Adam Frankish

Affiliations

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Publications (35)

GENCODE: reference annotation for the human and mouse genomes in 2023.

Nucleic acids research

Avec: Adam Frankish , Sílvia 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 , Andrew Berry , Alexandra Bignell , Carles Boix , Ferriol Calvet , Daniel Cerdán-Vélez , Fiona Cunningham , Claire Davidson , Sarah Donaldson , Cagatay Dursun , Reham Fatima , Stefano Giorgetti , Carlos Garcıa Giron , Jose Manuel Gonzalez , Matthew Hardy , Peter W Harrison , Thibaut Hourlier , Zoe Hollis , Toby Hunt , Benjamin James , Yunzhe Jiang , Rory Johnson , Mike Kay , Julien Lagarde , Fergal J Martin , Laura Martínez Gómez , Surag Nair , Pengyu Ni , Fernando Pozo , Vivek Ramalingam , Magali Ruffier , Bianca M Schmitt , Jacob M Schreiber , Emily Steed , Marie-Marthe Suner , Dulika Sumathipala , Irina Sycheva , Barbara Uszczynska-Ratajczak , Elizabeth Wass , Yucheng T Yang , Andrew Yates , Zahoor Zafrulla , Jyoti S Choudhary , Mark Gerstein , Roderic Guigo , Tim J P Hubbard , Manolis Kellis , Anshul Kundaje , Benedict Paten , Michael L Tress , Paul Flicek

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

bioRxiv : the preprint server for biology

Avec: Francisco J Pardo-Palacios , Dingjie Wang , Fairlie Reese , Mark Diekhans , Sílvia Carbonell-Sala , Brian Williams , Jane E Loveland , Maite De María , Matthew S Adams , Gabriela Balderrama-Gutierrez , Amit K Behera , Jose M Gonzalez , Toby Hunt , Julien Lagarde , Cindy E Liang , Haoran Li , Marcus Jerryd Meade , David A Moraga Amador , Andrey D Prjibelski , Inanc Birol , Hamed Bostan , Ashley M Brooks , Muhammed Hasan Çelik , Ying Chen , Mei R M Du , Colette Felton , Jonathan Göke , Saber Hafezqorani , Ralf Herwig , Hideya Kawaji , Joseph Lee , Jian Liang Li , Matthias Lienhard , Alla Mikheenko , Dennis Mulligan , Ka Ming Nip , Mihaela Pertea , Matthew E Ritchie , Andre D Sim , Alison D Tang , Yuk Kei Wan , Changqing Wang , Brandon Y Wong , Chen Yang , If Barnes , Andrew Berry , Salvador Capella , Namrita Dhillon , Jose M Fernandez-Gonzalez , Luis Ferrández-Peral , Natàlia Garcia-Reyero , Stefan Goetz , Carles Hernández-Ferrer , Liudmyla Kondratova , Tianyuan Liu , Alessandra Martinez-Martin , Carlos Menor , Jorge Mestre-Tomás , Jonathan M Mudge , Nedka G Panayotova , Alejandro Paniagua , Dmitry Repchevsky , Eric Rouchka , Brandon Saint-John , Enrique Sapena , Leon Sheynkman , Melissa Laird Smith , Marie-Marthe Suner , Hazuki Takahashi , Ingrid Ashley Youngworth , Piero Carninci , Nancy D Denslow , Roderic Guigó , Margaret E Hunter , Hagen U Tilgner , Barbara J Wold , Christopher Vollmers , Adam Frankish , Kin Fai Au , Gloria M Sheynkman , Ali Mortazavi , Ana Conesa , Angela N Brooks

The status of the human gene catalogue.

Nature

Avec: Paulo Amaral , Silvia Carbonell-Sala , Francisco M De La Vega , Tiago Faial , Adam Frankish , Thomas Gingeras , Roderic Guigo , Jennifer L Harrow , Artemis G Hatzigeorgiou , Rory Johnson , Terence D Murphy , Mihaela Pertea , Kim D Pruitt , Shashikant Pujar , Hazuki Takahashi , Igor Ulitsky , Ales Varabyou , Christine A Wells , Mark Yandell , Piero Carninci , Steven L Salzberg

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.

bioRxiv : the preprint server for biology

Avec: Eric W Deutsch , Leron W Kok , Jonathan M Mudge , Jorge Ruiz-Orera , Ivo Fierro-Monti , Zhi Sun , Jennifer G Abelin , M Mar Alba , Julie L Aspden , Ariel A Bazzini , Elspeth A Bruford , Marie A Brunet , Lorenzo Calviello , Steven A Carr , Anne-Ruxandra Carvunis , Sonia Chothani , Jim Clauwaert , Kellie Dean , Pouya Faridi , Adam Frankish , Norbert Hubner , Nicholas T Ingolia , Michele Magrane , Maria Jesus Martin , Thomas F Martinez , Gerben Menschaert , Uwe Ohler , Sandra Orchard , Owen Rackham , Xavier Roucou , Sarah A Slavoff , Eivind Valen , Aaron Wacholder , Jonathan S Weissman , Wei Wu , Zhi Xie , Jyoti Choudhary , Michal Bassani-Sternberg , Juan Antonio Vizcaíno , Nicola Ternette , Robert L Moritz , John R Prensner , Sebastiaan van Heesch

FODMAP intake in children with coeliac disease influences diet quality and health-related quality of life and has no impact on gastrointestinal symptoms.

