Roderic Guigo Lab

Roderic Guigo Lab

Computational biology of RNA processing group

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

    Chaturvedi A;Li X;Dhandapani V;Marshall H;Kissane S;Cuenca-Cambronero M;Asole G;Calvet F;Ruiz-Romero M;Marangio P;Guigó R;Rago D;Mirbahai L;Eastwood N;Colbourne JK;Zhou J;Mallon E;Orsini L

    Nucleic Acids Res

    Genome annotation: From human genetics to biodiversity genomics.

    Guigó R

    Cell Genom

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

    Pardo-Palacios FJ;Wang D;Reese F;Diekhans M;Carbonell-Sala S;Williams B;Loveland JE;De María M;Adams MS;Balderrama-Gutierrez G;Behera AK;Gonzalez JM;Hunt T;Lagarde J;Liang CE;Li H;Meade MJ;Amador DAM;Prjibelski AD;Birol I;Bostan H;Brooks AM;Çelik MH;Chen Y;Du MRM;Felton C;Göke J;Hafezqorani S;Herwig R;Kawaji H;Lee J;Li JL;Lienhard M;Mikheenko A;Mulligan D;Nip KM;Pertea M;Ritchie ME;Sim AD;Tang AD;Wan YK;Wang C;Wong BY;Yang C;Barnes I;Berry A;Capella S;Dhillon N;Fernandez-Gonzalez JM;Ferrández-Peral L;Garcia-Reyero N;Goetz S;Hernández-Ferrer C;Kondratova L;Liu T;Martinez-Martin A;Menor C;Mestre-Tomás J;Mudge JM;Panayotova NG;Paniagua A;Repchevsky D;Rouchka E;Saint-John B;Sapena E;Sheynkman L;Smith ML;Suner MM;Takahashi H;Youngworth IA;Carninci P;Denslow ND;Guigó R;Hunter ME;Tilgner HU;Wold BJ;Vollmers C;Frankish A;Au KF;Sheynkman GM;Mortazavi A;Conesa A;Brooks AN

    preprint

    bioRxiv

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

    Carbonell-Sala S;Lagarde J;Nishiyori H;Palumbo E;Arnan C;Takahashi H;Carninci P;Uszczynska-Ratajczak B;Guigó R

    preprint

    bioRxiv

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

    Reese F;Williams B;Balderrama-Gutierrez G;Wyman D;Çelik MH;Rebboah E;Rezaie N;Trout D;Razavi-Mohseni M;Jiang Y;Borsari B;Morabito S;Liang HY;McGill CJ;Rahmanian S;Sakr J;Jiang S;Zeng W;Carvalho K;Weimer AK;Dionne LA;McShane A;Bedi K;Elhajjajy SI;Upchurch S;Jou J;Youngworth I;Gabdank I;Sud P;Jolanki O;Strattan JS;Kagda MS;Snyder MP;Hitz BC;Moore JE;Weng Z;Bennett D;Reinholdt L;Ljungman M;Beer MA;Gerstein MB;Pachter L;Guigó R;Wold BJ;Mortazavi A

    preprint

    bioRxiv

    Putting hornets on the genomic map.

    Favreau E;Cini A;Taylor D;Câmara Ferreira F;Bentley MA;Cappa F;Cervo R;Privman E;Schneider J;Thiéry D;Mashoodh R;Wyatt CDR;Brown RL;Bodrug-Schepers A;Stralis-Pavese N;Dohm JC;Mead D;Himmelbauer H;Guigo R;Sumner S

    Sci Rep

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

    Rozowsky J;Gao J;Borsari B;Yang YT;Galeev T;Gürsoy G;Epstein CB;Xiong K;Xu J;Li T;Liu J;Yu K;Berthel A;Chen Z;Navarro F;Sun MS;Wright J;Chang J;Cameron CJF;Shoresh N;Gaskell E;Drenkow J;Adrian J;Aganezov S;Aguet F;Balderrama-Gutierrez G;Banskota S;Corona GB;Chee S;Chhetri SB;Cortez Martins GC;Danyko C;Davis CA;Farid D;Farrell NP;Gabdank I;Gofin Y;Gorkin DU;Gu M;Hecht V;Hitz BC;Issner R;Jiang Y;Kirsche M;Kong X;Lam BR;Li S;Li B;Li X;Lin KZ;Luo R;Mackiewicz M;Meng R;Moore JE;Mudge J;Nelson N;Nusbaum C;Popov I;Pratt HE;Qiu Y;Ramakrishnan S;Raymond J;Salichos L;Scavelli A;Schreiber JM;Sedlazeck FJ;See LH;Sherman RM;Shi X;Shi M;Sloan CA;Strattan JS;Tan Z;Tanaka FY;Vlasova A;Wang J;Werner J;Williams B;Xu M;Yan C;Yu L;Zaleski C;Zhang J;Ardlie K;Cherry JM;Mendenhall EM;Noble WS;Weng Z;Levine ME;Dobin A;Wold B;Mortazavi A;Ren B;Gillis J;Myers RM;Snyder MP;Choudhary J;Milosavljevic A;Schatz MC;Bernstein BE;Guigó R;Gingeras TR;Gerstein M

    Cell

    The status of the human gene catalogue.

    Amaral P;Carbonell-Sala S;Vega FM;Faial T;Frankish A;Gingeras T;Guigo R;Harrow JL;Hatzigeorgiou AG;Johnson R;Murphy TD;Pertea M;Pruitt KD;Pujar S;Takahashi H;Ulitsky I;Varabyou A;Wells CA;Yandell M;Carninci P;Salzberg SL

    preprint

    ArXiv

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

    Ferré A;Chauvigné F;Vlasova A;Norberg B;Bargelloni L;Guigó R;Finn RN;Cerdà J

    Mol Biol Evol

    RNAget: an API to securely retrieve RNA quantifications.

    Upchurch S;Palumbo E;Adams J;Bujold D;Bourque G;Nedzel J;Graham K;Kagda MS;Assis P;Hitz B;Righi E;Guigó R;Wold BJ;GA4GH RNA-Seq Task Team

    Bioinformatics

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

    García-Pérez R;Ramirez JM;Ripoll-Cladellas A;Chazarra-Gil R;Oliveros W;Soldatkina O;Bosio M;Rognon PJ;Capella-Gutierrez S;Calvo M;Reverter F;Guigó R;Aguet F;Ferreira PG;Ardlie KG;Melé M

    Cell Genom

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

    Wucher V;Sodaei R;Amador R;Irimia M;Guigó R

    PLoS Biol

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

    Frankish A;Carbonell-Sala S;Diekhans M;Jungreis I;Loveland JE;Mudge JM;Sisu C;Wright JC;Arnan C;Barnes I;Banerjee A;Bennett R;Berry A;Bignell A;Boix C;Calvet F;Cerdán-Vélez D;Cunningham F;Davidson C;Donaldson S;Dursun C;Fatima R;Giorgetti S;Giron CG;Gonzalez JM;Hardy M;Harrison PW;Hourlier T;Hollis Z;Hunt T;James B;Jiang Y;Johnson R;Kay M;Lagarde J;Martin FJ;Gómez LM;Nair S;Ni P;Pozo F;Ramalingam V;Ruffier M;Schmitt BM;Schreiber JM;Steed E;Suner MM;Sumathipala D;Sycheva I;Uszczynska-Ratajczak B;Wass E;Yang YT;Yates A;Zafrulla Z;Choudhary JS;Gerstein M;Guigo R;Hubbard TJP;Kellis M;Kundaje A;Paten B;Tress ML;Flicek P

    Nucleic Acids Res

    Brain transcriptomic profiling reveals common alterations across neurodegenerative and psychiatric disorders.

    Sadeghi I;Gispert JD;Palumbo E;Muñoz-Aguirre M;Wucher V;D'Argenio V;Santpere G;Navarro A;Guigo R;Vilor-Tejedor N

    Comput Struct Biotechnol J

    Genetically predicted telomere length and its relationship with neurodegenerative diseases and life expectancy.

    Rodríguez-Fernández B;Gispert JD;Guigo R;Navarro A;Vilor-Tejedor N;Crous-Bou M

    Comput Struct Biotechnol J

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

    Arnan C;Ullrich S;Pulido-Quetglas C;Nurtdinov R;Esteban A;Blanco-Fernandez J;Aparicio-Prat E;Johnson R;Pérez-Lluch S;Guigó R

    BMC Genomics

    How to ensure the Human Cell Atlas benefits humanity.

    Majumder P;Mhlanga M;Shalek A;Guigó R;Knoppers BM;Wold B

    Nature

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

    ENCODE Project Consortium;Moore JE;Purcaro MJ;Pratt HE;Epstein CB;Shoresh N;Adrian J;Kawli T;Davis CA;Dobin A;Kaul R;Halow J;Van Nostrand EL;Freese P;Gorkin DU;Shen Y;He Y;Mackiewicz M;Pauli-Behn F;Williams BA;Mortazavi A;Keller CA;Zhang XO;Elhajjajy SI;Huey J;Dickel DE;Snetkova V;Wei X;Wang X;Rivera-Mulia JC;Rozowsky J;Zhang J;Chhetri SB;Zhang J;Victorsen A;White KP;Visel A;Yeo GW;Burge CB;Lécuyer E;Gilbert DM;Dekker J;Rinn J;Mendenhall EM;Ecker JR;Kellis M;Klein RJ;Noble WS;Kundaje A;Guigó R;Farnham PJ;Cherry JM;Myers RM;Ren B;Graveley BR;Gerstein MB;Pennacchio LA;Snyder MP;Bernstein BE;Wold B;Hardison RC;Gingeras TR;Stamatoyannopoulos JA;Weng Z

    Nature

    Genomic and functional conservation of lncRNAs: lessons from flies.

    Camilleri-Robles C;Amador R;Klein CC;Guigó R;Corominas M;Ruiz-Romero M

    Mamm Genome

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

    Rehm HL;Page AJH;Smith L;Adams JB;Alterovitz G;Babb LJ;Barkley MP;Baudis M;Beauvais MJS;Beck T;Beckmann JS;Beltran S;Bernick D;Bernier A;Bonfield JK;Boughtwood TF;Bourque G;Bowers SR;Brookes AJ;Brudno M;Brush MH;Bujold D;Burdett T;Buske OJ;Cabili MN;Cameron DL;Carroll RJ;Casas-Silva E;Chakravarty D;Chaudhari BP;Chen SH;Cherry JM;Chung J;Cline M;Clissold HL;Cook-Deegan RM;Courtot M;Cunningham F;Cupak M;Davies RM;Denisko D;Doerr MJ;Dolman LI;Dove ES;Dursi LJ;Dyke SOM;Eddy JA;Eilbeck K;Ellrott KP;Fairley S;Fakhro KA;Firth HV;Fitzsimons MS;Fiume M;Flicek P;Fore IM;Freeberg MA;Freimuth RR;Fromont LA;Fuerth J;Gaff CL;Gan W;Ghanaim EM;Glazer D;Green RC;Griffith M;Griffith OL;Grossman RL;Groza T;Auvil JMG;Guigó R;Gupta D;Haendel MA;Hamosh A;Hansen DP;Hart RK;Hartley DM;Haussler D;Hendricks-Sturrup RM;Ho CWL;Hobb AE;Hoffman MM;Hofmann OM;Holub P;Hsu JS;Hubaux JP;Hunt SE;Husami A;Jacobsen JO;Jamuar SS;Janes EL;Jeanson F;Jené A;Johns AL;Joly Y;Jones SJM;Kanitz A;Kato K;Keane TM;Kekesi-Lafrance K;Kelleher J;Kerry G;Khor SS;Knoppers BM;Konopko MA;Kosaki K;Kuba M;Lawson J;Leinonen R;Li S;Lin MF;Linden M;Liu X;Udara Liyanage I;Lopez J;Lucassen AM;Lukowski M;Mann AL;Marshall J;Mattioni M;Metke-Jimenez A;Middleton A;Milne RJ;Molnár-Gábor F;Mulder N;Munoz-Torres MC;Nag R;Nakagawa H;Nasir J;Navarro A;Nelson TH;Niewielska A;Nisselle A;Niu J;Nyrönen TH;O'Connor BD;Oesterle S;Ogishima S;Wang VO;Paglione LAD;Palumbo E;Parkinson HE;Philippakis AA;Pizarro AD;Prlic A;Rambla J;Rendon A;Rider RA;Robinson PN;Rodarmer KW;Rodriguez LL;Rubin AF;Rueda M;Rushton GA;Ryan RS;Saunders GI;Schuilenburg H;Schwede T;Scollen S;Senf A;Sheffield NC;Skantharajah N;Smith AV;Sofia HJ;Spalding D;Spurdle AB;Stark Z;Stein LD;Suematsu M;Tan P;Tedds JA;Thomson AA;Thorogood A;Tickle TL;Tokunaga K;Törnroos J;Torrents D;Upchurch S;Valencia A;Guimera RV;Vamathevan J;Varma S;Vears DF;Viner C;Voisin C;Wagner AH;Wallace SE;Walsh BP;Williams MS;Winkler EC;Wold BJ;Wood GM;Woolley JP;Yamasaki C;Yates AD;Yung CK;Zass LJ;Zaytseva K;Zhang J;Goodhand P;North K;Birney E

    Cell Genom

    The European Genome-phenome Archive in 2021.

