Robert D Finn

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 24

Top Venues

Nucleic acids research

Scientific reports

Nature microbiology

Nature biotechnology

European Bioinformatics Institute

This page only lists publications with an associated author ORCID identifier.

Affiliation History

European Bioinformatics Institute Jan 01 2014

United Kingdom

Team Leder :: Sequence Families Team

Howard Hughes Medical Institute Janelia Farm Research Campus Dec 01 2012 - Dec 01 2013

United States

Manager, Computational Genomics :: Scientific Computing

Howard Hughes Medical Institute Janelia Farm Research Campus Jul 15 2010 - Dec 01 2012

United States

HMMER Project Leader :: Scientific Computing

Wellcome Trust Sanger Institute Sep 01 2004 - Jul 01 2010

United Kingdom

Project leader :: Informatics

Publications

Ellen S Cameron, Santiago Sanchez, Nick Goldman, Mark L Blaxter, Robert D Finn
Diversity and specificity of molecular functions in cyanobacterial symbionts. Scientific reports 14 (1) (2024)
Ellen S Cameron, Santiago Sanchez, Nick Goldman, Mark L Blaxter, Robert D Finn
Diversity and specificity of molecular functions in cyanobacterial symbionts. Scientific reports 14 (1) (2024)
Ellen S Cameron, Santiago Sanchez, Nick Goldman, Mark L Blaxter, Robert D Finn
Diversity and specificity of molecular functions in cyanobacterial symbionts. Scientific reports 14 (1) (2024)
Curtis Huttenhower, Robert D Finn, Alice Carolyn McHardy
Challenges and opportunities in sharing microbiome data and analyses. Nature microbiology (2023)
Guillermo Rangel-Pineros, Alexandre Almeida, Martin Beracochea, Ekaterina 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 computational biology 19 (8) (2023)
Thomas Sebastian Benedikt Schmidt, Anthony Fullam, Pamela Ferretti, Askarbek Orakov, Oleksandr M Maistrenko, Hans-Joachim Ruscheweyh, Ivica Letunic, Yiqian Duan, Thea Van Rossum, Shinichi Sunagawa, Daniel R Mende, Robert D Finn, Michael Kuhn, Luis Pedro Coelho, Peer Bork
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic acids research (2023)
Haris Zafeiropoulos, Martin Beracochea, Stelios Ninidakis, Katrina Exter, Antonis Potirakis, Gianluca De Moro, Lorna Richardson, Erwann Corre, João Machado, Evangelos Pafilis, Georgios Kotoulas, Ioulia Santi, Robert D Finn, Cymon J Cox, Christina Pavloudi
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data. GigaScience 12 (2023)
Peter W Harrison, M Ridwan Amode, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Lahcen I Campbell, Manuel Carbajo Martinez, Mehrnaz Charkhchi, Kapeel Chougule, Alexander Cockburn, Claire Davidson, Nishadi H De Silva, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcıa Giron, Thiago Genez, Dionysios Grigoriadis, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Tatiana A Gurbich, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Disha Lodha, Diego Marques-Coelho, Gareth Maslen, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Daniel Poppleton, Irina Prosovetskaia, Shriya Raj, José G Pérez-Silva, Ahamed Imran Abdul Salam, Shradha Saraf, Nuno Saraiva-Agostinho, Dan Sheppard, Swati Sinha, Botond Sipos, Vasily Sitnik, William Stark, Emily Steed, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Doreen H Ware, Elizabeth Wass, Natalie L Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jon Keatley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, Guy Naamati, John Tate, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Fiona Cunningham, Sarah Dyer, Robert D Finn, Fergal J Martin, Andrew D Yates
Ensembl 2024. Nucleic acids research (2023)
Fergal J Martin, M Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fiorretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcıa Giron, Thiago Genez, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike 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 Piližota, 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 Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, John 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 research (2022)
Maaly Nassar, Alexander B Rogers, Francesco Talo', Santiago Sanchez, Zunaira Shafique, Robert D Finn, Johanna McEntyre
A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications. GigaScience 11 (2022)