International journal of food sciences and nutrition

Avec: Samantha Cyrkot , Margaret Marcon , Herbert Brill , Heather Mileski , Jenna Dowhaniuk , Alena Frankish , Matthew W Carroll , Rabin Persad , Justine M Turner , Diana R Mager

GENCODE 2021.

Nucleic acids research

Avec: Adam Frankish , Mark Diekhans , Irwin Jungreis , Julien Lagarde , Jane E Loveland , Jonathan M Mudge , Cristina Sisu , James C Wright , Joel Armstrong , If Barnes , Andrew Berry , Alexandra Bignell , Carles Boix , Silvia Carbonell Sala , Fiona Cunningham , Tomás Di Domenico , Sarah Donaldson , Ian T Fiddes , Carlos García Girón , Jose Manuel Gonzalez , Tiago Grego , Matthew Hardy , Thibaut Hourlier , Kevin L Howe , Toby Hunt , Osagie G Izuogu , Rory Johnson , Fergal J Martin , Laura Martínez , Shamika Mohanan , Paul Muir , Fabio C P Navarro , Anne Parker , Baikang Pei , Fernando Pozo , Ferriol Calvet Riera , Magali Ruffier , Bianca M Schmitt , Eloise Stapleton , Marie-Marthe Suner , Irina Sycheva , Barbara Uszczynska-Ratajczak , Maxim Y Wolf , Jinuri Xu , Yucheng T Yang , Andrew Yates , Daniel Zerbino , Yan Zhang , Jyoti S Choudhary , Mark Gerstein , Roderic Guigó , Tim J P Hubbard , Manolis Kellis , Benedict Paten , Michael L Tress , Paul Flicek

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.

Nature communications

Avec: Anoushka Joglekar , Andrey Prjibelski , Ahmed Mahfouz , Paul Collier , Susan Lin , Anna Katharina Schlusche , Jordan Marrocco , Stephen R Williams , Bettina Haase , Ashley Hayes , Jennifer G Chew , Neil I Weisenfeld , Man Ying Wong , Alexander N Stein , Simon A Hardwick , Toby Hunt , Qi Wang , Christoph Dieterich , Zachary Bent , Olivier Fedrigo , Steven A Sloan , Davide Risso , Erich D Jarvis , Paul Flicek , Wenjie Luo , Geoffrey S Pitt , Adam Frankish , August B Smit , M Elizabeth Ross , Hagen U Tilgner

GENCODE reference annotation for the human and mouse genomes.

Nucleic acids research

Avec: Adam Frankish , Mark Diekhans , Anne-Maud Ferreira , Rory Johnson , Irwin Jungreis , Jane Loveland , Jonathan M Mudge , Cristina Sisu , James 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 Hardy , Thibaut Hourlier , Toby Hunt , Osagie G Izuogu , Julien Lagarde , Fergal J Martin , Laura Martínez , Shamika Mohanan , Paul 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 Yates , Daniel Zerbino , Yan Zhang , Bronwen Aken , Jyoti S Choudhary , Mark Gerstein , Roderic Guigó , Tim J P Hubbard , Manolis Kellis , Benedict Paten , Alexandre Reymond , Michael L Tress , Paul Flicek

Getting the Entire Message: Progress in Isoform Sequencing.

Frontiers in genetics

Avec: Simon A Hardwick , Anoushka Joglekar , Paul Flicek , Adam Frankish , Hagen U Tilgner

Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons.

BMC genomics

Avec: If H A Barnes , Ximena Ibarra-Soria , Stephen Fitzgerald , Jose M Gonzalez , Claire Davidson , Matthew P Hardy , Deepa Manthravadi , Laura Van Gerven , Mark Jorissen , Zhen Zeng , Mona Khan , Peter Mombaerts , Jennifer Harrow , Darren W Logan , Adam Frankish

SCN1A: bioinformatically informed revised boundaries for promoter and enhancer regions.

Human molecular genetics

Avec: Susanna Pagni , Helena Martins Custodio , Adam Frankish , Jonathan M Mudge , James D Mills , Sanjay M Sisodiya

A draft human pangenome reference.

