Works by Finn, Robert D.


Results: 91
    1

    InterPro: the integrative protein signature database.

    Published in:
    Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D211, doi. 10.1093/nar/gkn785
    By:
    • Hunter, Sarah;
    • Apweiler, Rolf;
    • Attwood, Teresa K.;
    • Bairoch, Amos;
    • Bateman, Alex;
    • Binns, David;
    • Bork, Peer;
    • Das, Ujjwal;
    • Daugherty, Louise;
    • Duquenne, Lauranne;
    • Finn, Robert D.;
    • Gough, Julian;
    • Haft, Daniel;
    • Hulo, Nicolas;
    • Kahn, Daniel;
    • Kelly, Elizabeth;
    • Laugraud, Aurélie;
    • Letunic, Ivica;
    • Lonsdale, David;
    • Lopez, Rodrigo
    Publication type:
    Article
    2

    Rfam: updates to the RNA families database.

    Published in:
    Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D136, doi. 10.1093/nar/gkn766
    By:
    • Gardner, Paul P.;
    • Daub, Jennifer;
    • Tate, John G.;
    • Nawrocki, Eric P.;
    • Kolbe, Diana L.;
    • Lindgreen, Stinus;
    • Wilkinson, Adam C.;
    • Finn, Robert D.;
    • Griffiths-Jones, Sam;
    • Eddy, Sean R.;
    • Bateman, Alex
    Publication type:
    Article
    3

    The Pfam protein families database.

    Published in:
    Nucleic Acids Research, 2008, v. 36, p. D281
    By:
    • Finn, Robert D.;
    • Tate, John;
    • Mistry, Jaina;
    • Coggill, Penny C.;
    • Sammut, Stephen John;
    • Hotz, Hans-Rudolf;
    • Ceric, Goran;
    • Forslund, Kristoffer;
    • Eddy, Sean R.;
    • Sonnhammer, Erik L. L.;
    • Bateman, Alex
    Publication type:
    Article
    4

    Pfam: clans, web tools and services.

    Published in:
    Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d247, doi. 10.1093/nar/gkj149
    By:
    • Finn, Robert D.;
    • Mistry, Jaina;
    • Schuster-Böckler, Benjamin;
    • Griffiths-Jones, Sam;
    • Hollich, Volker;
    • Lassmann, Timo;
    • Moxon, Simon;
    • Marshall, Mhairi;
    • Khanna, Ajay;
    • Durbin, Richard;
    • Eddy, Sean R.;
    • Sonnhammer, Erik L. L.;
    • Bateman, Alex
    Publication type:
    Article
    5

    The Pfam protein families database.

    Published in:
    Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d138
    By:
    • Bateman, Alex;
    • Coin, Lachlan;
    • Durbin, Richard;
    • Finn, Robert D.;
    • Hollich, Volker;
    • Griffiths‐Jones, Sam;
    • Khanna, Ajay;
    • Marshall, Mhairi;
    • Moxon, Simon;
    • Sonnhammer, Erik L. L.;
    • Studholme, David J.;
    • Yeats, Corin;
    • Eddy, Sean R.
    Publication type:
    Article
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    Experience using web services for biological sequence analysis.

    Published in:
    Briefings in Bioinformatics, 2008, v. 9, n. 6, p. 493, doi. 10.1093/bib/bbn029
    By:
    • Stockinger, Heinz;
    • Attwood, Teresa;
    • Nadeem Chohan, Shahid;
    • Côté, Richard;
    • Cudré-Mauroux, Philippe;
    • Falquet, Laurent;
    • Fernandes, Pedro;
    • Finn, Robert D.;
    • Hupponen, Taavi;
    • Korpelainen, Eija;
    • Labarga, Alberto;
    • Laugraud, Aurelie;
    • Lima, Tania;
    • Pafilis, Evangelos;
    • Pagni, Marco;
    • Pettifer, Steve;
    • Phan, Isabelle;
    • Rahman, Nazim
    Publication type:
    Article
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    An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.

