Roderic Guigó

Affiliations

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain.
Universitat Pompeu Fabra (UPF), Barcelona, E-08003 Catalonia, Spain.

Publications (52)

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

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

Processive Recoding and Metazoan Evolution of Selenoprotein P: Up to 132 UGAs in Molluscs.

Journal of molecular biology

Avec: Janinah Baclaocos , Didac Santesmasses , Marco Mariotti , Katarzyna Bierła , Michael B Vetick , Sharon Lynch , Rob McAllen , John J Mackrill , Gary Loughran , Roderic Guigó , Joanna Szpunar , Paul R Copeland , Vadim N Gladyshev , John F Atkins

Dynamic changes in intron retention are tightly associated with regulation of splicing factors and proliferative activity during B-cell development.

Nucleic acids research

Avec: Sebastian Ullrich , Roderic Guigó

Publisher Correction: The tuatara genome reveals ancient features of amniote evolution.

Nature

Avec: Neil J Gemmell , Kim Rutherford , Stefan Prost , Marc Tollis , David Winter , J Robert Macey , David L Adelson , Alexander Suh , Terry Bertozzi , José H Grau , Chris Organ , Paul P Gardner , Matthieu Muffato , Mateus Patricio , Konstantinos Billis , Fergal J Martin , Paul Flicek , Bent Petersen , Lin Kang , Pawel Michalak , Thomas R Buckley , Melissa Wilson , Yuanyuan Cheng , Hilary Miller , Ryan K Schott , Melissa D Jordan , Richard D Newcomb , José Ignacio Arroyo , Nicole Valenzuela , Tim A Hore , Jaime Renart , Valentina Peona , Claire R Peart , Vera M Warmuth , Lu Zeng , R Daniel Kortschak , Joy M Raison , Valeria Velásquez Zapata , Zhiqiang Wu , Didac Santesmasses , Marco Mariotti , Roderic Guigó , Shawn M Rupp , Victoria G Twort , Nicolas Dussex , Helen Taylor , Hideaki Abe , Donna M Bond , James M Paterson , Daniel G Mulcahy , Vanessa L Gonzalez , Charles G Barbieri , Dustin P DeMeo , Stephan Pabinger , Tracey Van Stijn , Shannon Clarke , Oliver Ryder , Scott V Edwards , Steven L Salzberg , Lindsay Anderson , Nicola Nelson , Clive Stone , Auteur inconnu

The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics.

NAR genomics and bioinformatics

Avec: Montserrat Corominas , Tomàs Marquès-Bonet , Miquel A Arnedo , Mònica Bayés , Jordina Belmonte , Hector Escrivà , Rosa Fernández , Toni Gabaldón , Teresa Garnatje , Josep Germain , Manel Niell , Ferran Palero , Joan Pons , Pere Puigdomènech , The Catalan Initiative For The Earth BioGenome Project , Auteur inconnu , Vanesa Arroyo , Cristian Cuevas-Caballé , Joan Ferrer Obiol , Ivo Gut , Marta Gut , Oriane Hidalgo , Guillem Izquierdo-Arànega , Laia Pérez-Sorribes , Emilio Righi , Marta Riutort , Joan Vallès , Julio Rozas , Tyler Alioto , Roderic Guigó

RNAget: an API to securely retrieve RNA quantifications.

Bioinformatics (Oxford, England)

Avec: Sean Upchurch , Emilio Palumbo , Jeremy Adams , David Bujold , Guillaume Bourque , Jared Nedzel , Keenan Graham , Meenakshi S Kagda , Pedro Assis , Benjamin Hitz , Emilio Righi , Roderic Guigó , Barbara J Wold , Auteur inconnu

Studying relative RNA localization From nucleus to the cytosol.

bioRxiv : the preprint server for biology

Avec: Vasilis F Ntasis , Roderic Guigó

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

Cell type-specific genetic regulation of gene expression across human tissues.

Science (New York, N.Y.)