Nature

Avec: Wen-Wei Liao , Mobin Asri , Jana Ebler , Daniel Doerr , Marina Haukness , Glenn Hickey , Shuangjia Lu , Julian K Lucas , Jean Monlong , Haley J Abel , Silvia Buonaiuto , Xian H Chang , Haoyu Cheng , Justin Chu , Vincenza Colonna , Jordan M Eizenga , Xiaowen Feng , Christian Fischer , Robert S Fulton , Shilpa Garg , Cristian Groza , Andrea Guarracino , William T Harvey , Simon Heumos , Kerstin Howe , Miten Jain , Tsung-Yu Lu , Charles Markello , Fergal J Martin , Matthew W Mitchell , Katherine M Munson , Moses Njagi Mwaniki , Adam M Novak , Hugh E Olsen , Trevor Pesout , David Porubsky , Pjotr Prins , Jonas A Sibbesen , Jouni Sirén , Chad Tomlinson , Flavia Villani , Mitchell R Vollger , Lucinda L Antonacci-Fulton , Gunjan Baid , Carl A Baker , Anastasiya Belyaeva , Konstantinos Billis , Andrew Carroll , Pi-Chuan Chang , Sarah Cody , Daniel E Cook , Robert M Cook-Deegan , Omar E Cornejo , Mark Diekhans , Peter Ebert , Susan Fairley , Olivier Fedrigo , Adam L Felsenfeld , Giulio Formenti , Adam Frankish , Yan Gao , Nanibaa' A Garrison , Carlos Garcia Giron , Richard E Green , Leanne Haggerty , Kendra Hoekzema , Thibaut Hourlier , Hanlee P Ji , Eimear E Kenny , Barbara A Koenig , Alexey Kolesnikov , Jan O Korbel , Jennifer Kordosky , Sergey Koren , HoJoon Lee , Alexandra P Lewis , Hugo Magalhães , Santiago Marco-Sola , Pierre Marijon , Ann McCartney , Jennifer McDaniel , Jacquelyn Mountcastle , Maria Nattestad , Sergey Nurk , Nathan D Olson , Alice B Popejoy , Daniela Puiu , Mikko Rautiainen , Allison A Regier , Arang Rhie , Samuel Sacco , Ashley D Sanders , Valerie A Schneider , Baergen I Schultz , Kishwar Shafin , Michael W Smith , Heidi J Sofia , Ahmad N Abou Tayoun , Françoise Thibaud-Nissen , Francesca Floriana Tricomi , Justin Wagner , Brian Walenz , Jonathan M D Wood , Aleksey V Zimin , Guillaume Bourque , Mark J P Chaisson , Paul Flicek , Adam M Phillippy , Justin M Zook , Evan E Eichler , David Haussler , Ting Wang , Erich D Jarvis , Karen H Miga , Erik Garrison , Tobias Marschall , Ira M Hall , Heng Li , Benedict Paten

Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas.

Haematologica

Avec: Luigi Grassi , Osagie G Izuogu , Natasha A N Jorge , Denis Seyres , Mariona Bustamante , Frances Burden , Samantha Farrow , Neda Farahi , Fergal J Martin , Adam Frankish , Jonathan M Mudge , Myrto Kostadima , Romina Petersen , John J Lambourne , Sophia Rowlston , Enca Martin-Rendon , Laura Clarke , Kate Downes , Xavier Estivill , Paul Flicek , Joost H A Martens , Marie-Laure Yaspo , Hendrik G Stunnenberg , Willem H Ouwehand , Fabio Passetti , Ernest Turro , Mattia Frontini

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in

NPJ genomic medicine

Avec: Charles A Steward , Jolien Roovers , Marie-Marthe Suner , Jose M Gonzalez , Barbara Uszczynska-Ratajczak , Dmitri Pervouchine , Stephen Fitzgerald , Margarida Viola , Hannah Stamberger , Fadi F Hamdan , Berten Ceulemans , Patricia Leroy , Caroline Nava , Anne Lepine , Electra Tapanari , Don Keiller , Stephen Abbs , Alba Sanchis-Juan , Detelina Grozeva , Anthony S Rogers , Mark Diekhans , Roderic Guigó , Robert Petryszak , Berge A Minassian , Gianpiero Cavalleri , Dimitrios Vitsios , Slavé Petrovski , Jennifer Harrow , Paul Flicek , F Lucy Raymond , Nicholas J Lench , Peter De Jonghe , Jonathan M Mudge , Sarah Weckhuysen , Sanjay M Sisodiya , Adam Frankish

Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay.

Nucleic acids research

Avec: Dmitri Pervouchine , Yaroslav Popov , Andy Berry , Beatrice Borsari , Adam Frankish , Roderic Guigó

Non-coding regulatory elements: Potential roles in disease and the case of epilepsy.

