M
Matthew P. Hardy
Researcher at European Bioinformatics Institute
Publications - 8
Citations - 2259
Matthew P. Hardy is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Genome & Biology. The author has an hindex of 2, co-authored 3 publications receiving 1257 citations.
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Journal ArticleDOI
GENCODE reference annotation for the human and mouse genomes.
Adam Frankish,Mark Diekhans,Anne-Maud Ferreira,Rory Johnson,Irwin Jungreis,Irwin Jungreis,Jane E. Loveland,Jonathan M. Mudge,Cristina Sisu,Cristina Sisu,James C. Wright,Joel Armstrong,If Barnes,Andrew Berry,Alexandra Bignell,Silvia Carbonell Sala,Jacqueline Chrast,Fiona Cunningham,Tomás Di Domenico,Sarah Donaldson,Ian T. Fiddes,Carlos García Girón,Jose Manuel Gonzalez,Tiago Grego,Matthew P. Hardy,Thibaut Hourlier,Toby Hunt,Osagie G. Izuogu,Julien Lagarde,Fergal J. Martin,Laura Martinez,Shamika Mohanan,Paul R. Muir,Fabio C. P. Navarro,Anne Parker,Baikang Pei,Fernando Pozo,Magali Ruffier,Bianca M. Schmitt,Eloise Stapleton,Marie-Marthe Suner,Irina Sycheva,Barbara Uszczynska-Ratajczak,Jinuri Xu,Andrew D. Yates,Daniel R. Zerbino,Yan Zhang,Yan Zhang,Bronwen Aken,Jyoti S. Choudhary,Mark Gerstein,Roderic Guigó,Tim Hubbard,Manolis Kellis,Manolis Kellis,Benedict Paten,Alexandre Reymond,Michael L. Tress,Paul Flicek +58 more
TL;DR: This work generates primary data, creates bioinformatics tools and provides analysis to support the work of expert manual gene annotators and automated gene annotation pipelines to identify and characterise gene loci to the highest standard.
Journal ArticleDOI
A joint NCBI and EMBL-EBI transcript set for clinical genomics and research
Joannella Morales,Shashikant Pujar,Jane E. Loveland,Alexander Astashyn,Ruth Bennett,Andrew Berry,Eric Cox,R. Davidson,Olga Ermolaeva,Catherine M. Farrell,Reham Fatima,Laurent Gil,Tamara Goldfarb,José M. González,Diana Haddad,Matthew P. Hardy,Toby Hunt,John D. Jackson,Vinita Joardar,M. Kay,Vamsi K Kodali,Kelly M. McGarvey,Aoife McMahon,Jonathan M. Mudge,Daniel N. Murphy,Michael R. Murphy,Bhanu Rajput,Sanjida H. Rangwala,Lillian D. Riddick,Françoise Thibaud-Nissen,Glen Threadgold,Anjana Raina Vatsan,Craig Wallin,David Webb,Paul Flicek,Ewan Birney,Kim D. Pruitt,Adam Frankish,Fiona Cunningham,Terence Murphy +39 more
TL;DR: The Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration as mentioned in this paper is a set of transcripts and corresponding proteins annotated for each human protein-coding gene.
Journal ArticleDOI
Ensembl 2023
Fergal J. Martin,M. Ridwan Amode,Alisha Aneja,Olanrewaju Austine-Orimoloye,Andrey G. Azov,If H. A. Barnes,Arne Becker,Ruth Bennett,Andrew Berry,Jyothish N Nair Thulasee 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,R. Davidson,K. Dodiya,Sarah Donaldson,Bilal El Houdaigui,Tamara El Naboulsi,Reham Fatima,Carlos García Girón,Thiago A. L. Genez,Gurpreet S. Ghattaoraya,J. Gonzalez Martinez,Cristina Guijarro,Matthew P. Hardy,Zoe Hollis,Thibaut Hourlier,Toby Hunt,M. Kay,Vinay Kaykala,Tuan Le,Diana Maria Guimarães Lemos,Diego Marques-Coelho,José Carlos Marugán,Gabriel Merino,Louisse Paola Mirabueno,Aleena Mushtaq,Syed Nakib Hossain,Denye Nathaniel Ogeh,Manoj Pandian Sakthivel,Anne Parker,Malcolm Stockbridge Perry,Ivana Piližota,Irina Prosovetskaia,J. Perez-Silva,Ahamed Imran Abdul Salam,Nuno Saraiva-Agostinho,Helen Schuilenburg,Daniel Sheppard,Swati Sinha,Botond Sipos,W. Stark,Emily Steed,Ranjit Sukumaran,Dulika S. 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,Beth Flint,Stefano Giorgetti,Leanne Haggerty,Garth R Ilsley,Jane E. Loveland,Benjamin L. 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 +95 more
TL;DR: Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years as mentioned in this paper . During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilize the Ensembl platform.
Journal ArticleDOI
Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons
If H. A. Barnes,Ximena Ibarra-Soria,Ximena Ibarra-Soria,Stephen Fitzgerald,Jose Manuel Gonzalez,Claire Davidson,Matthew P. Hardy,Deepa Manthravadi,Laura Van Gerven,Mark Jorissen,Zhen Zeng,Mona Khan,Peter Mombaerts,Jennifer Harrow,Darren W. Logan,Darren W. Logan,Adam Frankish +16 more
TL;DR: This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date, and challenges the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.
Journal ArticleDOI
GENCODE: reference annotation for the human and mouse genomes in 2023
Adam Frankish,S. Carbonell-Sala,Mark Diekhans,Irwin Jungreis,Jane E. Loveland,Jonathan M. Mudge,Cristina Sisu,James C. Wright,Carme Arnan,If H. A. Barnes,Abhimanyu Banerjee,Ruth Bennett,Andrew Berry,Alexandra Bignell,Carles Boix,Ferriol Calvet,Daniel Cerdán-Vélez,Fiona Cunningham,R. Davidson,Sarah Donaldson,Cagatay Dursun,Reham Fatima,Stefano Giorgetti,Carlos García Girón,José M. González,Matthew P. Hardy,Peter W. Harrison,Thibaut Hourlier,Zoe Hollis,Toby Hunt,Benjamin James,Yunzhe Jiang,Rory Johnson,M. Kay,Julien Lagarde,Fergal J. Martin,Laura Martínez Gómez,Surag Nair,Pengyu Ni,Fernando Pozo,Vivekanandan Ramalingam,Magali Ruffier,Bianca M. Schmitt,Jacob M. Schreiber,Emily Steed,Marie-Marthe Suner,Dulika S. Sumathipala,Irina Sergeyevna Sycheva,Barbara Uszczynska-Ratajczak,Elizabeth Wass,Yucheng T. Yang,Andrew D. Yates,Zahoor Zafrulla,Jyoti S. Choudhary,Mark Gerstein,Roderic Guigó,Tim Hubbard,Manolis Kellis,Anshul Kundaje,Benedict Paten,Michael L. Tress,Paul Flicek +61 more
TL;DR: The GENCODE consortium produces high quality gene and transcript annotation for the human and mouse genomes as mentioned in this paper , which is supported by experimental data and serves as a reference for genome biology and clinical genomics.