Works by Haft, Daniel H.

Results: 40

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.
Published in:
Nature Biotechnology, 2004, v. 22, n. 5, p. 554, doi. 10.1038/nbt959
By:
- Heidelberg, John F.;
- Seshadri, Rekha;
- Haveman, Shelley A.;
- Hemme, Christopher L.;
- Paulsen, Ian T.;
- Kolonay, James F.;
- Eisen, Jonathan A.;
- Ward, Naomi;
- Methe, Barbara;
- Brinkac, Lauren M.;
- Daugherty, Sean C.;
- Deboy, Robert T.;
- Dodson, Robert J.;
- Durkin, A. Scott;
- Madupu, Ramana;
- Nelson, William C.;
- Sullivan, Steven A.;
- Fouts, Derrick;
- Haft, Daniel H.;
- Selengut, Jeremy
Publication type:
Article
High-speed microbial community profiling.
Published in:
Nature Methods, 2012, v. 9, n. 8, p. 793, doi. 10.1038/nmeth.2080
By:
- Haft, Daniel H;
- Tovchigrechko, Andrey
Publication type:
Article
Sites Inferred by Metabolic Background AssertionLabeling (SIMBAL): adapting the PartialPhylogenetic Profiling algorithm to scansequences for signatures that predict proteinfunction.
Published in:
BMC Bioinformatics, 2010, v. 11, p. 52, doi. 10.1186/1471-2105-11-52
By:
- Selengut, Jeremy D.;
- Rusch, Douglas B.;
- Haft, Daniel H.
Publication type:
Article
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners.
Published in:
BMC Genomics, 2011, v. 12, n. 1, p. 1, doi. 10.1186/1471-2164-12-21
By:
- Haft, Daniel H.
Publication type:
Article
Expansion of ribosomally produced naturalproducts: a nitrile hydratase- and Nif11-relatedprecursor family.
Published in:
BMC Biology, 2010, v. 8, p. 70, doi. 10.1186/1741-7007-8-70
By:
- Haft, Daniel H.;
- Basu, Malay Kumar;
- Mitchell, Douglas A.
Publication type:
Article
A strain-variable bacteriocin in Bacillus anthracis and Bacillus cereus with repeated Cys-Xaa-Xaa motifs.
Published in:
Biology Direct, 2009, v. 4, p. 1, doi. 10.1186/1745-6150-4-15
By:
- Haft, Daniel H.
Publication type:
Article
Orphan SelD proteins and selenium-dependent molybdenum hydroxylases.
Published in:
Biology Direct, 2008, v. 3, p. 1, doi. 10.1186/1745-6150-3-4
By:
- Haft, Daniel H.;
- Self, William T.
Publication type:
Article
A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes.
Published in:
PLoS Computational Biology, 2005, v. 1, n. 6, p. 474, doi. 10.1371/journal.pcbi.0010060
By:
- Haft, Daniel H.;
- Selengut, Jeremy;
- Mongodin, Emmanuel F.;
- Nelson, Karen E.;
- Eisen, Jonathan A.
Publication type:
Article
Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima.
Published in:
Nature, 1999, v. 399, n. 6734, p. 323, doi. 10.1038/20601
By:
- Nelson, Karen E.;
- Clayton, Rebecca A.;
- Gill, Steven R.;
- Gwinn, Michelle L.;
- Dodson, Robert J.;
- Haft, Daniel H.;
- Hickey, Erin K.;
- Peterson, Jeremy D.;
- Nelson, William C.;
- Ketchum, Karen A.;
- McDonald, Lisa;
- Utterback, Teresa R.;
- Malek, Joel A.;
- Linher, Katja D.;
- Garrett, Mina M.;
- Stewart, Ashley M.;
- Cotton, Matthew D.;
- Pratt, Matthew S.;
- Phillips, Cheryl A.;
- Richardson, Delwood
Publication type:
Article
Cell Contact-Dependent Outer Membrane Exchange in Myxobacteria: Genetic Determinants and Mechanism.
Published in:
PLoS Genetics, 2012, v. 8, n. 4, p. 1, doi. 10.1371/journal.pgen.1002626
By:
- Pathak, Darshankumar T.;
- Wei, Xueming;
- Bucuvalas, Alex;
- Haft, Daniel H.;
- Gerloff, Dietlind L.;
- Wall, Daniel
Publication type:
Article
Correction: Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901.