Neuropathology and applied neurobiology

Avec: Susanna Pagni , James D Mills , Adam Frankish , Jonathan M Mudge , Sanjay M Sisodiya

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

Nature methods

Avec: Francisco J Pardo-Palacios , Dingjie Wang , Fairlie Reese , Mark Diekhans , Sílvia Carbonell-Sala , Brian Williams , Jane E Loveland , Maite De María , Matthew S Adams , Gabriela Balderrama-Gutierrez , Amit K Behera , Jose M Gonzalez Martinez , Toby Hunt , Julien Lagarde , Cindy E Liang , Haoran Li , Marcus Jerryd Meade , David A Moraga Amador , Andrey D Prjibelski , Inanc Birol , Hamed Bostan , Ashley M Brooks , Muhammed Hasan Çelik , Ying Chen , Mei R M Du , Colette Felton , Jonathan Göke , Saber Hafezqorani , Ralf Herwig , Hideya Kawaji , Joseph Lee , Jian-Liang Li , Matthias Lienhard , Alla Mikheenko , Dennis Mulligan , Ka Ming Nip , Mihaela Pertea , Matthew E Ritchie , Andre D Sim , Alison D Tang , Yuk Kei Wan , Changqing Wang , Brandon Y Wong , Chen Yang , If Barnes , Andrew E Berry , Salvador Capella-Gutierrez , Alyssa Cousineau , Namrita Dhillon , Jose M Fernandez-Gonzalez , Luis Ferrández-Peral , Natàlia Garcia-Reyero , Stefan Götz , Carles Hernández-Ferrer , Liudmyla Kondratova , Tianyuan Liu , Alessandra Martinez-Martin , Carlos Menor , Jorge Mestre-Tomás , Jonathan M Mudge , Nedka G Panayotova , Alejandro Paniagua , Dmitry Repchevsky , Xingjie Ren , Eric Rouchka , Brandon Saint-John , Enrique Sapena , Leon Sheynkman , Melissa Laird Smith , Marie-Marthe Suner , Hazuki Takahashi , Ingrid A Youngworth , Piero Carninci , Nancy D Denslow , Roderic Guigó , Margaret E Hunter , Rene Maehr , Yin Shen , Hagen U Tilgner , Barbara J Wold , Christopher Vollmers , Adam Frankish , Kin Fai Au , Gloria M Sheynkman , Ali Mortazavi , Ana Conesa , Angela N Brooks

Transcriptional activity and strain-specific history of mouse pseudogenes.

Nature communications

Avec: Cristina Sisu , Paul Muir , Adam Frankish , Ian Fiddes , Mark Diekhans , David Thybert , Duncan T Odom , Paul Flicek , Thomas M Keane , Tim Hubbard , Jennifer Harrow , Mark Gerstein

Perspectives on ENCODE.

Nature

Avec: Auteur inconnu , Michael P Snyder , Thomas R Gingeras , Jill E Moore , Zhiping Weng , Mark B Gerstein , Bing Ren , Ross C Hardison , John A Stamatoyannopoulos , Brenton R Graveley , Elise A Feingold , Michael J Pazin , Michael Pagan , Daniel A Gilchrist , Benjamin C Hitz , J Michael Cherry , Bradley E Bernstein , Eric M Mendenhall , Daniel R Zerbino , Adam Frankish , Paul Flicek , Richard M Myers

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.

Genome research

Avec: Jonathan M Mudge , Irwin Jungreis , Toby Hunt , Jose Manuel Gonzalez , James C Wright , Mike Kay , Claire Davidson , Stephen Fitzgerald , Ruth Seal , Susan Tweedie , Liang He , Robert M Waterhouse , Yue Li , Elspeth Bruford , Jyoti S Choudhary , Adam Frankish , Manolis Kellis

Ensembl 2019.

Nucleic acids research

Avec: Fiona Cunningham , Premanand Achuthan , Wasiu Akanni , James Allen , M Ridwan Amode , Irina M Armean , Ruth Bennett , Jyothish Bhai , Konstantinos Billis , Sanjay Boddu , Carla Cummins , Claire Davidson , Kamalkumar Jayantilal Dodiya , Astrid Gall , Carlos García Girón , Laurent Gil , Tiago Grego , Leanne Haggerty , Erin Haskell , Thibaut Hourlier , Osagie G Izuogu , Sophie H Janacek , Thomas Juettemann , Mike Kay , Matthew R Laird , Ilias Lavidas , Zhicheng Liu , Jane E Loveland , José C Marugán , Thomas Maurel , Aoife C McMahon , Benjamin Moore , Joannella Morales , Jonathan M Mudge , Michael Nuhn , Denye Ogeh , Anne Parker , Andrew Parton , Mateus Patricio , Ahamed Imran Abdul Salam , Bianca M Schmitt , Helen Schuilenburg , Dan Sheppard , Helen Sparrow , Eloise Stapleton , Marek Szuba , Kieron Taylor , Glen Threadgold , Anja Thormann , Alessandro Vullo , Brandon Walts , Andrea Winterbottom , Amonida Zadissa , Marc Chakiachvili , Adam Frankish , Sarah E Hunt , Myrto Kostadima , Nick Langridge , Fergal J Martin , Matthieu Muffato , Emily Perry , Magali Ruffier , Daniel M Staines , Stephen J Trevanion , Bronwen L Aken , Andrew D Yates , Daniel R Zerbino , Paul Flicek