Avec: Sarah Kim-Hellmuth , François Aguet , Meritxell Oliva , Manuel Muñoz-Aguirre , Silva Kasela , Valentin Wucher , Stephane E Castel , Andrew R Hamel , Ana Viñuela , Amy L Roberts , Serghei Mangul , Xiaoquan Wen , Gao Wang , Alvaro N Barbeira , Diego Garrido-Martín , Brian B Nadel , Yuxin Zou , Rodrigo Bonazzola , Jie Quan , Andrew Brown , Angel Martinez-Perez , José Manuel Soria , Auteur inconnu , Gad Getz , Emmanouil T Dermitzakis , Kerrin S Small , Matthew Stephens , Hualin S Xi , Hae Kyung Im , Roderic Guigó , Ayellet V Segrè , Barbara E Stranger , Kristin G Ardlie , Tuuli Lappalainen

FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow.

Genes

Avec: Anna Vlasova , Toni Hermoso Pulido , Francisco Camara , Julia Ponomarenko , Roderic Guigó

An encyclopedia of enhancer-gene regulatory interactions in the human genome.

bioRxiv : the preprint server for biology

Avec: Andreas R Gschwind , Kristy S Mualim , Alireza Karbalayghareh , Maya U Sheth , Kushal K Dey , Evelyn Jagoda , Ramil N Nurtdinov , Wang Xi , Anthony S Tan , Hank Jones , X Rosa Ma , David Yao , Joseph Nasser , Žiga Avsec , Benjamin T James , Muhammad S Shamim , Neva C Durand , Suhas S P Rao , Ragini Mahajan , Benjamin R Doughty , Kalina Andreeva , Jacob C Ulirsch , Kaili Fan , Elizabeth M Perez , Tri C Nguyen , David R Kelley , Hilary K Finucane , Jill E Moore , Zhiping Weng , Manolis Kellis , Michael C Bassik , Alkes L Price , Michael A Beer , Roderic Guigó , John A Stamatoyannopoulos , Erez Lieberman Aiden , William J Greenleaf , Christina S Leslie , Lars M Steinmetz , Anshul Kundaje , Jesse M Engreitz

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.

bioRxiv : the preprint server for biology

Avec: Fairlie Reese , Brian Williams , Gabriela Balderrama-Gutierrez , Dana Wyman , Muhammed Hasan Çelik , Elisabeth Rebboah , Narges Rezaie , Diane Trout , Milad Razavi-Mohseni , Yunzhe Jiang , Beatrice Borsari , Samuel Morabito , Heidi Yahan Liang , Cassandra J McGill , Sorena Rahmanian , Jasmine Sakr , Shan Jiang , Weihua Zeng , Klebea Carvalho , Annika K Weimer , Louise A Dionne , Ariel McShane , Karan Bedi , Shaimae I Elhajjajy , Sean Upchurch , Jennifer Jou , Ingrid Youngworth , Idan Gabdank , Paul Sud , Otto Jolanki , J Seth Strattan , Meenakshi S Kagda , Michael P Snyder , Ben C Hitz , Jill E Moore , Zhiping Weng , David Bennett , Laura Reinholdt , Mats Ljungman , Michael A Beer , Mark B Gerstein , Lior Pachter , Roderic Guigó , Barbara J Wold , Ali Mortazavi

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

Dynamics of microRNA expression during mouse prenatal development.

Genome research

Avec: Sorena Rahmanian , Rabi Murad , Alessandra Breschi , Weihua Zeng , Mark Mackiewicz , Brian Williams , Carrie A Davis , Brian Roberts , Sarah Meadows , Dianna Moore , Diane Trout , Chris Zaleski , Alex Dobin , Lei-Hoon Sei , Jorg Drenkow , Alex Scavelli , Thomas R Gingeras , Barbara J Wold , Richard M Myers , Roderic Guigó , Ali Mortazavi

NEAT1 Long Isoform Is Highly Expressed in Chronic Lymphocytic Leukemia Irrespectively of Cytogenetic Groups or Clinical Outcome.

