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Citing Pfam
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Latest publications
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`The Pfam protein families database: embracing AI/ML <https://doi.org/10.1093/nar/gkae997>`_ T. Paysan-Lafosse, A. Andreeva, M. Blum, S. Chuguransky, T. Grego, B. Lazaro Pinto, G.A. Salazar, M.L. Bileschi, F. Llinares-López, L. Meng-Papaxanthos, L.J. Colwell, NV. Grishin, R.D. Schaeffer, D.Clementel, S.C.E Tosatto, E. Sonnhammer, V. Wood, A. Bateman *Nucleic Acids Research* (2024) doi: 10.1093/nar/gkae997, PMID: `39540428 <https://europepmc.org/article/MED/39540428>`_

`Bridging the gap between sequence and structure classifications of proteins with AlphaFold models. <https://www.sciencedirect.com/science/article/pii/S002228362400384X?via%3Dihub>`_
J. Pei, A. Andreeva, S. Chuguransky, B. Lázaro Pinto, T. Paysan-Lafosse, D.R. Schaeffer, A. Bateman, Q. Cong, NV. Grishin *Journal of Molecular Biology* (2024) doi: 10.1016/j.jmb.2024.168764, PMID: `39197652 <https://europepmc.org/article/MED/39197652>`_

Previous publications
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`Pfam: The protein families database in 2021 <https://doi.org/10.1093/nar/gkaa913>`_  J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G.A. Salazar, E.L.L. Sonnhammer, S.C.E. Tosatto, L. Paladin, S. Raj, L.J. Richardson, R.D. Finn, A. Bateman *Nucleic Acids Research* (2020) Database Issue 49:D412–D419, PMID: `33125078 <https://europepmc.org/article/MED/33125078>`_

`The Pfam protein families database in 2019 <https://doi.org/10.1093/nar/gky995>`_: S. El-Gebali, J. Mistry, A. Bateman, S.R. Eddy, A. Luciani, S.C. Potter, M. Qureshi, L.J. Richardson, G.A. Salazar, A. Smart, E.L.L. Sonnhammer, L. Hirsh, L. Paladin, D. Piovesan, S.C.E. Tosatto, R.D. Finn *Nucleic Acids Research* (2019) Database Issue 47:D427–D432, PMID: `30357350 <https://europepmc.org/article/MED/30357350>`_

`The Pfam protein families database: towards a more sustainable future <https://nar.oxfordjournals.org/content/44/D1/D279.long>`_: R.D. Finn, P. Coggill, R.Y. Eberhardt, S.R. Eddy, J. Mistry, A.L. Mitchell, S.C. Potter, M. Punta, M. Qureshi, A. Sangrador-Vegas, G.A. Salazar, J. Tate, A. Bateman *Nucleic Acids Research* (2016) Database Issue 44:D279-D285, PMID: `26673716 <https://europepmc.org/article/MED/26673716>`_

`The Pfam protein families database <https://nar.oxfordjournals.org/content/42/D1/D222.long>`_: R.D. Finn, A. Bateman, J. Clements, P. Coggill, R.Y. Eberhardt, S.R. Eddy, A. Heger, K. Hetherington, L. Holm, J. Mistry, E.L.L. Sonnhammer, J. Tate, M. Punta *Nucleic Acids Research* (2014) Database Issue 42:D222-D230, PMID: `24288371 <https://europepmc.org/article/MED/24288371>`_

`The Pfam protein families database <https://nar.oxfordjournals.org/content/40/D1/D290.full>`_: M. Punta, P.C. Coggill, R.Y. Eberhardt, J. Mistry, J. Tate, C. Boursnell, N. Pang, K. Forslund, G. Ceric, J. Clements, A. Heger, L. Holm, E.L.L. Sonnhammer, S.R. Eddy, A. Bateman, R.D. Finn *Nucleic Acids Research* (2012) Database Issue 40:D290-D301, PMID: `22127870 <https://europepmc.org/article/MED/22127870>`_

`The Pfam protein families database <https://nar.oxfordjournals.org/cgi/content/full/38/suppl_1/D211>`_: R.D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J.E. Pollington, O.L. Gavin, P. Gunesekaran, G. Ceric, K. Forslund, L. Holm, E.L. Sonnhammer, S.R. Eddy, A. Bateman *Nucleic Acids Research* (2010) Database Issue 38:D211-D222, PMID: `19920124 <https://europepmc.org/article/MED/19920124>`_