Ensembl 2022.

Nucleic acids research

Avec: Fiona Cunningham , James E Allen , Jamie Allen , Jorge Alvarez-Jarreta , M Ridwan Amode , Irina M Armean , Olanrewaju Austine-Orimoloye , Andrey G Azov , If Barnes , Ruth Bennett , Andrew Berry , Jyothish Bhai , Alexandra Bignell , Konstantinos Billis , Sanjay Boddu , Lucy Brooks , Mehrnaz Charkhchi , Carla Cummins , Luca Da Rin Fioretto , Claire Davidson , Kamalkumar Dodiya , Sarah Donaldson , Bilal El Houdaigui , Tamara El Naboulsi , Reham Fatima , Carlos Garcia Giron , Thiago Genez , Jose Gonzalez Martinez , Cristina Guijarro-Clarke , Arthur Gymer , Matthew Hardy , Zoe Hollis , Thibaut Hourlier , Toby Hunt , Thomas Juettemann , Vinay Kaikala , Mike Kay , Ilias Lavidas , Tuan Le , Diana Lemos , José Carlos Marugán , Shamika Mohanan , Aleena Mushtaq , Marc Naven , Denye N Ogeh , Anne Parker , Andrew Parton , Malcolm Perry , Ivana Piližota , Irina Prosovetskaia , Manoj Pandian Sakthivel , Ahamed Imran Abdul Salam , Bianca M Schmitt , Helen Schuilenburg , Dan Sheppard , José G Pérez-Silva , William Stark , Emily Steed , Kyösti Sutinen , Ranjit Sukumaran , Dulika Sumathipala , Marie-Marthe Suner , Michal Szpak , Anja Thormann , Francesca Floriana Tricomi , David Urbina-Gómez , Andres Veidenberg , Thomas A Walsh , Brandon Walts , Natalie Willhoft , Andrea Winterbottom , Elizabeth Wass , Marc Chakiachvili , Bethany Flint , Adam Frankish , Stefano Giorgetti , Leanne Haggerty , Sarah E Hunt , Garth R IIsley , Jane E Loveland , Fergal J Martin , Benjamin Moore , Jonathan M Mudge , Matthieu Muffato , Emily Perry , Magali Ruffier , John Tate , David Thybert , Stephen J Trevanion , Sarah Dyer , Peter W Harrison , Kevin L Howe , Andrew D Yates , Daniel R Zerbino , Paul Flicek

Accuracy of the MedGem® portable indirect calorimeter for measuring resting energy expenditure in adults with class II or III obesity.

Clinical nutrition ESPEN

Avec: Sarah A Purcell , Carlene Johnson-Stoklossa , Jenneffer Rayane Braga Tibaes , Alena Frankish , Sarah A Elliott , Raj Padwal , Carla M Prado

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research.

Nature

Avec: Joannella Morales , Shashikant Pujar , Jane E Loveland , Alex Astashyn , Ruth Bennett , Andrew Berry , Eric Cox , Claire Davidson , Olga Ermolaeva , Catherine M Farrell , Reham Fatima , Laurent Gil , Tamara Goldfarb , Jose M Gonzalez , Diana Haddad , Matthew Hardy , Toby Hunt , John Jackson , Vinita S Joardar , Michael 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 R Vatsan , Craig Wallin , David Webb , Paul Flicek , Ewan Birney , Kim D Pruitt , Adam Frankish , Fiona Cunningham , Terence D Murphy

Ensembl 2024.