Non-coding RNA

Avec: Domenica Ronchetti , Vanessa Favasuli , Paola Monti , Giovanna Cutrona , Sonia Fabris , Ilaria Silvestris , Luca Agnelli , Monica Colombo , Paola Menichini , Serena Matis , Massimo Gentile , Ramil Nurtdinov , Roderic Guigó , Luca Baldini , Gilberto Fronza , Manlio Ferrarini , Fortunato Morabito , Antonino Neri , Elisa Taiana

The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues.

Genome medicine

Avec: Francesc Muyas , Luis Zapata , Roderic Guigó , Stephan Ossowski

Multivariate Analysis and Modelling of multiple Brain endOphenotypes: Let's MAMBO!

Computational and structural biotechnology journal

Avec: Natalia Vilor-Tejedor , Diego Garrido-Martín , Blanca Rodriguez-Fernandez , Sander Lamballais , Roderic Guigó , Juan Domingo Gispert

Conserved long-range base pairings are associated with pre-mRNA processing of human genes.

Nature communications

Avec: Svetlana Kalmykova , Marina Kalinina , Stepan Denisov , Alexey Mironov , Dmitry Skvortsov , Roderic Guigó , Dmitri Pervouchine

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

Cell genomics

Avec: Heidi L Rehm , Angela J H Page , Lindsay Smith , Jeremy B Adams , Gil Alterovitz , Lawrence J Babb , Maxmillian P Barkley , Michael Baudis , Michael J S Beauvais , Tim Beck , Jacques S Beckmann , Sergi Beltran , David Bernick , Alexander Bernier , James K Bonfield , Tiffany F Boughtwood , Guillaume Bourque , Sarion R Bowers , Anthony J Brookes , Michael Brudno , Matthew H Brush , David Bujold , Tony Burdett , Orion J Buske , Moran N Cabili , Daniel L Cameron , Robert J Carroll , Esmeralda Casas-Silva , Debyani Chakravarty , Bimal P Chaudhari , Shu Hui Chen , J Michael Cherry , Justina Chung , Melissa Cline , Hayley L Clissold , Robert M Cook-Deegan , Mélanie Courtot , Fiona Cunningham , Miro Cupak , Robert M Davies , Danielle Denisko , Megan J Doerr , Lena I Dolman , Edward S Dove , L Jonathan Dursi , Stephanie O M Dyke , James A Eddy , Karen Eilbeck , Kyle P Ellrott , Susan Fairley , Khalid A Fakhro , Helen V Firth , Michael S Fitzsimons , Marc Fiume , Paul Flicek , Ian M Fore , Mallory A Freeberg , Robert R Freimuth , Lauren A Fromont , Jonathan Fuerth , Clara L Gaff , Weiniu Gan , Elena M Ghanaim , David Glazer , Robert C Green , Malachi Griffith , Obi L Griffith , Robert L Grossman , Tudor Groza , Jaime M Guidry Auvil , Roderic Guigó , Dipayan Gupta , Melissa A Haendel , Ada Hamosh , David P Hansen , Reece K Hart , Dean Mitchell Hartley , David Haussler , Rachele M Hendricks-Sturrup , Calvin W L Ho , Ashley E Hobb , Michael M Hoffman , Oliver M Hofmann , Petr Holub , Jacob Shujui Hsu , Jean-Pierre Hubaux , Sarah E Hunt , Ammar Husami , Julius O Jacobsen , Saumya S Jamuar , Elizabeth L Janes , Francis Jeanson , Aina Jené , Amber L Johns , Yann Joly , Steven J M Jones , Alexander Kanitz , Kazuto Kato , Thomas M Keane , Kristina Kekesi-Lafrance , Jerome Kelleher , Giselle Kerry , Seik-Soon Khor , Bartha M Knoppers , Melissa A Konopko , Kenjiro Kosaki , Martin Kuba , Jonathan Lawson , Rasko Leinonen , Stephanie Li , Michael F Lin , Mikael Linden , Xianglin Liu , Isuru Udara Liyanage , Javier Lopez , Anneke M Lucassen , Michael Lukowski , Alice L Mann , John Marshall , Michele Mattioni , Alejandro Metke-Jimenez , Anna Middleton , Richard J Milne , Fruzsina Molnár-Gábor , Nicola Mulder , Monica C Munoz-Torres , Rishi Nag , Hidewaki Nakagawa , Jamal Nasir , Arcadi Navarro , Tristan H Nelson , Ania Niewielska , Amy Nisselle , Jeffrey Niu , Tommi H Nyrönen , Brian D O'Connor , Sabine Oesterle , Soichi Ogishima , Vivian Ota Wang , Laura A D Paglione , Emilio Palumbo , Helen E Parkinson , Anthony A Philippakis , Angel D Pizarro , Andreas Prlic , Jordi Rambla , Augusto Rendon , Renee A Rider , Peter N Robinson , Kurt W Rodarmer , Laura Lyman Rodriguez , Alan F Rubin , Manuel Rueda , Gregory A Rushton , Rosalyn S Ryan , Gary I Saunders , Helen Schuilenburg , Torsten Schwede , Serena Scollen , Alexander Senf , Nathan C Sheffield , Neerjah Skantharajah , Albert V Smith , Heidi J Sofia , Dylan Spalding , Amanda B Spurdle , Zornitza Stark , Lincoln D Stein , Makoto Suematsu , Patrick Tan , Jonathan A Tedds , Alastair A Thomson , Adrian Thorogood , Timothy L Tickle , Katsushi Tokunaga , Juha Törnroos , David Torrents , Sean Upchurch , Alfonso Valencia , Roman Valls Guimera , Jessica Vamathevan , Susheel Varma , Danya F Vears , Coby Viner , Craig Voisin , Alex H Wagner , Susan E Wallace , Brian P Walsh , Marc S Williams , Eva C Winkler , Barbara J Wold , Grant M Wood , J Patrick Woolley , Chisato Yamasaki , Andrew D Yates , Christina K Yung , Lyndon J Zass , Ksenia Zaytseva , Junjun Zhang , Peter Goodhand , Kathryn North , Ewan Birney

Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages.

BMC genomics

Avec: Carme Arnan , Sebastian Ullrich , Carlos Pulido-Quetglas , Ramil Nurtdinov , Alexandre Esteban , Joan Blanco-Fernandez , Estel Aparicio-Prat , Rory Johnson , Sílvia Pérez-Lluch , Roderic Guigó

Day-night and seasonal variation of human gene expression across tissues.

PLoS biology

Avec: Valentin Wucher , Reza Sodaei , Raziel Amador , Manuel Irimia , Roderic Guigó

The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.

Nucleic acids research

Avec: Anurag Chaturvedi , Xiaojing Li , Vignesh Dhandapani , Hollie Marshall , Stephen Kissane , Maria Cuenca-Cambronero , Giovanni Asole , Ferriol Calvet , Marina Ruiz-Romero , Paolo Marangio , Roderic Guigó , Daria Rago , Leda Mirbahai , Niamh Eastwood , John K Colbourne , Jiarui Zhou , Eamonn Mallon , Luisa Orsini

Molecular signatures of alternative reproductive strategies in a facultatively social hover wasp.

Molecular ecology

Avec: Benjamin A Taylor , Daisy Taylor , Alexandrina Bodrug-Schepers , Francisco Câmara Ferreira , Nancy Stralis-Pavese , Heinz Himmelbauer , Roderic Guigó , Max Reuter , Seirian Sumner

The tuatara genome reveals ancient features of amniote evolution.

Nature

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest.