    Published in:
    Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-89881-2
    By:
    • O'Sullivan, Denise M.;
    • Doyle, Ronan M.;
    • Temisak, Sasithon;
    • Redshaw, Nicholas;
    • Whale, Alexandra S.;
    • Logan, Grace;
    • Huang, Jiabin;
    • Fischer, Nicole;
    • Amos, Gregory C. A.;
    • Preston, Mark D.;
    • Marchesi, Julian R.;
    • Wagner, Josef;
    • Parkhill, Julian;
    • Motro, Yair;
    • Denise, Hubert;
    • Finn, Robert D.;
    • Harris, Kathryn A.;
    • Kay, Gemma L.;
    • O'Grady, Justin;
    • Ransom-Jones, Emma
    Publication type:
    Article
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    Microbial abundance, activity and population genomic profiling with mOTUs2.

    Published in:
    Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-08844-4
    By:
    • Milanese, Alessio;
    • Mende, Daniel R;
    • Paoli, Lucas;
    • Salazar, Guillem;
    • Ruscheweyh, Hans-Joachim;
    • Cuenca, Miguelangel;
    • Hingamp, Pascal;
    • Alves, Renato;
    • Costea, Paul I;
    • Coelho, Luis Pedro;
    • Schmidt, Thomas S. B.;
    • Almeida, Alexandre;
    • Mitchell, Alex L;
    • Finn, Robert D.;
    • Huerta-Cepas, Jaime;
    • Bork, Peer;
    • Zeller, Georg;
    • Sunagawa, Shinichi
    Publication type:
    Article
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    ProServer: a simple, extensible Perl DAS server.

    Published in:
    Bioinformatics, 2007, v. 23, n. 12, p. 1568, doi. 10.1093/bioinformatics/btl650
    By:
    • Robert D. Finn;
    • James W. Stalker;
    • David K. Jackson;
    • Eugene Kulesha;
    • Jody Clements;
    • Roger Pettett
    Publication type:
    Article
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    COVID-19 pandemic reveals the peril of ignoring metadata standards.

    Published in:
    Scientific Data, 2020, v. 7, n. 1, p. 1, doi. 10.1038/s41597-020-0524-5
    By:
    • Schriml, Lynn M.;
    • Chuvochina, Maria;
    • Davies, Neil;
    • Eloe-Fadrosh, Emiley A.;
    • Finn, Robert D.;
    • Hugenholtz, Philip;
    • Hunter, Christopher I.;
    • Hurwitz, Bonnie L.;
    • Kyrpides, Nikos C.;
    • Meyer, Folker;
    • Mizrachi, Ilene Karsch;
    • Sansone, Susanna-Assunta;
    • Sutton, Granger;
    • Tighe, Scott;
    • Walls, Ramona
    Publication type:
    Article
    26

    A unified catalog of 204,938 reference genomes from the human gut microbiome.

    Published in:
    Nature Biotechnology, 2021, v. 39, n. 1, p. 105, doi. 10.1038/s41587-020-0603-3
    By:
    • Almeida, Alexandre;
    • Nayfach, Stephen;
    • Boland, Miguel;
    • Strozzi, Francesco;
    • Beracochea, Martin;
    • Shi, Zhou Jason;
    • Pollard, Katherine S.;
    • Sakharova, Ekaterina;
    • Parks, Donovan H.;
    • Hugenholtz, Philip;
    • Segata, Nicola;
    • Kyrpides, Nikos C.;
    • Finn, Robert D.
    Publication type:
    Article
    27

    A human gut bacterial genome and culture collection for improved metagenomic analyses.