    Freeberg MA;Fromont LA;D'Altri T;Romero AF;Ciges JI;Jene A;Kerry G;Moldes M;Ariosa R;Bahena S;Barrowdale D;Barbero MC;Fernandez-Orth D;Garcia-Linares C;Garcia-Rios E;Haziza F;Juhasz B;Llobet OM;Milla G;Mohan A;Rueda M;Sankar A;Shaju D;Shimpi A;Singh B;Thomas C;de la Torre S;Uyan U;Vasallo C;Flicek P;Guigo R;Navarro A;Parkinson H;Keane T;Rambla J

    Nucleic Acids Res

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

    Vilor-Tejedor N;Garrido-Martín D;Rodriguez-Fernandez B;Lamballais S;Guigó R;Gispert JD

    Comput Struct Biotechnol J

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

    Vlasova A;Hermoso Pulido T;Camara F;Ponomarenko J;Guigó R

    Genes (Basel)

    Perivascular spaces are associated with tau pathophysiology and synaptic dysfunction in early Alzheimer's continuum.

    Vilor-Tejedor N;Ciampa I;Operto G;Falcón C;Suárez-Calvet M;Crous-Bou M;Shekari M;Arenaza-Urquijo EM;Milà-Alomà M;Grau-Rivera O;Minguillon C;Kollmorgen G;Zetterberg H;Blennow K;Guigo R;Molinuevo JL;Gispert JD;ALFA study

    Alzheimers Res Ther

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

    Borsari B;Villegas-Mirón P;Pérez-Lluch S;Turpin I;Laayouni H;Segarra-Casas A;Bertranpetit J;Guigó R;Acosta S

    Genome Res

    Genetic Influences on Hippocampal Subfields: An Emerging Area of Neuroscience Research.

    Vilor-Tejedor N;Evans TE;Adams HH;González-de-Echávarri JM;Molinuevo JL;Guigo R;Gispert JD;Operto G

    Neurol Genet

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

    Ciampa I;Operto G;Falcon C;Minguillon C;Castro de Moura M;Piñeyro D;Esteller M;Molinuevo JL;Guigó R;Navarro A;Gispert JD;Vilor-Tejedor N;For The Alfa Study

    Genes (Basel)

    The genomic basis of evolutionary differentiation among honey bees.

    Fouks B;Brand P;Nguyen HN;Herman J;Camara F;Ence D;Hagen DE;Hoff KJ;Nachweide S;Romoth L;Walden KKO;Guigo R;Stanke M;Narzisi G;Yandell M;Robertson HM;Koeniger N;Chantawannakul P;Schatz MC;Worley KC;Robinson GE;Elsik CG;Rueppell O

    Genome Res

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

    Kalmykova S;Kalinina M;Denisov S;Mironov A;Skvortsov D;Guigó R;Pervouchine D

    Nat Commun

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

    Wucher V;Sodaei R;Amador R;Irimia M;Guigó R

    preprint

    bioRxiv

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

    Garrido-Martín D;Borsari B;Calvo M;Reverter F;Guigó R

    Nat Commun

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

    Pérez-Lluch S;Klein CC;Breschi A;Ruiz-Romero M;Abad A;Palumbo E;Bekish L;Arnan C;Guigó R

    PLoS Genet

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

    Carbonell Sala S;Uszczyńska-Ratajczak B;Lagarde J;Johnson R;Guigó R

    Methods Mol Biol

    GENCODE 2021.

    Frankish A;Diekhans M;Jungreis I;Lagarde J;Loveland JE;Mudge JM;Sisu C;Wright JC;Armstrong J;Barnes I;Berry A;Bignell A;Boix C;Carbonell Sala S;Cunningham F;Di Domenico T;Donaldson S;Fiddes IT;García Girón C;Gonzalez JM;Grego T;Hardy M;Hourlier T;Howe KL;Hunt T;Izuogu OG;Johnson R;Martin FJ;Martínez L;Mohanan S;Muir P;Navarro FCP;Parker A;Pei B;Pozo F;Riera FC;Ruffier M;Schmitt BM;Stapleton E;Suner MM;Sycheva I;Uszczynska-Ratajczak B;Wolf MY;Xu J;Yang YT;Yates A;Zerbino D;Zhang Y;Choudhary JS;Gerstein M;Guigó R;Hubbard TJP;Kellis M;Paten B;Tress ML;Flicek P

    Nucleic Acids Res

    PyHIST: A Histological Image Segmentation Tool.

    Muñoz-Aguirre M;Ntasis VF;Rojas S;Guigó R

    PLoS Comput Biol

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

    De Palma FDE;Del Monaco V;Pol JG;Kremer M;D'Argenio V;Stoll G;Montanaro D;Uszczyńska-Ratajczak B;Klein CC;Vlasova A;Botti G;D'Aiuto M;Baldi A;Guigó R;Kroemer G;Maiuri MC;Salvatore F

    Pharmacol Res

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

    Rispe C;Legeai F;Nabity PD;Fernández R;Arora AK;Baa-Puyoulet P;Banfill CR;Bao L;Barberà M;Bouallègue M;Bretaudeau A;Brisson JA;Calevro F;Capy P;Catrice O;Chertemps T;Couture C;Delière L;Douglas AE;Dufault-Thompson K;Escuer P;Feng H;Forneck A;Gabaldón T;Guigó R;Hilliou F;Hinojosa-Alvarez S;Hsiao YM;Hudaverdian S;Jacquin-Joly E;James EB;Johnston S;Joubard B;Le Goff G;Le Trionnaire G;Librado P;Liu S;Lombaert E;Lu HL;Maïbèche M;Makni M;Marcet-Houben M;Martínez-Torres D;Meslin C;Montagné N;Moran NA;Papura D;Parisot N;Rahbé Y;Lopes MR;Ripoll-Cladellas A;Robin S;Roques C;Roux P;Rozas J;Sánchez-Gracia A;Sánchez-Herrero JF;Santesmasses D;Scatoni I;Serre RF;Tang M;Tian W;Umina PA;van Munster M;Vincent-Monégat C;Wemmer J;Wilson ACC;Zhang Y;Zhao C;Zhao J;Zhao S;Zhou X;Delmotte F;Tagu D

    BMC Biol

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

    Kim-Hellmuth S;Aguet F;Oliva M;Muñoz-Aguirre M;Kasela S;Wucher V;Castel SE;Hamel AR;Viñuela A;Roberts AL;Mangul S;Wen X;Wang G;Barbeira AN;Garrido-Martín D;Nadel BB;Zou Y;Bonazzola R;Quan J;Brown A;Martinez-Perez A;Soria JM;GTEx Consortium;Getz G;Dermitzakis ET;Small KS;Stephens M;Xi HS;Im HK;Guigó R;Segrè AV;Stranger BE;Ardlie KG;Lappalainen T

    Science

    The impact of sex on gene expression across human tissues.

    Oliva M;Muñoz-Aguirre M;Kim-Hellmuth S;Wucher V;Gewirtz ADH;Cotter DJ;Parsana P;Kasela S;Balliu B;Viñuela A;Castel SE;Mohammadi P;Aguet F;Zou Y;Khramtsova EA;Skol AD;Garrido-Martín D;Reverter F;Brown A;Evans P;Gamazon ER;Payne A;Bonazzola R;Barbeira AN;Hamel AR;Martinez-Perez A;Soria JM;GTEx Consortium;Pierce BL;Stephens M;Eskin E;Dermitzakis ET;Segrè AV;Im HK;Engelhardt BE;Ardlie KG;Montgomery SB;Battle AJ;Lappalainen T;Guigó R;Stranger BE

    Science

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

    Gemmell NJ;Rutherford K;Prost S;Tollis M;Winter D;Macey JR;Adelson DL;Suh A;Bertozzi T;Grau JH;Organ C;Gardner PP;Muffato M;Patricio M;Billis K;Martin FJ;Flicek P;Petersen B;Kang L;Michalak P;Buckley TR;Wilson M;Cheng Y;Miller H;Schott RK;Jordan MD;Newcomb RD;Arroyo JI;Valenzuela N;Hore TA;Renart J;Peona V;Peart CR;Warmuth VM;Zeng L;Kortschak RD;Raison JM;Zapata VV;Wu Z;Santesmasses D;Mariotti M;Guigó R;Rupp SM;Twort VG;Dussex N;Taylor H;Abe H;Bond DM;Paterson JM;Mulcahy DG;Gonzalez VL;Barbieri CG;DeMeo DP;Pabinger S;Van Stijn T;Clarke S;Ryder O;Edwards SV;Salzberg SL;Anderson L;Nelson N;Stone C;Ngatiwai Trust Board

    Nature

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

    Vilor-Tejedor N;Operto G;Evans TE;Falcon C;Crous-Bou M;Minguillón C;Cacciaglia R;Milà-Alomà M;Grau-Rivera O;Suárez-Calvet M;Garrido-Martín D;Morán S;Esteller M;Adams HH;Molinuevo JL;Guigó R;Gispert JD;ALFA Study

    Brain Struct Funct

    The tuatara genome reveals ancient features of amniote evolution.

    Gemmell NJ;Rutherford K;Prost S;Tollis M;Winter D;Macey JR;Adelson DL;Suh A;Bertozzi T;Grau JH;Organ C;Gardner PP;Muffato M;Patricio M;Billis K;Martin FJ;Flicek P;Petersen B;Kang L;Michalak P;Buckley TR;Wilson M;Cheng Y;Miller H;Schott RK;Jordan MD;Newcomb RD;Arroyo JI;Valenzuela N;Hore TA;Renart J;Peona V;Peart CR;Warmuth VM;Zeng L;Kortschak RD;Raison JM;Zapata VV;Wu Z;Santesmasses D;Mariotti M;Guigó R;Rupp SM;Twort VG;Dussex N;Taylor H;Abe H;Bond DM;Paterson JM;Mulcahy DG;Gonzalez VL;Barbieri CG;DeMeo DP;Pabinger S;Van Stijn T;Clarke S;Ryder O;Edwards SV;Salzberg SL;Anderson L;Nelson N;Stone C;Ngatiwai Trust Board

    Nature

    A limited set of transcriptional programs define major cell types.

    Breschi A;Muñoz-Aguirre M;Wucher V;Davis CA;Garrido-Martín D;Djebali S;Gillis J;Pervouchine DD;Vlasova A;Dobin A;Zaleski C;Drenkow J;Danyko C;Scavelli A;Reverter F;Snyder MP;Gingeras TR;Guigó R

    Genome Res

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

    ENCODE Project Consortium;Moore JE;Purcaro MJ;Pratt HE;Epstein CB;Shoresh N;Adrian J;Kawli T;Davis CA;Dobin A;Kaul R;Halow J;Van Nostrand EL;Freese P;Gorkin DU;Shen Y;He Y;Mackiewicz M;Pauli-Behn F;Williams BA;Mortazavi A;Keller CA;Zhang XO;Elhajjajy SI;Huey J;Dickel DE;Snetkova V;Wei X;Wang X;Rivera-Mulia JC;Rozowsky J;Zhang J;Chhetri SB;Zhang J;Victorsen A;White KP;Visel A;Yeo GW;Burge CB;Lécuyer E;Gilbert DM;Dekker J;Rinn J;Mendenhall EM;Ecker JR;Kellis M;Klein RJ;Noble WS;Kundaje A;Guigó R;Farnham PJ;Cherry JM;Myers RM;Ren B;Graveley BR;Gerstein MB;Pennacchio LA;Snyder MP;Bernstein BE;Wold B;Hardison RC;Gingeras TR;Stamatoyannopoulos JA;Weng Z

    Nature

    Functional annotation of human long noncoding RNAs via molecular phenotyping.

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    Genome Res

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

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    BMC Biol

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

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    Genome Med

    Gene duplications, divergence and recombination shape adaptive evolution of the fish ectoparasite Gyrodactylus bullatarudis.

    Konczal M;Przesmycka KJ;Mohammed RS;Phillips KP;Camara F;Chmielewski S;Hahn C;Guigo R;Cable J;Radwan J

    Mol Ecol

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

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    Noncoding RNA

    Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes.

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    Genome Biol

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

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    Nucleic Acids Res

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

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    NPJ Genom Med

    Dynamics of microRNA expression during mouse prenatal development.

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    Genome Res

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

    Baclaocos J;Santesmasses D;Mariotti M;Bierła K;Vetick MB;Lynch S;McAllen R;Mackrill JJ;Loughran G;Guigó R;Szpunar J;Copeland PR;Gladyshev VN;Atkins JF

    J Mol Biol

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

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    Nucleic Acids Res

    Recent advances in functional genome analysis.

    Guigo R;de Hoon M

    F1000Res

    Damage-responsive elements in

    Vizcaya-Molina E;Klein CC;Serras F;Mishra RK;Guigó R;Corominas M

    Genome Res

    GENCODE reference annotation for the human and mouse genomes.