`The Pfam protein families database <https://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D281>`_: R.D. Finn, J. Tate, J. Mistry, P.C. Coggill, J.S. Sammut, H.R. Hotz, G. Ceric, K. Forslund, S.R. Eddy, E.L. Sonnhammer and A. Bateman *Nucleic Acids Research* (2008) Database Issue 36:D281-D288

`Pfam: clans, web tools and services <https://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D247>`_: R.D. Finn, J. Mistry, B. Schuster-Böckler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S.R. Eddy, E.L.L. Sonnhammer and A. Bateman *Nucleic Acids Research* (2006) Database Issue 34:D247-D51

`Enhanced protein domain discovery by using language modeling techniques from speech recognition <https://www.ncbi.nlm.nih.gov/pubmed/12668763>`_: L. Coin, A. Bateman and R. Durbin *Proc. Natl. Acad. Sci.* USA. (2003) 100(8):4516-20

`The Pfam Protein Families Database <https://academic.oup.com/nar/article/42/D1/D222/1062431>`_: A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E.L.L. Sonnhammer, D.J. Studholme, C. Yeats and S.R. Eddy *Nucleic Acids Research* (2004) 32:D138-D141

`The Pfam Protein Families Database <https://nar.oxfordjournals.org/cgi/content/short/30/1/276>`_: A. Bateman, E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S.R. Eddy, S. Griffiths-Jones, K.L. Howe, M. Marshall and E.L. Sonnhammer *Nucleic Acids Research* (2002) 30(1):276-280

`The Pfam Protein Families Database <https://nar.oxfordjournals.org/cgi/content/full/28/1/263>`_: A. Bateman, E. Birney, R. Durbin, S.R. Eddy, K.L. Howe and E.L. Sonnhammer *Nucleic Acids Research*  (2000) 28:263-266

`Pfam 3.1: 1313 multiple alignments match the majority of proteins <https://nar.oxfordjournals.org/cgi/content/full/27/1/260>`_: A. Bateman, E. Birney, R. Durbin, S.R. Eddy, R.D. Finn and E.L.L. Sonnhammer *Nucleic Acids Research* (1999) 27:260-262

`Pfam: multiple sequence alignments and HMM-profiles of protein domains <https://nar.oxfordjournals.org/cgi/content/full/26/1/320>`_: E.L.L. Sonnhammer, S.R. Eddy, E. Birney, A. Bateman and R. Durbin *Nucleic Acids Research* (1998) 26:320-322

`Pfam: a comprehensive database of protein families based on seed alignments <https://www.ncbi.nlm.nih.gov/pubmed/9223186>`_: E.L.L. Sonnhammer, S.R. Eddy and R. Durbin *Proteins* (1997) 28:405-420

Book Chapters on Pfam
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`Homology-Based Annotation of Large Protein Datasets <https://doi.org/10.1007/978-1-4939-3572-7_8>`_ M. Punta, J. Mistry
*Data Mining Techniques for the Life Sciences. Methods in Molecular Biology* vol 1415 (2016) doi: 10.1007/978-1-4939-3572-7_8

`Identifying Protein Domains with the Pfam Database <https://doi.org/10.1002/0471250953.bi0205s23>`_ P. Coggill, R.D. Finn, A. Bateman
*Current Protocols in Bioinformatics* Chapter 2, Unit 2.5 (2008) doi: 10.1002/0471250953.bi0205s23

`Pfam: a domain-centric method for analysing proteins and proteomes <https://doi.org/10.1007/978-1-59745-515-2_4>`_ J. Mistry and R.D. Finn
*Comparative Genomics. Methods in Molecular Biology* vol 396 (2007) doi: 10.1007/978-1-59745-515-2_4

`Pfam: the protein families database <https://doi.org/10.1002/047001153X.g306303>`_ R.D. Finn (eds M.J. Dunn, L.B. Jorde, P.F.R. Little, S. Subramaniam)
*Genetics, Genomics, Proteomics and Bioinformatics*, Section 6: Protein Families (2005) doi: 10.1002/047001153X.g306303

`Identifying protein domains with the Pfam database <https://doi.org/10.1002/0471250953.bi0205s01>`_ R.D. Finn, A. Bateman and S. Griffiths-Jones
*Current Protocols in Bioinformatics* (2003) doi: 10.1002/0471250953.bi0205s01