Integrating genomic homology into gene structure prediction. - Ian Korf; Paul Flicek; Daniel Duan; Michael R. Brent (ISMB (Supplement of Bioinformatics), 2001)

Gene finding in the chicken genome. - Eduardo Eyras; Alexandre Reymond; Robert Castelo; Jacqueline M. Bye; Francisco Camara; Paul Flicek; Elizabeth J. Huckle; Genis Parra; David D. Shteynberg; Carine Wyss; Jane Rogers; Stylianos E. Antonarakis; et al. (BMC Bioinform., 2005)

Ensembl 2006. - Ewan Birney; T. Daniel Andrews; Mario Cáccamo; Yuan Chen 007; Laura Clarke; Guy Coates; Tony Cox 001; Fiona Cunningham; Val Curwen; Tim Cutts; Thomas A. Down; Richard Durbin; et al. (Nucleic Acids Res., 2006)

Optimized design and assessment of whole genome tiling arrays. - Stefan Gräf; Fiona G. G. Nielsen; Stefan Kurtz; Martijn A. Huynen; Ewan Birney; Henk Stunnenberg; Paul Flicek (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Optimising oligonucleotide array design for ChIP-on-chip. - Fiona G. G. Nielsen; Stefan Gräf; Xinmin Zhang; Stefan Kurtz; Sergei Denissov; Roland Green; Ewan Birney; Paul Flicek; Martijn A. Huynen; Henk Stunnenberg (BMC Bioinform., 2007)

Ensembl 2007. - Tim J. P. Hubbard; Bronwen L. Aken; Kathryn Beal; Benoît Ballester; Mario Cáccamo; Yuan Chen 007; Laura Clarke; Guy Coates; Fiona Cunningham; Tim Cutts; Thomas A. Down; S. C. Dyer; et al. (Nucleic Acids Res., 2007)

nGASP - the nematode genome annotation assessment project. - Avril Coghlan; Tristan J. Fiedler; Sheldon J. McKay; Paul Flicek; Todd W. Harris; Darin Blasiar; Lincoln D. Stein (BMC Bioinform., 2008)

Ensembl 2008. - Paul Flicek; Bronwen L. Aken; Kathryn Beal; Benoît Ballester; Mario Cáccamo; Yuan Chen 007; Laura Clarke; Guy Coates; Fiona Cunningham; Tim Cutts; Thomas A. Down; S. C. Dyer; et al. (Nucleic Acids Res., 2008)

Ensembl 2009. - Tim J. P. Hubbard; Bronwen L. Aken; Sarah C. Ayling; Benoît Ballester; Kathryn Beal; Eugene Bragin; Simon Brent; Yuan Chen 007; Peter Clapham; Laura Clarke; Guy Coates; Susan Fairley; et al. (Nucleic Acids Res., 2009)

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. - Damian Smedley; Paul N. Schofield; Chao-Kung Chen; Vassilis Aidinis; Crysanthi Ainali; Jonathan B. L. Bard; Rudi Balling; Ewan Birney; Andrew Blake 003; Erik Bongcam-Rudloff; Anthony J. Brookes; Gianni Cesareni; et al. (Database J. Biol. Databases Curation, 2010)

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. - William M. McLaren; Bethan Pritchard; Daniel Rios; Yuan Chen 007; Paul Flicek; Fiona Cunningham (Bioinform., 2010)

A database and API for variation, dense genotyping and resequencing data. - Daniel Rios; William M. McLaren; Yuan Chen 007; Ewan Birney; Arne Stabenau; Paul Flicek; Fiona Cunningham (BMC Bioinform., 2010)

eHive: An Artificial Intelligence workflow system for genomic analysis. - Jessica Severin; Kathryn Beal; Albert J. Vilella; Stephen Fitzgerald; Michael Schuster; Leo Gordon; Abel Ureta-Vidal; Paul Flicek; Javier Herrero (BMC Bioinform., 2010)

Ensembl's 10th year. - Paul Flicek; Bronwen L. Aken; Benoît Ballester; Kathryn Beal; Eugene Bragin; Simon Brent; Yuan Chen 007; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Julio Fernandez-Banet; et al. (Nucleic Acids Res., 2010)

Ensembl BioMarts: a hub for data retrieval across taxonomic space. - Rhoda Kinsella; Andreas Kähäri; Syed Haider; Jorge Zamora; Glenn Proctor; Giulietta Spudich; Jeff Almeida-King; Daniel M. Staines; Paul S. Derwent; Arnaud Kerhornou; Paul J. Kersey; Paul Flicek (Database J. Biol. Databases Curation, 2011)

Ensembl 2011. - Paul Flicek; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Yuan Chen 007; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Leo Gordon; Maurice Hendrix; et al. (Nucleic Acids Res., 2011)