    Published in:
    Nature Biotechnology, 2019, v. 37, n. 2, p. 186, doi. 10.1038/s41587-018-0009-7
    By:
    • Forster, Samuel C.;
    • Kumar, Nitin;
    • Anonye, Blessing O.;
    • Almeida, Alexandre;
    • Viciani, Elisa;
    • Stares, Mark D.;
    • Dunn, Matthew;
    • Mkandawire, Tapoka T.;
    • Zhu, Ana;
    • Shao, Yan;
    • Pike, Lindsay J.;
    • Louie, Thomas;
    • Browne, Hilary P.;
    • Mitchell, Alex L.;
    • Neville, B. Anne;
    • Finn, Robert D.;
    • Lawley, Trevor D.
    Publication type:
    Article
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    Integrating biological data -- the Distributed Annotation System.

    Published in:
    BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-S8-S3
    By:
    • Jenkinson, Andrew M.;
    • Albrecht, Mario;
    • Birney, Ewan;
    • Blankenburg, Hagen;
    • Down, Thomas;
    • Finn, Robert D.;
    • Hermjakob, Henning;
    • Hubbard, Tim J. P.;
    • Jimenez, Rafael C.;
    • Jones, Philip;
    • Kähäri, Andreas;
    • Kulesha, Eugene;
    • Macías, José R.;
    • Reeves, Gabrielle A.;
    • Prlić, Andreas
    Publication type:
    Article
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    CELEBRIMBOR: core and accessory genes from metagenomes.

    Published in:
    Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae542
    By:
    • Hellewell, Joel;
    • Horsfield, Samuel T;
    • Wachsmann, Johanna von;
    • Gurbich, Tatiana A;
    • Finn, Robert D;
    • Iqbal, Zamin;
    • Roberts, Leah W;
    • Lees, John A
    Publication type:
    Article
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    Pfam: The protein families database in 2021.

    Published in:
    Nucleic Acids Research, 2021, v. 49, n. D1, p. D412, doi. 10.1093/nar/gkaa913
    By:
    • Mistry, Jaina;
    • Chuguransky, Sara;
    • Williams, Lowri;
    • Qureshi, Matloob;
    • Salazar, Gustavo A;
    • Sonnhammer, Erik L L;
    • Tosatto, Silvio C E;
    • Paladin, Lisanna;
    • Raj, Shriya;
    • Richardson, Lorna J;
    • Finn, Robert D;
    • Bateman, Alex
    Publication type:
    Article
    40

    Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

    Published in:
    Nucleic Acids Research, 2021, v. 49, n. D1, p. D192, doi. 10.1093/nar/gkaa1047
    By:
    • Kalvari, Ioanna;
    • Nawrocki, Eric P;
    • Ontiveros-Palacios, Nancy;
    • Argasinska, Joanna;
    • Lamkiewicz, Kevin;
    • Marz, Manja;
    • Griffiths-Jones, Sam;
    • Toffano-Nioche, Claire;
    • Gautheret, Daniel;
    • Weinberg, Zasha;
    • Rivas, Elena;
    • Eddy, Sean R;
    • Finn, Robert D;
    • Bateman, Alex;
    • Petrov, Anton I
    Publication type:
    Article
    41

    Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.

    Published in:
    Nucleic Acids Research, 2020, v. 48, n. D1, p. D314, doi. 10.1093/nar/gkz967
    By:
    • Sillitoe, Ian;
    • Andreeva, Antonina;
    • Blundell, Tom L;
    • Buchan, Daniel W A;
    • Finn, Robert D;
    • Gough, Julian;
    • Jones, David;
    • Kelley, Lawrence A;
    • Paysan-Lafosse, Typhaine;
    • Lam, Su Datt;
    • Murzin, Alexey G;
    • Pandurangan, Arun Prasad;
    • Salazar, Gustavo A;
    • Skwark, Marcin J;
    • Sternberg, Michael J E;
    • Velankar, Sameer;
    • Orengo, Christine
    Publication type:
    Article
    42

    MGnify: the microbiome analysis resource in 2020.