BMC biology

Avec: Claude Rispe , Fabrice Legeai , Paul D Nabity , Rosa Fernández , Arinder K Arora , Patrice Baa-Puyoulet , Celeste R Banfill , Leticia Bao , Miquel Barberà , Maryem Bouallègue , Anthony Bretaudeau , Jennifer A Brisson , Federica Calevro , Pierre Capy , Olivier Catrice , Thomas Chertemps , Carole Couture , Laurent Delière , Angela E Douglas , Keith Dufault-Thompson , Paula Escuer , Honglin Feng , Astrid Forneck , Toni Gabaldón , Roderic Guigó , Frédérique Hilliou , Silvia Hinojosa-Alvarez , Yi-Min Hsiao , Sylvie Hudaverdian , Emmanuelle Jacquin-Joly , Edward B James , Spencer Johnston , Benjamin Joubard , Gaëlle Le Goff , Gaël Le Trionnaire , Pablo Librado , Shanlin Liu , Eric Lombaert , Hsiao-Ling Lu , Martine Maïbèche , Mohamed Makni , Marina Marcet-Houben , David Martínez-Torres , Camille Meslin , Nicolas Montagné , Nancy A Moran , Daciana Papura , Nicolas Parisot , Yvan Rahbé , Mélanie Ribeiro Lopes , Aida Ripoll-Cladellas , Stéphanie Robin , Céline Roques , Pascale Roux , Julio Rozas , Alejandro Sánchez-Gracia , Jose F Sánchez-Herrero , Didac Santesmasses , Iris Scatoni , Rémy-Félix Serre , Ming Tang , Wenhua Tian , Paul A Umina , Manuella van Munster , Carole Vincent-Monégat , Joshua Wemmer , Alex C C Wilson , Ying Zhang , Chaoyang Zhao , Jing Zhao , Serena Zhao , Xin Zhou , François Delmotte , Denis Tagu

Effect of BDNF Val66Met on hippocampal subfields volumes and compensatory interaction with APOE-ε4 in middle-age cognitively unimpaired individuals from the ALFA study.

Brain structure & function

Avec: Natalia Vilor-Tejedor , Grégory Operto , Tavia E Evans , Carles Falcon , Marta Crous-Bou , Carolina Minguillón , Raffaele Cacciaglia , Marta Milà-Alomà , Oriol Grau-Rivera , Marc Suárez-Calvet , Diego Garrido-Martín , Sebastián Morán , Manel Esteller , Hieab H Adams , José Luis Molinuevo , Roderic Guigó , Juan Domingo Gispert , Auteur inconnu

Day-night and seasonal variation of human gene expression across tissues.

bioRxiv : the preprint server for biology

Avec: Valentin Wucher , Reza Sodaei , Raziel Amador , Manuel Irimia , Roderic Guigó

bsAS, an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage.

PLoS genetics

Avec: Sílvia Pérez-Lluch , Cecilia C Klein , Alessandra Breschi , Marina Ruiz-Romero , Amaya Abad , Emilio Palumbo , Lyazzat Bekish , Carme Arnan , Roderic Guigó

The impact of sex on gene expression across human tissues.

Science (New York, N.Y.)

Avec: Meritxell Oliva , Manuel Muñoz-Aguirre , Sarah Kim-Hellmuth , Valentin Wucher , Ariel D H Gewirtz , Daniel J Cotter , Princy Parsana , Silva Kasela , Brunilda Balliu , Ana Viñuela , Stephane E Castel , Pejman Mohammadi , François Aguet , Yuxin Zou , Ekaterina A Khramtsova , Andrew D Skol , Diego Garrido-Martín , Ferran Reverter , Andrew Brown , Patrick Evans , Eric R Gamazon , Anthony Payne , Rodrigo Bonazzola , Alvaro N Barbeira , Andrew R Hamel , Angel Martinez-Perez , José Manuel Soria , Auteur inconnu , Brandon L Pierce , Matthew Stephens , Eleazar Eskin , Emmanouil T Dermitzakis , Ayellet V Segrè , Hae Kyung Im , Barbara E Engelhardt , Kristin G Ardlie , Stephen B Montgomery , Alexis J Battle , Tuuli Lappalainen , Roderic Guigó , Barbara E Stranger

Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest.

BMC biology

Genome annotation: From human genetics to biodiversity genomics.

Cell genomics

Avec: Roderic Guigó

Functional Evolution of Clustered Aquaporin Genes Reveals Insights into the Oceanic Success of Teleost Eggs.