Ensembl 2012. - Paul Flicek; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Laurent Gil; Leo Gordon; et al. (Nucleic Acids Res., 2012)

Ensembl 2013. - Paul Flicek; Ikhlak Ahmed; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Laurent Gil; et al. (Nucleic Acids Res., 2013)

dbVar and DGVa: public archives for genomic structural variation. - Ilkka Lappalainen; John Lopez; Lisa Skipper; Timothy Hefferon; J. Dylan Spalding; John Garner; Chao Chen; Michael Maguire; Matthew Corbett; George Zhou; Justin E. Paschall; Victor Ananiev; et al. (Nucleic Acids Res., 2013)

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. - Daniel R. Zerbino; Nathan Johnson; Thomas Juettemann; Steven P. Wilder; Paul Flicek (Bioinform., 2014)

Ensembl 2014. - Paul Flicek; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Konstantinos Billis; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Stephen Fitzgerald; Laurent Gil; Carlos García-Girón; et al. (Nucleic Acids Res., 2014)

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. - Gautier Koscielny; Gagarine Yaikhom; Vivek Iyer; Terrence F. Meehan; Hugh Morgan; Julian Atienza-Herrero; Andrew Blake 003; Chao-Kung Chen; Richard Easty; Armida Di Fenza; Tanja Fiegel; Mark Grifiths; et al. (Nucleic Acids Res., 2014)

Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants. - Jacqueline A. L. MacArthur; Joannella Morales; Ray E. Tully; Alex Astashyn; Laurent Gil; Elspeth A. Bruford; Pontus Larsson; Paul Flicek; Raymond Dalgleish; Donna R. Maglott; Fiona Cunningham (Nucleic Acids Res., 2014)

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. - Danielle Welter; Jacqueline A. L. MacArthur; Joannella Morales; Tony Burdett; Peggy Hall; Heather Junkins; Alan Klemm; Paul Flicek; Teri Manolio; Lucia Hindorff; Helen E. Parkinson (Nucleic Acids Res., 2014)

The Ensembl REST API: Ensembl Data for Any Language. - Andrew D. Yates; Kathryn Beal; Stephen Keenan; William M. McLaren; Miguel Pignatelli; Graham R. S. Ritchie; Magali Ruffier; Kieron R. Taylor; Alessandro Vullo; Paul Flicek (Bioinform., 2015)

Ensembl 2015. - Fiona Cunningham; M. Ridwan Amode; Daniel Barrell; Kathryn Beal; Konstantinos Billis; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Stephen Fitzgerald; Laurent Gil; Carlos García-Girón; et al. (Nucleic Acids Res., 2015)

The IPD and IMGT/HLA database: allele variant databases. - James Robinson; Jason A. Halliwell; James D. Hayhurst; Paul Flicek; Peter Parham; Steven G. E. Marsh (Nucleic Acids Res., 2015)

The Ensembl gene annotation system. - Bronwen L. Aken; Sarah C. Ayling; Daniel Barrell; Laura Clarke; Valery Curwen; Susan Fairley; Julio Fernandez-Banet; Konstantinos Billis; Carlos García-Girón; Thibaut Hourlier; Kevin Lee Howe; Andreas Kähäri; et al. (Database J. Biol. Databases Curation, 2016)

Ensembl comparative genomics resources. - Javier Herrero; Matthieu Muffato; Kathryn Beal; Stephen Fitzgerald; Leo Gordon; Miguel Pignatelli; Albert J. Vilella; Stephen M. J. Searle; M. Ridwan Amode; Simon Brent; William Spooner; Eugene Kulesha; et al. (Database J. Biol. Databases Curation, 2016)

ncRNA orthologies in the vertebrate lineage. - Miguel Pignatelli; Albert J. Vilella; Matthieu Muffato; Leo Gordon; Simon White; Paul Flicek; Javier Herrero (Database J. Biol. Databases Curation, 2016)

Ensembl regulation resources. - Daniel R. Zerbino; Nathan Johnson; Thomas Juettemann; Daniel Sheppard; Steven P. Wilder; Ilias Lavidas; Michael Nuhn; Emily Perry; Quentin Raffaillac-Desfosses; Daniel Sobral; Damian Keefe; Stefan Gräf; et al. (Database J. Biol. Databases Curation, 2016)

Ensembl 2016. - Andrew D. Yates; Wasiu A. Akanni; M. Ridwan Amode; Daniel Barrell; Konstantinos Billis; Denise Carvalho-Silva; Carla A. Cummins; Peter Clapham; Stephen Fitzgerald; Laurent Gil; Carlos García-Girón; Leo Gordon; et al. (Nucleic Acids Res., 2016)