    Published in:
    Nucleic Acids Research, 2020, v. 48, n. D1, p. D570, doi. 10.1093/nar/gkz1035
    By:
    • Mitchell, Alex L;
    • Almeida, Alexandre;
    • Beracochea, Martin;
    • Boland, Miguel;
    • Burgin, Josephine;
    • Cochrane, Guy;
    • Crusoe, Michael R;
    • Kale, Varsha;
    • Potter, Simon C;
    • Richardson, Lorna J;
    • Sakharova, Ekaterina;
    • Scheremetjew, Maxim;
    • Korobeynikov, Anton;
    • Shlemov, Alex;
    • Kunyavskaya, Olga;
    • Lapidus, Alla;
    • Finn, Robert D
    Publication type:
    Article
    43

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

    Published in:
    Nucleic Acids Research, 2019, v. 47, n. W1, p. W636, doi. 10.1093/nar/gkz268
    By:
    • Madeira, Fábio;
    • Park, Young mi;
    • Lee, Joon;
    • Buso, Nicola;
    • Gur, Tamer;
    • Madhusoodanan, Nandana;
    • Basutkar, Prasad;
    • Tivey, Adrian R N;
    • Potter, Simon C;
    • Finn, Robert D;
    • Lopez, Rodrigo
    Publication type:
    Article
    44

    The Pfam protein families database in 2019.

    Published in:
    Nucleic Acids Research, 2019, v. 47, n. D1, p. D427, doi. 10.1093/nar/gky995
    By:
    • El-Gebali, Sara;
    • Mistry, Jaina;
    • Bateman, Alex;
    • Eddy, Sean R;
    • Luciani, Aurélien;
    • Potter, Simon C;
    • Qureshi, Matloob;
    • Richardson, Lorna J;
    • Salazar, Gustavo A;
    • Smart, Alfredo;
    • Sonnhammer, Erik L L;
    • Hirsh, Layla;
    • Paladin, Lisanna;
    • Piovesan, Damiano;
    • Tosatto, Silvio C E;
    • Finn, Robert D
    Publication type:
    Article
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    HMMER web server: 2018 update.

    Published in:
    Nucleic Acids Research, 2018, v. 46, n. W1, p. W200, doi. 10.1093/nar/gky448
    By:
    • Potter, Simon C.;
    • Luciani, Aurélien;
    • Eddy, Sean R.;
    • Park, Youngmi;
    • Lopez, Rodrigo;
    • Finn, Robert D.
    Publication type:
    Article
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    InterPro in 2017--beyond protein family and domain annotations.

    Published in:
    Nucleic Acids Research, 2017, v. 45, n. D1, p. D190, doi. 10.1093/nar/gkw1107
    By:
    • Finn, Robert D.;
    • Attwood, Teresa K.;
    • Babbitt, Patricia C.;
    • Bateman, Alex;
    • Bork, Peer;
    • Bridge, Alan J.;
    • Hsin-Yu Chang;
    • Dosztányi, Zsuzsanna;
    • El-Gebali, Sara;
    • Fraser, Matthew;
    • Gough, Julian;
    • Haft, David;
    • Holliday, Gemma L.;
    • Hongzhan Huang;
    • Xiaosong Huang;
    • Letunic, Ivica;
    • Lopez, Rodrigo;
    • Lu, Shennan;
    • Marchler-Bauer, Aron;
    • Huaiyu Mi
    Publication type:
    Article
    50

    The Pfam protein families database: towards a more sustainable future.

    Published in:
    Nucleic Acids Research, 2016, v. 44, p. D279, doi. 10.1093/nar/gkv1344
    By:
    • Finn, Robert D.;
    • Coggill, Penelope;
    • Eberhardt, Ruth Y.;
    • Eddy, Sean R.;
    • Mistry, Jaina;
    • Mitchell, Alex L.;
    • Potter, Simon C.;
    • Punta, Marco;
    • Qureshi, Matloob;
    • Sangrador-Vegas, Amaia;
    • Salazar, Gustavo A.;
    • Tate, John;
    • Bateman, Alex
    Publication type:
    Article