Nucleic acids research

Avec: Peter W Harrison , M Ridwan Amode , Olanrewaju Austine-Orimoloye , Andrey G Azov , Matthieu Barba , If Barnes , Arne Becker , Ruth Bennett , Andrew Berry , Jyothish Bhai , Simarpreet Kaur Bhurji , Sanjay Boddu , Paulo R Branco Lins , Lucy Brooks , Shashank Budhanuru Ramaraju , Lahcen I Campbell , Manuel Carbajo Martinez , Mehrnaz Charkhchi , Kapeel Chougule , Alexander Cockburn , Claire Davidson , Nishadi H De Silva , Kamalkumar Dodiya , Sarah Donaldson , Bilal El Houdaigui , Tamara El Naboulsi , Reham Fatima , Carlos Garcia Giron , Thiago Genez , Dionysios Grigoriadis , Gurpreet S Ghattaoraya , Jose Gonzalez Martinez , Tatiana A Gurbich , Matthew Hardy , Zoe Hollis , Thibaut Hourlier , Toby Hunt , Mike Kay , Vinay Kaykala , Tuan Le , Diana Lemos , Disha Lodha , Diego Marques-Coelho , Gareth Maslen , Gabriela Alejandra Merino , Louisse Paola Mirabueno , Aleena Mushtaq , Syed Nakib Hossain , Denye N Ogeh , Manoj Pandian Sakthivel , Anne Parker , Malcolm Perry , Ivana Piližota , Daniel Poppleton , Irina Prosovetskaia , Shriya Raj , José G Pérez-Silva , Ahamed Imran Abdul Salam , Shradha Saraf , Nuno Saraiva-Agostinho , Dan Sheppard , Swati Sinha , Botond Sipos , Vasily Sitnik , William Stark , Emily Steed , Marie-Marthe Suner , Likhitha Surapaneni , Kyösti Sutinen , Francesca Floriana Tricomi , David Urbina-Gómez , Andres Veidenberg , Thomas A Walsh , Doreen Ware , Elizabeth Wass , Natalie L Willhoft , Jamie Allen , Jorge Alvarez-Jarreta , Marc Chakiachvili , Bethany Flint , Stefano Giorgetti , Leanne Haggerty , Garth R Ilsley , Jon Keatley , Jane E Loveland , Benjamin Moore , Jonathan M Mudge , Guy Naamati , John Tate , Stephen J Trevanion , Andrea Winterbottom , Adam Frankish , Sarah E Hunt , Fiona Cunningham , Sarah Dyer , Robert D Finn , Fergal J Martin , Andrew D Yates

Ensembl 2020.

Nucleic acids research

Avec: Andrew D Yates , Premanand Achuthan , Wasiu Akanni , James Allen , Jamie Allen , Jorge Alvarez-Jarreta , M Ridwan Amode , Irina M Armean , Andrey G Azov , Ruth Bennett , Jyothish Bhai , Konstantinos Billis , Sanjay Boddu , José Carlos Marugán , Carla Cummins , Claire Davidson , Kamalkumar Dodiya , Reham Fatima , Astrid Gall , Carlos Garcia Giron , Laurent Gil , Tiago Grego , Leanne Haggerty , Erin Haskell , Thibaut Hourlier , Osagie G Izuogu , Sophie H Janacek , Thomas Juettemann , Mike Kay , Ilias Lavidas , Tuan Le , Diana Lemos , Jose Gonzalez Martinez , Thomas Maurel , Mark McDowall , Aoife McMahon , Shamika Mohanan , Benjamin Moore , Michael Nuhn , Denye N Oheh , Anne Parker , Andrew Parton , Mateus Patricio , Manoj Pandian Sakthivel , Ahamed Imran Abdul Salam , Bianca M Schmitt , Helen Schuilenburg , Dan Sheppard , Mira Sycheva , Marek Szuba , Kieron Taylor , Anja Thormann , Glen Threadgold , Alessandro Vullo , Brandon Walts , Andrea Winterbottom , Amonida Zadissa , Marc Chakiachvili , Bethany Flint , Adam Frankish , Sarah E Hunt , Garth IIsley , Myrto Kostadima , Nick Langridge , Jane E Loveland , Fergal J Martin , Joannella Morales , Jonathan M Mudge , Matthieu Muffato , Emily Perry , Magali Ruffier , Stephen J Trevanion , Fiona Cunningham , Kevin L Howe , Daniel R Zerbino , Paul Flicek

Accuracy and reliability of a portable indirect calorimeter compared to whole-body indirect calorimetry for measuring resting energy expenditure.

Clinical nutrition ESPEN

Avec: Sarah A Purcell , Carlene Johnson-Stoklossa , Jenneffer Rayane Braga Tibaes , Alena Frankish , Sarah A Elliott , Raj Padwal , Carla M Prado

Progress, Challenges, and Surprises in Annotating the Human Genome.

Annual review of genomics and human genetics

Avec: Daniel R Zerbino , Adam Frankish , Paul Flicek

The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data.

