Daniel H. Haft

According to our database, Daniel H. Haft authored at least 26 papers between 1997 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

InterPro in 2022.

Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan J. Bridge, Lucy J. Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman

Nucleic Acids Res., January, 2023

2021

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.

Wenjun Li, Kathleen O'Neill, Daniel H. Haft, Michael DiCuccio, Vyacheslav Chetvernin, Azat Badretdin, George Coulouris, Farideh Chitsaz, Myra K. Derbyshire, A. Scott Durkin, Noreen R. Gonzales, Marc Gwadz, Christopher J. Lanczycki, James S. Song, Narmada Thanki, Jiyao Wang, Roxanne A. Yamashita, Mingzhang Yang, Chanjuan Zheng, Aron Marchler-Bauer, Françoise Thibaud-Nissen

Nucleic Acids Res., 2021

The InterPro protein families and domains database: 20 years on.

Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasamy, Alex L. Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna J. Richardson, Gustavo A. Salazar, Lowri Williams, Peer Bork, Alan J. Bridge, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman, Robert D. Finn

Nucleic Acids Res., 2021

2018

RefSeq: an update on prokaryotic genome annotation and curation.

Daniel H. Haft, Michael DiCuccio, Azat Badretdin, Vyacheslav Brover, Vyacheslav Chetvernin, Kathleen O'Neill, Wenjun Li, Farideh Chitsaz, Myra K. Derbyshire, Noreen R. Gonzales, Marc Gwadz, Fu Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Françoise Thibaud-Nissen, Lewis Y. Geer, Aron Marchler-Bauer, Kim D. Pruitt

Nucleic Acids Res., 2018

2016

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

Nuala A. O'Leary, Mathew W. Wright, J. Rodney Brister, Stacy Ciufo, Diana Haddad, Richard McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-Adjei, Alexander Astashyn, Azat Badretdin, Yiming Bao, Olga Blinkova, Vyacheslav Brover, Vyacheslav Chetvernin, Jinna Choi, Eric Cox, Olga D. Ermolaeva, Catherine M. Farrell, Tamara Goldfarb, Tripti Gupta, Daniel H. Haft, Eneida Hatcher, Wratko Hlavina, Vinita S. Joardar, Vamsi K. Kodali, Wenjun Li, Donna R. Maglott, Patrick Masterson, Kelly M. McGarvey, Michael R. Murphy, Kathleen O'Neill, Shashikant Pujar, Sanjida H. Rangwala, Daniel Rausch, Lillian D. Riddick, Conrad L. Schoch, Andrei Shkeda, Susan S. Storz, Hanzhen Sun, Françoise Thibaud-Nissen, Igor Tolstoy, Raymond E. Tully, Anjana R. Vatsan, Craig Wallin, David Webb, Wendy Wu, Melissa J. Landrum, Avi Kimchi, Tatiana A. Tatusova, Michael DiCuccio, Paul A. Kitts, Terence D. Murphy, Kim D. Pruitt

Nucleic Acids Res., 2016

2015

The InterPro protein families database: the classification resource after 15 years.

Alex L. Mitchell, Hsin-Yu Chang, Louise C. Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew, Claudia Rato, Siew-Yit Yong, Alex Bateman, Marco Punta, Teresa K. Attwood, Christian J. A. Sigrist, Nicole Redaschi, Catherine Rivoire, Ioannis Xenarios, Daniel Kahn, Dominique Guyot, Peer Bork, Ivica Letunic, Julian Gough, Matt E. Oates, Daniel H. Haft, Hongzhan Huang, Darren A. Natale, Cathy H. Wu, Christine A. Orengo, Ian Sillitoe, Huaiyu Mi, Paul D. Thomas, Robert D. Finn

Nucleic Acids Res., 2015

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David E. Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Ísberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O'Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Åke Västermark, Gerrit Vriend

Database J. Biol. Databases Curation, 2015

2013

TIGRFAMs and Genome Properties in 2013.

Daniel H. Haft, Jeremy D. Selengut, Roland A. Richter, Derek M. Harkins, Malay Kumar Basu, Erin Beck

Nucleic Acids Res., 2013

2012

CharProtDB: a database of experimentally characterized protein annotations.

Ramana Madupu, Alexander R. Richter, Robert J. Dodson, Lauren M. Brinkac, Derek M. Harkins, A. Scott Durkin, Susmita Shrivastava, Granger G. Sutton, Daniel H. Haft

Nucleic Acids Res., 2012

InterPro in 2011: new developments in the family and domain prediction database.

