremy D., White, Owen
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature...
Buell, C. Robin, Joardar, Vinita, Lindeberg, Magdalen, Selengut, Jeremy, Paulsen, Ian T., Gwinn, Michelle L., ...
We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome...
Complete Genome Sequence of the Oral Pathogenic Bacterium Porphyromonas gingivalis Strain W83
Nelson, Karen E., Fleischmann, Robert D., DeBoy, Robert T., Paulsen, Ian T., Fouts, Derrick E., Eisen, Jonathan A., ...
The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium Porphyromonas gingivalis strain W83, a major contributor to periodontal disease, was determined. Whole-genome...
Complete Genome Sequence of the Oral Pathogenic Bacterium Porphyromonas gingivalis Strain W83
Nelson, Karen E., Fleischmann, Robert D., DeBoy, Robert T., Paulsen, Ian T., Fouts, Derrick E., Eisen, Jonathan A., ...
Nelson, Karen E., Fouts, Derrick E., Mongodin, Emmanuel F., Ravel, Jacques, DeBoy, Robert T., Kolonay, James F., ...
The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69...
Structural flexibility in the Burkholderia mallei genome
Nierman, William C., DeShazer, David, Kim, H. Stanley, Tettelin, Herve, Nelson, Karen E., Feldblyum, Tamara, ...
The complete genome sequence of Burkholderia mallei ATCC 23344 provides insight into this highly infectious bacterium's pathogenicity and evolutionary history. B. mallei, the etiologic agent of...
Gill, Steven R., Fouts, Derrick E., Archer, Gordon L., Mongodin, Emmanuel F., DeBoy, Robert T., Ravel, Jacques, ...
Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent...
Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., ...
The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single...
Haft, Daniel H, Selengut, Jeremy, Mongodin, Emmanuel F, Nelson, Karen E
Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. Repeats of 21–37 bp typically show weak dyad symmetry and...
Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C., Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, ...
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an...
Wu, Martin, Ren, Qinghu, Durkin, A. Scott, Daugherty, Sean C, Brinkac, Lauren M, Dodson, Robert J, ...
Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents
Dunning Hotopp, Julie C, Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan A, ...
Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens
Myers, Garry S.A., Rasko, David A., Cheung, Jackie K., Ravel, Jacques, Seshadri, Rekha, DeBoy, Robert T., ...
Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide...
Badger, Jonathan H., Hoover, Timothy R., Brun, Yves V., Weiner, Ronald M., Laub, Michael T., Alexandre, Gladys, ...
The dimorphic prosthecate bacteria (DPB) are α-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this...
Selengut, Jeremy D., Haft, Daniel H., Davidsen, Tanja, Ganapathy, Anurhada, Gwinn-Giglio, Michelle, Nelson, William C., ...
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff...
Orphan SelD proteins and selenium-dependent molybdenum hydroxylases
Haft, Daniel H, Self, William T
Bacterial and Archaeal cells use selenium structurally in selenouridine-modified tRNAs, in proteins translated with selenocysteine, and in the selenium-dependent molybdenum hydroxylases (SDMH). The...
Bacteriocins are peptide antibiotics from ribosomally translated precursors, produced by bacteria often through extensive post-translational modification. Minimal sequence conservation, short gene...
Ward, Naomi L., Challacombe, Jean F., Janssen, Peter H., Henrissat, Bernard, Coutinho, Pedro M., Wu, Martin, ...
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria,...