Molecular biology and evolution

Avec: Alba Ferré , François Chauvigné , Anna Vlasova , Birgitta Norberg , Luca Bargelloni , Roderic Guigó , Roderick Nigel Finn , Joan Cerdà

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.

Cell

Avec: Joel Rozowsky , Jiahao Gao , Beatrice Borsari , Yucheng T Yang , Timur Galeev , Gamze Gürsoy , Charles B Epstein , Kun Xiong , Jinrui Xu , Tianxiao Li , Jason Liu , Keyang Yu , Ana Berthel , Zhanlin Chen , Fabio Navarro , Maxwell S Sun , James Wright , Justin Chang , Christopher J F Cameron , Noam Shoresh , Elizabeth Gaskell , Jorg Drenkow , Jessika Adrian , Sergey Aganezov , François Aguet , Gabriela Balderrama-Gutierrez , Samridhi Banskota , Guillermo Barreto Corona , Sora Chee , Surya B Chhetri , Gabriel Conte Cortez Martins , Cassidy Danyko , Carrie A Davis , Daniel Farid , Nina P Farrell , Idan Gabdank , Yoel Gofin , David U Gorkin , Mengting Gu , Vivian Hecht , Benjamin C Hitz , Robbyn Issner , Yunzhe Jiang , Melanie Kirsche , Xiangmeng Kong , Bonita R Lam , Shantao Li , Bian Li , Xiqi Li , Khine Zin Lin , Ruibang Luo , Mark Mackiewicz , Ran Meng , Jill E Moore , Jonathan Mudge , Nicholas Nelson , Chad Nusbaum , Ioann Popov , Henry E Pratt , Yunjiang Qiu , Srividya Ramakrishnan , Joe Raymond , Leonidas Salichos , Alexandra Scavelli , Jacob M Schreiber , Fritz J Sedlazeck , Lei Hoon See , Rachel M Sherman , Xu Shi , Minyi Shi , Cricket Alicia Sloan , J Seth Strattan , Zhen Tan , Forrest Y Tanaka , Anna Vlasova , Jun Wang , Jonathan Werner , Brian Williams , Min Xu , Chengfei Yan , Lu Yu , Christopher Zaleski , Jing Zhang , Kristin Ardlie , J Michael Cherry , Eric M Mendenhall , William S Noble , Zhiping Weng , Morgan E Levine , Alexander Dobin , Barbara Wold , Ali Mortazavi , Bing Ren , Jesse Gillis , Richard M Myers , Michael P Snyder , Jyoti Choudhary , Aleksandar Milosavljevic , Michael C Schatz , Bradley E Bernstein , Roderic Guigó , Thomas R Gingeras , Mark Gerstein

CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing.

Nature communications

Avec: Sílvia Carbonell-Sala , Tamara Perteghella , Julien Lagarde , Hiromi Nishiyori , Emilio Palumbo , Carme Arnan , Hazuki Takahashi , Piero Carninci , Barbara Uszczynska-Ratajczak , Roderic Guigó

