Protein Sequence Annotation in the Genome Era: The Annotation Concept of SWISS-PROT + TREMBL. - Rolf Apweiler; Alain Gateau; Sergio Contrino; Maria Jesus Martin; Vivien Junker; Claire O'Donovan; Fiona Lang; Nicoletta Mitaritonna; Stephanie Kappus; Amos Bairoch (ISMB, 1997)

SPTR: A comprehensive, non redundant and up-to-date view of the protein sequence world. - Henning Hermjakob; Claire O'Donovan; Maria Jesus Martin; Fiona Lang; Rolf Apweiler (German Conference on Bioinformatics, 1998)

Removing redundancy in SWISS-PROT and TrEMBL. - Claire O'Donovan; Maria Jesus Martin; Eric Glémet; Jean-Jacques Codani; Rolf Apweiler (Bioinform., 1999)

High-quality Protein Knowledge Resource: SWISS-PROT and TrEMBL. - Claire O'Donovan; Maria Jesus Martin; Alexandre Gattiker; Elisabeth Gasteiger; Amos Bairoch; Rolf Apweiler (Briefings Bioinform., 2002)

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. - 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 (Nucleic Acids Res., 2003)

The European Bioinformatics Institute's data resources. - 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; et al. (Nucleic Acids Res., 2003)

UniProt: the Universal Protein knowledgebase. - 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; et al. (Nucleic Acids Res., 2004)

The Universal Protein Resource (UniProt). - 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; et al. (Nucleic Acids Res., 2005)

The Universal Protein Resource (UniProt): an expanding universe of protein information. - 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; et al. (Nucleic Acids Res., 2006)

UniProtJAPI: a remote API for accessing UniProt data. - Samuel Patient; Daniela Wieser; Michael Kleen; Ernst Kretschmann; Maria Jesus Martin; Rolf Apweiler (Bioinform., 2008)

Infrastructure for the life sciences: design and implementation of the UniProt website. - Eric Jain; Amos Bairoch; Severine Duvaud; Isabelle Phan; Nicole Redaschi; Baris E. Suzek; Maria Jesus Martin; Peter B. McGarvey; Elisabeth Gasteiger (BMC Bioinform., 2009)

Annotating UniProt Metagenomic and Environmental Sequences in UniMES. - Samuel Patient; Maria Jesus Martin (BIOINFORMATICS, 2011)

Dasty3, a WEB framework for DAS. - 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 (Bioinform., 2011)

AntiFam: a tool to help identify spurious ORFs in protein annotation. - Ruth Y. Eberhardt; Daniel H. Haft; Marco Punta; Maria Jesus Martin; Claire O'Donovan; Alex Bateman (Database J. Biol. Databases Curation, 2012)

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. - 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; et al. (Database J. Biol. Databases Curation, 2012)

The UniProt-GO Annotation database in 2011. - 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; et al. (Nucleic Acids Res., 2012)

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. - Prudence Mutowo-Meullenet; Rachael P. Huntley; Emily C. Dimmer; Yasmin Alam-Faruque; Tony Sawford; Maria Jesus Martin; Claire O'Donovan; Rolf Apweiler (Database J. Biol. Databases Curation, 2013)

BioJS: an open source JavaScript framework for biological data visualization. - 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; et al. (Bioinform., 2013)

The EBI enzyme portal. - 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; et al. (Nucleic Acids Res., 2013)

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. - 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 (Nucleic Acids Res., 2013)

The EBI RDF platform: linked open data for the life sciences. - 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; et al. (Bioinform., 2014)

Big data and other challenges in the quest for orthologs. - Erik L. L. Sonnhammer; Toni Gabaldón; Alan W. Sousa da Silva; Maria Jesus Martin; Marc Robinson-Rechavi; Brigitte Boeckmann; Paul D. Thomas; Christophe Dessimoz; Quest for Orthologs Consortium (Bioinform., 2014)

UniProt-GOA: A Central Resource for Data Integration and GO Annotation. - Mélanie Courtot; Aleksandra Shypitsyna; Elena Speretta; Alexander Holmes; Tony Sawford; Tony Wardell; Maria Jesus Martin; Claire O'Donovan (SWAT4LS, 2015)

The GOA database: Gene Ontology annotation updates for 2015. - Rachael P. Huntley; Tony Sawford; Prudence Mutowo-Meullenet; Aleksandra Shypitsyna; Carlos Bonilla; Maria Jesus Martin; Claire O'Donovan (Nucleic Acids Res., 2015)

A Graph-based Taxonomy RESTful Data Service. - Leyla J. García; Leonardo Gonzales; Maria Jesus Martin (SWAT4LS, 2016)

Minimizing proteome redundancy in the UniProt Knowledgebase. - Borisas Bursteinas; Ramona Britto; Benoit Bely; Andrea H. Auchincloss; Catherine Rivoire; Nicole Redaschi; Claire O'Donovan; Maria Jesus Martin (Database J. Biol. Databases Curation, 2016)

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. - 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 (Database J. Biol. Databases Curation, 2016)

UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. - Tunca Dogan; Alistair MacDougall; Rabie Saidi; Diego Poggioli; Alex Bateman; Claire O'Donovan; Maria Jesus Martin (Bioinform., 2016)

Using the Gene Ontology to Annotate Key Players in Parkinson's Disease. - Rebecca E. Foulger; Paul Denny 002; John Hardy; Maria Jesus Martin; Tony Sawford; Ruth C. Lovering (Neuroinformatics, 2016)

ProtVista: visualization of protein sequence annotations. - Xavier Watkins; Leyla J. García; Sangya Pundir; Maria Jesus Martin; UniProt Consortium (Bioinform., 2017)

Open Targets: a platform for therapeutic target identification and validation. - 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; et al. (Nucleic Acids Res., 2017)

Uniclust databases of clustered and deeply annotated protein sequences and alignments. - Milot Mirdita; Lars von den Driesch; Clovis Galiez; Maria Jesus Martin; Johannes Söding; Martin Steinegger (Nucleic Acids Res., 2017)

The Proteins API: accessing key integrated protein and genome information. - Andrew Nightingale; Ricardo Antunes; Emanuele Alpi; Borisas Bursteinas; Leonardo Gonzales; Wudong Liu; Jie Luo; Guoying Qi; Edd Turner; Maria Jesus Martin (Nucleic Acids Res., 2017)

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. - Alperen Dalkiran; Ahmet Süreyya Rifaioglu; Maria Jesus Martin; Rengül Çetin-Atalay; Volkan Atalay; Tunca Dogan (BMC Bioinform., 2018)

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. - Ahmet Süreyya Rifaioglu; Heval Atas; Maria Jesus Martin; Rengül Çetin-Atalay; Volkan Atalay; Tunca Dogan (Briefings Bioinform., 2019)

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. - Jose M. Dana; Aleksandras Gutmanas; Nidhi Tyagi; Guoying Qi; Claire O'Donovan; Maria Jesus Martin; Sameer Velankar (Nucleic Acids Res., 2019)

GlyGen data model and processing workflow. - 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; et al. (Bioinform., 2020)

The Quest for Orthologs benchmark service and consensus calls in 2020. - 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 001; Laia Codó; Quest for Orthologs Consortium; et al. (Nucleic Acids Res., 2020)

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. - 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; et al. (Briefings Bioinform., 2021)

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. - 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; et al. (Bioinform., 2021)

MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery. - Ahmet Süreyya Rifaioglu; Rengül Çetin-Atalay; Deniz Cansen Kahraman; Tunca Dogan; Maria Jesus Martin; Volkan Atalay (Bioinform., 2021)

UniProt: the universal protein knowledgebase in 2021. - 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; et al. (Nucleic Acids Res., 2021)

The Gene Ontology resource: enriching a GOld mine. - 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; et al. (Nucleic Acids Res., 2021)

Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases. - Tunca Dogan; Ece Akhan Güzelcan; Marcus Baumann; Altay Koyas; Heval Atas; Ian R. Baxendale; Maria Jesus Martin; Rengül Çetin-Atalay (PLoS Comput. Biol., 2021)

A roadmap for the functional annotation of protein families: a community perspective. - 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; et al. (Database J. Biol. Databases Curation, 2022)

Hierarchical deep learning for predicting GO annotations by integrating protein knowledge. - Gabriela Alejandra Merino; Rabie Saidi; Diego H. Milone; Georgina Stegmayer; Maria Jesus Martin (Bioinform., 2022)

SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins. - Gökhan Özsari; Ahmet Süreyya Rifaioglu; Ahmet Atakan; Tunca Dogan; Maria Jesus Martin; Rengül Çetin-Atalay; Volkan Atalay (Bioinform., 2022)

The IntAct database: efficient access to fine-grained molecular interaction data. - 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; et al. (Nucleic Acids Res., 2022)

Transfer learning for drug-target interaction prediction. - Alperen Dalkiran; Ahmet Atakan; Ahmet Süreyya Rifaioglu; Maria Jesus Martin; Rengül Çetin-Atalay; Aybar C. Acar; Tunca Dogan; Volkan Atalay (Bioinform., 2023)

Annotation of biologically relevant ligands in UniProtKB using ChEBI. - Elisabeth Coudert; Sebastien Gehant; Edouard De Castro; Monica Pozzato; Delphine Baratin; Teresa Batista Neto; Christian J. A. Sigrist; Nicole Redaschi; Alan J. Bridge; Lucila Aimo; Ghislaine Argoud-Puy; Andrea H. Auchincloss; et al. (Bioinform., 2023)

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. - Karina Martinez; Jon Agirre; Yukie Akune; Kiyoko F. Aoki-Kinoshita; Cecilia N. Arighi; Kristian B. Axelsen; Evan Bolton; Emily Bordeleau; Nathan J. Edwards; Elisa Fadda; Ten Feizi; Catherine A. Hayes; et al. (Database J. Biol. Databases Curation, 2024)