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    Nucleic Acids Res

    Using geneid to Identify Genes.

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    Curr Protoc Bioinformatics

    Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk.

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    Nat Genet

    ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization.

    Garrido-Martín D;Palumbo E;Guigó R;Breschi A

    PLoS Comput Biol

    Towards a complete map of the human long non-coding RNA transcriptome.

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    Nat Rev Genet

    The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.

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    Nat Med

    Expression of the transcribed ultraconserved region 70 and the related long non-coding RNA AC092652.2-202 has prognostic value in Chronic Lymphocytic Leukaemia.

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    Br J Haematol

    Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity.

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    Aging Cell

    The effects of death and post-mortem cold ischemia on human tissue transcriptomes.

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    Nat Commun

    The discovery potential of RNA processing profiles.

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    Nucleic Acids Res

    High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.

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    Nat Genet

    Data Resources for Human Functional Genomics.

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    Curr Opin Syst Biol

    Selenoprofiles: A Computational Pipeline for Annotation of Selenoproteins.

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    Methods Mol Biol

    Comparative transcriptomics in human and mouse.

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    Nat Rev Genet

    LncATLAS database for subcellular localization of long noncoding RNAs.

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    Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease.

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    Front Aging Neurosci

    Genomic history of the origin and domestication of common bean unveils its closest sister species.

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    Genome Biol

    Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

    Pulido-Quetglas C;Aparicio-Prat E;Arnan C;Polidori T;Hermoso T;Palumbo E;Ponomarenko J;Guigo R;Johnson R

    PLoS Comput Biol

    Computational identification of the selenocysteine tRNA (tRNASec) in genomes.

    Santesmasses D;Mariotti M;Guigó R

    PLoS Comput Biol

    Ten Simple Rules on How to Organize a Scientific Retreat.

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    PLoS Comput Biol

    Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features.

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    Sci Rep

    ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.

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    BMC Genomics

    Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

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    Genome Biol

    Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements.

    Wu S;Mariotti M;Santesmasses D;Hill KE;Baclaocos J;Aparicio-Prat E;Li S;Mackrill J;Wu Y;Howard MT;Capecchi M;Guigó R;Burk RF;Atkins JF

    Open Biol

    The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

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    Cell

    Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

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    Cell

    Selenoprotein Gene Nomenclature.

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    J Biol Chem

    Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.

    Ferreira PG;Oti M;Barann M;Wieland T;Ezquina S;Friedländer MR;Rivas MA;Esteve-Codina A;GEUVADIS Consortium;Rosenstiel P;Strom TM;Lappalainen T;Guigó R;Sammeth M

    Sci Rep

    Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

    Lagarde J;Uszczynska-Ratajczak B;Santoyo-Lopez J;Gonzalez JM;Tapanari E;Mudge JM;Steward CA;Wilming L;Tanzer A;Howald C;Chrast J;Vela-Boza A;Rueda A;Lopez-Domingo FJ;Dopazo J;Reymond A;Guigó R;Harrow J

    Nat Commun

    Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems.

    Mariotti M;Lobanov AV;Manta B;Santesmasses D;Bofill A;Guigó R;Gabaldón T;Gladyshev VN

    Mol Biol Evol

    Gene-specific patterns of expression variation across organs and species.

    Breschi A;Djebali S;Gillis J;Pervouchine DD;Dobin A;Davis CA;Gingeras TR;Guigó R

    Genome Biol

    Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells.

    Carlevaro-Fita J;Rahim A;Guigó R;Vardy LA;Johnson R

    RNA

    Erratum to: Promoter-like epigenetic signatures in exons displaying cell type-specific splicing.

    Curado J;Iannone C;Tilgner H;Valcárcel J;Guigó R

    Genome Biol

    Erratum to: 'DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs'.

    Aparicio-Prat E;Arnan C;Sala I;Bosch N;Guigó R;Johnson R

    BMC Genomics

    Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life.

    Figueras A;Robledo D;Corvelo A;Hermida M;Pereiro P;Rubiolo JA;Gómez-Garrido J;Carreté L;Bello X;Gut M;Gut IG;Marcet-Houben M;Forn-Cuní G;Galán B;García JL;Abal-Fabeiro JL;Pardo BG;Taboada X;Fernández C;Vlasova A;Hermoso-Pulido A;Guigó R;Álvarez-Dios JA;Gómez-Tato A;Viñas A;Maside X;Gabaldón T;Novoa B;Bouza C;Alioto T;Martínez P

    DNA Res

    Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.

    Vlasova A;Capella-Gutiérrez S;Rendón-Anaya M;Hernández-Oñate M;Minoche AE;Erb I;Câmara F;Prieto-Barja P;Corvelo A;Sanseverino W;Westergaard G;Dohm JC;Pappas GJ;Saburido-Alvarez S;Kedra D;Gonzalez I;Cozzuto L;Gómez-Garrido J;Aguilar-Morón MA;Andreu N;Aguilar OM;Garcia-Mas J;Zehnsdorf M;Vázquez MP;Delgado-Salinas A;Delaye L;Lowy E;Mentaberry A;Vianello-Brondani RP;García JL;Alioto T;Sánchez F;Himmelbauer H;Santalla M;Notredame C;Gabaldón T;Herrera-Estrella A;Guigó R

    Genome Biol

    Spatiotemporal Control of Forkhead Binding to DNA Regulates the Meiotic Gene Expression Program.

    Alves-Rodrigues I;Ferreira PG;Moldón A;Vivancos AP;Hidalgo E;Guigó R;Ayté J

    Cell Rep

    Active transcription without histone modifications.

    Pérez-Lluch S;Guigó R;Corominas M

    Oncotarget

    Corrigendum: Domains of genome-wide gene expression dysregulation in Down's syndrome.

    Letourneau A;Santoni FA;Bonilla X;Sailani MR;Gonzalez D;Kind J;Chevalier C;Thurman R;Sandstrom RS;Hibaoui Y;Garieri M;Popadin K;Falconnet E;Gagnebin M;Gehrig C;Vannier A;Guipponi M;Farinelli L;Robyr D;Migliavacca E;Borel C;Deutsch S;Feki A;Stamatoyannopoulos JA;Herault Y;van Steensel B;Guigo R;Antonarakis SE

    Nature

    Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.

    Mesquita RD;Vionette-Amaral RJ;Lowenberger C;Rivera-Pomar R;Monteiro FA;Minx P;Spieth J;Carvalho AB;Panzera F;Lawson D;Torres AQ;Ribeiro JM;Sorgine MH;Waterhouse RM;Montague MJ;Abad-Franch F;Alves-Bezerra M;Amaral LR;Araujo HM;Araujo RN;Aravind L;Atella GC;Azambuja P;Berni M;Bittencourt-Cunha PR;Braz GR;Calderón-Fernández G;Carareto CM;Christensen MB;Costa IR;Costa SG;Dansa M;Daumas-Filho CR;De-Paula IF;Dias FA;Dimopoulos G;Emrich SJ;Esponda-Behrens N;Fampa P;Fernandez-Medina RD;da Fonseca RN;Fontenele M;Fronick C;Fulton LA;Gandara AC;Garcia ES;Genta FA;Giraldo-Calderón GI;Gomes B;Gondim KC;Granzotto A;Guarneri AA;Guigó R;Harry M;Hughes DS;Jablonka W;Jacquin-Joly E;Juárez MP;Koerich LB;Lange AB;Latorre-Estivalis JM;Lavore A;Lawrence GG;Lazoski C;Lazzari CR;Lopes RR;Lorenzo MG;Lugon MD;Majerowicz D;Marcet PL;Mariotti M;Masuda H;Megy K;Melo AC;Missirlis F;Mota T;Noriega FG;Nouzova M;Nunes RD;Oliveira RL;Oliveira-Silveira G;Ons S;Orchard I;Pagola L;Paiva-Silva GO;Pascual A;Pavan MG;Pedrini N;Peixoto AA;Pereira MH;Pike A;Polycarpo C;Prosdocimi F;Ribeiro-Rodrigues R;Robertson HM;Salerno AP;Salmon D;Santesmasses D;Schama R;Seabra-Junior ES;Silva-Cardoso L;Silva-Neto MA;Souza-Gomes M;Sterkel M;Taracena ML;Tojo M;Tu ZJ;Tubio JM;Ursic-Bedoya R;Venancio TM;Walter-Nuno AB;Wilson D;Warren WC;Wilson RK;Huebner E;Dotson EM;Oliveira PL

    Proc Natl Acad Sci U S A

    Promoter-like epigenetic signatures in exons displaying cell type-specific splicing.

    Curado J;Iannone C;Tilgner H;Valcárcel J;Guigó R

    Genome Biol

    DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs.

    Aparicio-Prat E;Arnan C;Sala I;Bosch N;Guigó R;Johnson R

    BMC Genomics

    Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.

    Patalano S;Vlasova A;Wyatt C;Ewels P;Camara F;Ferreira PG;Asher CL;Jurkowski TP;Segonds-Pichon A;Bachman M;González-Navarrete I;Minoche AE;Krueger F;Lowy E;Marcet-Houben M;Rodriguez-Ales JL;Nascimento FS;Balasubramanian S;Gabaldon T;Tarver JE;Andrews S;Himmelbauer H;Hughes WO;Guigó R;Reik W;Sumner S

    Proc Natl Acad Sci U S A

    CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis.

    Ounzain S;Micheletti R;Arnan C;Plaisance I;Cecchi D;Schroen B;Reverter F;Alexanian M;Gonzales C;Ng SY;Bussotti G;Pezzuto I;Notredame C;Heymans S;Guigó R;Johnson R;Pedrazzini T

    J Mol Cell Cardiol

    Identification of a selenium-dependent glutathione peroxidase in the blood-sucking insect Rhodnius prolixus.

    Dias FA;Gandara AC;Perdomo HD;Gonçalves RS;Oliveira CR;Oliveira RL;Citelli M;Polycarpo CR;Santesmasses D;Mariotti M;Guigó R;Braz GR;Missirlis F;Oliveira PL

    Insect Biochem Mol Biol

    Absence of canonical marks of active chromatin in developmentally regulated genes.

    Pérez-Lluch S;Blanco E;Tilgner H;Curado J;Ruiz-Romero M;Corominas M;Guigó R

    Nat Genet

    Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization.

    Mariotti M;Santesmasses D;Capella-Gutierrez S;Mateo A;Arnan C;Johnson R;D'Aniello S;Yim SH;Gladyshev VN;Serras F;Corominas M;Gabaldón T;Guigó R

    Genome Res

    Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

    Frankish A;Uszczynska B;Ritchie GR;Gonzalez JM;Pervouchine D;Petryszak R;Mudge JM;Fonseca N;Brazma A;Guigo R;Harrow J

    BMC Genomics

    Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

    Rivas MA;Pirinen M;Conrad DF;Lek M;Tsang EK;Karczewski KJ;Maller JB;Kukurba KR;DeLuca DS;Fromer M;Ferreira PG;Smith KS;Zhang R;Zhao F;Banks E;Poplin R;Ruderfer DM;Purcell SM;Tukiainen T;Minikel EV;Stenson PD;Cooper DN;Huang KH;Sullivan TJ;Nedzel J;GTEx Consortium;Geuvadis Consortium;Bustamante CD;Li JB;Daly MJ;Guigo R;Donnelly P;Ardlie K;Sammeth M;Dermitzakis ET;McCarthy MI;Montgomery SB;Lappalainen T;MacArthur DG

    Science

    Human genomics. The human transcriptome across tissues and individuals.

    Melé M;Ferreira PG;Reverter F;DeLuca DS;Monlong J;Sammeth M;Young TR;Goldmann JM;Pervouchine DD;Sullivan TJ;Johnson R;Segrè AV;Djebali S;Niarchou A;GTEx Consortium;Wright FA;Lappalainen T;Calvo M;Getz G;Dermitzakis ET;Ardlie KG;Guigó R

    Science

    The genomes of two key bumblebee species with primitive eusocial organization.

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    Genome Biol

    Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing.

    Tejedor JR;Tilgner H;Iannone C;Guigó R;Valcárcel J

    RNA

    Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation.

    Delmore KE;Hübner S;Kane NC;Schuster R;Andrew RL;Câmara F;Guigó R;Irwin DE

    Mol Ecol

    Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

    Pervouchine DD;Djebali S;Breschi A;Davis CA;Barja PP;Dobin A;Tanzer A;Lagarde J;Zaleski C;See LH;Fastuca M;Drenkow J;Wang H;Bussotti G;Pei B;Balasubramanian S;Monlong J;Harmanci A;Gerstein M;Beer MA;Notredame C;Guigó R;Gingeras TR

    Nat Commun

    RNA. Prescribing splicing.

