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2020 – today
- 2021
- [j100]Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida
, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman
, Jan Baumbach
, Niko Beerenwinkel, Christian Brandt
, Marco Cacciabue, Sara Chuguransky
, Oliver Drechsel, Robert D. Finn
, Adrian Fritz, Stephan Fuchs, Georges Hattab
, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari
, Max von Kleist, Renó Kmiecinski, Denise Kühnert
, Gorka Lasso, Pieter Libin
, Markus List, Hannah F. Löchel
, Maria Jesus Martin
, Roman Martin
, Julian O. Matschinske, Alice C. McHardy, Pedro Mendes
, Jaina Mistry
, Vincent Navratil
, Eric P. Nawrocki, Áine Niamh O'toole, Nancy Ontiveros-Palacios
, Anton I. Petrov
, Guillermo Rangel-Pineros
, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes
, Lorna J. Richardson
, David L. Robertson, Sepideh Sadegh
, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz
:
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. 22(2): 642-663 (2021) - [j99]Ioanna Kalvari
, Eric P. Nawrocki
, Nancy Ontiveros-Palacios
, Joanna Argasinska
, Kevin Lamkiewicz
, Manja Marz
, Sam Griffiths-Jones
, Claire Toffano-Nioche
, Daniel Gautheret
, Zasha Weinberg
, Elena Rivas
, Sean R. Eddy
, Robert D. Finn
, Alex Bateman
, Anton I. Petrov
:
Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. 49(Database-Issue): D192-D200 (2021) - [j98]Blake A. Sweeney
, Anton I. Petrov, Carlos Eduardo Ribas, Robert D. Finn, Alex Bateman
, Maciej Szymanski, Wojciech M. Karlowski, Stefan E. Seemann, Jan Gorodkin, Jamie J. Cannone, Robin Ray Gutell
, Simon Kay, Steven J. Marygold, Gilberto dos Santos, Adam Frankish
, Jonathan M. Mudge
, Ruth Barshir, Simon Fishilevich, Patricia P. Chan, Todd M. Lowe, Ruth L. Seal, Elspeth A. Bruford
, Simona Panni, Pablo Porras
, Dimitra Karagkouni, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J. Peterson, Ioanna Kalvari, Eric P. Nawrocki, Anton S. Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle S. Scott, Lauren M. Lui, David Hoksza, Ruth C. Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, Zasha Weinberg:
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 49(Database-Issue): D212-D220 (2021) - [j97]Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni
, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm
, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou
, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo
, Helen Attrill, Nick H. Brown, Phani V. Garapati
, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond
, Penelope Garmiri
, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio
, Martin Kuiper, Astrid Lægreid, Colin Logie
, Ruth C. Lovering
, Barbara Kramarz
, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow
, Marcus C. Chibucos
, Michelle G. Giglio, Suvarna Nadendla, James B. Munro
, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal
, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras
, Sandra E. Orchard
, Anjali Shrivastava, Hsin-Yu Chang
, Robert D. Finn
, Alex L. Mitchell
, Neil D. Rawlings, Lorna J. Richardson
, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford
, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek
, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry
, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann
, Pascale Gaudet
, Anne Morgat, Erica Bakker, Tanya Z. Berardini
, Leonore Reiser
, Shabari Subramaniam, Eva Huala
, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman
, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan Bridge, Ramona Britto
, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny
, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou
, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko
, Florence Jungo, Kati Laiho, Philippe Le Mercier
, Damien Lieberherr, Antonia Lock
, Yvonne Lussi, Alistair MacDougall, Michele Magrane
, Maria Jesus Martin
, Patrick Masson
, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi
, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta
, Shyamala Sundaram, Nidhi Tyagi, Kate Warner
, Rossana Zaru, Cathy H. Wu
, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe
, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper
, Justin Elser:
The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49(Database-Issue): D325-D334 (2021) - [j96]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 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
:
The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 49(Database-Issue): D344-D354 (2021) - [j95]Jaina Mistry
, Sara Chuguransky
, Lowri Williams
, Matloob Qureshi
, Gustavo A. Salazar
, Erik L. L. Sonnhammer, Silvio C. E. Tosatto
, Lisanna Paladin
, Shriya Raj
, Lorna J. Richardson
, Robert D. Finn
, Alex Bateman
:
Pfam: The protein families database in 2021. Nucleic Acids Res. 49(Database-Issue): D412-D419 (2021) - [j94]Alex Bateman
, Maria Jesus Martin
, Sandra E. Orchard
, Michele Magrane
, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett
, Ramona Britto
, Borisas Bursteinas, Hema Bye-A-Jee
, Ray Coetzee, Austra Cukura, Alan W. Sousa da Silva, Paul Denny
, Tunca Dogan
, Thankgod Ebenezer, Jun Fan, Leyla Jael García Castro
, Penelope Garmiri
, George E. Georghiou
, Leonardo Gonzales, Emma Hatton-Ellis
, Abdulrahman Hussein
, Alexandr Ignatchenko
, Giuseppe Insana
, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock
, Rodrigo Lopez
, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira
, Mahdi Mahmoudy, Manuela Menchi
, Alok Mishra, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj
, Daniel Rice, Milagros Rodríguez-López, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta
, Edward Turner
, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner
, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal
, Delphine Baratin, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet
, Lionel Breuza, Cristina Casals-Casas, Edouard De Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Béatrice A. Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann
, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier
, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson
, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi
, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire
, Christian J. A. Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Cathy H. Wu
, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter B. McGarvey
, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh, Jian Zhang, Patrick Ruch
, Douglas Teodoro
:
UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49(Database-Issue): D480-D489 (2021) - [j93]Loïc Lannelongue, Jason Grealey, Alex Bateman
, Michael Inouye
:
Ten simple rules to make your computing more environmentally sustainable. PLoS Comput. Biol. 17(9) (2021) - 2020
- [j92]Rachel Drysdale, Charles E. Cook
, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl
, Jürgen Haas, Jerry Lanfear, Rodrigo Lopez
, Nicole Redaschi
, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman
, Alan Bridge, Guy Cochrane
, Robert D. Finn
, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Andrew Leach, Luana Licata
, Per Oksvold, Sandra E. Orchard
, Christine A. Orengo, Helen E. Parkinson
, Bengt Persson, Pablo Porras
, Jordi Rambla, Ana Rath, Charlotte Rodwell, Ugis Sarkans
, Dietmar Schomburg, Ian Sillitoe, J. Dylan Spalding
, Mathias Uhlén, Sameer Velankar
, Juan Antonio Vizcaíno
, Kalle von Feilitzen, Christian von Mering, Andrew D. Yates
, Niklas Blomberg
, Christine Durinx, Johanna R. McEntyre
:
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinform. 36(8): 2636-2642 (2020)
2010 – 2019
- 2019
- [j91]Aleix Lafita
, Pengfei Tian
, Robert B. Best
, Alex Bateman
:
TADOSS: computational estimation of tandem domain swap stability. Bioinform. 35(14): 2507-2508 (2019) - [j90]Sara El-Gebali
, Jaina Mistry
, Alex Bateman
, Sean R. Eddy
, Aurelien Luciani
, Simon C. Potter
, Matloob Qureshi
, Lorna J. Richardson
, Gustavo A. Salazar
, Alfredo Smart, Erik L. L. Sonnhammer, Layla Hirsh
, Lisanna Paladin
, Damiano Piovesan
, Silvio C. E. Tosatto
, Robert D. Finn
:
The Pfam protein families database in 2019. Nucleic Acids Res. 47(Database-Issue): D427-D432 (2019) - 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 Res. 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 Res. 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. Bioinform. 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 J. 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 Res. 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. Bioinform. 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 Res. 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 J. Biol. Databases Curation 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 Res. 43(Database-Issue): 130-137 (2015) - [j81]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
:
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 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 Res. 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 Bioinform. 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 Res. 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 Res. 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 Res. 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 Res. 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 J. Biol. Databases Curation 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 J. Biol. Databases Curation 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 J. Biol. Databases Curation 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 Bioinform. 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 Bioinform. 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 Bioinform. 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 Res. 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 Comput. Biol. 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 J. Biol. Databases Curation 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 J. Biol. Databases Curation 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 J. Biol. Databases Curation 2012 (2012) - [j63]Hanchuan Peng, Alex Bateman