Published in:
2006
By:
- Wu, Martin;
- Ren, Qinghu;
- Durkin, A. Scott;
- Daugherty, Sean C.;
- Brinkac, Lauren M.;
- Dodson, Robert J.;
- Madupu, Ramana;
- Sullivan, Steven A.;
- Kolonay, James F.;
- Haft, Daniel H.;
- Nelson, William C.;
- Tallon, Luke J.;
- Jones, Kristine M.;
- Ulrich, Luke E.;
- Gonzalez, Juan M.;
- Zhulin, Igor B.;
- Robb, Frank T.;
- Eisen, Jonathan A.
Publication type:
Correction Notice
An updated evolutionary classification of CRISPR-Cas systems.
Published in:
Nature Reviews Microbiology, 2015, v. 13, n. 11, p. 722, doi. 10.1038/nrmicro3569
By:
- Makarova, Kira S.;
- Wolf, Yuri I.;
- Alkhnbashi, Omer S.;
- Costa, Fabrizio;
- Shah, Shiraz A.;
- Saunders, Sita J.;
- Barrangou, Rodolphe;
- Brouns, Stan J. J.;
- Charpentier, Emmanuelle;
- Haft, Daniel H.;
- Horvath, Philippe;
- Moineau, Sylvain;
- Mojica, Francisco J. M.;
- Terns, Rebecca M.;
- Terns, Michael P.;
- White, Malcolm F.;
- Yakunin, Alexander F.;
- Garrett, Roger A.;
- van der Oost, John;
- Backofen, Rolf
Publication type:
Article
Evolution and classification of the CRISPR-Cas systems.
Published in:
2011
By:
- Makarova, Kira S.;
- Haft, Daniel H.;
- Barrangou, Rodolphe;
- Brouns, Stan J. J.;
- Charpentier, Emmanuelle;
- Horvath, Philippe;
- Moineau, Sylvain;
- Mojica, Francisco J. M.;
- Wolf, Yuri I.;
- Yakunin, Alexander F.;
- van der Oost, John;
- Koonin, Eugene V.
Publication type:
Opinion
Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors.
Published in:
Scientific Reports, 2017, p. 41074, doi. 10.1038/srep41074
By:
- Haft, Daniel H.;
- Pierce, Phillip G.;
- Mayclin, Stephen J.;
- Sullivan, Amy;
- Gardberg, Anna S.;
- Abendroth, Jan;
- Begley, Darren W.;
- Phan, Isabelle Q.;
- Staker, Bart L.;
- Myler, Peter J.;
- Marathias, Vasilios M.;
- Lorimer, Donald D.;
- Edwards, Thomas E.
Publication type:
Article
Both widespread PEP‐CTERM proteins and exopolysaccharides are required for floc formation of <italic>Zoogloea resiniphila</italic> and other activated sludge bacteria.
Published in:
Environmental Microbiology, 2018, v. 20, n. 5, p. 1677, doi. 10.1111/1462-2920.14080
By:
- Gao, Na;
- Xia, Ming;
- Dai, Jingcheng;
- Yu, Dianzhen;
- An, Weixing;
- Li, Shuyang;
- Liu, Shuangyuan;
- He, Penghui;
- Zhang, Liping;
- Wu, Zhenbin;
- Bi, Xuezhi;
- Chen, Shouwen;
- Haft, Daniel H.;
- Qiu, Dongru
Publication type:
Article
Methanobactin and MmoD work in concert to act as the 'copper-switch' in methanotrophs.
Published in:
Environmental Microbiology, 2013, v. 15, n. 11, p. 3077, doi. 10.1111/1462-2920.12150
By:
- Semrau, Jeremy D.;
- Jagadevan, Sheeja;
- DiSpirito, Alan A.;
- Khalifa, Ashraf;
- Scanlan, Julie;
- Bergman, Brandt H.;
- Freemeier, Brittani C.;
- Baral, Bipin S.;
- Bandow, Nathan L.;
- Vorobev, Alexey;
- Haft, Daniel H.;
- Vuilleumier, Stéphane;
- Murrell, J. Colin
Publication type:
Article
Pathogenomic Inference of Virulence-Associated Genes in Leptospira interrogans.