    Guigó R;Valcárcel J

    Science

    The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

    Chipman AD;Ferrier DE;Brena C;Qu J;Hughes DS;Schröder R;Torres-Oliva M;Znassi N;Jiang H;Almeida FC;Alonso CR;Apostolou Z;Aqrawi P;Arthur W;Barna JC;Blankenburg KP;Brites D;Capella-Gutiérrez S;Coyle M;Dearden PK;Du Pasquier L;Duncan EJ;Ebert D;Eibner C;Erikson G;Evans PD;Extavour CG;Francisco L;Gabaldón T;Gillis WJ;Goodwin-Horn EA;Green JE;Griffiths-Jones S;Grimmelikhuijzen CJ;Gubbala S;Guigó R;Han Y;Hauser F;Havlak P;Hayden L;Helbing S;Holder M;Hui JH;Hunn JP;Hunnekuhl VS;Jackson L;Javaid M;Jhangiani SN;Jiggins FM;Jones TE;Kaiser TS;Kalra D;Kenny NJ;Korchina V;Kovar CL;Kraus FB;Lapraz F;Lee SL;Lv J;Mandapat C;Manning G;Mariotti M;Mata R;Mathew T;Neumann T;Newsham I;Ngo DN;Ninova M;Okwuonu G;Ongeri F;Palmer WJ;Patil S;Patraquim P;Pham C;Pu LL;Putman NH;Rabouille C;Ramos OM;Rhodes AC;Robertson HE;Robertson HM;Ronshaugen M;Rozas J;Saada N;Sánchez-Gracia A;Scherer SE;Schurko AM;Siggens KW;Simmons D;Stief A;Stolle E;Telford MJ;Tessmar-Raible K;Thornton R;van der Zee M;von Haeseler A;Williams JM;Willis JH;Wu Y;Zou X;Lawson D;Muzny DM;Worley KC;Gibbs RA;Akam M;Richards S

    PLoS Biol

    A comparative encyclopedia of DNA elements in the mouse genome.

    Yue F;Cheng Y;Breschi A;Vierstra J;Wu W;Ryba T;Sandstrom R;Ma Z;Davis C;Pope BD;Shen Y;Pervouchine DD;Djebali S;Thurman RE;Kaul R;Rynes E;Kirilusha A;Marinov GK;Williams BA;Trout D;Amrhein H;Fisher-Aylor K;Antoshechkin I;DeSalvo G;See LH;Fastuca M;Drenkow J;Zaleski C;Dobin A;Prieto P;Lagarde J;Bussotti G;Tanzer A;Denas O;Li K;Bender MA;Zhang M;Byron R;Groudine MT;McCleary D;Pham L;Ye Z;Kuan S;Edsall L;Wu YC;Rasmussen MD;Bansal MS;Kellis M;Keller CA;Morrissey CS;Mishra T;Jain D;Dogan N;Harris RS;Cayting P;Kawli T;Boyle AP;Euskirchen G;Kundaje A;Lin S;Lin Y;Jansen C;Malladi VS;Cline MS;Erickson DT;Kirkup VM;Learned K;Sloan CA;Rosenbloom KR;Lacerda de Sousa B;Beal K;Pignatelli M;Flicek P;Lian J;Kahveci T;Lee D;Kent WJ;Ramalho Santos M;Herrero J;Notredame C;Johnson A;Vong S;Lee K;Bates D;Neri F;Diegel M;Canfield T;Sabo PJ;Wilken MS;Reh TA;Giste E;Shafer A;Kutyavin T;Haugen E;Dunn D;Reynolds AP;Neph S;Humbert R;Hansen RS;De Bruijn M;Selleri L;Rudensky A;Josefowicz S;Samstein R;Eichler EE;Orkin SH;Levasseur D;Papayannopoulou T;Chang KH;Skoultchi A;Gosh S;Disteche C;Treuting P;Wang Y;Weiss MJ;Blobel GA;Cao X;Zhong S;Wang T;Good PJ;Lowdon RF;Adams LB;Zhou XQ;Pazin MJ;Feingold EA;Wold B;Taylor J;Mortazavi A;Weissman SM;Stamatoyannopoulos JA;Snyder MP;Guigo R;Gingeras TR;Gilbert DM;Hardison RC;Beer MA;Ren B;Mouse ENCODE Consortium

    Nature

    Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

    Kellis M;Wold B;Snyder MP;Bernstein BE;Kundaje A;Marinov GK;Ward LD;Birney E;Crawford GE;Dekker J;Dunham I;Elnitski LL;Farnham PJ;Feingold EA;Gerstein M;Giddings MC;Gilbert DM;Gingeras TR;Green ED;Guigo R;Hubbard T;Kent J;Lieb JD;Myers RM;Pazin MJ;Ren B;Stamatoyannopoulos J;Weng Z;White KP;Hardison RC

    Proc Natl Acad Sci U S A

    Transcriptional diversity during lineage commitment of human blood progenitors.

    Chen L;Kostadima M;Martens JHA;Canu G;Garcia SP;Turro E;Downes K;Macaulay IC;Bielczyk-Maczynska E;Coe S;Farrow S;Poudel P;Burden F;Jansen SBG;Astle WJ;Attwood A;Bariana T;de Bono B;Breschi A;Chambers JC;Consortium B;Choudry FA;Clarke L;Coupland P;van der Ent M;Erber WN;Jansen JH;Favier R;Fenech ME;Foad N;Freson K;van Geet C;Gomez K;Guigo R;Hampshire D;Kelly AM;Kerstens HHD;Kooner JS;Laffan M;Lentaigne C;Labalette C;Martin T;Meacham S;Mumford A;Nürnberg S;Palumbo E;van der Reijden BA;Richardson D;Sammut SJ;Slodkowicz G;Tamuri AU;Vasquez L;Voss K;Watt S;Westbury S;Flicek P;Loos R;Goldman N;Bertone P;Read RJ;Richardson S;Cvejic A;Soranzo N;Ouwehand WH;Stunnenberg HG;Frontini M;Rendon A

    Science

    Comparative analysis of the transcriptome across distant species.

    Gerstein MB;Rozowsky J;Yan KK;Wang D;Cheng C;Brown JB;Davis CA;Hillier L;Sisu C;Li JJ;Pei B;Harmanci AO;Duff MO;Djebali S;Alexander RP;Alver BH;Auerbach R;Bell K;Bickel PJ;Boeck ME;Boley NP;Booth BW;Cherbas L;Cherbas P;Di C;Dobin A;Drenkow J;Ewing B;Fang G;Fastuca M;Feingold EA;Frankish A;Gao G;Good PJ;Guigó R;Hammonds A;Harrow J;Hoskins RA;Howald C;Hu L;Huang H;Hubbard TJ;Huynh C;Jha S;Kasper D;Kato M;Kaufman TC;Kitchen RR;Ladewig E;Lagarde J;Lai E;Leng J;Lu Z;MacCoss M;May G;McWhirter R;Merrihew G;Miller DM;Mortazavi A;Murad R;Oliver B;Olson S;Park PJ;Pazin MJ;Perrimon N;Pervouchine D;Reinke V;Reymond A;Robinson G;Samsonova A;Saunders GI;Schlesinger F;Sethi A;Slack FJ;Spencer WC;Stoiber MH;Strasbourger P;Tanzer A;Thompson OA;Wan KH;Wang G;Wang H;Watkins KL;Wen J;Wen K;Xue C;Yang L;Yip K;Zaleski C;Zhang Y;Zheng H;Brenner SE;Graveley BR;Celniker SE;Gingeras TR;Waterston R

    Nature

    Identification of genetic variants associated with alternative splicing using sQTLseekeR.

    Monlong J;Calvo M;Ferreira PG;Guigó R

    Nat Commun

    The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs.

    Johnson R;Guigó R

    RNA

    Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs.

    Ounzain S;Micheletti R;Beckmann T;Schroen B;Alexanian M;Pezzuto I;Crippa S;Nemir M;Sarre A;Johnson R;Dauvillier J;Burdet F;Ibberson M;Guigó R;Xenarios I;Heymans S;Pedrazzini T

    Eur Heart J

    Defining functional DNA elements in the human genome.

    Kellis M;Wold B;Snyder MP;Bernstein BE;Kundaje A;Marinov GK;Ward LD;Birney E;Crawford GE;Dekker J;Dunham I;Elnitski LL;Farnham PJ;Feingold EA;Gerstein M;Giddings MC;Gilbert DM;Gingeras TR;Green ED;Guigo R;Hubbard T;Kent J;Lieb JD;Myers RM;Pazin MJ;Ren B;Stamatoyannopoulos JA;Weng Z;White KP;Hardison RC

    Proc Natl Acad Sci U S A

    Domains of genome-wide gene expression dysregulation in Down's syndrome.

    Letourneau A;Santoni FA;Bonilla X;Sailani MR;Gonzalez D;Kind J;Chevalier C;Thurman R;Sandstrom RS;Hibaoui Y;Garieri M;Popadin K;Falconnet E;Gagnebin M;Gehrig C;Vannier A;Guipponi M;Farinelli L;Robyr D;Migliavacca E;Borel C;Deutsch S;Feki A;Stamatoyannopoulos JA;Herault Y;van Steensel B;Guigo R;Antonarakis SE

    Nature

    Finding the missing honey bee genes: lessons learned from a genome upgrade.

    Elsik CG;Worley KC;Bennett AK;Beye M;Camara F;Childers CP;de Graaf DC;Debyser G;Deng J;Devreese B;Elhaik E;Evans JD;Foster LJ;Graur D;Guigo R;HGSC production teams;Hoff KJ;Holder ME;Hudson ME;Hunt GJ;Jiang H;Joshi V;Khetani RS;Kosarev P;Kovar CL;Ma J;Maleszka R;Moritz RF;Munoz-Torres MC;Murphy TD;Muzny DM;Newsham IF;Reese JT;Robertson HM;Robinson GE;Rueppell O;Solovyev V;Stanke M;Stolle E;Tsuruda JM;Vaerenbergh MV;Waterhouse RM;Weaver DB;Whitfield CW;Wu Y;Zdobnov EM;Zhang L;Zhu D;Gibbs RA;Honey Bee Genome Sequencing Consortium

    BMC Genomics

    ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection.

    Alioto T;Picardi E;Guigó R;Pesole G

    Biomed Res Int

    Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia.

    Ferreira PG;Jares P;Rico D;Gómez-López G;Martínez-Trillos A;Villamor N;Ecker S;González-Pérez A;Knowles DG;Monlong J;Johnson R;Quesada V;Djebali S;Papasaikas P;López-Guerra M;Colomer D;Royo C;Cazorla M;Pinyol M;Clot G;Aymerich M;Rozman M;Kulis M;Tamborero D;Gouin A;Blanc J;Gut M;Gut I;Puente XS;Pisano DG;Martin-Subero JI;López-Bigas N;López-Guillermo A;Valencia A;López-Otín C;Campo E;Guigó R

    Genome Res

    SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans.

    Romagné F;Santesmasses D;White L;Sarangi GK;Mariotti M;Hübler R;Weihmann A;Parra G;Gladyshev VN;Guigó R;Castellano S

    Nucleic Acids Res

    Assessment of transcript reconstruction methods for RNA-seq.

    Steijger T;Abril JF;Engström PG;Kokocinski F;RGASP Consortium;Hubbard TJ;Guigó R;Harrow J;Bertone P

    Nat Methods

    Systematic evaluation of spliced alignment programs for RNA-seq data.

    Engström PG;Steijger T;Sipos B;Grant GR;Kahles A;Rätsch G;Goldman N;Hubbard TJ;Harrow J;Guigó R;Bertone P;RGASP Consortium

    Nat Methods

    Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.

    't Hoen PA;Friedländer MR;Almlöf J;Sammeth M;Pulyakhina I;Anvar SY;Laros JF;Buermans HP;Karlberg O;Brännvall M;GEUVADIS Consortium;den Dunnen JT;van Ommen GJ;Gut IG;Guigó R;Estivill X;Syvänen AC;Dermitzakis ET;Lappalainen T

    Nat Biotechnol

    Transcriptome and genome sequencing uncovers functional variation in humans.

    Lappalainen T;Sammeth M;Friedländer MR;'t Hoen PA;Monlong J;Rivas MA;Gonzàlez-Porta M;Kurbatova N;Griebel T;Ferreira PG;Barann M;Wieland T;Greger L;van Iterson M;Almlöf J;Ribeca P;Pulyakhina I;Esser D;Giger T;Tikhonov A;Sultan M;Bertier G;MacArthur DG;Lek M;Lizano E;Buermans HP;Padioleau I;Schwarzmayr T;Karlberg O;Ongen H;Kilpinen H;Beltran S;Gut M;Kahlem K;Amstislavskiy V;Stegle O;Pirinen M;Montgomery SB;Donnelly P;McCarthy MI;Flicek P;Strom TM;Geuvadis Consortium;Lehrach H;Schreiber S;Sudbrak R;Carracedo A;Antonarakis SE;Häsler R;Syvänen AC;van Ommen GJ;Brazma A;Meitinger T;Rosenstiel P;Guigó R;Gut IG;Estivill X;Dermitzakis ET

    Nature

    Topoisomerase II regulates yeast genes with singular chromatin architectures.

    Nikolaou C;Bermúdez I;Manichanh C;García-Martinez J;Guigó R;Pérez-Ortín JE;Roca J

    Nucleic Acids Res

    SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins.