Lorna Richardson, Ben Allen, Germana Baldi, Martin Beracochea, Maxwell L Bileschi, Tony Burdett, Josephine Burgin, Juan Caballero Pérez, Guy Cochrane, Lucy J Colwell, Tom Curtis, Alejandra Escobar-Zepeda, Tatiana A Gurbich, Varsha Kale, Anton Korobeynikov, Shriya Raj, Alexander B Rogers, Ekaterina Sakharova, Santiago Sanchez, Darren J Wilkinson, Robert D Finn
MGnify: the microbiome sequence data analysis resource in 2023. Nucleic acids research (2022)
Qiang Lin, Xavier Basil Britto, Blaise T F Alako, Alex L Mitchell, Sahaya Glingston Rajakani, Youri Glupczynski, Robert D Finn, Guy Cochrane, Surbhi Malhotra-Kumar
Screening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes. Communications biology 5 (1) (2022)
Nishadi H De Silva, Jyothish Bhai, Marc Chakiachvili, Bruno Contreras-Moreira, Carla Cummins, Adam Frankish, Astrid Gall, Thiago Genez, Kevin L Howe, Sarah E Hunt, Fergal J Martin, Benjamin Moore, Denye Ogeh, Anne Parker, Andrew Parton, Magali Ruffier, Manoj Pandian Sakthivel, Dan Sheppard, John 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 research (2021)
Andrew D Yates, James Allen, Ridwan M Amode, Andrey G Azov, Matthieu Barba, Andrés Becerra, Jyothish Bhai, Lahcen I Campbell, Manuel Carbajo Martinez, Marc Chakiachvili, Kapeel Chougule, Mikkel Christensen, Bruno Contreras-Moreira, Alayne Cuzick, Luca Da Rin Fioretto, Paul Davis, Nishadi H 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 L 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 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 research (2021)
Blake A Sweeney, David Hoksza, Eric P Nawrocki, Carlos Eduardo Ribas, Fábio Madeira, Jamie J Cannone, Robin Gutell, Aparna Maddala, Caeden D Meade, Loren Dean Williams, Anton S Petrov, Patricia P Chan, Todd M Lowe, Robert D Finn, Anton I Petrov
R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nature communications 12 (1) (2021)
Cynthia Maria Chibani, Alexander Mahnert, Guillaume Borrel, Alexandre Almeida, Almut Werner, Jean-François Brugère, Simonetta Gribaldo, Robert D Finn, Ruth Anne Schmitz, Christine Moissl-Eichinger
A catalogue of 1,167 genomes from the human gut archaeome. Nature microbiology 7 (1) (2021)
Sara Saheb Kashaf, Diana M Proctor, Clay Deming, Paul Saary, Martin Hölzer, null null, Monica E Taylor, Heidi H Kong, Julie A Segre, Alexandre Almeida, Robert D Finn
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. Nature microbiology 7 (1) (2021)
Muzaffer Arıkan, Alex L Mitchell, Robert D Finn, Filiz Gürel
Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics. Journal of food science 85 (2) (2020)
Lynn M Schriml, Maria Chuvochina, Neil Davies, Emiley A Eloe-Fadrosh, Robert D Finn, Philip Hugenholtz, Christopher I Hunter, Bonnie L Hurwitz, Nikos C Kyrpides, Folker Meyer, Ilene Karsch Mizrachi, Susanna-Assunta Sansone, Granger G Sutton, Scott W Tighe, Ramona L Walls
COVID-19 pandemic reveals the peril of ignoring metadata standards. Scientific data 7 (1) (2020)
Alexandre Almeida, Stephen Nayfach, Miguel Boland, Francesco Strozzi, Martin Beracochea, Zhou Jason Shi, Katherine S Pollard, Ekaterina Sakharova, Donovan H Parks, Philip Hugenholtz, Nicola Segata, Nikos C Kyrpides, Robert D Finn
A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature biotechnology 39 (1) (2020)
Samuel C Forster, Nitin Kumar, Blessing O Anonye, Alexandre Almeida, Elisa Viciani, Mark D Stares, Matthew Dunn, Tapoka T Mkandawire, Ana Zhu, Yan Shao, Lindsay J Pike, Thomas Louie, Hilary P Browne, Alex L Mitchell, B Anne Neville, Robert D Finn, Trevor D Lawley
A human gut bacterial genome and culture collection for improved metagenomic analyses. Nature biotechnology 37 (2) (2019)
Alessio Milanese, Daniel R Mende, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Jc Alves, Paul Igor Costea, Luis Pedro Coelho, Thomas Sebastian Benedikt Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller, Shinichi Sunagawa
Microbial abundance, activity and population genomic profiling with mOTUs2. Nature communications 10 (1) (2019)
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 computational biology 14 (12) (2018)
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 (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Robert D Finn