Published in:
PLoS Neglected Tropical Diseases, 2013, v. 7, n. 10, p. 1, doi. 10.1371/journal.pntd.0002468
By:
- Lehmann, Jason S.;
- Fouts, Derrick E.;
- Haft, Daniel H.;
- Cannella, Anthony P.;
- Ricaldi, Jessica N.;
- Brinkac, Lauren;
- Harkins, Derek;
- Durkin, Scott;
- Sanka, Ravi;
- Sutton, Granger;
- Moreno, Angelo;
- Vinetz, Joseph M.;
- Matthias, Michael A.
Publication type:
Article
Pathogenomic Inference of Virulence-Associated Genes in <i>Leptospira interrogans</i>.
Published in:
PLoS Neglected Tropical Diseases, 2013, v. 7, n. 10, p. 1, doi. 10.1371/journal.pntd.0002468
By:
- Lehmann, Jason S.;
- Fouts, Derrick E.;
- Haft, Daniel H.;
- Cannella, Anthony P.;
- Ricaldi, Jessica N.;
- Brinkac, Lauren;
- Harkins, Derek;
- Durkin, Scott;
- Sanka, Ravi;
- Sutton, Granger;
- Moreno, Angelo;
- Vinetz, Joseph M.;
- Matthias, Michael A.
Publication type:
Article
A comprehensive software suite for protein family construction and functional site prediction.
Published in:
PLoS ONE, 2017, v. 12, n. 2, p. 1, doi. 10.1371/journal.pone.0171758
By:
- Haft, David Renfrew;
- Haft, Daniel H.
Publication type:
Article
Proposal for assignment of allele numbers for mobile colistin resistance (mcr) genes.
Published in:
2018
By:
- Partridge, Sally R;
- Pilato, Vincenzo Di;
- Doi, Yohei;
- Feldgarden, Michael;
- Haft, Daniel H;
- Klimke, William;
- Kumar-Singh, Samir;
- Liu, Jian-Hua;
- Malhotra-Kumar, Surbhi;
- Prasad, Arjun;
- Di Pilato, Vincenzo;
- Rossolini, Gian Maria;
- Schwarz, Stefan;
- Shen, Jianzhong;
- Walsh, Timothy;
- Wang, Yang;
- Xavier, Basil Britto
Publication type:
journal article
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.
Published in:
Nucleic Acids Research, 2007, v. 35, p. d260, doi. 10.1093/nar/gkl1043
By:
- Selengut, Jeremy D.;
- Haft, Daniel H.;
- Davidsen, Tanja;
- Ganapathy, Anurhada;
- Gwinn-Giglio, Michelle;
- Nelson, William C.;
- Richter, Alexander R.;
- White, Owen
Publication type:
Article
The TIGRFAMs database of protein families.
Published in:
Nucleic Acids Research, 2003, v. 31, n. 1, p. 371, doi. 10.1093/nar/gkg128
By:
- Haft, Daniel H.;
- Selengut, Jeremy D.;
- White, Owen
Publication type:
Article
TIGRFAMs: a protein family resource for the functional identification of proteins.
Published in:
Nucleic Acids Research, 2001, v. 29, n. 1, p. 41, doi. 10.1093/nar/29.1.41
By:
- Haft, Daniel H.;
- Loftus, Brendan J.;
- Richardson, Delwood L.;
- Yang, Fan;
- Eisen, Jonathan A.;
- Paulsen, Ian T.;
- White, Owen
Publication type:
Article
The PIR‐International Protein Sequence Database.
Published in:
Nucleic Acids Research, 1998, v. 26, n. 1, p. 27, doi. 10.1093/nar/26.1.27
By:
- Barker, Winona C.;
- Garavelli, John S.;
- Haft, Daniel H.;
- Hunt, Lois T.;
- Marzec, Christopher R.;
- Orcutt, Bruce C.;
- Srinivasarao, Geetha Y.;
- Yeh, Lai‐Su L.;
- Ledley, Robert S.;
- Mewes, Hans‐Werner;
- Pfeiffer, Friedhelm;
- Tsugita, Akira
Publication type:
Article
The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database.
Published in:
Nucleic Acids Research, 1997, v. 25, n. 1, p. 24, doi. 10.1093/nar/25.1.24
By:
- George, David G.;
- Dodson, Robert J.;
- Garavelli, John S.;
- Haft, Daniel H.;
- Hunt, Lois T.;
- Marzec, Christopher R.;
- Orcutt, Bruce C.;
- Sidman, Kathryn E.;
- Srinivasarao, Geetha Y.;
- Yeh, Lai-Su L.;
- Arminski, Leslie M.;
- Ledley, Robert S.;
- Tsugita, Akira;
- Barker, Winona C.