    Mariotti M;Lobanov AV;Guigo R;Gladyshev VN

    Nucleic Acids Res

    Unravelling the hidden DNA structural/physical code provides novel insights on promoter location.

    Durán E;Djebali S;González S;Flores O;Mercader JM;Guigó R;Torrents D;Soler-López M;Orozco M

    Nucleic Acids Res

    Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes.

    Ferreira PG;Patalano S;Chauhan R;Ffrench-Constant R;Gabaldón T;Guigó R;Sumner S

    Genome Biol

    CPEB1 coordinates alternative 3'-UTR formation with translational regulation.

    Bava FA;Eliscovich C;Ferreira PG;Miñana B;Ben-Dov C;Guigó R;Valcárcel J;Méndez R

    Nature

    Grape RNA-Seq analysis pipeline environment.

    Knowles DG;Röder M;Merkel A;Guigó R

    Bioinformatics

    Intron-centric estimation of alternative splicing from RNA-seq data.

    Pervouchine DD;Knowles DG;Guigó R

    Bioinformatics

    The GEM mapper: fast, accurate and versatile alignment by filtration.

    Marco-Sola S;Sammeth M;Guigó R;Ribeca P

    Nat Methods

    Modelling and simulating generic RNA-Seq experiments with the flux simulator.

    Griebel T;Zacher B;Ribeca P;Raineri E;Lacroix V;Guigó R;Sammeth M

    Nucleic Acids Res

    The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

    Derrien T;Johnson R;Bussotti G;Tanzer A;Djebali S;Tilgner H;Guernec G;Martin D;Merkel A;Knowles DG;Lagarde J;Veeravalli L;Ruan X;Ruan Y;Lassmann T;Carninci P;Brown JB;Lipovich L;Gonzalez JM;Thomas M;Davis CA;Shiekhattar R;Gingeras TR;Hubbard TJ;Notredame C;Harrow J;Guigó R

    Genome Res

    GENCODE: the reference human genome annotation for The ENCODE Project.

    Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ

    Genome Res

    Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

    Howald C;Tanzer A;Chrast J;Kokocinski F;Derrien T;Walters N;Gonzalez JM;Frankish A;Aken BL;Hourlier T;Vogel JH;White S;Searle S;Harrow J;Hubbard TJ;Guigó R;Reymond A

    Genome Res

    Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

    Cheng C;Alexander R;Min R;Leng J;Yip KY;Rozowsky J;Yan KK;Dong X;Djebali S;Ruan Y;Davis CA;Carninci P;Lassman T;Gingeras TR;Guigó R;Birney E;Weng Z;Snyder M;Gerstein M

    Genome Res

    Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.

    Tilgner H;Knowles DG;Johnson R;Davis CA;Chakrabortty S;Djebali S;Curado J;Snyder M;Gingeras TR;Guigó R

    Genome Res

    Landscape of transcription in human cells.

    Djebali S;Davis CA;Merkel A;Dobin A;Lassmann T;Mortazavi A;Tanzer A;Lagarde J;Lin W;Schlesinger F;Xue C;Marinov GK;Khatun J;Williams BA;Zaleski C;Rozowsky J;Röder M;Kokocinski F;Abdelhamid RF;Alioto T;Antoshechkin I;Baer MT;Bar NS;Batut P;Bell K;Bell I;Chakrabortty S;Chen X;Chrast J;Curado J;Derrien T;Drenkow J;Dumais E;Dumais J;Duttagupta R;Falconnet E;Fastuca M;Fejes-Toth K;Ferreira P;Foissac S;Fullwood MJ;Gao H;Gonzalez D;Gordon A;Gunawardena H;Howald C;Jha S;Johnson R;Kapranov P;King B;Kingswood C;Luo OJ;Park E;Persaud K;Preall JB;Ribeca P;Risk B;Robyr D;Sammeth M;Schaffer L;See LH;Shahab A;Skancke J;Suzuki AM;Takahashi H;Tilgner H;Trout D;Walters N;Wang H;Wrobel J;Yu Y;Ruan X;Hayashizaki Y;Harrow J;Gerstein M;Hubbard T;Reymond A;Antonarakis SE;Hannon G;Giddings MC;Ruan Y;Wold B;Carninci P;Guigó R;Gingeras TR

    Nature

    Modeling gene expression using chromatin features in various cellular contexts.

    Dong X;Greven MC;Kundaje A;Djebali S;Brown JB;Cheng C;Gingeras TR;Gerstein M;Guigó R;Birney E;Weng Z

    Genome Biol

    An encyclopedia of mouse DNA elements (Mouse ENCODE).

    Mouse ENCODE Consortium;Stamatoyannopoulos JA;Snyder M;Hardison R;Ren B;Gingeras T;Gilbert DM;Groudine M;Bender M;Kaul R;Canfield T;Giste E;Johnson A;Zhang M;Balasundaram G;Byron R;Roach V;Sabo PJ;Sandstrom R;Stehling AS;Thurman RE;Weissman SM;Cayting P;Hariharan M;Lian J;Cheng Y;Landt SG;Ma Z;Wold BJ;Dekker J;Crawford GE;Keller CA;Wu W;Morrissey C;Kumar SA;Mishra T;Jain D;Byrska-Bishop M;Blankenberg D;Lajoie BR;Jain G;Sanyal A;Chen KB;Denas O;Taylor J;Blobel GA;Weiss MJ;Pimkin M;Deng W;Marinov GK;Williams BA;Fisher-Aylor KI;Desalvo G;Kiralusha A;Trout D;Amrhein H;Mortazavi A;Edsall L;McCleary D;Kuan S;Shen Y;Yue F;Ye Z;Davis CA;Zaleski C;Jha S;Xue C;Dobin A;Lin W;Fastuca M;Wang H;Guigo R;Djebali S;Lagarde J;Ryba T;Sasaki T;Malladi VS;Cline MS;Kirkup VM;Learned K;Rosenbloom KR;Kent WJ;Feingold EA;Good PJ;Pazin M;Lowdon RF;Adams LB

    Genome Biol

    The genome of melon (Cucumis melo L.).

    Garcia-Mas J;Benjak A;Sanseverino W;Bourgeois M;Mir G;González VM;Hénaff E;Câmara F;Cozzuto L;Lowy E;Alioto T;Capella-Gutiérrez S;Blanca J;Cañizares J;Ziarsolo P;Gonzalez-Ibeas D;Rodríguez-Moreno L;Droege M;Du L;Alvarez-Tejado M;Lorente-Galdos B;Melé M;Yang L;Weng Y;Navarro A;Marques-Bonet T;Aranda MA;Nuez F;Picó B;Gabaldón T;Roma G;Guigó R;Casacuberta JM;Arús P;Puigdomènech P

    Proc Natl Acad Sci U S A

    Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

    Frenkel-Morgenstern M;Lacroix V;Ezkurdia I;Levin Y;Gabashvili A;Prilusky J;Del Pozo A;Tress M;Johnson R;Guigo R;Valencia A

    Genome Res

    Composition and evolution of the vertebrate and mammalian selenoproteomes.

    Mariotti M;Ridge PG;Zhang Y;Lobanov AV;Pringle TH;Guigo R;Hatfield DL;Gladyshev VN

    PLoS One

    BLUEPRINT to decode the epigenetic signature written in blood.

    Adams D;Altucci L;Antonarakis SE;Ballesteros J;Beck S;Bird A;Bock C;Boehm B;Campo E;Caricasole A;Dahl F;Dermitzakis ET;Enver T;Esteller M;Estivill X;Ferguson-Smith A;Fitzgibbon J;Flicek P;Giehl C;Graf T;Grosveld F;Guigo R;Gut I;Helin K;Jarvius J;Küppers R;Lehrach H;Lengauer T;Lernmark Å;Leslie D;Loeffler M;Macintyre E;Mai A;Martens JH;Minucci S;Ouwehand WH;Pelicci PG;Pendeville H;Porse B;Rakyan V;Reik W;Schrappe M;Schübeler D;Seifert M;Siebert R;Simmons D;Soranzo N;Spicuglia S;Stratton M;Stunnenberg HG;Tanay A;Torrents D;Valencia A;Vellenga E;Vingron M;Walter J;Willcocks S

    Nat Biotechnol

    The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter".

    Derrien T;Guigó R;Johnson R

    Front Genet

    Fast computation and applications of genome mappability.

    Derrien T;Estellé J;Marco Sola S;Knowles DG;Raineri E;Guigó R;Ribeca P

    PLoS One

    Evidence for transcript networks composed of chimeric RNAs in human cells.

    Djebali S;Lagarde J;Kapranov P;Lacroix V;Borel C;Mudge JM;Howald C;Foissac S;Ucla C;Chrast J;Ribeca P;Martin D;Murray RR;Yang X;Ghamsari L;Lin C;Bell I;Dumais E;Drenkow J;Tress ML;Gelpí JL;Orozco M;Valencia A;van Berkum NL;Lajoie BR;Vidal M;Stamatoyannopoulos J;Batut P;Dobin A;Harrow J;Hubbard T;Dekker J;Frankish A;Salehi-Ashtiani K;Reymond A;Antonarakis SE;Guigó R;Gingeras TR

    PLoS One

    Estimation of alternative splicing variability in human populations.

    Gonzàlez-Porta M;Calvo M;Sammeth M;Guigó R

    Genome Res

    Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer.

    Maxwell CA;Benítez J;Gómez-Baldó L;Osorio A;Bonifaci N;Fernández-Ramires R;Costes SV;Guinó E;Chen H;Evans GJ;Mohan P;Català I;Petit A;Aguilar H;Villanueva A;Aytes A;Serra-Musach J;Rennert G;Lejbkowicz F;Peterlongo P;Manoukian S;Peissel B;Ripamonti CB;Bonanni B;Viel A;Allavena A;Bernard L;Radice P;Friedman E;Kaufman B;Laitman Y;Dubrovsky M;Milgrom R;Jakubowska A;Cybulski C;Gorski B;Jaworska K;Durda K;Sukiennicki G;Lubiński J;Shugart YY;Domchek SM;Letrero R;Weber BL;Hogervorst FB;Rookus MA;Collee JM;Devilee P;Ligtenberg MJ;Luijt RB;Aalfs CM;Waisfisz Q;Wijnen J;Roozendaal CE;HEBON;EMBRACE;Easton DF;Peock S;Cook M;Oliver C;Frost D;Harrington P;Evans DG;Lalloo F;Eeles R;Izatt L;Chu C;Eccles D;Douglas F;Brewer C;Nevanlinna H;Heikkinen T;Couch FJ;Lindor NM;Wang X;Godwin AK;Caligo MA;Lombardi G;Loman N;Karlsson P;Ehrencrona H;Wachenfeldt Av;SWE-BRCA;Barkardottir RB;Hamann U;Rashid MU;Lasa A;Caldés T;Andrés R;Schmitt M;Assmann V;Stevens K;Offit K;Curado J;Tilgner H;Guigó R;Aiza G;Brunet J;Castellsagué J;Martrat G;Urruticoechea A;Blanco I;Tihomirova L;Goldgar DE;Buys S;John EM;Miron A;Southey M;Daly MB;BCFR;Schmutzler RK;Wappenschmidt B;Meindl A;Arnold N;Deissler H;Varon-Mateeva R;Sutter C;Niederacher D;Imyamitov E;Sinilnikova OM;Stoppa-Lyonne D;Mazoyer S;Verny-Pierre C;Castera L;de Pauw A;Bignon YJ;Uhrhammer N;Peyrat JP;Vennin P;Fert Ferrer S;Collonge-Rame MA;Mortemousque I;GEMO Study Collaborators;Spurdle AB;Beesley J;Chen X;Healey S;kConFab;Barcellos-Hoff MH;Vidal M;Gruber SB;Lázaro C;Capellá G;McGuffog L;Nathanson KL;Antoniou AC;Chenevix-Trench G;Fleisch MC;Moreno V;Pujana MA

    PLoS Biol

    Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.

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    Nature

    Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.

    Martin D;Pantoja C;Fernández Miñán A;Valdes-Quezada C;Moltó E;Matesanz F;Bogdanović O;de la Calle-Mustienes E;Domínguez O;Taher L;Furlan-Magaril M;Alcina A;Cañón S;Fedetz M;Blasco MA;Pereira PS;Ovcharenko I;Recillas-Targa F;Montoliu L;Manzanares M;Guigó R;Serrano M;Casares F;Gómez-Skarmeta JL

    Nat Struct Mol Biol

    The origins, evolution, and functional potential of alternative splicing in vertebrates.

    Mudge JM;Frankish A;Fernandez-Banet J;Alioto T;Derrien T;Howald C;Reymond A;Guigó R;Hubbard T;Harrow J

    Mol Biol Evol

    [Long non-coding RNAs with enhancer-like function in human cells].

    Derrien T;Guigó R

    Med Sci (Paris)

    Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae.

    Nikolaou C;Althammer S;Beato M;Guigó R

    Epigenetics Chromatin

    Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

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    Science

    Long noncoding RNAs with enhancer-like function in human cells.

