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Maria Jesus Martin

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affiliation: European Bioinformatics Institute, Hinxton, UK

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2023
[j45]
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Elisabeth Coudert, Sebastien Gehant, Edouard De Castro, Monica Pozzato, Delphine Baratin, Teresa Batista Neto, Christian J. A. Sigrist, Nicole Redaschi, Alan Bridge, Alan J. Bridge, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Béatrice A. Cuche, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Manuela Pruess, Catherine Rivoire, Karin Sonesson, Shyamala Sundaram, Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Hema Bye-A-Jee, Austra Cukura, Paul Denny, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Alok Mishra, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James D. Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang:
Annotation of biologically relevant ligands in UniProtKB using ChEBI. Bioinform. 39(1) (2023)
[j44]
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Alperen Dalkiran, Ahmet Atakan, Ahmet Süreyya Rifaioglu, Maria Jesus Martin, Rengül Çetin-Atalay, Aybar C. Acar, Tunca Dogan, Volkan Atalay:
Transfer learning for drug-target interaction prediction. Bioinform. 39(Supplement-1): 103-110 (2023)
2022
[j43]
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  - journals/biodb/Crecy-LagardHAB22
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Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu:
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022(2022) (2022)
[j42]
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Gökhan Özsari, Ahmet Süreyya Rifaioglu, Ahmet Atakan, Tunca Dogan, Maria Jesus Martin, Rengül Çetin-Atalay, Volkan Atalay:
SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins. Bioinform. 38(17): 4226-4229 (2022)
[j41]
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  - journals/bioinformatics/MerinoSMSM22
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Gabriela Alejandra Merino, Rabie Saidi, Diego H. Milone, Georgina Stegmayer, Maria Jesus Martin:
Hierarchical deep learning for predicting GO annotations by integrating protein knowledge. Bioinform. 38(19): 4488-4496 (2022)
[j40]
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  - journals/nar/del-ToroSRMCBPH22
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Noemi del-Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal, Colin W. Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa Ratan, Gautam Shirodkar, Odilia Lu, Bálint Mészáros, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret J. Duesbury, Sylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwínski, Sandra E. Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob:
The IntAct database: efficient access to fine-grained molecular interaction data. Nucleic Acids Res. 50(D1): 648-653 (2022)
2021
[j39]
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  - journals/bib/HufskyLAAABBBBC21
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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)
[j38]
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Alistair MacDougall, Vladimir Volynkin, Rabie Saidi, Diego Poggioli, Hermann Zellner, Emma Hatton-Ellis, Vishal Joshi, Claire O'Donovan, Sandra E. Orchard, Andrea H. Auchincloss, Delphine Baratin, Jerven T. Bolleman, Elisabeth Coudert, Edouard De Castro, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Cecilia N. Arighi, Qinghua Wang, Chuming Chen, Hongzhan Huang, John Garavelli, C. R. Vinayaka, Lai-Su Yeh, Darren A. Natale, Kati Laiho, Maria Jesus Martin, Alexandre Renaux, Klemens Pichler:
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. Bioinform. 36(22-23): 5562 (2021)
[j37]
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Ahmet Süreyya Rifaioglu, Rengül Çetin-Atalay, Deniz Cansen Kahraman, Tunca Dogan, Maria Jesus Martin, Volkan Atalay:
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery. Bioinform. 37(5): 693-704 (2021)
[j36]
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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)
[j35]
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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 J. 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)
[j34]
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  - journals/ploscb/DoganGBKABMC21
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Tunca Dogan, Ece Akhan Güzelcan, Marcus Baumann, Altay Koyas, Heval Atas, Ian R. Baxendale, Maria Jesus Martin, Rengül Çetin-Atalay:
Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases. PLoS Comput. Biol. 17(11) (2021)
2020
[j33]
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  - journals/bioinformatics/KahsayVNMFHPRMW20
