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ORCIDRobert D. Finn
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- affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)
- affiliation: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn
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Journal Articles
- 2023
[j73]Fotis A. Baltoumas, Evangelos Karatzas, David Páez-Espino, Nefeli K. Venetsianou, Eleni Aplakidou, Anastasis Oulas, Robert D. Finn
, Sergey Ovchinnikov, Evangelos Pafilis, Nikos Kyrpides, Georgios A. Pavlopoulos:
Exploring microbial functional biodiversity at the protein family level - From metagenomic sequence reads to annotated protein clusters. Frontiers Bioinform. 3 (2023)- [j72]Lorna J. Richardson, Ben Allen, Germana Baldi, Martin Beracochea, Maxwell L. Bileschi, Tony Burdett, Josephine Burgin, Juan Caballero, Guy Cochrane, Lucy J. Colwell, Tom Curtis, Alejandra Escobar-Zepeda, Tatiana A. Gurbich, Varsha Kale, Anton I. Korobeynikov, Shriya Raj, Alexander B. Rogers, Ekaterina A. Sakharova, Santiago Sanchez, Darren J. Wilkinson, Robert D. Finn:
MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Res. 51(D1): 753-759 (2023) - [j71]Fergal J. Martin, M. Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew E. Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R. B. Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Jayantilal Dodiya, Sarah M. Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos García-Girón, Thiago Augusto Lopes Genez, Gurpreet S. Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike P. Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, José Carlos Marugán, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N. Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Pilizota, Irina Prosovetskaia, José G. Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Elizabeth Wass, Natalie L. Willhoft, Jamie Allen, Jorge Álvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E. Loveland, Benjamin Moore, Jonathan M. Mudge, John G. Tate, David Thybert, Stephen J. Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E. Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D. Finn, Kevin L. Howe, Peter W. Harrison, Andrew D. Yates, Paul Flicek:
Ensembl 2023. Nucleic Acids Res. 51(D1): 933-941 (2023) - [j70]Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina A. Sakharova, Manja Marz, Alejandro Reyes, Martin Hölzer, Robert D. Finn:
VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models. PLoS Comput. Biol. 19(8) (2023) - 2022
- [j69]Nishadi De Silva, Jyothish Bhai, Marc Chakiachvili, Bruno Contreras-Moreira, Carla A. Cummins, Adam Frankish, Astrid Gall, Thiago Augusto Lopes Genez, Kevin L. Howe, Sarah E. Hunt, Fergal J. Martin, Benjamin Moore, Denye N. Oheh, Anne Parker, Andrew Parton, Magali Ruffier, Manoj Pandian Sakthivel, Dan Sheppard, John G. Tate, Anja Thormann, David Thybert, Stephen J. Trevanion, Andrea Winterbottom, Daniel R. Zerbino, Robert D. Finn, Paul Flicek, Andrew D. Yates:
The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. Nucleic Acids Res. 50(D1): 765-770 (2022) - [j68]Andrew D. Yates, James E. Allen, M. Ridwan Amode, Andrey G. Azov, Matthieu Barba, Andrés Becerra, Jyothish Bhai, Lahcen I. Campbell, Manuel Carbajo Martinez, Marc Chakiachvili, Kapeel Chougule, Mikkel B. Christensen, Bruno Contreras-Moreira, Alayne Cuzick, Luca Da Rin Fioretto, Paul Davis, Nishadi De Silva, Stavros Diamantakis, Sarah Dyer, Justin Elser, Carla V. Filippi, Astrid Gall, Dionysios Grigoriadis, Cristina Guijarro-Clarke, Parul Gupta, Kim E. Hammond-Kosack, Kevin L. Howe, Pankaj Jaiswal, Vinay Kaikala, Vivek Kumar, Sunita Kumari, Nick Langridge, Tuan Le, Manuel Luypaert, Gareth Maslen, Thomas Maurel, Benjamin Moore, Matthieu Muffato, Aleena Mushtaq, Guy Naamati, Sushma Naithani, Andrew Olson, Anne Parker, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Mark Quinton-Tulloch, Faye Rodgers, Marc Rosello, Magali Ruffier, James Seager, Vasily Sitnik, Michal Szpak, John G. Tate, Marcela K. Tello-Ruiz, Stephen J. Trevanion, Martin Urban, Doreen Ware, Sharon Wei, Gary Williams, Andrea Winterbottom, Magdalena Zarowiecki, Robert D. Finn, Paul Flicek:
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Res. 50(D1): 996-1003 (2022) - 2021
- [j67]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) - [j66]Ioanna Kalvari, Eric P. Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska, Kevin Lamkiewicz, Manja Marz, Sam Griffiths-Jones, Claire Toffano-Nioche, Daniel Gautheret, Zasha Weinberg, Elena Rivas, Sean R. Eddy, Robert D. Finn, Alex Bateman, Anton I. Petrov:
Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. 49(Database-Issue): D192-D200 (2021) - [j65]Blake A. Sweeney, Anton I. Petrov, Carlos Eduardo Ribas, Robert D. Finn, Alex Bateman, Maciej Szymanski, Wojciech M. Karlowski, Stefan E. Seemann, Jan Gorodkin, Jamie J. Cannone, Robin Ray Gutell, Simon Kay, Steven J. Marygold, Gilberto dos Santos, Adam Frankish, Jonathan M. Mudge, Ruth Barshir, Simon Fishilevich, Patricia P. Chan, Todd M. Lowe, Ruth L. Seal, Elspeth A. Bruford, Simona Panni, Pablo Porras, Dimitra Karagkouni, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J. Peterson, Ioanna Kalvari, Eric P. Nawrocki, Anton S. Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle S. Scott, Lauren M. Lui, David Hoksza, Ruth C. Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, Zasha Weinberg:
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 49(Database-Issue): D212-D220 (2021) - [j64]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) - [j63]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) - [j62]Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A. Salazar, Erik L. L. Sonnhammer, Silvio C. E. Tosatto, Lisanna Paladin, Shriya Raj, Lorna J. Richardson, Robert D. Finn, Alex Bateman:
Pfam: The protein families database in 2021. Nucleic Acids Res. 49(Database-Issue): D412-D419 (2021) - 2020
- [j61]Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jürgen Haas, Jerry Lanfear, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman, Alan J. Bridge, Guy Cochrane, Robert D. Finn, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Andrew Leach, Luana Licata, Per Oksvold, Sandra E. Orchard, Christine A. Orengo, Helen E. Parkinson, Bengt Persson, Pablo Porras, Jordi Rambla, Ana Rath, Charlotte Rodwell, Ugis Sarkans, Dietmar Schomburg, Ian Sillitoe, J. Dylan Spalding, Mathias Uhlén, Sameer Velankar, Juan Antonio Vizcaíno, Kalle von Feilitzen, Christian von Mering, Andrew D. Yates, Niklas Blomberg, Christine Durinx, Johanna R. McEntyre:
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinform. 36(8): 2636-2642 (2020) - [j60]Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Robert D. Finn, Julian Gough, David T. Jones, Lawrence A. Kelley, Typhaine Paysan-Lafosse, Su Datt Lam, Alexey G. Murzin, Arun Prasad Pandurangan, Gustavo A. Salazar, Marcin J. Skwark, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo:
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Nucleic Acids Res. 48(Database-Issue): D314-D319 (2020) - [j59]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
- [j58]David Jakubec, Jirí Vondrásek, Robert D. Finn:
3DPatch: fast 3D structure visualization with residue conservation. Bioinform. 35(2): 332-334 (2019) - [j57]Haiming Tang, Robert D. Finn, Paul D. Thomas:
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Bioinform. 35(3): 518-520 (2019) - [j56]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) - [j55]Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R. Eddy, Aurelien Luciani, Simon C. Potter, Matloob Qureshi, Lorna J. Richardson, Gustavo A. Salazar, Alfredo Smart, Erik L. L. Sonnhammer, Layla Hirsh, Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto, Robert D. Finn:
The Pfam protein families database in 2019. Nucleic Acids Res. 47(Database-Issue): D427-D432 (2019) - [j54]Lorna J. Richardson, Neil D. Rawlings, Gustavo A. Salazar, Alexandre Almeida, David Haft, Gregory Ducq, Granger G. Sutton, Robert D. Finn:
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. Nucleic Acids Res. 47(Database-Issue): D564-D572 (2019) - [j53]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:
The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 47(Webserver-Issue): W636-W641 (2019) - 2018
- [j52]Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P. Nawrocki, Elena Rivas, Sean R. Eddy, Alex Bateman, Robert D. Finn, Anton I. Petrov:
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 46(Database-Issue): D335-D342 (2018) - [j51]Neil D. Rawlings, Alan J. Barrett, Paul D. Thomas, Xiaosong Huang, Alex Bateman, Robert D. Finn:
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res. 46(Database-Issue): D624-D632 (2018) - [j50]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) - [j49]Paul Julian Kersey, James E. Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu, Thomas Maurel, Benjamin Moore, Mark D. McDowall, Uma Maheswari, Guy Naamati, Victoria Newman, Chuang Kee Ong, Michael Paulini, Helder Pedro, Emily Perry, Matthew Russell, Helen Sparrow, Electra Tapanari, Kieron R. Taylor, Alessandro Vullo, Gareth Williams, Amonida Zadissa, Andrew Olson, Joshua C. Stein, Sharon Wei, Marcela K. Tello-Ruiz, Doreen Ware, Aurelien Luciani, Simon C. Potter, Robert D. Finn, Martin Urban, Kim E. Hammond-Kosack, Dan M. Bolser, Nishadi De Silva, Kevin L. Howe, Nicholas Langridge, Gareth Maslen, Daniel Michael Staines, Andrew D. Yates:
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res. 46(Database-Issue): D802-D808 (2018) - [j48]Simon C. Potter, Aurelien Luciani, Sean R. Eddy, Young Mi Park, Rodrigo Lopez, Robert D. Finn:
HMMER web server: 2018 update. Nucleic Acids Res. 46(Webserver-Issue): W200-W204 (2018) - [j47]Aleksandra Tarkowska, Denise Carvalho-Silva, Charles E. Cook, Edd Turner, Robert D. Finn, Andrew D. Yates:
Eleven quick tips to build a usable REST API for life sciences. PLoS Comput. Biol. 14(12) (2018) - 2017
- [j46]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
- [j45]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) - [j44]Charles E. Cook, Mary Todd Bergman, Robert D. Finn, Guy Cochrane, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute in 2016: Data growth and integration. Nucleic Acids Res. 44(Database-Issue): 20-26 (2016) - [j43]Robert Hubley, Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Weidong Bao, Arian F. A. Smit, Travis J. Wheeler:
The Dfam database of repetitive DNA families. Nucleic Acids Res. 44(Database-Issue): 81-89 (2016) - [j42]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) - [j41]Neil D. Rawlings, Alan J. Barrett, Robert D. Finn:
Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res. 44(Database-Issue): 343-350 (2016) - [j40]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) - [j39]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) - [j38]Amit Upadhyay, Aaron D. Fleetwood, Ogun Adebali, Robert D. Finn, Igor B. Zhulin:
Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. PLoS Comput. Biol. 12(4) (2016) - 2015
- [j37]Zachary Chiang, Åke Västermark, Marco Punta, Penelope Coggill, Jaina Mistry, Robert D. Finn, Milton H. Saier Jr.:
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. Briefings Bioinform. 16(5): 865-872 (2015) - [j36]Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David E. Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Ísberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O'Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Åke Västermark, Gerrit Vriend:
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database J. Biol. Databases Curation 2015 (2015) - [j35]Eric P. Nawrocki, Sarah W. Burge, Alex Bateman, Jennifer Daub, Ruth Y. Eberhardt, Sean R. Eddy, Evan W. Floden, Paul P. Gardner, Thomas A. Jones, John G. Tate, Robert D. Finn:
Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 43(Database-Issue): 130-137 (2015) - [j34]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) - [j33]Robert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy:
HMMER web server: 2015 update. Nucleic Acids Res. 43(Webserver-Issue): W30-W38 (2015) - 2014
- [j32]Travis J. Wheeler, Jody Clements, Robert D. Finn:
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. BMC Bioinform. 15: 7 (2014) - [j31]Debanu Das, Alexey G. Murzin, Neil D. Rawlings, Robert D. Finn, Penelope Coggill, Alex Bateman, Adam Godzik, L. Aravind:
Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis. BMC Bioinform. 15: 75 (2014) - [j30]Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John G. Tate, Marco Punta:
Pfam: the protein families database. Nucleic Acids Res. 42(Database-Issue): 222-230 (2014) - [j29]Robert D. Finn, Benjamin L. Miller, Jody Clements, Alex Bateman:
iPfam: a database of protein family and domain interactions found in the Protein Data Bank. Nucleic Acids Res. 42(Database-Issue): 364-373 (2014) - 2013
- [j28]Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta:
The challenge of increasing Pfam coverage of the human proteome. Database J. Biol. Databases Curation 2013 (2013) - [j27]Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta:
The challenge of increasing Pfam coverage of the human proteome. Database J. Biol. Databases Curation 2013 (2013) - [j26]Penelope Coggill, Ruth Y. Eberhardt, Robert D. Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L. Axelrod, L. Aravind, Alexey G. Murzin, Alex Bateman:
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila. BMC Bioinform. 14: 265 (2013) - [j25]Travis J. Wheeler, Jody Clements, Sean R. Eddy, Robert Hubley, Thomas A. Jones, Jerzy Jurka, Arian F. A. Smit, Robert D. Finn:
Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res. 41(Database-Issue): 70-82 (2013) - 2012
- [j24]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) - [j23]Robert D. Finn, Paul P. Gardner, Alex Bateman:
Making your database available through Wikipedia: the pros and cons. Nucleic Acids Res. 40(Database-Issue): 9-12 (2012) - [j22]Marco Punta, Penny C. Coggill, Ruth Y. Eberhardt, Jaina Mistry, John G. Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn:
The Pfam protein families database. Nucleic Acids Res. 40(Database-Issue): 290-301 (2012) - [j21]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) - 2011
- [j20]Paul P. Gardner, Jennifer Daub, John G. Tate, Benjamin L. Moore, Isabelle H. Osuch, Sam Griffiths-Jones, Robert D. Finn, Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy, Alex Bateman:
Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res. 39(Database-Issue): 141-145 (2011) - [j19]Robert D. Finn, Jody Clements, Sean R. Eddy:
HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39(Web-Server-Issue): 29-37 (2011) - 2010
- [j18]Robert D. Finn, Jaina Mistry, John G. Tate, Penny C. Coggill, Andreas Heger, Joanne E. Pollington, O. Luke Gavin, Prasad Gunasekaran, Goran Ceric, Kristoffer Forslund, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman:
The Pfam protein families database. Nucleic Acids Res. 38(Database-Issue): 211-222 (2010) - 2009
- [j17]Alex Bateman, Robert D. Finn, Peter J. Sims, Therese Wiedmer, Andreas Biegert, Johannes Söding:
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. Bioinform. 25(2): 159-162 (2009) - [j16]Hagen Blankenburg, Robert D. Finn, Andreas Prlic, Andrew M. Jenkinson, Fidel Ramírez, Dorothea Emig, Sven-Eric Schelhorn, Joachim Büch, Thomas Lengauer, Mario Albrecht:
DASMI: exchanging, annotating and assessing molecular interaction data. Bioinform. 25(10): 1321-1328 (2009) - [j15]Paul P. Gardner, Jennifer Daub, John G. Tate, Eric P. Nawrocki, Diana L. Kolbe, Stinus Lindgreen, Adam C. Wilkinson, Robert D. Finn, Sam Griffiths-Jones, Sean R. Eddy, Alex Bateman:
Rfam: updates to the RNA families database. Nucleic Acids Res. 37(Database-Issue): 136-140 (2009) - [j14]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) - 2008
- [j13]Stephen John Sammut, Robert D. Finn, Alex Bateman:
Pfam 10 years on: 10 000 families and still growing. Briefings Bioinform. 9(3): 210-219 (2008) - [j12]Heinz Stockinger, Teresa K. Attwood, Shahid Nadeem Chohan, Richard G. Côté, Philippe Cudré-Mauroux, Laurent Falquet, Pedro L. Fernandes, Robert D. Finn, Taavi Hupponen, Eija Korpelainen, Alberto Labarga, Aurélie Laugraud, Tania Lima, Evangelos Pafilis, Marco Pagni, Steve Pettifer, Isabelle Phan, Nazim Rahman:
Experience using web services for biological sequence analysis. Briefings Bioinform. 9(6): 493-505 (2008) - [j11]Andrew M. Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas A. Down, Robert D. Finn, Henning Hermjakob, Tim J. P. Hubbard, Rafael C. Jiménez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R. Macías, Gabrielle A. Reeves, Andreas Prlic:
Integrating biological data - the Distributed Annotation System. BMC Bioinform. 9(S-8) (2008) - [j10]Robert D. Finn, John G. Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
The Pfam protein families database. Nucleic Acids Res. 36(Database-Issue): 281-288 (2008) - 2007
- [j9]Alex Bateman, Robert D. Finn:
SCOOP: a simple method for identification of novel protein superfamily relationships. Bioinform. 23(7): 809-814 (2007) - [j8]Robert D. Finn, James W. Stalker, David K. Jackson, Eugene Kulesha, Jody Clements, Roger Pettett:
ProServer: a simple, extensible Perl DAS server. Bioinform. 23(12): 1568-1570 (2007) - [j7]Jaina Mistry, Alex Bateman, Robert D. Finn:
Predicting active site residue annotations in the Pfam database. BMC Bioinform. 8 (2007) - [j6]Andreas Prlic, Thomas A. Down, Eugene Kulesha, Robert D. Finn, Andreas Kähäri, Tim J. P. Hubbard:
Integrating sequence and structural biology with DAS. BMC Bioinform. 8 (2007) - [j5]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) - 2006
- [j4]Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
Pfam: clans, web tools and services. Nucleic Acids Res. 34(Database-Issue): 247-251 (2006) - 2005
- [j3]Robert D. Finn, Mhairi Marshall, Alex Bateman:
iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions. Bioinform. 21(3): 410-412 (2005) - 2004
- [j2]Alex Bateman, Lachlan James M. Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, Sean R. Eddy:
The Pfam protein families database. Nucleic Acids Res. 32(Database-Issue): 138-141 (2004) - 1999
- [j1]Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L. Sonnhammer:
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 27(1): 260-262 (1999)
Conference and Workshop Papers
- 2016
- [c2]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 - 2006
- [c1]Andreas Prlic, Ewan Birney, Tony Cox, Thomas A. Down, Robert D. Finn, Stefan Gräf, David K. Jackson, Andreas Kähäri, Eugene Kulesha, Roger Pettett, James A. Smith, Jim Stalker, Tim J. P. Hubbard:
The Distributed Annotation System for Integration of Biological Data. DILS 2006: 195-203
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
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