    Ørom UA;Derrien T;Beringer M;Gumireddy K;Gardini A;Bussotti G;Lai F;Zytnicki M;Notredame C;Huang Q;Guigo R;Shiekhattar R

    Cell

    Reshaping the gut microbiome with bacterial transplantation and antibiotic intake.

    Manichanh C;Reeder J;Gibert P;Varela E;Llopis M;Antolin M;Guigo R;Knight R;Guarner F

    Genome Res

    Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).

    Stajich JE;Wilke SK;Ahrén D;Au CH;Birren BW;Borodovsky M;Burns C;Canbäck B;Casselton LA;Cheng CK;Deng J;Dietrich FS;Fargo DC;Farman ML;Gathman AC;Goldberg J;Guigó R;Hoegger PJ;Hooker JB;Huggins A;James TY;Kamada T;Kilaru S;Kodira C;Kües U;Kupfer D;Kwan HS;Lomsadze A;Li W;Lilly WW;Ma LJ;Mackey AJ;Manning G;Martin F;Muraguchi H;Natvig DO;Palmerini H;Ramesh MA;Rehmeyer CJ;Roe BA;Shenoy N;Stanke M;Ter-Hovhannisyan V;Tunlid A;Velagapudi R;Vision TJ;Zeng Q;Zolan ME;Pukkila PJ

    Proc Natl Acad Sci U S A

    International network of cancer genome projects.

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    Nature

    From chromatin to splicing: RNA-processing as a total artwork.

    Tilgner H;Guigó R

    Epigenetics

    Transcriptome genetics using second generation sequencing in a Caucasian population.

    Montgomery SB;Sammeth M;Gutierrez-Arcelus M;Lach RP;Ingle C;Nisbett J;Guigo R;Dermitzakis ET

    Nature

    The histone variant macroH2A is an epigenetic regulator of key developmental genes.

    Buschbeck M;Uribesalgo I;Wibowo I;Rué P;Martin D;Gutierrez A;Morey L;Guigó R;López-Schier H;Di Croce L

    Nat Struct Mol Biol

    Nucleosome positioning as a determinant of exon recognition.

    Tilgner H;Nikolaou C;Althammer S;Sammeth M;Beato M;Valcárcel J;Guigó R

    Nat Struct Mol Biol

    Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls.

    Makrythanasis P;Kapranov P;Bartoloni L;Reymond A;Deutsch S;Guigó R;Denoeud F;Drenkow J;Rossier C;Ariani F;Capra V;Excoffier L;Renieri A;Gingeras TR;Antonarakis SE

    Hum Mutat

    Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins.

    Castellano S;Andrés AM;Bosch E;Bayes M;Guigó R;Clark AG

    Mol Biol Evol

    The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells.

    Arman M;Aguilera-Montilla N;Mas V;Puig-Kröger A;Pignatelli M;Guigó R;Corbí AL;Lozano F

    Mol Immunol

    The genome sequence of taurine cattle: a window to ruminant biology and evolution.

    Bovine Genome Sequencing and Analysis Consortium;Elsik CG;Tellam RL;Worley KC;Gibbs RA;Muzny DM;Weinstock GM;Adelson DL;Eichler EE;Elnitski L;Guigó R;Hamernik DL;Kappes SM;Lewin HA;Lynn DJ;Nicholas FW;Reymond A;Rijnkels M;Skow LC;Zdobnov EM;Schook L;Womack J;Alioto T;Antonarakis SE;Astashyn A;Chapple CE;Chen HC;Chrast J;Câmara F;Ermolaeva O;Henrichsen CN;Hlavina W;Kapustin Y;Kiryutin B;Kitts P;Kokocinski F;Landrum M;Maglott D;Pruitt K;Sapojnikov V;Searle SM;Solovyev V;Souvorov A;Ucla C;Wyss C;Anzola JM;Gerlach D;Elhaik E;Graur D;Reese JT;Edgar RC;McEwan JC;Payne GM;Raison JM;Junier T;Kriventseva EV;Eyras E;Plass M;Donthu R;Larkin DM;Reecy J;Yang MQ;Chen L;Cheng Z;Chitko-McKown CG;Liu GE;Matukumalli LK;Song J;Zhu B;Bradley DG;Brinkman FS;Lau LP;Whiteside MD;Walker A;Wheeler TT;Casey T;German JB;Lemay DG;Maqbool NJ;Molenaar AJ;Seo S;Stothard P;Baldwin CL;Baxter R;Brinkmeyer-Langford CL;Brown WC;Childers CP;Connelley T;Ellis SA;Fritz K;Glass EJ;Herzig CT;Iivanainen A;Lahmers KK;Bennett AK;Dickens CM;Gilbert JG;Hagen DE;Salih H;Aerts J;Caetano AR;Dalrymple B;Garcia JF;Gill CA;Hiendleder SG;Memili E;Spurlock D;Williams JL;Alexander L;Brownstein MJ;Guan L;Holt RA;Jones SJ;Marra MA;Moore R;Moore SS;Roberts A;Taniguchi M;Waterman RC;Chacko J;Chandrabose MM;Cree A;Dao MD;Dinh HH;Gabisi RA;Hines S;Hume J;Jhangiani SN;Joshi V;Kovar CL;Lewis LR;Liu YS;Lopez J;Morgan MB;Nguyen NB;Okwuonu GO;Ruiz SJ;Santibanez J;Wright RA;Buhay C;Ding Y;Dugan-Rocha S;Herdandez J;Holder M;Sabo A;Egan A;Goodell J;Wilczek-Boney K;Fowler GR;Hitchens ME;Lozado RJ;Moen C;Steffen D;Warren JT;Zhang J;Chiu R;Schein JE;Durbin KJ;Havlak P;Jiang H;Liu Y;Qin X;Ren Y;Shen Y;Song H;Bell SN;Davis C;Johnson AJ;Lee S;Nazareth LV;Patel BM;Pu LL;Vattathil S;Williams RL;Curry S;Hamilton C;Sodergren E;Wheeler DA;Barris W;Bennett GL;Eggen A;Green RD;Harhay GP;Hobbs M;Jann O;Keele JW;Kent MP;Lien S;McKay SD;McWilliam S;Ratnakumar A;Schnabel RD;Smith T;Snelling WM;Sonstegard TS;Stone RT;Sugimoto Y;Takasuga A;Taylor JF;Van Tassell CP;Macneil MD;Abatepaulo AR;Abbey CA;Ahola V;Almeida IG;Amadio AF;Anatriello E;Bahadue SM;Biase FH;Boldt CR;Carroll JA;Carvalho WA;Cervelatti EP;Chacko E;Chapin JE;Cheng Y;Choi J;Colley AJ;de Campos TA;De Donato M;Santos IK;de Oliveira CJ;Deobald H;Devinoy E;Donohue KE;Dovc P;Eberlein A;Fitzsimmons CJ;Franzin AM;Garcia GR;Genini S;Gladney CJ;Grant JR;Greaser ML;Green JA;Hadsell DL;Hakimov HA;Halgren R;Harrow JL;Hart EA;Hastings N;Hernandez M;Hu ZL;Ingham A;Iso-Touru T;Jamis C;Jensen K;Kapetis D;Kerr T;Khalil SS;Khatib H;Kolbehdari D;Kumar CG;Kumar D;Leach R;Lee JC;Li C;Logan KM;Malinverni R;Marques E;Martin WF;Martins NF;Maruyama SR;Mazza R;McLean KL;Medrano JF;Moreno BT;Moré DD;Muntean CT;Nandakumar HP;Nogueira MF;Olsaker I;Pant SD;Panzitta F;Pastor RC;Poli MA;Poslusny N;Rachagani S;Ranganathan S;Razpet A;Riggs PK;Rincon G;Rodriguez-Osorio N;Rodriguez-Zas SL;Romero NE;Rosenwald A;Sando L;Schmutz SM;Shen L;Sherman L;Southey BR;Lutzow YS;Sweedler JV;Tammen I;Telugu BP;Urbanski JM;Utsunomiya YT;Verschoor CP;Waardenberg AJ;Wang Z;Ward R;Weikard R;Welsh TH;White SN;Wilming LG;Wunderlich KR;Yang J;Zhao FQ

    Science

    CROC: finding chromosomal clusters in eukaryotic genomes.

    Pignatelli M;Serras F;Moya A;Guigó R;Corominas M

    Bioinformatics

    Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver.

    Servitja JM;Pignatelli M;Maestro MA;Cardalda C;Boj SF;Lozano J;Blanco E;Lafuente A;McCarthy MI;Sumoy L;Guigó R;Ferrer J

    Mol Cell Biol

    Identifying protein-coding genes in genomic sequences.

    Harrow J;Nagy A;Reymond A;Alioto T;Patthy L;Antonarakis SE;Guigó R

    Genome Biol

    A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins.

    Takeuchi A;Schmitt D;Chapple C;Babaylova E;Karpova G;Guigo R;Krol A;Allmang C

    Nucleic Acids Res

    Functional targets of the monogenic diabetes transcription factors HNF-1alpha and HNF-4alpha are highly conserved between mice and humans.

    Boj SF;Servitja JM;Martin D;Rios M;Talianidis I;Guigo R;Ferrer J

    Diabetes

    SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.

    Chapple CE;Guigó R;Krol A

    Bioinformatics

    ASTD: The Alternative Splicing and Transcript Diversity database.

    Koscielny G;Le Texier V;Gopalakrishnan C;Kumanduri V;Riethoven JJ;Nardone F;Stanley E;Fallsehr C;Hofmann O;Kull M;Harrington E;Boué S;Eyras E;Plass M;Lopez F;Ritchie W;Moucadel V;Ara T;Pospisil H;Herrmann A;G Reich J;Guigó R;Bork P;Doeberitz Mv;Vilo J;Hide W;Apweiler R;Thanaraj TA;Gautheret D

    Genomics

    Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila.

    Blanco E;Pignatelli M;Beltran S;Punset A;Pérez-Lluch S;Serras F;Guigó R;Corominas M

    Genome Biol

    Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes.

    Chapple CE;Guigó R

    PLoS One

    A general definition and nomenclature for alternative splicing events.

    Sammeth M;Foissac S;Guigó R

    PLoS Comput Biol

    A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

    Manichanh C;Chapple CE;Frangeul L;Gloux K;Guigo R;Dore J

    Nucleic Acids Res

    Efficient targeted transcript discovery via array-based normalization of RACE libraries.

    Djebali S;Kapranov P;Foissac S;Lagarde J;Reymond A;Ucla C;Wyss C;Drenkow J;Dumais E;Murray RR;Lin C;Szeto D;Denoeud F;Calvo M;Frankish A;Harrow J;Makrythanasis P;Vidal M;Salehi-Ashtiani K;Antonarakis SE;Gingeras TR;Guigó R

    Nat Methods

    SNP and haplotype mapping for genetic analysis in the rat.

    STAR Consortium;Saar K;Beck A;Bihoreau MT;Birney E;Brocklebank D;Chen Y;Cuppen E;Demonchy S;Dopazo J;Flicek P;Foglio M;Fujiyama A;Gut IG;Gauguier D;Guigo R;Guryev V;Heinig M;Hummel O;Jahn N;Klages S;Kren V;Kube M;Kuhl H;Kuramoto T;Kuroki Y;Lechner D;Lee YA;Lopez-Bigas N;Lathrop GM;Mashimo T;Medina I;Mott R;Patone G;Perrier-Cornet JA;Platzer M;Pravenec M;Reinhardt R;Sakaki Y;Schilhabel M;Schulz H;Serikawa T;Shikhagaie M;Tatsumoto S;Taudien S;Toyoda A;Voigt B;Zelenika D;Zimdahl H;Hubner N

    Nat Genet

    Using geneid to identify genes.

    Blanco E;Parra G;Guigó R

    Curr Protoc Bioinformatics

    In silico meets in vivo.

    Weng Z;Guigó R

    Genome Biol

    A combinatorial code for CPE-mediated translational control.

    Piqué M;López JM;Foissac S;Guigó R;Méndez R

    Cell

    Interoperability with Moby 1.0--it's better than sharing your toothbrush!

    BioMoby Consortium;Wilkinson MD;Senger M;Kawas E;Bruskiewich R;Gouzy J;Noirot C;Bardou P;Ng A;Haase D;Saiz Ede A;Wang D;Gibbons F;Gordon PM;Sensen CW;Carrasco JM;Fernández JM;Shen L;Links M;Ng M;Opushneva N;Neerincx PB;Leunissen JA;Ernst R;Twigger S;Usadel B;Good B;Wong Y;Stein L;Crosby W;Karlsson J;Royo R;Párraga I;Ramírez S;Gelpi JL;Trelles O;Pisano DG;Jimenez N;Kerhornou A;Rosset R;Zamacola L;Tarraga J;Huerta-Cepas J;Carazo JM;Dopazo J;Guigo R;Navarro A;Orozco M;Valencia A;Claros MG;Pérez AJ;Aldana J;Rojano M;Fernandez-Santa Cruz R;Navas I;Schiltz G;Farmer A;Gessler D;Schoof H;Groscurth A

    Brief Bioinform

    SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

    Castellano S;Gladyshev VN;Guigó R;Berry MJ

    Nucleic Acids Res

    Evolution of genes and genomes on the Drosophila phylogeny.