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Robel Y. Kahsay, Jeet Vora, Rahi Navelkar, Reza Mousavi, Brian C. Fochtman, Xavier Holmes, Nagarajan Pattabiraman, René Ranzinger, Rupali Mahadik, Tatiana Williamson, Sujeet Kulkarni, Gaurav Agarwal, Maria Jesus Martin, Preethi Vasudev, Leyla J. García, Nathan Edwards, Wenjin Zhang, Darren A. Natale, Karen Ross, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, William S. York, Raja Mazumder:
GlyGen data model and processing workflow. Bioinform. 36(12): 3941-3943 (2020)
[j32]
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  - journals/nar/AltenhoffGCEGHN20
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Adrian M. Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M. Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José María Fernández, Laia Codó, The Quest for Orthologs Consortium, Josep Lluis Gelpí, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria Jesus Martin, Salvador Capella-Gutiérrez, Paul D. Thomas, Erik L. L. Sonnhammer, Christophe Dessimoz:
The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res. 48(Webserver-Issue): W538-W545 (2020)
2019
[j31]
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Ahmet Süreyya Rifaioglu, Heval Atas, Maria Jesus Martin, Rengül Çetin-Atalay, Volkan Atalay, Tunca Dogan:
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. Briefings Bioinform. 20(5): 1878-1912 (2019)
[j30]
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  - journals/nar/DanaGTQOMV19
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Jose M. Dana, Aleksandras Gutmanas, Nidhi Tyagi, Guoying Qi, Claire O'Donovan, Maria Jesus Martin, Sameer Velankar:
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. Nucleic Acids Res. 47(Database-Issue): D482-D489 (2019)
2018
[j29]
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  - journals/bmcbi/DalkiranRMCAD18
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Alperen Dalkiran, Ahmet Süreyya Rifaioglu, Maria Jesus Martin, Rengül Çetin-Atalay, Volkan Atalay, Tunca Dogan:
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. BMC Bioinform. 19(1): 334:1-334:13 (2018)
2017
[j28]
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  - journals/bioinformatics/WatkinsGPMC17
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Xavier Watkins, Leyla J. García, Sangya Pundir, Maria Jesus Martin, The UniProt Consortium:
ProtVista: visualization of protein sequence annotations. Bioinform. 33(13): 2040-2041 (2017)
[j27]
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  - journals/nar/MirditaDGMSS17
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Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria Jesus Martin, Johannes Söding, Martin Steinegger:
Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Res. 45(Database-Issue): D170-D176 (2017)
[j26]
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  - journals/nar/KoscielnyACCFGH17
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Gautier Koscielny, Peter An, Denise Carvalho-Silva, Jennifer A. Cham, Luca Fumis, Rippa Gasparyan, Samiul Hasan, Nikiforos Karamanis, Michael Maguire, Eliseo Papa, Andrea Pierleoni, Miguel Pignatelli, Theo Platt, Francis Rowland, Priyanka Wankar, A. Patrícia Bento, Tony Burdett, Antonio Fabregat, Simon A. Forbes, Anna Gaulton, Cristina Yenyxe González, Henning Hermjakob, Anne Hersey, Steven Jupe, Senay Kafkas, Maria Keays, Catherine Leroy, Francisco-Javier Lopez, María P. Magariños, James Malone, Johanna R. McEntyre, Alfonso Muñoz-Pomer Fuentes, Claire O'Donovan, Irene Papatheodorou, Helen E. Parkinson, Barbara Palka, Justin E. Paschall, Robert Petryszak, Naruemon Pratanwanich, Sirarat Sarntivijai, Gary Saunders, Konstantinos Sidiropoulos, Thomas Smith, Zbyslaw Sondka, Oliver Stegle, Y. Amy Tang, Edward Turner, Brendan W. Vaughan, Olga Vrousgou, Xavier Watkins, Maria Jesus Martin, Philippe Sanseau, Jessica Vamathevan, Ewan Birney, Jeffrey Barrett, Ian Dunham:
Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 45(Database-Issue): D985-D994 (2017)
[j25]
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  - journals/nar/NightingaleAABG17
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Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Jesus Martin:
The Proteins API: accessing key integrated protein and genome information. Nucleic Acids Res. 45(Webserver-Issue): W539-W544 (2017)
2016
[j24]
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  - journals/biodb/BursteinasBBARR16
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Borisas Bursteinas, Ramona Britto, Benoit Bely, Andrea H. Auchincloss, Catherine Rivoire, Nicole Redaschi, Claire O'Donovan, Maria Jesus Martin:
Minimizing proteome redundancy in the UniProt Knowledgebase. Database J. Biol. Databases Curation 2016 (2016)
[j23]
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Sefa Kiliç, Dinara M. Sagitova, Shoshannah Wolfish, Benoit Bely, Mélanie Courtot, Stacy Ciufo, Tatiana A. Tatusova, Claire O'Donovan, Marcus C. Chibucos, Maria Jesus Martin, Ivan Erill:
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. Database J. Biol. Databases Curation 2016 (2016)
[j22]
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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)
[j21]
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Rebecca E. Foulger, Paul Denny, John Hardy, Maria Jesus Martin, Tony Sawford, Ruth C. Lovering:
Using the Gene Ontology to Annotate Key Players in Parkinson's Disease. Neuroinformatics 14(3): 297-304 (2016)
2015
[j20]
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  - journals/nar/HuntleySMSBMO15
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Rachael P. Huntley, Tony Sawford, Prudence Mutowo-Meullenet, Aleksandra Shypitsyna, Carlos Bonilla, Maria Jesus Martin, Claire O'Donovan:
The GOA database: Gene Ontology annotation updates for 2015. Nucleic Acids Res. 43(Database-Issue): 1057-1063 (2015)
2014
[j19]
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Simon Jupp, James Malone, Jerven T. Bolleman, Marco Brandizi, Mark Davies, Leyla J. García, Anna Gaulton, Sebastien Gehant, Camille Laibe, Nicole Redaschi, Sarala M. Wimalaratne, Maria Jesus Martin, Nicolas Le Novère, Helen E. Parkinson, Ewan Birney, Andrew M. Jenkinson:
The EBI RDF platform: linked open data for the life sciences. Bioinform. 30(9): 1338-1339 (2014)
[j18]
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  - journals/bioinformatics/SonnhammerGSMRBTDa14
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Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, The Quest for Orthologs Consortium:
Big data and other challenges in the quest for orthologs. Bioinform. 30(21): 2993-2998 (2014)
2013
[j17]
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  - journals/biodb/Mutowo-MeullenetHDASMOA13
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Prudence Mutowo-Meullenet, Rachael P. Huntley, Emily C. Dimmer, Yasmin Alam-Faruque, Tony Sawford, Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler:
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database J. Biol. Databases Curation 2013 (2013)
[j16]
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  - journals/bioinformatics/GomezGSVGGMLAdDOVHZPCJ13
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John Gómez, Leyla J. García, Gustavo A. Salazar, Jose M. Villaveces, Swanand P. Gore, Alexander García Castro, Maria Jesus Martin, Guillaume Launay, Rafael Alcántara, Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Sameer Velankar, Henning Hermjakob, Chenggong Zong, Peipei Ping, Manuel Corpas, Rafael C. Jiménez:
BioJS: an open source JavaScript framework for biological data visualization. Bioinform. 29(8): 1103-1104 (2013)
[j15]
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Sameer Velankar, Jose M. Dana, Julius O. B. Jacobsen, Glen van Ginkel, Paul J. Gane, Jie Luo, Thomas J. Oldfield, Claire O'Donovan, Maria Jesus Martin, Gerard J. Kleywegt:
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res. 41(Database-Issue): 483-489 (2013)
[j14]
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Rafael Alcántara, Joseph Onwubiko, Hong Cao, Paula de Matos, Jennifer A. Cham, Julius O. B. Jacobsen, Gemma L. Holliday, Julia D. Fischer, Syed Asad Rahman, Bijay Jassal, Mickael Goujon, Francis Rowland, Sameer Velankar, Rodrigo Lopez, John P. Overington, Gerard J. Kleywegt, Henning Hermjakob, Claire O'Donovan, Maria Jesus Martin, Janet M. Thornton, Christoph Steinbeck:
The EBI enzyme portal. Nucleic Acids Res. 41(Database-Issue): 773-780 (2013)
2012
[j13]
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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)
[j12]
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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)
[j11]
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  - journals/nar/DimmerHA12
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Emily C. Dimmer, Rachael P. Huntley, Yasmin Alam-Faruque, Tony Sawford, Claire O'Donovan, Maria Jesus Martin, Benoit Bely, Paul Browne, Wei Mun Chan, Ruth Y. Eberhardt, Michael Gardner, Kati Laiho, Duncan Legge, Michele Magrane, Klemens Pichler, Diego Poggioli, Harminder Sehra, Andrea H. Auchincloss, Kristian B. Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Silvia Braconi-Quintaje, Lionel Breuza, Alan J. Bridge, Elisabeth Coudert, Anne Estreicher, Maria Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Phillippe Lemercier, Damien Lieberherr, Patrick Masson, Madelaine Moinat, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Lydie Bougueleret, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek-Roggli, Ioannis Xenarios, Rolf Apweiler:
The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 40(Database-Issue): 565-570 (2012)
2011
[j10]
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Jose M. Villaveces, Rafael C. Jiménez, Leyla J. García, Gustavo A. Salazar, Bernat Gel, Nicola J. Mulder, Maria Jesus Martin, Alexander García Castro, Henning Hermjakob:
Dasty3, a WEB framework for DAS. Bioinform. 27(18): 2616-2617 (2011)
2009
[j9]
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Eric Jain, Amos Bairoch, Severine Duvaud, Isabelle Phan, Nicole Redaschi, Baris E. Suzek, Maria Jesus Martin, Peter B. McGarvey, Elisabeth Gasteiger:
Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinform. 10 (2009)
2008
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Samuel Patient, Daniela Wieser, Michael Kleen, Ernst Kretschmann, Maria Jesus Martin, Rolf Apweiler:
UniProtJAPI: a remote API for accessing UniProt data. Bioinform. 24(10): 1321-1322 (2008)
2006
[j7]
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Cathy H. Wu, Rolf Apweiler, Amos Bairoch, Darren A. Natale, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Raja Mazumder, Claire O'Donovan, Nicole Redaschi, Baris E. Suzek:
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 34(Database-Issue): 187-191 (2006)
2005
[j6]
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Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L. Yeh:
The Universal Protein Resource (UniProt). Nucleic Acids Res. 33(Database-Issue): 154-159 (2005)
2004
[j5]
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Rolf Apweiler, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L. Yeh:
UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32(Database-Issue): 115-119 (2004)
2003
[j4]
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Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola J. Mulder, Claire O'Donovan, Helen E. Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron:
The European Bioinformatics Institute's data resources. Nucleic Acids Res. 31(1): 43-50 (2003)
[j3]
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Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-Claude Blatter, Anne Estreicher, Elisabeth Gasteiger, Maria Jesus Martin, Karine Michoud, Claire O'Donovan, Isabelle Phan, Sandrine Pilbout, Michel Schneider:
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31(1): 365-370 (2003)
2002
[j2]
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Claire O'Donovan, Maria Jesus Martin, Alexandre Gattiker, Elisabeth Gasteiger, Amos Bairoch, Rolf Apweiler:
High-quality Protein Knowledge Resource: SWISS-PROT and TrEMBL. Briefings Bioinform. 3(3): 275-284 (2002)
1999
[j1]
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  - journals/bioinformatics/ODonovanMGCA99
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Claire O'Donovan, Maria Jesus Martin, Eric Glémet, Jean-Jacques Codani, Rolf Apweiler:
Removing redundancy in SWISS-PROT and TrEMBL. Bioinform. 15(3): 258-259 (1999)

Conference and Workshop Papers

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2016
[c6]
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Leyla J. García, Leonardo Gonzales, Maria Jesus Martin:
A Graph-based Taxonomy RESTful Data Service. SWAT4LS 2016
2015
[c5]
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Mélanie Courtot, Aleksandra Shypitsyna, Elena Speretta, Alexander Holmes, Tony Sawford, Tony Wardell, Maria Jesus Martin, Claire O'Donovan:
UniProt-GOA: A Central Resource for Data Integration and GO Annotation. SWAT4LS 2015: 227-228
2011
[c4]
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Samuel Patient, Maria Jesus Martin:
Annotating UniProt Metagenomic and Environmental Sequences in UniMES. BIOINFORMATICS 2011: 367-368
1998
[c3]
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Henning Hermjakob, Claire O'Donovan, Maria Jesus Martin, Fiona Lang, Rolf Apweiler:
SPTR: A comprehensive, non redundant and up-to-date view of the protein sequence world. German Conference on Bioinformatics 1998
[c2]
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Claire O'Donovan, Maria Jesus Martin, Eric Glémet, Jean-Jacques Codani, Rolf Apweiler:
Removing Redundancy in SWISS-PROT and TrEMBL. German Conference on Bioinformatics 1998
1997
[c1]
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Rolf Apweiler, Alain Gateau, Sergio Contrino, Maria Jesus Martin, Vivien Junker, Claire O'Donovan, Fiona Lang, Nicoletta Mitaritonna, Stephanie Kappus, Amos Bairoch:
Protein Sequence Annotation in the Genome Era: The Annotation Concept of SWISS-PROT + TREMBL. ISMB 1997: 33-43

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