Publication type:
Article
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
Published in:
2015
By:
- Babbitt, Patricia C.;
- Bagos, Pantelis G.;
- Bairoch, Amos;
- Bateman, Alex;
- Chatonnet, Arnaud;
- Jinan Chen, Mark;
- Craik, David J.;
- Finn, Robert D.;
- Gloriam, David;
- Haft, Daniel H.;
- Henrissat, Bernard;
- Holliday, Gemma L.;
- Isberg, Vignir;
- Kaas, Quentin;
- Landsman, David;
- Lenfant, Nicolas;
- Manning, Gerard;
- Nozomi Nagano;
- Srinivasan, Narayanaswamy;
- O'Donovan, Claire
Publication type:
Proceeding
AntiFam: a tool to help identify spurious ORFs in protein annotation.
Published in:
Database: The Journal of Biological Databases & Curation, 2012, v. 2012, p. 1, doi. 10.1093/database/bas003
By:
- Eberhardt, Ruth Y.;
- Haft, Daniel H.;
- Punta, Marco;
- Martin, Maria;
- O'Donovan, Claire;
- Bateman, Alex
Publication type:
Article
InterPro: the protein sequence classification resource in 2025.
Published in:
Nucleic Acids Research, 2025, v. 53, n. D1, p. D444, doi. 10.1093/nar/gkae1082
By:
- Blum, Matthias;
- Andreeva, Antonina;
- Florentino, Laise Cavalcanti;
- Chuguransky, Sara Rocio;
- Grego, Tiago;
- Hobbs, Emma;
- Pinto, Beatriz Lazaro;
- Orr, Ailsa;
- Paysan-Lafosse, Typhaine;
- Ponamareva, Irina;
- Salazar, Gustavo A;
- Bordin, Nicola;
- Bork, Peer;
- Bridge, Alan;
- Colwell, Lucy;
- Gough, Julian;
- Haft, Daniel H;
- Letunic, Ivica;
- Llinares-López, Felipe;
- Marchler-Bauer, Aron
Publication type:
Article
RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes.
Published in:
Nucleic Acids Research, 2024, v. 52, n. D1, p. D762, doi. 10.1093/nar/gkad988
By:
- Haft, Daniel H;
- Badretdin, Azat;
- Coulouris, George;
- DiCuccio, Michael;
- Durkin, A Scott;
- Jovenitti, Eric;
- Li, Wenjun;
- Mersha, Megdelawit;
- O'Neill, Kathleen R;
- Virothaisakun, Joel;
- Thibaud-Nissen, Françoise
Publication type:
Article
InterPro in 2022.
Published in:
Nucleic Acids Research, 2023, v. 51, n. D1, p. D418, doi. 10.1093/nar/gkac993
By:
- Paysan-Lafosse, Typhaine;
- Blum, Matthias;
- Chuguransky, Sara;
- Grego, Tiago;
- Pinto, Beatriz Lázaro;
- Salazar, Gustavo A;
- Bileschi, Maxwell L;
- Bork, Peer;
- Bridge, Alan;
- Colwell, Lucy;
- Gough, Julian;
- Haft, Daniel H;
- Letunić, Ivica;
- Marchler-Bauer, Aron;
- Mi, Huaiyu;
- Natale, Darren A;
- Orengo, Christine A;
- Pandurangan, Arun P;
- Rivoire, Catherine;
- Sigrist, Christian J A
Publication type:
Article
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
Published in:
Nature, 2000, v. 406, n. 6795, p. 477, doi. 10.1038/35020000
By:
- Heidelberg, John F.;
- Eisen, Jonathan A.;
- Nelson, William C.;
- Clayton, Rebecca A.;
- Gwinn, Michelle L.;
- Dodson, Robert J.;
- Haft, Daniel H.;
- Hickey, Erin K.;
- Peterson, Jeremy D.;
- Umayam, Lowell;
- Gill, Steven R.;
- Nelson, Karen E.;
- Read, Timothy D.;
- Tettelin, Herve;
- Richardson, Delwood;
- Ermolaeva, Marie D.;
- Vamathevan, Jessica;
- Bass, Steven;
- Haiying Qin;
- Dragoi, Ioana
Publication type:
Article
Folding the unfoldable: using AlphaFold to explore spurious proteins.
