Fábio Madeira

• Nandana Madhusoodanan7
• Rodrigo Lopez6
• Geoffrey J. Barton5
• Joon Lee5
• Adrian R. Tivey3
• Alberto Eusebi3
• Ania Niewielska3
• David Hoksza3
• Sarah Butcher3
• Abdulrahman Hussein2
• Adrian R. N. Tivey2
• Alex Bateman2
• Alexandr Ignatchenko2
• Anton I. Petrov2
• Anton S. Petrov2
• Aurelien Luciani2
• Austra Cukura2
• Blake Sweeney2
• Caeden D. Meade2
• Carlos Eduardo Ribas2
• Carol MacKintosh2
• Dushyanth Jyothi2
• Emanuele Alpi2
• Emma Hatton-Ellis2

1. UniProt: the Universal Protein Knowledgebase in 2023

   著者: Alex Bateman, María Martin, Sandra Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily Bowler-Barnett, Ramona Britto, Hema Bye‐A‐Jee, Austra Cukura, Paul Denny, Tunca Doğan, ThankGod E. 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 Kandasaamy, Antonia Lock, Aurélien 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 L Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James Stephenson, Prabhat Totoo, E. B. Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan Bridge, Lucila Aimo, Ghislaine Argoud‐Puy, Andrea H Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Teresa M Batista Neto, Marie-Claude Blatter, Jerven Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals‐Casas, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Edouard de Castro, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Sébastien Géhant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz, 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, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Christian J A Sigrist, Karin Sonesson, Shyamala Sundaram ほか 14 名 - Nucleic Acids Research, Nucleic Acids Res. 2022 被引用: 7,020

2. UniProt: the universal protein knowledgebase in 2021

   著者: 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 ほか 33 名 - Nucleic Acids Research, Nucleic Acids Res. 2020 被引用: 7,040

3. Search and sequence analysis tools services from EMBL-EBI in 2022

   著者: Fábio Madeira, Matt Pearce, Adrian R. N. Tivey, Prasad Basutkar, Joon Lee, Ossama Edbali, Nandana Madhusoodanan, Anton Kolesnikov, Rodrigo Lopez - Nucleic Acids Research, Nucleic Acids Res. 2022 被引用: 2,513

4. The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024

   著者: Fábio Madeira, Nandana Madhusoodanan, Joon Lee, Alberto Eusebi, Ania Niewielska, Adrian R. Tivey, Rodrigo López, Sarah Butcher - Nucleic Acids Research 2024 被引用: 1,575

5. The EMBL-EBI search and sequence analysis tools APIs in 2019

   著者: Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R. N. Tivey, Simon C. Potter, Robert D. Finn, Rodrigo Lopez - Nucleic Acids Research, Nucleic Acids Res. 2019 被引用: 4,653

6. Annotation of biologically relevant ligands in UniProtKB using ChEBI

   著者: Elisabeth Coudert, Sébastien Géhant, Edouard de Castro, Monica Pozzato, Delphine Baratin, Teresa Batista Neto, Christian J A Sigrist, Nicole Redaschi, Alan Bridge, Alan Bridge, Lucila Aimo, Ghislaine Argoud‐Puy, Andrea H Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Teresa M Batista Neto, Marie-Claude Blatter, Jerven Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals‐Casas, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Edouard de Castro, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Sébastien Géhant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz, 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, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Christian J A Sigrist, Karin Sonesson, Shyamala Sundaram, Alex Bateman, María Martin, Sandra Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily Bowler-Barnett, Ramona Britto, Hema Bye- A-Jee, Austra Cukura, Paul Denny, Tunca Doğan, ThankGod E. 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 Kandasaamy, Antonia Lock, Aurélien 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 L Rice, Rabie Saidi, Rafael Santos, Elena Speretta ほか 22 名 - Bioinformatics, Bioinform. 2022 被引用: 319

7. InterPro in 2019: improving coverage, classification and access to protein sequence annotations

   著者: 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 - Nucleic Acids Research, Nucleic Acids Res. 2018 被引用: 1,539

8. R2DT is a framework for predicting and visualising RNA secondary structure using templates

   著者: Blake Sweeney, David Hoksza, Eric P. Nawrocki, Carlos Eduardo Ribas, Fábio Madeira, Jamie J. Cannone, Robin R. Gutell, Aparna Maddala, Caeden D. Meade, Loren Dean Williams, Anton S. Petrov, Patricia P. Chan, Todd M. Lowe, ROBERT FINN, Anton I. Petrov - Nature Communications 2021 被引用: 147