    Drosophila 12 Genomes Consortium;Clark AG;Eisen MB;Smith DR;Bergman CM;Oliver B;Markow TA;Kaufman TC;Kellis M;Gelbart W;Iyer VN;Pollard DA;Sackton TB;Larracuente AM;Singh ND;Abad JP;Abt DN;Adryan B;Aguade M;Akashi H;Anderson WW;Aquadro CF;Ardell DH;Arguello R;Artieri CG;Barbash DA;Barker D;Barsanti P;Batterham P;Batzoglou S;Begun D;Bhutkar A;Blanco E;Bosak SA;Bradley RK;Brand AD;Brent MR;Brooks AN;Brown RH;Butlin RK;Caggese C;Calvi BR;Bernardo de Carvalho A;Caspi A;Castrezana S;Celniker SE;Chang JL;Chapple C;Chatterji S;Chinwalla A;Civetta A;Clifton SW;Comeron JM;Costello JC;Coyne JA;Daub J;David RG;Delcher AL;Delehaunty K;Do CB;Ebling H;Edwards K;Eickbush T;Evans JD;Filipski A;Findeiss S;Freyhult E;Fulton L;Fulton R;Garcia AC;Gardiner A;Garfield DA;Garvin BE;Gibson G;Gilbert D;Gnerre S;Godfrey J;Good R;Gotea V;Gravely B;Greenberg AJ;Griffiths-Jones S;Gross S;Guigo R;Gustafson EA;Haerty W;Hahn MW;Halligan DL;Halpern AL;Halter GM;Han MV;Heger A;Hillier L;Hinrichs AS;Holmes I;Hoskins RA;Hubisz MJ;Hultmark D;Huntley MA;Jaffe DB;Jagadeeshan S;Jeck WR;Johnson J;Jones CD;Jordan WC;Karpen GH;Kataoka E;Keightley PD;Kheradpour P;Kirkness EF;Koerich LB;Kristiansen K;Kudrna D;Kulathinal RJ;Kumar S;Kwok R;Lander E;Langley CH;Lapoint R;Lazzaro BP;Lee SJ;Levesque L;Li R;Lin CF;Lin MF;Lindblad-Toh K;Llopart A;Long M;Low L;Lozovsky E;Lu J;Luo M;Machado CA;Makalowski W;Marzo M;Matsuda M;Matzkin L;McAllister B;McBride CS;McKernan B;McKernan K;Mendez-Lago M;Minx P;Mollenhauer MU;Montooth K;Mount SM;Mu X;Myers E;Negre B;Newfeld S;Nielsen R;Noor MA;O'Grady P;Pachter L;Papaceit M;Parisi MJ;Parisi M;Parts L;Pedersen JS;Pesole G;Phillippy AM;Ponting CP;Pop M;Porcelli D;Powell JR;Prohaska S;Pruitt K;Puig M;Quesneville H;Ram KR;Rand D;Rasmussen MD;Reed LK;Reenan R;Reily A;Remington KA;Rieger TT;Ritchie MG;Robin C;Rogers YH;Rohde C;Rozas J;Rubenfield MJ;Ruiz A;Russo S;Salzberg SL;Sanchez-Gracia A;Saranga DJ;Sato H;Schaeffer SW;Schatz MC;Schlenke T;Schwartz R;Segarra C;Singh RS;Sirot L;Sirota M;Sisneros NB;Smith CD;Smith TF;Spieth J;Stage DE;Stark A;Stephan W;Strausberg RL;Strempel S;Sturgill D;Sutton G;Sutton GG;Tao W;Teichmann S;Tobari YN;Tomimura Y;Tsolas JM;Valente VL;Venter E;Venter JC;Vicario S;Vieira FG;Vilella AJ;Villasante A;Walenz B;Wang J;Wasserman M;Watts T;Wilson D;Wilson RK;Wing RA;Wolfner MF;Wong A;Wong GK;Wu CI;Wu G;Yamamoto D;Yang HP;Yang SP;Yorke JA;Yoshida K;Zdobnov E;Zhang P;Zhang Y;Zimin AV;Baldwin J;Abdouelleil A;Abdulkadir J;Abebe A;Abera B;Abreu J;Acer SC;Aftuck L;Alexander A;An P;Anderson E;Anderson S;Arachi H;Azer M;Bachantsang P;Barry A;Bayul T;Berlin A;Bessette D;Bloom T;Blye J;Boguslavskiy L;Bonnet C;Boukhgalter B;Bourzgui I;Brown A;Cahill P;Channer S;Cheshatsang Y;Chuda L;Citroen M;Collymore A;Cooke P;Costello M;D'Aco K;Daza R;De Haan G;DeGray S;DeMaso C;Dhargay N;Dooley K;Dooley E;Doricent M;Dorje P;Dorjee K;Dupes A;Elong R;Falk J;Farina A;Faro S;Ferguson D;Fisher S;Foley CD;Franke A;Friedrich D;Gadbois L;Gearin G;Gearin CR;Giannoukos G;Goode T;Graham J;Grandbois E;Grewal S;Gyaltsen K;Hafez N;Hagos B;Hall J;Henson C;Hollinger A;Honan T;Huard MD;Hughes L;Hurhula B;Husby ME;Kamat A;Kanga B;Kashin S;Khazanovich D;Kisner P;Lance K;Lara M;Lee W;Lennon N;Letendre F;LeVine R;Lipovsky A;Liu X;Liu J;Liu S;Lokyitsang T;Lokyitsang Y;Lubonja R;Lui A;MacDonald P;Magnisalis V;Maru K;Matthews C;McCusker W;McDonough S;Mehta T;Meldrim J;Meneus L;Mihai O;Mihalev A;Mihova T;Mittelman R;Mlenga V;Montmayeur A;Mulrain L;Navidi A;Naylor J;Negash T;Nguyen T;Nguyen N;Nicol R;Norbu C;Norbu N;Novod N;O'Neill B;Osman S;Markiewicz E;Oyono OL;Patti C;Phunkhang P;Pierre F;Priest M;Raghuraman S;Rege F;Reyes R;Rise C;Rogov P;Ross K;Ryan E;Settipalli S;Shea T;Sherpa N;Shi L;Shih D;Sparrow T;Spaulding J;Stalker J;Stange-Thomann N;Stavropoulos S;Stone C;Strader C;Tesfaye S;Thomson T;Thoulutsang Y;Thoulutsang D;Topham K;Topping I;Tsamla T;Vassiliev H;Vo A;Wangchuk T;Wangdi T;Weiand M;Wilkinson J;Wilson A;Yadav S;Young G;Yu Q;Zembek L;Zhong D;Zimmer A;Zwirko Z;Jaffe DB;Alvarez P;Brockman W;Butler J;Chin C;Gnerre S;Grabherr M;Kleber M;Mauceli E;MacCallum I

    Nature

    Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.

    Lyle R;Prandini P;Osoegawa K;ten Hallers B;Humphray S;Zhu B;Eyras E;Castelo R;Bird CP;Gagos S;Scott C;Cox A;Deutsch S;Ucla C;Cruts M;Dahoun S;She X;Bena F;Wang SY;Van Broeckhoven C;Eichler EE;Guigo R;Rogers J;de Jong PJ;Reymond A;Antonarakis SE

    Genome Res

    Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

    ENCODE Project Consortium;Birney E;Stamatoyannopoulos JA;Dutta A;Guigó R;Gingeras TR;Margulies EH;Weng Z;Snyder M;Dermitzakis ET;Thurman RE;Kuehn MS;Taylor CM;Neph S;Koch CM;Asthana S;Malhotra A;Adzhubei I;Greenbaum JA;Andrews RM;Flicek P;Boyle PJ;Cao H;Carter NP;Clelland GK;Davis S;Day N;Dhami P;Dillon SC;Dorschner MO;Fiegler H;Giresi PG;Goldy J;Hawrylycz M;Haydock A;Humbert R;James KD;Johnson BE;Johnson EM;Frum TT;Rosenzweig ER;Karnani N;Lee K;Lefebvre GC;Navas PA;Neri F;Parker SC;Sabo PJ;Sandstrom R;Shafer A;Vetrie D;Weaver M;Wilcox S;Yu M;Collins FS;Dekker J;Lieb JD;Tullius TD;Crawford GE;Sunyaev S;Noble WS;Dunham I;Denoeud F;Reymond A;Kapranov P;Rozowsky J;Zheng D;Castelo R;Frankish A;Harrow J;Ghosh S;Sandelin A;Hofacker IL;Baertsch R;Keefe D;Dike S;Cheng J;Hirsch HA;Sekinger EA;Lagarde J;Abril JF;Shahab A;Flamm C;Fried C;Hackermüller J;Hertel J;Lindemeyer M;Missal K;Tanzer A;Washietl S;Korbel J;Emanuelsson O;Pedersen JS;Holroyd N;Taylor R;Swarbreck D;Matthews N;Dickson MC;Thomas DJ;Weirauch MT;Gilbert J;Drenkow J;Bell I;Zhao X;Srinivasan KG;Sung WK;Ooi HS;Chiu KP;Foissac S;Alioto T;Brent M;Pachter L;Tress ML;Valencia A;Choo SW;Choo CY;Ucla C;Manzano C;Wyss C;Cheung E;Clark TG;Brown JB;Ganesh M;Patel S;Tammana H;Chrast J;Henrichsen CN;Kai C;Kawai J;Nagalakshmi U;Wu J;Lian Z;Lian J;Newburger P;Zhang X;Bickel P;Mattick JS;Carninci P;Hayashizaki Y;Weissman S;Hubbard T;Myers RM;Rogers J;Stadler PF;Lowe TM;Wei CL;Ruan Y;Struhl K;Gerstein M;Antonarakis SE;Fu Y;Green ED;Karaöz U;Siepel A;Taylor J;Liefer LA;Wetterstrand KA;Good PJ;Feingold EA;Guyer MS;Cooper GM;Asimenos G;Dewey CN;Hou M;Nikolaev S;Montoya-Burgos JI;Löytynoja A;Whelan S;Pardi F;Massingham T;Huang H;Zhang NR;Holmes I;Mullikin JC;Ureta-Vidal A;Paten B;Seringhaus M;Church D;Rosenbloom K;Kent WJ;Stone EA;NISC Comparative Sequencing Program;Baylor College of Medicine Human Genome Sequencing Center;Washington University Genome Sequencing Center;Broad Institute;Children's Hospital Oakland Research Institute;Batzoglou S;Goldman N;Hardison RC;Haussler D;Miller W;Sidow A;Trinklein ND;Zhang ZD;Barrera L;Stuart R;King DC;Ameur A;Enroth S;Bieda MC;Kim J;Bhinge AA;Jiang N;Liu J;Yao F;Vega VB;Lee CW;Ng P;Shahab A;Yang A;Moqtaderi Z;Zhu Z;Xu X;Squazzo S;Oberley MJ;Inman D;Singer MA;Richmond TA;Munn KJ;Rada-Iglesias A;Wallerman O;Komorowski J;Fowler JC;Couttet P;Bruce AW;Dovey OM;Ellis PD;Langford CF;Nix DA;Euskirchen G;Hartman S;Urban AE;Kraus P;Van Calcar S;Heintzman N;Kim TH;Wang K;Qu C;Hon G;Luna R;Glass CK;Rosenfeld MG;Aldred SF;Cooper SJ;Halees A;Lin JM;Shulha HP;Zhang X;Xu M;Haidar JN;Yu Y;Ruan Y;Iyer VR;Green RD;Wadelius C;Farnham PJ;Ren B;Harte RA;Hinrichs AS;Trumbower H;Clawson H;Hillman-Jackson J;Zweig AS;Smith K;Thakkapallayil A;Barber G;Kuhn RM;Karolchik D;Armengol L;Bird CP;de Bakker PI;Kern AD;Lopez-Bigas N;Martin JD;Stranger BE;Woodroffe A;Davydov E;Dimas A;Eyras E;Hallgrímsdóttir IB;Huppert J;Zody MC;Abecasis GR;Estivill X;Bouffard GG;Guan X;Hansen NF;Idol JR;Maduro VV;Maskeri B;McDowell JC;Park M;Thomas PJ;Young AC;Blakesley RW;Muzny DM;Sodergren E;Wheeler DA;Worley KC;Jiang H;Weinstock GM;Gibbs RA;Graves T;Fulton R;Mardis ER;Wilson RK;Clamp M;Cuff J;Gnerre S;Jaffe DB;Chang JL;Lindblad-Toh K;Lander ES;Koriabine M;Nefedov M;Osoegawa K;Yoshinaga Y;Zhu B;de Jong PJ

    Nature

    Structured RNAs in the ENCODE selected regions of the human genome.

