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2020 – today
- 2020
[j32]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)
2010 – 2019
- 2019
- [j31]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]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]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]Xavier Watkins, Leyla J. Garcia, Sangya Pundir, Maria Jesus Martin, The UniProt Consortium:
ProtVista: visualization of protein sequence annotations. Bioinform. 33(13): 2040-2041 (2017) - [j27]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]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]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]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]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]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]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) - [c6]Leyla J. García, Leonardo Gonzales, Maria Jesus Martin:
A Graph-based Taxonomy RESTful Data Service. SWAT4LS 2016 - 2015
- [j20]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) - [c5]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 - 2014
- [j19]Simon Jupp, James Malone, Jerven T. Bolleman, Marco Brandizi, Mark Davies, Leyla J. Garcia, 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]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]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]John Gómez, Leyla J. Garcia, 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. Jimenez:
BioJS: an open source JavaScript framework for biological data visualization. Bioinform. 29(8): 1103-1104 (2013) - [j15]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]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]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]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]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 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]Jose M. Villaveces, Rafael C. Jimenez, Leyla J. Garcia, 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) - [c4]Samuel Patient, Maria Jesus Martin:
Annotating UniProt Metagenomic and Environmental Sequences in UniMES. BIOINFORMATICS 2011: 367-368
2000 – 2009
- 2009
- [j9]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
- [j8]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]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]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]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]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]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]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)
1990 – 1999
- 1999
- [j1]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) - 1998
- [c3]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]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]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
Coauthor Index
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