Nucleic acids research

Avec: Nishadi H De Silva , Jyothish Bhai , Marc Chakiachvili , Bruno Contreras-Moreira , Carla Cummins , Adam Frankish , Astrid Gall , Thiago Genez , Kevin L Howe , Sarah E Hunt , Fergal J Martin , Benjamin Moore , Denye Ogeh , Anne Parker , Andrew Parton , Magali Ruffier , Manoj Pandian Sakthivel , Dan Sheppard , John Tate , Anja Thormann , David Thybert , Stephen J Trevanion , Andrea Winterbottom , Daniel R Zerbino , Robert D Finn , Paul Flicek , Andrew D Yates

Ensembl 2021.

Nucleic acids research

Avec: Kevin L Howe , Premanand Achuthan , James Allen , Jamie Allen , Jorge Alvarez-Jarreta , M Ridwan Amode , Irina M Armean , Andrey G Azov , Ruth Bennett , Jyothish Bhai , Konstantinos Billis , Sanjay Boddu , Mehrnaz Charkhchi , Carla Cummins , Luca Da Rin Fioretto , Claire Davidson , Kamalkumar Dodiya , Bilal El Houdaigui , Reham Fatima , Astrid Gall , Carlos Garcia Giron , Tiago Grego , Cristina Guijarro-Clarke , Leanne Haggerty , Anmol Hemrom , Thibaut Hourlier , Osagie G Izuogu , Thomas Juettemann , Vinay Kaikala , Mike Kay , Ilias Lavidas , Tuan Le , Diana Lemos , Jose Gonzalez Martinez , José Carlos Marugán , Thomas Maurel , Aoife C McMahon , Shamika Mohanan , Benjamin Moore , Matthieu Muffato , Denye N Oheh , Dimitrios Paraschas , Anne Parker , Andrew Parton , Irina Prosovetskaia , Manoj P Sakthivel , Ahamed I Abdul Salam , Bianca M Schmitt , Helen Schuilenburg , Dan Sheppard , Emily Steed , Michal Szpak , Marek Szuba , Kieron Taylor , Anja Thormann , Glen Threadgold , Brandon Walts , Andrea Winterbottom , Marc Chakiachvili , Ameya Chaubal , Nishadi De Silva , Bethany Flint , Adam Frankish , Sarah E Hunt , Garth R IIsley , Nick Langridge , Jane E Loveland , Fergal J Martin , Jonathan M Mudge , Joanella Morales , Emily Perry , Magali Ruffier , John Tate , David Thybert , Stephen J Trevanion , Fiona Cunningham , Andrew D Yates , Daniel R Zerbino , Paul Flicek

The value of primary transcripts to the clinical and non-clinical genomics community: Survey results and roadmap for improvements.

Molecular genetics & genomic medicine

Avec: Joannella Morales , Aoife C McMahon , Jane Loveland , Emily Perry , Adam Frankish , Sarah Hunt , Irina M Armean , Paul Flicek , Fiona Cunningham

SCN1A overexpression, associated with a genomic region marked by a risk variant for a common epilepsy, raises seizure susceptibility.

Acta neuropathologica

Avec: Katri Silvennoinen , Kinga Gawel , Despina Tsortouktzidis , Julika Pitsch , Saud Alhusaini , Karen M J van Loo , Richard Picardo , Zuzanna Michalak , Susanna Pagni , Helena Martins Custodio , James Mills , Christopher D Whelan , Greig I de Zubicaray , Katie L McMahon , Wietske van der Ent , Karolina J Kirstein-Smardzewska , Ettore Tiraboschi , Jonathan M Mudge , Adam Frankish , Maria Thom , Margaret J Wright , Paul M Thompson , Susanne Schoch , Albert J Becker , Camila V Esguerra , Sanjay M Sisodiya

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms.

bioRxiv : the preprint server for biology

Avec: Luke Lambourne , Kaia Mattioli , Clarissa Santoso , Gloria Sheynkman , Sachi Inukai , Babita Kaundal , Anna Berenson , Kerstin Spirohn-Fitzgerald , Anukana Bhattacharjee , Elisabeth Rothman , Shaleen Shrestha , Florent Laval , Zhipeng Yang , Deepa Bisht , Jared A Sewell , Guangyuan Li , Anisa Prasad , Sabrina Phanor , Ryan Lane , Devlin M Campbell , Toby Hunt , Dawit Balcha , Marinella Gebbia , Jean-Claude Twizere , Tong Hao , Adam Frankish , Josh A Riback , Nathan Salomonis , Michael A Calderwood , David E Hill , Nidhi Sahni , Marc Vidal , Martha L Bulyk , Juan I Fuxman Bass

Ensembl 2023.