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Genome research

Avec: Jordan A Ramilowski , Chi Wai Yip , Saumya Agrawal , Jen-Chien Chang , Yari Ciani , Ivan V Kulakovskiy , Mickaël Mendez , Jasmine Li Ching Ooi , John F Ouyang , Nick Parkinson , Andreas Petri , Leonie Roos , Jessica Severin , Kayoko Yasuzawa , Imad Abugessaisa , Altuna Akalin , Ivan V Antonov , Erik Arner , Alessandro Bonetti , Hidemasa Bono , Beatrice Borsari , Frank Brombacher , Christopher JF Cameron , Carlo Vittorio Cannistraci , Ryan Cardenas , Melissa Cardon , Howard Chang , Josée Dostie , Luca Ducoli , Alexander Favorov , Alexandre Fort , Diego Garrido , Noa Gil , Juliette Gimenez , Reto Guler , Lusy Handoko , Jayson Harshbarger , Akira Hasegawa , Yuki Hasegawa , Kosuke Hashimoto , Norihito Hayatsu , Peter Heutink , Tetsuro Hirose , Eddie L Imada , Masayoshi Itoh , Bogumil Kaczkowski , Aditi Kanhere , Emily Kawabata , Hideya Kawaji , Tsugumi Kawashima , S Thomas Kelly , Miki Kojima , Naoto Kondo , Haruhiko Koseki , Tsukasa Kouno , Anton Kratz , Mariola Kurowska-Stolarska , Andrew Tae Jun Kwon , Jeffrey Leek , Andreas Lennartsson , Marina Lizio , Fernando López-Redondo , Joachim Luginbühl , Shiori Maeda , Vsevolod J Makeev , Luigi Marchionni , Yulia A Medvedeva , Aki Minoda , Ferenc Müller , Manuel Muñoz-Aguirre , Mitsuyoshi Murata , Hiromi Nishiyori , Kazuhiro R Nitta , Shuhei Noguchi , Yukihiko Noro , Ramil Nurtdinov , Yasushi Okazaki , Valerio Orlando , Denis Paquette , Callum J C Parr , Owen J L Rackham , Patrizia Rizzu , Diego Fernando Sánchez Martinez , Albin Sandelin , Pillay Sanjana , Colin A M Semple , Youtaro Shibayama , Divya M Sivaraman , Takahiro Suzuki , Suzannah C Szumowski , Michihira Tagami , Martin S Taylor , Chikashi Terao , Malte Thodberg , Supat Thongjuea , Vidisha Tripathi , Igor Ulitsky , Roberto Verardo , Ilya E Vorontsov , Chinatsu Yamamoto , Robert S Young , J Kenneth Baillie , Alistair R R Forrest , Roderic Guigó , Michael M Hoffman , Chung Chau Hon , Takeya Kasukawa , Sakari Kauppinen , Juha Kere , Boris Lenhard , Claudio Schneider , Harukazu Suzuki , Ken Yagi , Michiel J L de Hoon , Jay W Shin , Piero Carninci

A limited set of transcriptional programs define major cell types.

Genome research

Avec: Alessandra Breschi , Manuel Muñoz-Aguirre , Valentin Wucher , Carrie A Davis , Diego Garrido-Martín , Sarah Djebali , Jesse Gillis , Dmitri D Pervouchine , Anna Vlasova , Alexander Dobin , Chris Zaleski , Jorg Drenkow , Cassidy Danyko , Alexandra Scavelli , Ferran Reverter , Michael P Snyder , Thomas R Gingeras , Roderic Guigó

PyHIST: A Histological Image Segmentation Tool.

PLoS computational biology

Avec: Manuel Muñoz-Aguirre , Vasilis F Ntasis , Santiago Rojas , Roderic Guigó

The abundance of the long intergenic non-coding RNA 01087 differentiates between luminal and triple-negative breast cancers and predicts patient outcome.

Pharmacological research

Avec: Fatima Domenica Elisa De Palma , Valentina Del Monaco , Jonathan G Pol , Margerie Kremer , Valeria D'Argenio , Gautier Stoll , Donatella Montanaro , Barbara Uszczyńska-Ratajczak , Cecilia C Klein , Anna Vlasova , Gerardo Botti , Massimiliano D'Aiuto , Alfonso Baldi , Roderic Guigó , Guido Kroemer , Maria Chiara Maiuri , Francesco Salvatore