, Alfonso Valencia, Jonathan D. Wren
:
Bioimage informatics: a new category in Bioinformatics. Bioinform. 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 Res. 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 Res. 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 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
:
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 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 Res. 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 J. 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 J. Biol. Databases Curation 2011 (2011) - [j57]Lars Juhl Jensen
, Alex Bateman
:
The rise and fall of supervised machine learning techniques. Bioinform. 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 J. 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 Res. 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 Res. 39(Database-Issue): 141-145 (2011) - 2010
- [j54]Alex Bateman
:
Curators of the world unite: the International Society of Biocuration. Bioinform. 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 Res. 38(Database-Issue): 211-222 (2010) - [j52]Neil D. Rawlings
, Alan J. Barrett
, Alex Bateman
:
MEROPS: the peptidase database. Nucleic Acids Res. 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 Comput. Biol. 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. Bioinform. 25(2): 159-162 (2009) - [j49]Alex Bateman
, John Quackenbush
:
Editorial. Bioinform. 25(4): 429 (2009) - [j48]Alex Bateman
, Matt Wood:
Cloud computing. Bioinform. 25(12): 1475 (2009) - [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 Res. 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 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:
InterPro: the integrative protein signature database. Nucleic Acids Res. 37(Database-Issue): 211-215 (2009) - [j45]Alex Bateman
, Philip E. Bourne:
Ten Simple Rules for Chairing a Scientific Session. PLoS Comput. Biol. 5(9) (2009) - 2008
- [j44]Stephen John Sammut, Robert D. Finn
, Alex Bateman
:
Pfam 10 years on: 10 000 families and still growing. Briefings Bioinform. 9(3): 210-219 (2008) - [j43]Jonathan D. Wren
, Alex Bateman
:
Databases, data tombs and dust in the wind. Bioinform. 24(19): 2127-2128 (2008) - [j42]Alex Bateman
:
Editorial. Nucleic Acids Res. 36(Database-Issue): 1 (2008) - [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 Res. 36(Database-Issue): 281-288 (2008) - 2007
- [j40]Alfonso Valencia, Alex Bateman
:
Editorial. Bioinform. 23(2): 133 (2007) - [j39]Alex Bateman
, Robert D. Finn
:
SCOOP: a simple method for identification of novel protein superfamily relationships. Bioinform. 23(7): 809-814 (2007) - [j38]Jaina Mistry
, Alex Bateman
, Robert D. Finn
:
Predicting active site residue annotations in the Pfam database. BMC Bioinform. 8 (2007) - [j37]Benjamin Schuster-Böckler
, Alex Bateman
:
Reuse of structural domain-domain interactions in protein networks. BMC Bioinform. 8 (2007) - [j36]Alex Bateman:
Editorial. Nucleic Acids Res. 35(Database-Issue): 1-2 (2007) - [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 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:
New developments in the InterPro database. Nucleic Acids Res. 35(Database-Issue): 224-228 (2007) - 2006
- [j34]Alex Bateman
:
Bioinformatics - The new home for protein sequence motifs. Bioinform. 22(1): 2 (2006) - [j33]Alfonso Valencia, Alex Bateman
:
Software patents in Bioinformatics. Bioinform. 22(12): 1415 (2006) - [j32]Alex Bateman
, Alfonso Valencia:
Structural genomics meets computational biology. Bioinform. 22(19): 2319 (2006) - [j31]Alex Bateman:
EDITORIAL. Nucleic Acids Res. 34(Database-Issue): 1 (2006) - [j30]Sam Griffiths-Jones
, Russell J. Grocock, Stijn van Dongen, Alex Bateman
, Anton J. Enright
:
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 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 Res. 34(Database-Issue): 247-251 (2006) - 2005
- [j28]Alfonso Valencia, Alex Bateman
:
Increasing the Impact of Bioinformatics. Bioinform. 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. Bioinform. 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. Bioinform. 21(8): 1301-1303 (2005) - [j25]Benjamin Schuster-Böckler
, Alex Bateman
:
Visualizing profile-profile alignment: pairwise HMM logos. Bioinform. 21(12): 2912-2913 (2005) - [j24]Alex Bateman
, Alfonso Valencia:
An update from the Bioinformatics Editors. Bioinform. 21(24): 4319 (2005) - [j23]Alex Bateman
:
Editorial. Nucleic Acids Res. 33(Database-Issue): 1 (2005) - [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 Res. 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 Res. 33(Database-Issue): 201-205 (2005) - 2004
- [j20]Alex Bateman