Nucleic acids research

Avec: Fergal J Martin , M Ridwan Amode , Alisha Aneja , Olanrewaju Austine-Orimoloye , Andrey G Azov , If Barnes , Arne Becker , Ruth Bennett , Andrew Berry , Jyothish 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 , Claire Davidson , Kamalkumar Dodiya , Sarah Donaldson , Bilal El Houdaigui , Tamara El Naboulsi , Reham Fatima , Carlos Garcia Giron , Thiago Genez , Gurpreet S Ghattaoraya , Jose Gonzalez Martinez , Cristi Guijarro , Matthew Hardy , Zoe Hollis , Thibaut Hourlier , Toby Hunt , Mike Kay , Vinay Kaykala , Tuan Le , Diana Lemos , Diego Marques-Coelho , José Carlos Marugán , Gabriela Alejandra Merino , Louisse Paola Mirabueno , Aleena Mushtaq , Syed Nakib Hossain , Denye N Ogeh , Manoj Pandian Sakthivel , Anne Parker , Malcolm Perry , Ivana Piližota , Irina Prosovetskaia , José G Pérez-Silva , Ahamed Imran Abdul Salam , Nuno Saraiva-Agostinho , Helen Schuilenburg , Dan Sheppard , Swati Sinha , Botond Sipos , William Stark , Emily Steed , Ranjit Sukumaran , Dulika 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 , Bethany Flint , Stefano Giorgetti , Leanne Haggerty , Garth R Ilsley , Jane E Loveland , Benjamin 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

The status of the human gene catalogue.

ArXiv

Réseau de co-auteurs

Jonathan M Mudge 19 collaborations

Paul Flicek 19 collaborations

Toby Hunt 12 collaborations

Fergal J Martin 12 collaborations

Jane E Loveland 11 collaborations

Fiona Cunningham 11 collaborations

Claire Davidson 10 collaborations

Thibaut Hourlier 10 collaborations

Magali Ruffier 9 collaborations

Marie-Marthe Suner 9 collaborations

Anne Parker 9 collaborations

Mark Diekhans 8 collaborations

If Barnes 8 collaborations

Ruth Bennett 8 collaborations

Andrew Berry 8 collaborations

Mike Kay 8 collaborations

Reham Fatima 7 collaborations

Matthew Hardy 7 collaborations

Bianca M Schmitt 7 collaborations

Leanne Haggerty 7 collaborations

Daniel R Zerbino 7 collaborations

Jyothish Bhai 7 collaborations

Benjamin Moore 7 collaborations

Dan Sheppard 7 collaborations

Andrea Winterbottom 7 collaborations

Marc Chakiachvili 7 collaborations

Sarah E Hunt 7 collaborations

Stephen J Trevanion 7 collaborations

Andrew D Yates 7 collaborations

Sarah Donaldson 6 collaborations

Roderic Guigó 6 collaborations

Kevin L Howe 6 collaborations

Osagie G Izuogu 6 collaborations

Carlos Garcia Giron 6 collaborations

M Ridwan Amode 6 collaborations

Sanjay Boddu 6 collaborations

Alexandra Bignell 5 collaborations

Rory Johnson 5 collaborations

Julien Lagarde 5 collaborations

Emily Steed 5 collaborations

Tiago Grego 5 collaborations

Shamika Mohanan 5 collaborations

Konstantinos Billis 5 collaborations

David Thybert 5 collaborations

Irina M Armean 5 collaborations

Carla Cummins 5 collaborations

Andrew Parton 5 collaborations

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Anja Thormann 5 collaborations

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Andrey G Azov 5 collaborations

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Jose Gonzalez Martinez 5 collaborations

Tuan Le 5 collaborations

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Bethany Flint 5 collaborations

John Tate 5 collaborations

Irwin Jungreis 4 collaborations

Cristina Sisu 4 collaborations

Stefano Giorgetti 4 collaborations

Jose Manuel Gonzalez 4 collaborations

Peter W Harrison 4 collaborations

Zoe Hollis 4 collaborations

Barbara Uszczynska-Ratajczak 4 collaborations

Elizabeth Wass 4 collaborations

Jyoti S Choudhary 4 collaborations

Mark Gerstein 4 collaborations

Manolis Kellis 4 collaborations

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Jose M Gonzalez 4 collaborations

Mihaela Pertea 4 collaborations

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Piero Carninci 4 collaborations

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Astrid Gall 4 collaborations

Thomas Juettemann 4 collaborations

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Glen Threadgold 4 collaborations

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Sílvia Carbonell-Sala 3 collaborations

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Fernando Pozo 3 collaborations

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Andrew Yates 3 collaborations

Roderic Guigo 3 collaborations

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Thomas Maurel 3 collaborations

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Nick Langridge 3 collaborations

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Lucy Brooks 3 collaborations

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William Stark 3 collaborations

Kyösti Sutinen 3 collaborations

Michal Szpak 3 collaborations

David Urbina-Gómez 3 collaborations

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Thomas A Walsh 3 collaborations

Sarah Dyer 3 collaborations

Robert D Finn 3 collaborations

Carles Boix 2 collaborations

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