InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites - Nicola J. Mulder; Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Philipp Bucher; Richard R. Copley; Emmanuel Courcelle; et al. (Briefings Bioinform., 2002)

The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs. - Sam Griffiths-Jones; Alex Bateman (Bioinform., 2002)

The Pfam Protein Families Database. - Alex Bateman; Ewan Birney; Lorenzo Cerutti; Richard Durbin; Laurence Ettwiller; Sean R. Eddy; Sam Griffiths-Jones; Kevin L. Howe; Mhairi Marshall; Erik L. L. Sonnhammer (Nucleic Acids Res., 2002)

Rfam: an RNA family database. - Sam Griffiths-Jones; Alex Bateman; Mhairi Marshall; Ajay Khanna; Sean R. Eddy (Nucleic Acids Res., 2003)

The InterPro Database, 2003 brings increased coverage and new features. - Nicola J. Mulder; Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Daniel Barrell; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Philipp Bucher; Richard R. Copley; et al. (Nucleic Acids Res., 2003)

The Pfam protein families database. - 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; et al. (Nucleic Acids Res., 2004)

The microRNA Registry. - Sam Griffiths-Jones (Nucleic Acids Res., 2004)

RALEE–RNA ALignment Editor in Emacs. - Sam Griffiths-Jones (Bioinform., 2005)

Rfam: annotating non-coding RNAs in complete genomes. - Sam Griffiths-Jones; Simon Moxon; Mhairi Marshall; Ajay Khanna; Sean R. Eddy; Alex Bateman (Nucleic Acids Res., 2005)

Pfam: clans, web tools and services. - 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; et al. (Nucleic Acids Res., 2006)

miRBase: microRNA sequences, targets and gene nomenclature. - Sam Griffiths-Jones; Russell J. Grocock; Stijn van Dongen; Alex Bateman; Anton J. Enright (Nucleic Acids Res., 2006)

miRBase: tools for microRNA genomics. - Sam Griffiths-Jones; Harpreet Kaur Saini; Stijn van Dongen; Anton J. Enright (Nucleic Acids Res., 2008)

Rfam: updates to the RNA families database. - 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 (Nucleic Acids Res., 2009)

Rfam: Wikipedia, clans and the "decimal" release. - 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 (Nucleic Acids Res., 2011)

miRBase: integrating microRNA annotation and deep-sequencing data. - Ana Kozomara; Sam Griffiths-Jones (Nucleic Acids Res., 2011)

Detection of microRNAs in color space. - Antonio Marco; Sam Griffiths-Jones (Bioinform., 2012)

miRBase: annotating high confidence microRNAs using deep sequencing data. - Ana Kozomara; Sam Griffiths-Jones (Nucleic Acids Res., 2014)

Bias in microRNA functional enrichment analysis. - Thomas Bleazard; Janine A. Lamb; Sam Griffiths-Jones (Bioinform., 2015)

miRBase: from microRNA sequences to function. - Ana Kozomara; Maria Birgaoanu; Sam Griffiths-Jones (Nucleic Acids Res., 2019)

Rfam 14: expanded coverage of metagenomic, viral and microRNA families. - 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; et al. (Nucleic Acids Res., 2021)

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. - 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; et al. (Nucleic Acids Res., 2021)

LitSumm: large language models for literature summarization of noncoding RNAs. - Andrew Green 001; Carlos Eduardo Ribas; Nancy Ontiveros-Palacios; Sam Griffiths-Jones; Anton I. Petrov; Alex Bateman; Blake A. Sweeney (Database J. Biol. Databases Curation, 2025)