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Nature

Avec: Auteur inconnu , Jill E Moore , Michael J Purcaro , Henry E Pratt , Charles B Epstein , Noam Shoresh , Jessika Adrian , Trupti Kawli , Carrie A Davis , Alexander Dobin , Rajinder Kaul , Jessica Halow , Eric L Van Nostrand , Peter Freese , David U Gorkin , Yin Shen , Yupeng He , Mark Mackiewicz , Florencia Pauli-Behn , Brian A Williams , Ali Mortazavi , Cheryl A Keller , Xiao-Ou Zhang , Shaimae I Elhajjajy , Jack Huey , Diane E Dickel , Valentina Snetkova , Xintao Wei , Xiaofeng Wang , Juan Carlos Rivera-Mulia , Joel Rozowsky , Jing Zhang , Surya B Chhetri , Jialing Zhang , Alec Victorsen , Kevin P White , Axel Visel , Gene W Yeo , Christopher B Burge , Eric Lécuyer , David M Gilbert , Job Dekker , John Rinn , Eric M Mendenhall , Joseph R Ecker , Manolis Kellis , Robert J Klein , William S Noble , Anshul Kundaje , Roderic Guigó , Peggy J Farnham , J Michael Cherry , Richard M Myers , Bing Ren , Brenton R Graveley , Mark B Gerstein , Len A Pennacchio , Michael P Snyder , Bradley E Bernstein , Barbara Wold , Ross C Hardison , Thomas R Gingeras , John A Stamatoyannopoulos , Zhiping Weng

Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome.

Nature communications

Avec: Diego Garrido-Martín , Beatrice Borsari , Miquel Calvo , Ferran Reverter , Roderic Guigó

Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS).

Methods in molecular biology (Clifton, N.J.)

Avec: Sílvia Carbonell Sala , Barbara Uszczyńska-Ratajczak , Julien Lagarde , Rory Johnson , Roderic Guigó

Genetic Predisposition to Alzheimer's Disease Is Associated with Enlargement of Perivascular Spaces in Centrum Semiovale Region.

Genes

Avec: Iacopo Ciampa , Grégory Operto , Carles Falcon , Carolina Minguillon , Manuel Castro de Moura , David Piñeyro , Manel Esteller , Jose Luis Molinuevo , Roderic Guigó , Arcadi Navarro , Juan Domingo Gispert , Natalia Vilor-Tejedor , For The Alfa Study

Enhancers with tissue-specific activity are enriched in intronic regions.

Genome research

Avec: Beatrice Borsari , Pablo Villegas-Mirón , Sílvia Pérez-Lluch , Isabel Turpin , Hafid Laayouni , Alba Segarra-Casas , Jaume Bertranpetit , Roderic Guigó , Sandra Acosta

Genomic and functional conservation of lncRNAs: lessons from flies.

Mammalian genome : official journal of the International Mammalian Genome Society

Avec: Carlos Camilleri-Robles , Raziel Amador , Cecilia C Klein , Roderic Guigó , Montserrat Corominas , Marina Ruiz-Romero

The landscape of expression and alternative splicing variation across human traits.

Cell genomics

Avec: Raquel García-Pérez , Jose Miguel Ramirez , Aida Ripoll-Cladellas , Ruben Chazarra-Gil , Winona Oliveros , Oleksandra Soldatkina , Mattia Bosio , Paul Joris Rognon , Salvador Capella-Gutierrez , Miquel Calvo , Ferran Reverter , Roderic Guigó , François Aguet , Pedro G Ferreira , Kristin G Ardlie , Marta Melé

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

CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing.

bioRxiv : the preprint server for biology

Avec: Silvia Carbonell-Sala , Julien Lagarde , Hiromi Nishiyori , Emilio Palumbo , Carme Arnan , Hazuki Takahashi , Piero Carninci , Barbara Uszczynska-Ratajczak , Roderic Guigó

A fast non-parametric test of association for multiple traits.

Genome biology

Avec: Diego Garrido-Martín , Miquel Calvo , Ferran Reverter , Roderic Guigó

Integration of transcription regulation and functional genomic data reveals lncRNA SNHG6's role in hematopoietic differentiation and leukemia.

Journal of biomedical science

Avec: Joshua M Hazan , Raziel Amador , Tahleel Ali-Nasser , Tamar Lahav , Stav Roni Shotan , Miryam Steinberg , Ziv Cohen , Dvir Aran , David Meiri , Yehuda G Assaraf , Roderic Guigó , Assaf C Bester

Long non-coding RNAs involved in

NAR genomics and bioinformatics

Avec: Carlos Camilleri-Robles , Raziel Amador , Marcel Tiebe , Aurelio A Teleman , Florenci Serras , Roderic Guigó , Montserrat Corominas

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None None 8 collaborations

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