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ORCIDAlex L. Mitchell
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- affiliation: European Molecular Biology Laboratory, EMBL-EBI, Hinxton, UK
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Journal Articles
- 2021
[j26]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 J. 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)- [j25]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:
The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 49(Database-Issue): D344-D354 (2021) - 2020
- [j24]Alex L. Mitchell, Alexandre Almeida, Martin Beracochea, Miguel A. Boland, Josephine Burgin, Guy Cochrane, Michael R. Crusoe, Varsha Kale, Simon C. Potter, Lorna J. Richardson, Ekaterina A. Sakharova, Maxim Scheremetjew, Anton I. Korobeynikov, Alexander Shlemov, Olga Kunyavskaya, Alla L. Lapidus, Robert D. Finn:
MGnify: the microbiome analysis resource in 2020. Nucleic Acids Res. 48(Database-Issue): D570-D578 (2020) - 2019
- [j23]Alex L. Mitchell, Teresa K. Attwood, Patricia C. Babbitt, Matthias Blum, Peer Bork, Alan J. Bridge, Shoshana D. Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Hongzhan Huang, Ivica Letunic, Rodrigo Lopez, Aurelien Luciani, Fábio Madeira, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Arun Prasad Pandurangan, Typhaine Paysan-Lafosse, Sebastien Pesseat, Simon C. Potter, Matloob Qureshi, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Gustavo A. Salazar, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Siew-Yit Yong, Robert D. Finn:
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47(Database-Issue): D351-D360 (2019) - 2018
- [j22]Alex L. Mitchell, Maxim Scheremetjew, Hubert Denise, Simon C. Potter, Aleksandra Tarkowska, Matloob Qureshi, Gustavo A. Salazar, Sebastien Pesseat, Miguel A. Boland, Fiona M. I. Hunter, Petra ten Hoopen, Blaise T. F. Alako, Clara Amid, Darren J. Wilkinson, Thomas P. Curtis, Guy Cochrane, Robert D. Finn:
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. Nucleic Acids Res. 46(Database-Issue): D726-D735 (2018) - 2017
- [j21]Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. 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, Young Mi 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
- [j20]Amaia Sangrador-Vegas, Alex L. Mitchell, Hsin-Yu Chang, Siew-Yit Yong, Robert D. Finn:
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. Database J. Biol. Databases Curation 2016 (2016) - [j19]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) - [j18]Alex L. Mitchell, François Bucchini, Guy Cochrane, Hubert Denise, Petra ten Hoopen, Matthew Fraser, Sebastien Pesseat, Simon C. Potter, Maxim Scheremetjew, Peter Sterk, Robert D. Finn:
EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data. Nucleic Acids Res. 44(Database-Issue): 595-603 (2016) - [j17]Samuel C. Forster, Hilary P. Browne, Nitin Kumar, Martin Hunt, Hubert Denise, Alex L. Mitchell, Robert D. Finn, Trevor D. Lawley:
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. Nucleic Acids Res. 44(Database-Issue): 604-609 (2016) - 2015
- [j16]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) - 2014
- [j15]Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex L. Mitchell, Gift Nuka, Sebastien Pesseat, Antony F. Quinn, Amaia Sangrador-Vegas, Maxim Scheremetjew, Siew-Yit Yong, Rodrigo Lopez, Sarah Hunter:
InterProScan 5: genome-scale protein function classification. Bioinform. 30(9): 1236-1240 (2014) - [j14]Sarah Hunter, Matthew Corbett, Hubert Denise, Matthew Fraser, Alejandra N. González-Beltrán, Christopher I. Hunter, Philip Jones, Rasko Leinonen, Craig McAnulla, Eamonn Maguire, John Maslen, Alex L. Mitchell, Gift Nuka, Arnaud Oisel, Sebastien Pesseat, Rajesh Radhakrishnan, Philippe Rocca-Serra, Maxim Scheremetjew, Peter Sterk, Daniel Vaughan, Guy Cochrane, Dawn Field, Susanna-Assunta Sansone:
EBI metagenomics - a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Res. 42(Database-Issue): 600-606 (2014) - 2013
