Roderic Guigo Lab

Roderic Guigo Lab

Computational biology of RNA processing group

Genomic and functional conservation of lncRNAs: lessons from flies

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

Mammalian Genome

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; Perez-Lluch, S; Guigo, R

Bmc Genomics

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 Research

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

Nature Communications

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

Vlasova, A; Pulido, TH; Camara, F; Ponomarenko, J; Guigo, R

Genes

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 Research & Therapy

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 Research

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 Research

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

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

Nature Communications

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

Nucleic Acids Research

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

Ullrich, Sebastian; Guigo, Roderic

Nucleic Acids Research

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 In Molecular Biology

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC,, Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH FANTOM consortium

Nature Communications

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

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

Computational And Structural Biotechnology Journal

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

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

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

RESEARCH ARTICLE 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 Genetics

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 Structure & Function

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

Pharmacological Research

PyHIST: A Histological Image Segmentation Tool

Munoz-Aguirre, M; Ntasis, VF; Rojas, S; Guigo, R

Plos Computational Biology

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,, 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 GTEx Consortium

Science

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,, Getz G, Dermitzakis ET, Small KS, Stephens M, Xi HS, Im HK, Guigó R, Segrè AV, Stranger BE, Ardlie KG, Lappalainen T GTEx Consortium

Science

Erratum: Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest (BMC biology (2020) 18 1 (90))

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

Bmc Biology

The GTEx Consortium atlas of genetic regulatory effects across human tissues

Aguet, F; Barbeira, AN; Bonazzola, R; Brown, A; Castel, SE; Jo, B; Kasela, S; Kim-Hellmuth, S; Liang, YY; Parsana, P; Flynn, E; Fresard, L; Gamazon, ER; Hamel, AR; He, Y; Hormozdiari, F; Mohammadi, P; Munoz-Aguirre, M; Ardlie, KG; Battle, A; Bonazzola, R; Brown, CD; Cox, N; Dermitzakis, ET; Engelhardt, BE; Garrido-Martin, D; Gay, NR; Getz, G; Guigo, R; Hamel, AR; Handsaker, RE; He, Y; Hoffman, PJ; Hormozdiari, F; Im, HK; Jo, B; Kasela, S; Kashin, S; Kim-Hellmuth, S; Kwong, A; Lappalainen, T; Li, X; Liang, YY; MacArthur, DG; Mohammadi, P; Montgomery, SB; Munoz-Aguirre, M; Rouhana, JM; Hormozdiari, F; Im, HK; Kim-Hellmuth, S; Ardlie, KG; Getz, G; Guigo, R; Im, HK; Lappalainen, T; Montgomery, SB; Im, HK; Lappalainen, T; Lappalainen, T; Anand, S; Gabriel, S; Getz, G; Graubert, A; Hadley, K; Handsaker, RE; Huang, KH; Kashin, S; Li, X; MacArthur, DG; Meier, SR; Nedzel, JL; Balliu, B; Conrad, D; Cotter, DJ; Das, S; de Goede, OM; Eskin, E; Eulalio, TY; Ferraro, NM; Garrido-Martin, D; Gay, NR; Getz, G; Graubert, A; Guigo, R; Hadley, K; Hamel, AR; Handsaker, RE; He, Y; Hoffman, PJ; Hormozdiari, F; Hou, L; Huang, KH; Im, HK; Jo, B; Kasela, S; Kashin, S; Kellis, M; Kim-Hellmuth, S; Kwong, A; Lappalainen, T; Li, X; Li, X; Liang, YY; MacArthur, DG; Mangul, S; Meier, SR; Mohammadi, P; Montgomery, SB; Munoz-Aguirre, M; Nachun, DC; Nedzel, JL; Nguyen, DY; Nobel, AB; Park, Y; Reverter, F; Sabatti, C; Saha, A; Segre, AV; Stephens, M; Strober, BJ; Teran, NA; Todres, E; Vinuela, A; Wang, G; Wen, XQ; Wright, F; Wucher, V; Zou, YX; Ferreira, PG; Li, G; Mele, M; Yeger-Lotem, E; Barcus, ME; Bradbury, D; Krubit, T; McLean, JA; Qi, LQ; Robinson, K; Roche, NV; Smith, AM; Tabor, DE; Undale, A; Bridge, J; Brigham, LE; Foster, BA; Gillard, BM; Hasz, R; Hunter, M; Johns, C; Johnson, M; Karasik, E; Kopen, G; Leinweber, WF; McDonald, A; Moser, MT; Myer, K; Ramsey, KD; Roe, B; Shad, S; Thomas, JA; Walters, G; Washington, M; Wheeler, J; Jewell, SD; Rohrer, DC; Valley, DR; Davis, DA; Mash, DC; Branton, PA; Sobin, L; Barker, LK; Gardiner, HM; Mosavel, M; Siminoff, LA; Flicek, P; Haeussler, M; Juettemann, T; Kent, WJ; Lee, CM; Powell, CC; Rosenbloom, KR; Ruffier, M; Sheppard, D; Taylor, K; Trevanion, SJ; Zerbino, DR; Abell, NS; Akey, J; Chen, L; Demanelis, K; Doherty, JA; Feinberg, AP; Hansen, KD; Hickey, PF; Hou, L; Jasmine, F; Jiang, LH; Kaul, R; Kellis, M; Kibriya, MG; Li, JB; Li, Q; Lin, S; Linder, SE; Montgomery, SB; Oliva, M; Park, Y; Pierce, BL; Rizzardi, LF; Skol, AD; Smith, KS; Snyder, M; Stamatoyannopoulos, J; Tang, H; Wang, M; Carithers, LJ; Guan, P; Koester, SE; Little, AR; Moore, HM; Nierras, CR; Rao, AK; Vaught, JB; Volpi, S