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. - Magali Ruffier; Andreas Kähäri; Monika Komorowska; Stephen Keenan; Matthew R. Laird; Ian Longden; Glenn Proctor; Steve Searle; Daniel M. Staines; Kieron R. Taylor; Alessandro Vullo; Andrew D. Yates; et al. (Database J. Biol. Databases Curation, 2017)

Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks. - Jean Louis Raisaro; Florian Tramèr; Zhanglong Ji; Diyue Bu; Yongan Zhao; W. Knox Carey; David D. Lloyd; Heidi Sofia; Dixie Baker; Paul Flicek; Suyash S. Shringarpure; Carlos D. Bustamante; et al. (J. Am. Medical Informatics Assoc., 2017)

Ensembl 2017. - Bronwen L. Aken; Premanand Achuthan; Wasiu A. Akanni; M. Ridwan Amode; Friederike Bernsdorff; Jyothish Bhai; Konstantinos Billis; Denise Carvalho-Silva; Carla A. Cummins; Peter Clapham; Laurent Gil; Carlos García-Girón; et al. (Nucleic Acids Res., 2017)

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data. - Laura Clarke; Susan Fairley; Xiangqun Zheng Bradley; Ian Streeter; Emily Perry; Ernesto Lowy-Gallego; Anne-Marie Tassé; Paul Flicek (Nucleic Acids Res., 2017)

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). - Jacqueline A. L. MacArthur; Emily Bowler; Maria Cerezo; Laurent Gil; Peggy Hall; Emma Hastings; Heather Junkins; Aoife McMahon; Annalisa Milano; Joannella Morales; Zoë May Pendlington; Danielle Welter; et al. (Nucleic Acids Res., 2017)

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex. - Giuseppe Maccari; James Robinson; Keith Ballingall; Lisbeth A. Guethlein; Unni Grimholt; Jim Kaufman; Chak-Sum Ho; Natasja de Groot; Paul Flicek; Ronald Bontrop; John A. Hammond; Steven G. E. Marsh (Nucleic Acids Res., 2017)

The human-induced pluripotent stem cell initiative - data resources for cellular genetics. - Ian Streeter; Peter W. Harrison; Adam Faulconbridge; HipSci Consortium; Paul Flicek; Helen E. Parkinson; Laura Clarke (Nucleic Acids Res., 2017)

Ensembl variation resources. - Sarah E. Hunt; William M. McLaren; Laurent Gil; Anja Thormann; Helen Schuilenburg; Daniel Sheppard; Andrew Parton; Irina M. Armean; Stephen J. Trevanion; Paul Flicek; Fiona Cunningham (Database J. Biol. Databases Curation, 2018)

Ensembl 2018. - Daniel R. Zerbino; Premanand Achuthan; Wasiu A. Akanni; M. Ridwan Amode; Daniel Barrell; Jyothish Bhai; Konstantinos Billis; Carla A. Cummins; Astrid Gall; Carlos García-Girón; Laurent Gil; Leo Gordon; et al. (Nucleic Acids Res., 2018)

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. - Annalisa Buniello; Jacqueline A. L. MacArthur; Maria Cerezo; Laura W. Harris; James D. Hayhurst; Cinzia Malangone; Aoife McMahon; Joannella Morales; Edward Mountjoy; Elliot Sollis; Daniel Suveges; Olga Vrousgou; et al. (Nucleic Acids Res., 2019)

Ensembl 2019. - Fiona Cunningham; Premanand Achuthan; Wasiu A. Akanni; James E. Allen; M. Ridwan Amode; Irina M. Armean; Ruth Bennett; Jyothish Bhai; Konstantinos Billis; Sanjay Boddu; Carla A. Cummins; Claire Davidson; et al. (Nucleic Acids Res., 2019)

GENCODE reference annotation for the human and mouse genomes. - Adam Frankish; Mark Diekhans; Anne-Maud Ferreira; Rory Johnson; Irwin Jungreis; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Joel Armstrong; If Barnes; Andrew E. Berry; et al. (Nucleic Acids Res., 2019)

Soft windowing application to improve analysis of high-throughput phenotyping data. - Hamed Haselimashhadi; Jeremy C. Mason; Violeta Muñoz-Fuentes; Federico López-Gómez; Kolawole O. Babalola; Elif F. Acar; Vivek Kumar; Jacqui White; Ann M. Flenniken; Ruairidh King; Ewan Straiton; John Richard Seavitt; et al. (Bioinform., 2020)

The International Genome Sample Resource (IGSR) collection of open human genomic variation resources. - Susan Fairley; Ernesto Lowy-Gallego; Emily Perry; Paul Flicek (Nucleic Acids Res., 2020)

