Works matching AU Haft, Daniel H.

Results: 40

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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