9. PDBe-KB: a community-driven resource for structural and functional annotations

   著者: Mihaly Varadi, John M. Berrisford, Mandar S. Deshpande, Sreenath Nair, Aleksandras Gutmanas, David R. Armstrong, Lukás Pravda, Bissan Al-Lazikani, Stephen Anyango, Geoffrey J. Barton, Karel Berka, Tom L. Blundell, Neera Borkakoti, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Fábio Madeira, M. S. Madhusudhan, Henry J. Martell, Stuart A. MacGowan, Jake E. McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro G. Radusky, António J. M. Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodová Vareková, Jonathan D. Tyzack, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar - Nucleic Acids Research, Nucleic Acids Res. 2019 被引用: 137

10. The European Nucleotide Archive in 2021

    著者: Carla A. Cummins, Alisha Ahamed, Raheela Aslam, Josephine Burgin, Rajkumar Devraj, Ossama Edbali, Dipayan Gupta, Peter W. Harrison, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Simon Kay, Manish Kumar, Ankur Lathi, Rasko Leinonen, Fábio Madeira, Nandana Madhusoodanan, Milena Mansurova, Colman O'Cathail, Matt Pearce, Stephane Pesant, Nadim Rahman, Jeena Rajan, Gabriele Rinck, Sandeep Selvakumar, Alexey Sokolov, Swati Suman, Ross Thorne, Prabhat Totoo, Senthilnathan Vijayaraja, Zahra Waheed, Ahmad Zyoud, Rodrigo Lopez, Tony Burdett, Guy Cochrane - Nucleic Acids Research, Nucleic Acids Res. 2021 被引用: 131

11. 14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides

    著者: Fábio Madeira, Michele Tinti, Gavuthami Murugesan, Emily Berrett, Margaret Stafford, Rachel Toth, Christian Cole, Carol MacKintosh, Geoffrey J. Barton - Bioinformatics, Bioinform. 2015 被引用: 226

12. JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure

    著者: Peter V. Troshin, James B. Procter, Alexander Sherstnev, Daniel L. Barton, Fábio Madeira, Geoffrey J. Barton - Bioinformatics, Bioinform. 2018 被引用: 72

13. Recommendations for the packaging and containerizing of bioinformatics software

    著者: Björn A. Grüning, Olivier Sallou, Pablo A. Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel J. Blankenberg, Rafael C. Jiménez, Daniel Blankenberg, Yasset Pérez-Riverol - F1000Research 2018 被引用: 56

14. The Dundee Resource for Sequence Analysis and Structure Prediction

    著者: Stuart A. MacGowan, Fábio Madeira, Thiago Britto‐Borges, Mateusz Warowny, Alexey Drozdetskiy, James B Procter, Geoffrey J. Barton - Protein Science 2019 被引用: 27

15. R2DT: a comprehensive platform for visualizing RNA secondary structure

    著者: Holly McCann, Caeden D. Meade, Loren Dean Williams, Anton S. Petrov, Philip Z. Johnson, Anne E. Simon, David Hoksza, Eric P. Nawrocki, Patricia P. Chan, Todd M. Lowe, Carlos Eduardo Ribas, Blake Sweeney, Fábio Madeira, Stephen Anyango, Sri Devan Appasamy, Mandar Deshpande, Mihály Váradi, Sameer Velankar, Craig L. Zirbel, Aleksei Naiden, Fabrice Jossinet, Anton I. Petrov - Nucleic Acids Research 2025 被引用: 23

16. Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services

    著者: Fábio Madeira, Nandana Madhusoodanan, Joon Lee, Alberto Eusebi, Ania Niewielska, Adrian R. Tivey, Stuart Meacham, Rodrigo López, Sarah Butcher - Current Protocols 2024 被引用: 21

17. Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services

    著者: Fábio Madeira, Nandana Madhusoodanan, Joon Lee, Adrian R. Tivey, Rodrigo López - Current Protocols in Bioinformatics 2019 被引用: 52

18. A unified analysis of evolutionary and population constraint in protein domains highlights structural features and pathogenic sites

    著者: Stuart A. MacGowan, Fábio Madeira, Thiago Britto‐Borges, Geoffrey J. Barton - Communications Biology 2024 被引用: 6

19. ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome

    著者: Michele Tinti, Fábio Madeira, Gavuthami Murugesan, Gerta Hoxhaj, Rachel Toth, Carol MacKintosh - Database, Database J. Biol. Databases Curation 2014 被引用: 63

20. Constraining Protein Docking with Coevolution Data for Medical Research

    著者: Ludwig Krippahl, Fábio Madeira, Pedro Barahona - Lecture notes in computer science, AIME 2013 被引用: 4

21. Pycoevol - A Python Workflow to Study Protein-protein Coevolution

    著者: Fábio Madeira, Ludwig Krippahl - Conference on Bioinformatics Models 2012 被引用: 2

22. Taxonomy Resolver: A Python package for building and filtering taxonomy trees

    著者: Fábio Madeira, Nandana Madhusoodanan, Joonheung Lee, Alberto Eusebi, Ania Niewielska, Sarah Butcher - The Journal of Open Source Software, J. Open Source Softw. 2025 被引用: 0

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