Ensembl Genomes 2020 - enabling non-vertebrate genomic research. - Kevin L. Howe; Bruno Contreras-Moreira; Nishadi De Silva; Gareth Maslen; Wasiu A. Akanni; James E. Allen; Jorge Álvarez-Jarreta; Matthieu Barba; Dan M. Bolser; Lahcen Cambell; Manuel Carbajo; Marc Chakiachvili; et al. (Nucleic Acids Res., 2020)

IPD-IMGT/HLA Database. - James Robinson; Dominic J. Barker; Xenia Georgiou; Michael A. Cooper; Paul Flicek; Steven G. E. Marsh (Nucleic Acids Res., 2020)

Ensembl 2020. - Andrew D. Yates; Premanand Achuthan; Wasiu A. Akanni; James E. Allen; Jamie Allen; Jorge Álvarez-Jarreta; M. Ridwan Amode; Irina M. Armean; Andrey G. Azov; Ruth Bennett; Jyothish Bhai; Konstantinos Billis; et al. (Nucleic Acids Res., 2020)

The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. - Gaia Cantelli; Guy Cochrane; Cath Brooksbank; Ellen M. McDonagh; Paul Flicek; Johanna R. McEntyre; Ewan Birney; Rolf Apweiler (Nucleic Acids Res., 2021)

GENCODE 2021. - Adam Frankish; Mark Diekhans; Irwin Jungreis; Julien Lagarde; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Joel Armstrong; If Barnes; Andrew E. Berry; Alexandra Bignell; et al. (Nucleic Acids Res., 2021)

Ensembl 2021. - Kevin L. Howe; Premanand Achuthan; James E. Allen; Jamie Allen; Jorge Álvarez-Jarreta; M. Ridwan Amode; Irina M. Armean; Andrey G. Azov; Ruth Bennett; Jyothish Bhai; Konstantinos Billis; Sanjay Boddu; et al. (Nucleic Acids Res., 2021)

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. - Marcela K. Tello-Ruiz; Sushma Naithani; Parul Gupta; Andrew Olson; Sharon Wei; Justin Preece; Yinping Jiao; Bo Wang 117; Kapeel Chougule; Priyanka Garg; Justin Elser; Sunita Kumari; et al. (Nucleic Acids Res., 2021)

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. - Beatrice Amos; Cristina Aurrecoechea; Matthieu Barba; Ana Barreto; Evelina Y. Basenko; Wojciech Bazant; Robert Belnap; Ann S. Blevins; Ulrike Böhme; John Brestelli; Brian P. Brunk; Mark J. Caddick; et al. (Nucleic Acids Res., 2022)

The European Bioinformatics Institute (EMBL-EBI) in 2021. - Gaia Cantelli; Alex Bateman; Cath Brooksbank; Anton I. Petrov; Rahuman S. Malik-Sheriff; Michele Ide-Smith; Henning Hermjakob; Paul Flicek; Rolf Apweiler; Ewan Birney; Johanna R. McEntyre (Nucleic Acids Res., 2022)

The European Variation Archive: a FAIR resource of genomic variation for all species. - Timothee Cezard; Fiona Cunningham; Sarah E. Hunt; Baron Koylass; Nitin Kumar 004; Gary Saunders; April Shen; Andres f Silva; Kirill Tsukanov; Sundararaman Venkataraman; Paul Flicek; Helen E. Parkinson; et al. (Nucleic Acids Res., 2022)

Ensembl 2022. - Fiona Cunningham; James E. Allen; Jamie Allen; Jorge Álvarez-Jarreta; M. Ridwan Amode; Irina M. Armean; Olanrewaju Austine-Orimoloye; Andrey G. Azov; If Barnes; Ruth Bennett; Andrew E. Berry; Jyothish Bhai; et al. (Nucleic Acids Res., 2022)

The European Genome-phenome Archive in 2021. - Mallory Ann Freeberg; Lauren A. Fromont; Teresa D'altri; Anna Foix Romero; Jorge Izquierdo Ciges; Aina Jene; Giselle Kerry; Mauricio Moldes; Roberto Ariosa; Silvia Bahena; Daniel Barrowdale; Marcos Casado Barbero; et al. (Nucleic Acids Res., 2022)

The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. - 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; et al. (Nucleic Acids Res., 2022)

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. - 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; et al. (Nucleic Acids Res., 2022)

The IPD-IMGT/HLA Database. - Dominic J. Barker; Giuseppe Maccari; Xenia Georgiou; Michael A. Cooper; Paul Flicek; James Robinson; Steven G. E. Marsh (Nucleic Acids Res., 2023)

GENCODE: reference annotation for the human and mouse genomes in 2023. - Adam Frankish; Silvia Carbonell Sala; Mark Diekhans; Irwin Jungreis; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Carme Arnan; If Barnes; Abhimanyu Banerjee; Ruth Bennett; et al. (Nucleic Acids Res., 2023)

Ensembl 2023. - 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; et al. (Nucleic Acids Res., 2023)