Sarah Hunter, Philip Jones, Alex L. Mitchell, Rolf Apweiler, Teresa K. Attwood, Alex Bateman, Thomas Bernard, David Binns, Peer Bork, Sarah W. Burge, Edouard De Castro, Penny C. Coggill, Matthew Corbett, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn, Matthew Fraser, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Conor McMenamin, Huaiyu Mi, Prudence Mutowo-Meullenet, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Sebastien Pesseat, Marco Punta, Antony F. Quinn, Catherine Rivoire, Amaia Sangrador-Vegas, Jeremy D. Selengut, Christian J. A. Sigrist, Maxim Scheremetjew, John G. Tate, Manjulapramila Thimmajanarthanan, Paul D. Thomas, Cathy H. Wu, Corin Yeats, Siew-Yit Yong

Nucleic Acids Res., 2012

AntiFam: a tool to help identify spurious ORFs in protein annotation.

Ruth Y. Eberhardt, Daniel H. Haft, Marco Punta, Maria Jesus Martin, Claire O'Donovan, Alex Bateman

Database J. Biol. Databases Curation, 2012

2011

ProPhylo: Partial Phylogenetic Profiling to guide protein family construction and assignment of biological process.

Malay Kumar Basu, Jeremy D. Selengut, Daniel H. Haft

BMC Bioinform., 2011

2010

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, Douglas B. Rusch, Daniel H. Haft

BMC Bioinform., 2010

2009

InterPro: the integrative protein signature database.

Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Aurélie Laugraud, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex L. Mitchell, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Antony F. Quinn, Jeremy D. Selengut, Christian J. A. Sigrist, Manjula Thimma, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats

Nucleic Acids Res., 2009

2007

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.

Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle Gwinn-Giglio, William C. Nelson, Alexander R. Richter, Owen White

Nucleic Acids Res., 2007

New developments in the InterPro database.

Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Louise C. Daugherty, Mark Dibley, Robert D. Finn, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicolas Hulo, Sarah Hunter, Daniel Kahn, Alexander Kanapin, Anish Kejariwal, Alberto Labarga, Petra S. Langendijk-Genevaux, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex L. Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Christine A. Orengo, Robert Petryszak, Jeremy D. Selengut, Christian J. A. Sigrist, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats

Nucleic Acids Res., 2007

2005

A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes.

Daniel H. Haft, Jeremy D. Selengut, Emmanuel F. Mongodin, Karen E. Nelson

PLoS Comput. Biol., 2005

InterPro, progress and status in 2005.

Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex L. Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu

Nucleic Acids Res., 2005

Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.

Daniel H. Haft, Jeremy D. Selengut, Lauren M. Brinkac, Nikhat Zafar, Owen White

Bioinform., 2005

2003

The InterPro Database, 2003 brings increased coverage and new features.

Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, Evgeni M. Zdobnov

Nucleic Acids Res., 2003

The TIGRFAMs database of protein families.

Daniel H. Haft, Jeremy D. Selengut, Owen White

Nucleic Acids Res., 2003

2002

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites

Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Sam Griffiths-Jones, Daniel H. Haft, Henning Hermjakob, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, Sue Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Florence Servant, Christian J. A. Sigrist

Briefings Bioinform., 2002

HMM-based databases in InterPro.

Alex Bateman, Daniel H. Haft

Briefings Bioinform., 2002

2001

TIGRFAMs: a protein family resource for the functional identification of proteins.

Daniel H. Haft, Brendan J. Loftus, Delwood L. Richardson, Fan Yang, Jonathan A. Eisen, Ian T. Paulsen, Owen White

Nucleic Acids Res., 2001

1998

The PIR-International Protein Sequence Database.

Winona C. Barker, John S. Garavelli, Daniel H. Haft, Lois T. Hunt, Christopher R. Marzec, Bruce C. Orcutt, Geetha Y. Srinivasarao, Lai-Su L. Yeh, Robert S. Ledley, Hans-Werner Mewes, Friedhelm Pfeiffer, Akira Tsugita

Nucleic Acids Res., 1998

1997

The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database.

David G. George, Robert J. Dodson, John S. Garavelli, Daniel H. Haft, Lois T. Hunt, Christopher R. Marzec, Bruce C. Orcutt, Kathryn E. Sidman, Geetha Y. Srinivasarao, Lai-Su L. Yeh, Leslie Arminski, Robert S. Ledley, Akira Tsugita, Winona C. Barker

Nucleic Acids Res., 1997