Published in:
Bioinformatics Advances, 2022, v. 2, n. 1, p. 1, doi. 10.1093/bioadv/vbab043
By:
- Monzon, Vivian;
- Haft, Daniel H;
- Bateman, Alex
Publication type:
Article
HMM-based databases in InterPro.
Published in:
Briefings in Bioinformatics, 2002, v. 3, n. 3, p. 236, doi. 10.1093/bib/3.3.236
By:
- Bateman, Alex;
- Haft, Daniel H.
Publication type:
Article
AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence.
Published in:
Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-91456-0
By:
- Feldgarden, Michael;
- Brover, Vyacheslav;
- Gonzalez-Escalona, Narjol;
- Frye, Jonathan G.;
- Haendiges, Julie;
- Haft, Daniel H.;
- Hoffmann, Maria;
- Pettengill, James B.;
- Prasad, Arjun B.;
- Tillman, Glenn E.;
- Tyson, Gregory H.;
- Klimke, William
Publication type:
Article
The InterPro protein families and domains database: 20 years on.
Published in:
Nucleic Acids Research, 2021, v. 49, n. D1, p. D344, doi. 10.1093/nar/gkaa977
By:
- Blum, Matthias;
- Chang, Hsin-Yu;
- Chuguransky, Sara;
- Grego, Tiago;
- Kandasaamy, Swaathi;
- Mitchell, Alex;
- Nuka, Gift;
- Paysan-Lafosse, Typhaine;
- Qureshi, Matloob;
- Raj, Shriya;
- Richardson, Lorna;
- Salazar, Gustavo A;
- Williams, Lowri;
- Bork, Peer;
- Bridge, Alan;
- Gough, Julian;
- Haft, Daniel H;
- Letunic, Ivica;
- Marchler-Bauer, Aron;
- Mi, Huaiyu
Publication type:
Article
RefSeq: an update on prokaryotic genome annotation and curation.
Published in:
Nucleic Acids Research, 2018, v. 46, n. D1, p. D851, doi. 10.1093/nar/gkx1068
By:
- Haft, Daniel H;
- DiCuccio, Michael;
- Badretdin, Azat;
- Brover, Vyacheslav;
- Chetvernin, Vyacheslav;
- O'Neill, Kathleen;
- Li, Wenjun;
- Chitsaz, Farideh;
- Derbyshire, Myra K;
- Gonzales, Noreen R
Publication type:
Article
Simultaneous non-contiguous deletions using large synthetic DNA and site-specific recombinases.
Published in:
Nucleic Acids Research, 2014, v. 42, n. 14, p. e111, doi. 10.1093/nar/gku509
By:
- Krishnakumar, Radha;
- Grose, Carissa;
- Haft, Daniel H.;
- Zaveri, Jayshree;
- Alperovich, Nina;
- Gibson, Daniel G.;
- Merryman, Chuck;
- Glass, John I.
Publication type:
Article
TIGRFAMs and Genome Properties in 2013.
Published in:
Nucleic Acids Research, 2013, v. 41, p. D387, doi. 10.1093/nar/gks1234
By:
- Haft, Daniel H.;
- Selengut, Jeremy D.;
- Beck, Erin;
- Harkins, Derek;
- Basu, Malay K.;
- Richter, Roland A.
Publication type:
Article
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.
Published in:
PLoS Neglected Tropical Diseases, 2016, v. 10, n. 2, p. 1, doi. 10.1371/journal.pntd.0004403
By:
- Fouts, Derrick E.;
- Matthias, Michael A.;
- Adhikarla, Haritha;
- Adler, Ben;
- Amorim-Santos, Luciane;
- Berg, Douglas E.;
- Bulach, Dieter;
- Buschiazzo, Alejandro;
- Chang, Yung-Fu;
- Galloway, Renee L.;
- Haake, David A.;
- Haft, Daniel H.;
- Hartskeerl, Rudy;
- Ko, Albert I.;
- Levett, Paul N.;
- Matsunaga, James;
- Mechaly, Ariel E.;
- Monk, Jonathan M.;
- Nascimento, Ana L. T.;
- Nelson, Karen E.
Publication type:
Article
GlyGly-CTERM and Rhombosortase: A C-Terminal Protein Processing Signal in a Many-to-One Pairing with a Rhomboid Family Intramembrane Serine Protease.
Published in:
PLoS ONE, 2011, v. 6, n. 12, p. 1, doi. 10.1371/journal.pone.0028886
By:
- Haft, Daniel H.;
- Varghese, Neha
Publication type:
Article