- [j13]Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Alison L. Cuff, Jose M. Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Alex L. Mitchell, Alexey G. Murzin, Bernardo Ochoa-Montaño, Owen J. L. Rackham, James Smith, Michael J. E. Sternberg, Sameer Velankar, Corin Yeats, Christine A. Orengo:
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res. 41(Database-Issue): 499-507 (2013) - 2012
- [j12]Chris I. Hunter, Alex L. Mitchell, Philip Jones, Craig McAnulla, Sebastien Pesseat, Maxim Scheremetjew, Sarah Hunter:
Metagenomic analysis: the challenge of the data bonanza. Briefings Bioinform. 13(6): 743-746 (2012) - [j11]Teresa K. Attwood, Alain Coletta, Gareth Muirhead, Athanasia Pavlopoulou, Peter B. Philippou, Ivan Popov, Carlos Romá-Mateo, Athina Theodosiou, Alex L. Mitchell:
The PRINTS database: a fine-grained protein sequence annotation and analysis resource - its status in 2012. Database J. Biol. Databases Curation 2012 (2012) - [j10]Sarah W. Burge, Elizabeth Kelly, David Lonsdale, Prudence Mutowo-Meullenet, Craig McAnulla, Alex L. Mitchell, Amaia Sangrador-Vegas, Siew-Yit Yong, Nicola J. Mulder, Sarah Hunter:
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database J. Biol. Databases Curation 2012 (2012) - [j9]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) - 2009
- [j8]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) - 2007
- [j7]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) - 2005
- [j6]Alex L. Mitchell, Anna Divoli, Jee-Hyub Kim, Melanie Hilario, I. Selimas, Teresa K. Attwood:
METIS: multiple extraction techniques for informative sentences. Bioinform. 21(22): 4196-4197 (2005) - [j5]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) - 2003
- [j4]Alex L. Mitchell, Jacqueline Renée Reich, Terri K. Attwood:
PRECIS: Protein reports engineered from concise information in SWISS-PROT. Bioinform. 19(13): 1664-1671 (2003) - [j3]Terri K. Attwood, Paul Bradley, Darren R. Flower, Anna Gaulton, Neil Maudling, Alex L. Mitchell, G. Moulton, A. Nordle, K. Paine, P. Taylor, A. Uddin, Christianna Zygouri:
PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res. 31(1): 400-402 (2003) - 2002
- [j2]Terri K. Attwood, Martin J. Blythe, Darren R. Flower, Anna Gaulton, J. E. Mabey, Neil Maudling, L. McGregor, Alex L. Mitchell, G. Moulton, K. Paine, Philip Scordis:
PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res. 30(1): 239-241 (2002) - 2001
- [j1]Jacqueline Renée Reich, Alex L. Mitchell, Carole A. Goble, Terri K. Attwood:
Toward More Intelligent Annotation Tools: A Prototype. IEEE Intell. Syst. 16(6): 42-51 (2001)
Conference and Workshop Papers
- 2016
- [c4]Mélanie Courtot, Alex L. Mitchell, Maxim Scheremetjew, Janet Piñero González, Laura I. Furlong, Robert D. Finn, Helen E. Parkinson:
Slim-o-matic: a Semi-Automated Way to Generate Gene Ontology Slims. SWAT4LS 2016 - 2007
- [c3]Jee-Hyub Kim, Alex L. Mitchell, Teresa K. Attwood, Melanie Hilario:
Learning to extract relations for protein annotation. ISMB/ECCB (Supplement of Bioinformatics) 2007: 256-263 - 2004
- [c2]Melanie Hilario, Alex L. Mitchell, Jee-Hyub Kim, Paul Bradley, Terri K. Attwood:
Classifying Protein Fingerprints. PKDD 2004: 197-208 - 2001
- [c1]Phillip W. Lord, Jacqueline Renée Reich, Alex L. Mitchell, Robert D. Stevens, Terri K. Attwood, Carole A. Goble:
PRECIS: An Automated Pipeline for Producing Concise Reports About Proteins. BIBE 2001: 57-64
Reference Works
- 2019
- [r1]Teresa K. Attwood, Alex L. Mitchell:
The Evolution of Protein Family Databases. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 34-45
Informal and Other Publications
- 2018
- [i2]Folker Meyer, Robert D. Finn, Wolfgang Gerlach, Alex L. Mitchell, Travis Harrison, Andreas Wilke:
On the way to research objects for environmental genomics (or metagenomics). RO 2018 - 2017
- [i1]Espen Mikal Robertsen, Hubert Denise, Alex L. Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen:
ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services. F1000Research 6: 70- (2017)
Coauthor Index
Terri K. Attwood
aka: Teresa K. Attwood
aka: Teresa K. Attwood
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