    Washietl S;Pedersen JS;Korbel JO;Stocsits C;Gruber AR;Hackermüller J;Hertel J;Lindemeyer M;Reiche K;Tanzer A;Ucla C;Wyss C;Antonarakis SE;Denoeud F;Lagarde J;Drenkow J;Kapranov P;Gingeras TR;Guigó R;Snyder M;Gerstein MB;Reymond A;Hofacker IL;Stadler PF

    Genome Res

    Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

    Zheng D;Frankish A;Baertsch R;Kapranov P;Reymond A;Choo SW;Lu Y;Denoeud F;Antonarakis SE;Snyder M;Ruan Y;Wei CL;Gingeras TR;Guigó R;Harrow J;Gerstein MB

    Genome Res

    Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.

    Denoeud F;Kapranov P;Ucla C;Frankish A;Castelo R;Drenkow J;Lagarde J;Alioto T;Manzano C;Chrast J;Dike S;Wyss C;Henrichsen CN;Holroyd N;Dickson MC;Taylor R;Hance Z;Foissac S;Myers RM;Rogers J;Hubbard T;Harrow J;Guigó R;Gingeras TR;Antonarakis SE;Reymond A

    Genome Res

    The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.

    Rozowsky JS;Newburger D;Sayward F;Wu J;Jordan G;Korbel JO;Nagalakshmi U;Yang J;Zheng D;Guigó R;Gingeras TR;Weissman S;Miller P;Snyder M;Gerstein MB

    Genome Res

    BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations.

    Kerhornou A;Guigó R

    Bioinformatics

    Multiple non-collinear TF-map alignments of promoter regions.

    Blanco E;Guigó R;Messeguer X

    BMC Bioinformatics

    The implications of alternative splicing in the ENCODE protein complement.

    Tress ML;Martelli PL;Frankish A;Reeves GA;Wesselink JJ;Yeats C;Olason PI;Albrecht M;Hegyi H;Giorgetti A;Raimondo D;Lagarde J;Laskowski RA;López G;Sadowski MI;Watson JD;Fariselli P;Rossi I;Nagy A;Kai W;Størling Z;Orsini M;Assenov Y;Blankenburg H;Huthmacher C;Ramírez F;Schlicker A;Denoeud F;Jones P;Kerrien S;Orchard S;Antonarakis SE;Reymond A;Birney E;Brunak S;Casadio R;Guigo R;Harrow J;Hermjakob H;Jones DT;Lengauer T;Orengo CA;Patthy L;Thornton JM;Tramontano A;Valencia A

    Proc Natl Acad Sci U S A

    Improving gene annotation using peptide mass spectrometry.

    Tanner S;Shen Z;Ng J;Florea L;Guigó R;Briggs SP;Bafna V

    Genome Res

    Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

    Aury JM;Jaillon O;Duret L;Noel B;Jubin C;Porcel BM;Ségurens B;Daubin V;Anthouard V;Aiach N;Arnaiz O;Billaut A;Beisson J;Blanc I;Bouhouche K;Câmara F;Duharcourt S;Guigo R;Gogendeau D;Katinka M;Keller AM;Kissmehl R;Klotz C;Koll F;Le Mouël A;Lepère G;Malinsky S;Nowacki M;Nowak JK;Plattner H;Poulain J;Ruiz F;Serrano V;Zagulski M;Dessen P;Bétermier M;Weissenbach J;Scarpelli C;Schächter V;Sperling L;Meyer E;Cohen J;Wincker P

    Nature

    GENCODE: producing a reference annotation for ENCODE.

    Harrow J;Denoeud F;Frankish A;Reymond A;Chen CK;Chrast J;Lagarde J;Gilbert JG;Storey R;Swarbreck D;Rossier C;Ucla C;Hubbard T;Antonarakis SE;Guigo R

    Genome Biol

    EGASP: the human ENCODE Genome Annotation Assessment Project.

    Guigó R;Flicek P;Abril JF;Reymond A;Lagarde J;Denoeud F;Antonarakis S;Ashburner M;Bajic VB;Birney E;Castelo R;Eyras E;Ucla C;Gingeras TR;Harrow J;Hubbard T;Lewis SE;Reese MG

    Genome Biol

    EGASP: Introduction.

    Reese MG;Guigó R

    Genome Biol

    Unweaving the meanings of messenger RNA sequences.

    Guigó R;Valcárcel J

    Mol Cell

    Transcription factor map alignment of promoter regions.

    Blanco E;Messeguer X;Smith TF;Guigó R

    PLoS Comput Biol

    Mutation patterns of amino acid tandem repeats in the human proteome.

    Mularoni L;Guigó R;Albà MM

    Genome Biol

    ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

    Blanco E;Farré D;Albà MM;Messeguer X;Guigó R

    Nucleic Acids Res

    Tandem chimerism as a means to increase protein complexity in the human genome.

    Parra G;Reymond A;Dabbouseh N;Dermitzakis ET;Castelo R;Thomson TM;Antonarakis SE;Guigó R

    Genome Res

    Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family.

    Castellano S;Lobanov AV;Chapple C;Novoselov SV;Albrecht M;Hua D;Lescure A;Lengauer T;Krol A;Gladyshev VN;Guigó R

    Proc Natl Acad Sci U S A

    Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition.

    Izquierdo JM;Majós N;Bonnal S;Martínez C;Castelo R;Guigó R;Bilbao D;Valcárcel J

    Mol Cell

    EGASP: collaboration through competition to find human genes.

    Guigó R;Reese MG

    Nat Methods

    Gene finding in the chicken genome.

    Eyras E;Reymond A;Castelo R;Bye JM;Camara F;Flicek P;Huckle EJ;Parra G;Shteynberg DD;Wyss C;Rogers J;Antonarakis SE;Birney E;Guigo R;Brent MR

    BMC Bioinformatics

    Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?

    Taskov K;Chapple C;Kryukov GV;Castellano S;Lobanov AV;Korotkov KV;Guigó R;Gladyshev VN

    Nucleic Acids Res

    Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

    Castelo R;Reymond A;Wyss C;Câmara F;Parra G;Antonarakis SE;Guigó R;Eyras E

    Nucleic Acids Res

    Are splicing mutations the most frequent cause of hereditary disease?

    López-Bigas N;Audit B;Ouzounis C;Parra G;Guigó R

    FEBS Lett

    Gene organization features in A/T-rich organisms.

    Szafranski K;Lehmann R;Parra G;Guigo R;Glöckner G

    J Mol Evol

    Comparison of splice sites in mammals and chicken.

    Abril JF;Castelo R;Guigó R

    Genome Res

    Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.

    Jaillon O;Aury JM;Brunet F;Petit JL;Stange-Thomann N;Mauceli E;Bouneau L;Fischer C;Ozouf-Costaz C;Bernot A;Nicaud S;Jaffe D;Fisher S;Lutfalla G;Dossat C;Segurens B;Dasilva C;Salanoubat M;Levy M;Boudet N;Castellano S;Anthouard V;Jubin C;Castelli V;Katinka M;Vacherie B;Biémont C;Skalli Z;Cattolico L;Poulain J;De Berardinis V;Cruaud C;Duprat S;Brottier P;Coutanceau JP;Gouzy J;Parra G;Lardier G;Chapple C;McKernan KJ;McEwan P;Bosak S;Kellis M;Volff JN;Guigó R;Zody MC;Mesirov J;Lindblad-Toh K;Birren B;Nusbaum C;Kahn D;Robinson-Rechavi M;Laudet V;Schachter V;Quétier F;Saurin W;Scarpelli C;Wincker P;Lander ES;Weissenbach J;Roest Crollius H

    Nature

    Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome.

    Castresana J;Guigó R;Albà MM

    J Mol Evol

    Splice site identification by idlBNs.

    Castelo R;Guigó R

    Bioinformatics

    Recent advances in gene structure prediction.

    Brent MR;Guigó R

    Curr Opin Struct Biol

    Comparative analysis of amino acid repeats in rodents and humans.

    Albà MM;Guigó R

    Genome Res

    Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

    Gibbs RA;Weinstock GM;Metzker ML;Muzny DM;Sodergren EJ;Scherer S;Scott G;Steffen D;Worley KC;Burch PE;Okwuonu G;Hines S;Lewis L;DeRamo C;Delgado O;Dugan-Rocha S;Miner G;Morgan M;Hawes A;Gill R;Celera;Holt RA;Adams MD;Amanatides PG;Baden-Tillson H;Barnstead M;Chin S;Evans CA;Ferriera S;Fosler C;Glodek A;Gu Z;Jennings D;Kraft CL;Nguyen T;Pfannkoch CM;Sitter C;Sutton GG;Venter JC;Woodage T;Smith D;Lee HM;Gustafson E;Cahill P;Kana A;Doucette-Stamm L;Weinstock K;Fechtel K;Weiss RB;Dunn DM;Green ED;Blakesley RW;Bouffard GG;De Jong PJ;Osoegawa K;Zhu B;Marra M;Schein J;Bosdet I;Fjell C;Jones S;Krzywinski M;Mathewson C;Siddiqui A;Wye N;McPherson J;Zhao S;Fraser CM;Shetty J;Shatsman S;Geer K;Chen Y;Abramzon S;Nierman WC;Havlak PH;Chen R;Durbin KJ;Egan A;Ren Y;Song XZ;Li B;Liu Y;Qin X;Cawley S;Worley KC;Cooney AJ;D'Souza LM;Martin K;Wu JQ;Gonzalez-Garay ML;Jackson AR;Kalafus KJ;McLeod MP;Milosavljevic A;Virk D;Volkov A;Wheeler DA;Zhang Z;Bailey JA;Eichler EE;Tuzun E;Birney E;Mongin E;Ureta-Vidal A;Woodwark C;Zdobnov E;Bork P;Suyama M;Torrents D;Alexandersson M;Trask BJ;Young JM;Huang H;Wang H;Xing H;Daniels S;Gietzen D;Schmidt J;Stevens K;Vitt U;Wingrove J;Camara F;Mar Albà M;Abril JF;Guigo R;Smit A;Dubchak I;Rubin EM;Couronne O;Poliakov A;Hübner N;Ganten D;Goesele C;Hummel O;Kreitler T;Lee YA;Monti J;Schulz H;Zimdahl H;Himmelbauer H;Lehrach H;Jacob HJ;Bromberg S;Gullings-Handley J;Jensen-Seaman MI;Kwitek AE;Lazar J;Pasko D;Tonellato PJ;Twigger S;Ponting CP;Duarte JM;Rice S;Goodstadt L;Beatson SA;Emes RD;Winter EE;Webber C;Brandt P;Nyakatura G;Adetobi M;Chiaromonte F;Elnitski L;Eswara P;Hardison RC;Hou M;Kolbe D;Makova K;Miller W;Nekrutenko A;Riemer C;Schwartz S;Taylor J;Yang S;Zhang Y;Lindpaintner K;Andrews TD;Caccamo M;Clamp M;Clarke L;Curwen V;Durbin R;Eyras E;Searle SM;Cooper GM;Batzoglou S;Brudno M;Sidow A;Stone EA;Venter JC;Payseur BA;Bourque G;López-Otín C;Puente XS;Chakrabarti K;Chatterji S;Dewey C;Pachter L;Bray N;Yap VB;Caspi A;Tesler G;Pevzner PA;Haussler D;Roskin KM;Baertsch R;Clawson H;Furey TS;Hinrichs AS;Karolchik D;Kent WJ;Rosenbloom KR;Trumbower H;Weirauch M;Cooper DN;Stenson PD;Ma B;Brent M;Arumugam M;Shteynberg D;Copley RR;Taylor MS;Riethman H;Mudunuri U;Peterson J;Guyer M;Felsenfeld A;Old S;Mockrin S;Collins F;Rat Genome Sequencing Project Consortium

    Nature

    Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution.

    Castellano S;Novoselov SV;Kryukov GV;Lescure A;Blanco E;Krol A;Gladyshev VN;Guigó R

    EMBO Rep

    gff2aplot: Plotting sequence comparisons.

    Abril JF;Guigó R;Wiehe T

    Bioinformatics

    Characterization of mammalian selenoproteomes.

    Kryukov GV;Castellano S;Novoselov SV;Lobanov AV;Zehtab O;Guigó R;Gladyshev VN

    Science

    Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster.

    Beltran S;Blanco E;Serras F;Pérez-Villamil B;Guigó R;Artavanis-Tsakonas S;Corominas M

    Proc Natl Acad Sci U S A

    Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.

    Guigo R;Dermitzakis ET;Agarwal P;Ponting CP;Parra G;Reymond A;Abril JF;Keibler E;Lyle R;Ucla C;Antonarakis SE;Brent MR

    Proc Natl Acad Sci U S A

    Comparative gene prediction in human and mouse.

    Parra G;Agarwal P;Abril JF;Wiehe T;Fickett JW;Guigó R

    Genome Res

    Initial sequencing and comparative analysis of the mouse genome.

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    Nature

    The genome sequence of the malaria mosquito Anopheles gambiae.

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    Science

    Sequence and analysis of chromosome 2 of Dictyostelium discoideum.

    Glöckner G;Eichinger L;Szafranski K;Pachebat JA;Bankier AT;Dear PH;Lehmann R;Baumgart C;Parra G;Abril JF;Guigó R;Kumpf K;Tunggal B;Cox E;Quail MA;Platzer M;Rosenthal A;Noegel AA;Dictyostelium Genome Sequencing Consortium

    Nature