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2010 – today
- 2018
[j89]Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P. Nawrocki, Elena Rivas, Sean R. Eddy, Alex Bateman, Robert D. Finn, Anton I. Petrov:
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Research 46(Database-Issue): D335-D342 (2018)- [j88]Neil D. Rawlings, Alan J. Barrett, Paul D. Thomas, Xiaosong Huang, Alex Bateman, Robert D. Finn:
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Research 46(Database-Issue): D624-D632 (2018) - 2017
- [j87]Sylvain Poux, Cecilia N. Arighi, Michele Magrane, Alex Bateman, Chih-Hsuan Wei, Zhiyong Lu, Emmanuel Boutet, Hema Bye-A-Jee, Maria Livia Famiglietti, Bernd Roechert, The UniProt Consortium:
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. Bioinformatics 33(21): 3454-3460 (2017) - [j86]Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Youngmi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell:
InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Research 45(Database-Issue): D190-D199 (2017) - 2016
- [j85]Tunca Dogan, Alistair MacDougall, Rabie Saidi, Diego Poggioli, Alex Bateman, Claire O'Donovan, Maria Jesus Martin:
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. Bioinformatics 32(15): 2264-2271 (2016) - [j84]Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John G. Tate, Alex Bateman:
The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research 44(Database-Issue): 279-285 (2016) - [c1]Matt Jeffryes, Maria Liakata, Alex Bateman:
Crowdsourcing Protein Family Database Curation. ICBO/BioCreative 2016 - 2015
- [j83]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:
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database 2015 (2015) - [j82]Eric P. Nawrocki, Sarah W. Burge, Alex Bateman, Jennifer Daub, Ruth Y. Eberhardt, Sean R. Eddy, Evan W. Floden, Paul P. Gardner, Thomas A. Jones, John G. Tate, Robert D. Finn:
Rfam 12.0: updates to the RNA families database. Nucleic Acids Research 43(Database-Issue): 130-137 (2015) - [j81]Alex L. Mitchell, Hsin-Yu Chang, Louise 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:
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Research 43(Database-Issue): 213-221 (2015) - [j80]Robert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy:
HMMER web server: 2015 update. Nucleic Acids Research 43(Webserver-Issue): W30-W38 (2015) - 2014
- [j79]Debanu Das, Alexey G. Murzin, Neil D. Rawlings, Robert D. Finn, Penelope Coggill, Alex Bateman, Adam Godzik, L. Aravind:
Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis. BMC Bioinformatics 15: 75 (2014) - [j78]Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John G. Tate, Marco Punta:
Pfam: the protein families database. Nucleic Acids Research 42(Database-Issue): 222-230 (2014) - [j77]Robert D. Finn, Benjamin L. Miller, Jody Clements, Alex Bateman:
iPfam: a database of protein family and domain interactions found in the Protein Data Bank. Nucleic Acids Research 42(Database-Issue): 364-373 (2014) - [j76]Neil D. Rawlings, Matthew Waller, Alan J. Barrett, Alex Bateman:
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Research 42(Database-Issue): 503-509 (2014) - [j75]Fabian Schreiber, Mateus Patricio, Matthieu Muffato, Miguel Pignatelli, Alex Bateman:
TreeFam v9: a new website, more species and orthology-on-the-fly. Nucleic Acids Research 42(Database-Issue): 922-925 (2014) - 2013
- [j74]Pascale Gaudet, Monica C. Munoz-Torres, Marc Robinson-Rechavi, Teresa K. Attwood, Alex Bateman, J. Michael Cherry, Renate Kania, Claire O'Donovan, Chisato Yamasaki:
DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration. Database 2013 (2013) - [j73]Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta:
The challenge of increasing Pfam coverage of the human proteome. Database 2013 (2013) - [j72]Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta:
The challenge of increasing Pfam coverage of the human proteome. Database 2013 (2013) - [j71]Penelope Coggill, Ruth Y. Eberhardt, Robert D. Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L. Axelrod, L. Aravind, Alexey G. Murzin, Alex Bateman:
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila. BMC Bioinformatics 14: 265 (2013) - [j70]Ruth Y. Eberhardt, Yuanyuan Chang, Alex Bateman, Alexey G. Murzin, Herbert L. Axelrod, William C. Hwang, L. Aravind:
Filling out the structural map of the NTF2-like superfamily. BMC Bioinformatics 14: 327 (2013) - [j69]William C. Hwang, Constantina Bakolitsa, Marco Punta, Penelope Coggill, Alex Bateman, Herbert L. Axelrod, Neil D. Rawlings, Mayya Sedova, Scott N. Peterson, Ruth Y. Eberhardt, L. Aravind, Jaime Pascual, Adam Godzik:
LUD, a new protein domain associated with lactate utilization. BMC Bioinformatics 14: 341 (2013) - [j68]Sarah W. Burge, Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, Lars Barquist, Eric P. Nawrocki, Sean R. Eddy, Paul P. Gardner, Alex Bateman:
Rfam 11.0: 10 years of RNA families. Nucleic Acids Research 41(Database-Issue): 226-232 (2013) - [j67]Alex Bateman, Janet Kelso, Daniel Mietchen, Geoff MacIntyre, Tomás Di Domenico, Thomas Abeel, Darren W. Logan, Predrag Radivojac, Burkhard Rost:
ISCB Computational Biology Wikipedia Competition. PLoS Computational Biology 9(9) (2013) - 2012
- [j66]Sarah W. Burge, Teresa K. Attwood, Alex Bateman, Tanya Z. Berardini, J. Michael Cherry, Claire O'Donovan, Ioannis Xenarios, Pascale Gaudet:
Biocurators and Biocuration: surveying the 21st century challenges. Database 2012 (2012) - [j65]Ruth Y. Eberhardt, Daniel H. Haft, Marco Punta, Maria Jesus Martin, Claire O'Donovan, Alex Bateman:
AntiFam: a tool to help identify spurious ORFs in protein annotation. Database 2012 (2012) - [j64]Pascale Gaudet, Cecilia N. Arighi, Frederic B. Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D'Eustachio, Robert D. Finn, Michelle G. Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Darren A. Natale, Claire O'Donovan, B. F. Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul N. Schofield, Granger G. Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy H. Wu, Jasmine Young, Raja Mazumder:
Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database 2012 (2012) - [j63]Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren:
Bioimage informatics: a new category in Bioinformatics. Bioinformatics 28(8): 1057 (2012) - [j62]Robert D. Finn, Paul P. Gardner, Alex Bateman:
Making your database available through Wikipedia: the pros and cons. Nucleic Acids Research 40(Database-Issue): 9-12 (2012) - [j61]Marco Punta, Penny C. Coggill, Ruth Y. Eberhardt, Jaina Mistry, John G. Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn:
The Pfam protein families database. Nucleic Acids Research 40(Database-Issue): 290-301 (2012) - [j60]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 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:
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research 40(Database-Issue): 306-312 (2012) - [j59]Neil D. Rawlings, Alan J. Barrett, Alex Bateman:
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Research 40(Database-Issue): 343-350 (2012) - 2011
- [j58]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Database 2011 (2011) - [j57]Lars Juhl Jensen, Alex Bateman:
The rise and fall of supervised machine learning techniques. Bioinformatics 27(24): 3331-3332 (2011) - [j56]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research 39(Database-Issue): 7-10 (2011) - [j55]Paul P. Gardner, Jennifer Daub, John G. Tate, Benjamin L. Moore, Isabelle H. Osuch, Sam Griffiths-Jones, Robert D. Finn, Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy, Alex Bateman:
Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Research 39(Database-Issue): 141-145 (2011) - 2010
- [j54]Alex Bateman:
Curators of the world unite: the International Society of Biocuration. Bioinformatics 26(8): 991 (2010) - [j53]Robert D. Finn, Jaina Mistry, John G. Tate, Penny C. Coggill, Andreas Heger, Joanne E. Pollington, O. Luke Gavin, Prasad Gunasekaran, Goran Ceric, Kristoffer Forslund, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman:
The Pfam protein families database. Nucleic Acids Research 38(Database-Issue): 211-222 (2010) - [j52]Neil D. Rawlings, Alan J. Barrett, Alex Bateman:
MEROPS: the peptidase database. Nucleic Acids Research 38(Database-Issue): 227-233 (2010) - [j51]Darren W. Logan, Massimo Sandal, Paul P. Gardner, Magnus Manske, Alex Bateman:
Ten Simple Rules for Editing Wikipedia. PLoS Computational Biology 6(9) (2010)
2000 – 2009
- 2009
- [j50]Alex Bateman, Robert D. Finn, Peter J. Sims, Therese Wiedmer, Andreas Biegert, Johannes Söding:
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. Bioinformatics 25(2): 159-162 (2009) - [j49]
- [j48]
- [j47]Paul P. Gardner, Jennifer Daub, John G. Tate, Eric P. Nawrocki, Diana L. Kolbe, Stinus Lindgreen, Adam C. Wilkinson, Robert D. Finn, Sam Griffiths-Jones, Sean R. Eddy, Alex Bateman:
Rfam: updates to the RNA families database. Nucleic Acids Research 37(Database-Issue): 136-140 (2009) - [j46]Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise 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:
InterPro: the integrative protein signature database. Nucleic Acids Research 37(Database-Issue): 211-215 (2009) - [j45]Alex Bateman, Philip E. Bourne:
Ten Simple Rules for Chairing a Scientific Session. PLoS Computational Biology 5(9) (2009) - 2008
- [j44]Stephen John Sammut, Robert D. Finn, Alex Bateman:
Pfam 10 years on: 10 000 families and still growing. Briefings in Bioinformatics 9(3): 210-219 (2008) - [j43]Jonathan D. Wren, Alex Bateman:
Databases, data tombs and dust in the wind. Bioinformatics 24(19): 2127-2128 (2008) - [j42]
- [j41]Robert D. Finn, John G. Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
The Pfam protein families database. Nucleic Acids Research 36(Database-Issue): 281-288 (2008) - 2007
- [j40]
- [j39]Alex Bateman, Robert D. Finn:
SCOOP: a simple method for identification of novel protein superfamily relationships. Bioinformatics 23(7): 809-814 (2007) - [j38]Jaina Mistry, Alex Bateman, Robert D. Finn:
Predicting active site residue annotations in the Pfam database. BMC Bioinformatics 8 (2007) - [j37]Benjamin Schuster-Böckler, Alex Bateman:
Reuse of structural domain-domain interactions in protein networks. BMC Bioinformatics 8 (2007) - [j36]
- [j35]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 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:
New developments in the InterPro database. Nucleic Acids Research 35(Database-Issue): 224-228 (2007) - 2006
- [j34]Alex Bateman:
Bioinformatics - The new home for protein sequence motifs. Bioinformatics 22(1): 2 (2006) - [j33]Alfonso Valencia, Alex Bateman:
Software patents in Bioinformatics. Bioinformatics 22(12): 1415 (2006) - [j32]Alex Bateman, Alfonso Valencia:
Structural genomics meets computational biology. Bioinformatics 22(19): 2319 (2006) - [j31]
- [j30]Sam Griffiths-Jones, Russell J. Grocock, Stijn van Dongen, Alex Bateman, Anton J. Enright:
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Research 34(Database-Issue): 140-144 (2006) - [j29]Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
Pfam: clans, web tools and services. Nucleic Acids Research 34(Database-Issue): 247-251 (2006) - 2005
- [j28]Alfonso Valencia, Alex Bateman:
Increasing the Impact of Bioinformatics. Bioinformatics 21(1): 1-1 (2005) - [j27]Robert D. Finn, Mhairi Marshall, Alex Bateman:
iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions. Bioinformatics 21(3): 410-412 (2005) - [j26]Alex Bateman, Matthew T. G. Holden, Corin Yeats:
The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation. Bioinformatics 21(8): 1301-1303 (2005) - [j25]Benjamin Schuster-Böckler, Alex Bateman:
Visualizing profile-profile alignment: pairwise HMM logos. Bioinformatics 21(12): 2912-2913 (2005) - [j24]Alex Bateman, Alfonso Valencia:
An update from the Bioinformatics Editors. Bioinformatics 21(24): 4319 (2005) - [j23]
- [j22]Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, Alex Bateman:
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Research 33(Database-Issue): 121-124 (2005) - [j21]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:
InterPro, progress and status in 2005. Nucleic Acids Research 33(Database-Issue): 201-205 (2005) - 2004
- [j20]Alex Bateman, Alfonso Valencia:
New Leadership for Bioinformatics. Bioinformatics 20(12): 1821 (2004) - [j19]Lachlan James M. Coin, Alex Bateman, Richard Durbin:
Enhanced protein domain discovery using taxonomy. BMC Bioinformatics 5: 56 (2004) - [j18]Shane C. Dillon, Alex Bateman:
The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. BMC Bioinformatics 5: 109 (2004) - [j17]Alex Bateman, Lachlan James M. Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, Sean R. Eddy:
The Pfam protein families database. Nucleic Acids Research 32(Database-Issue): 138-141 (2004) - 2003
- [j16]David J. Studholme, Neil D. Rawlings, Alan J. Barrett, Alex Bateman:
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised. BMC Bioinformatics 4: 17 (2003) - [j15]Alex Bateman, Valerie A. Kickhoefer:
The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins. BMC Bioinformatics 4: 49 (2003) - [j14]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:
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Research 31(1): 315-318 (2003) - [j13]Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, Sean R. Eddy:
Rfam: an RNA family database. Nucleic Acids Research 31(1): 439-441 (2003) - 2002
- [j12]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:
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites. Briefings in Bioinformatics 3(3): 225-235 (2002) - [j11]Alex Bateman, Daniel H. Haft:
HMM-based databases in InterPro. Briefings in Bioinformatics 3(3): 236-245 (2002) - [j10]Sam Griffiths-Jones, Alex Bateman:
The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs. Bioinformatics 18(9): 1243-1249 (2002) - [j9]Kevin L. Howe, Alex Bateman, Richard Durbin:
QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics 18(11): 1546-1547 (2002) - [j8]
- [j7]Alex Bateman, Ewan Birney, Lorenzo Cerutti, Richard Durbin, Laurence Ettwiller, Sean R. Eddy, Sam Griffiths-Jones, Kevin L. Howe, Mhairi Marshall, Erik L. L. Sonnhammer:
The Pfam Protein Families Database. Nucleic Acids Research 30(1): 276-280 (2002) - 2001
- [j6]Paul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, Jiye Shi, Hiroki Shirai, Tom L. Blundell:
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. Bioinformatics 17(8): 748-749 (2001) - [j5]Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov:
The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29(1): 37-40 (2001) - 2000
- [j4]Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov:
InterPro-an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16(12): 1145-1150 (2000) - [j3]Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik L. L. Sonnhammer:
The Pfam Protein Families Database. Nucleic Acids Research 28(1): 263-266 (2000)
1990 – 1999
- 1999
- [j2]Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L. Sonnhammer:
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Research 27(1): 260-262 (1999) - 1998
- [j1]Erik L. L. Sonnhammer, Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin:
Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Research 26(1): 320-322 (1998)