Science

Functional annotation of human long noncoding RNAs via molecular phenotyping (vol 30, pg 1060, 2020)

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

Genome Research

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; Stone C; Smillie J; Edmonds H; Ngatiwai Trust Board

Nature

Expanded encyclopaedias of DNA elements in the human and mouse genomes

, 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, 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 ENCODE Project Consortium

Nature

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

Bmc Biology

A limited set of transcriptional programs define major cell types

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

Genome Research

Functional annotation of human long noncoding RNAs via molecular phenotyping

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

Genome Research

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

Muyas F; Zapata L; Guigó R; Ossowski S

Genome Medicine

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

Molecular Ecology

NEAT1 long isoform is highly expressed in chronic lymphocytic leukemia irrespectively of cytogenetic groups or clinical outcome

Ronchetti D; Favasuli V; Monti P; Cutrona G; Fabris S; Silvestris I; Agnelli L; Colombo M; Menichini P; Matis S; Gentile M; Nurtdinov R; Guigó R; Baldini L; Fronza G; Ferrarini M; Morabito F; Neri A; Taiana E

Noncoding Rna

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

Bou Sleiman M, Frochaux MV, Andreani T, Osman D, Guigo R, Deplancke B

Genome Biology

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

Ullrich S, Guigó R

Nucleic Acids Research

Perspectives on ENCODE

, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM ENCODE Project Consortium

Nature

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

Steward CA, Roovers J, Suner MM, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D, Fitzgerald S, Viola M, Stamberger H, Hamdan FF, Ceulemans B, Leroy P, Nava C, Lepine A, Tapanari E, Keiller D, Abbs S, Sanchis-Juan A, Grozeva D, Rogers AS, Diekhans M, Guigó R, Petryszak R, Minassian BA, Cavalleri G, Vitsios D, Petrovski S, Harrow J, Flicek P, Lucy Raymond F, Lench NJ, Jonghe P, Mudge JM, Weckhuysen S, Sisodiya SM, Frankish A

Npj Genomic Medicine

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

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

Journal Of Molecular Biology

Dynamics of microRNA expression during mouse prenatal development

Rahmanian S, Murad R, Breschi A, Zeng W, Mackiewicz M, Williams B, Davis CA, Roberts B, Meadows S, Moore D, Trout D, Zaleski C, Dobin A, Sei LH, Drenkow J, Scavelli A, Gingeras TR, Wold BJ, Myers RM, Guigó R, Mortazavi A

Genome Research

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry

Terrazas M; Genna V; Portella G; Villegas N; Sánchez D; Arnan C; Pulido-Quetglas C; Johnson R; Guigó R; Brun-Heath I; Aviñó A; Eritja R; Orozco M

Chem

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

Pervouchine D, Popov Y, Berry A, Borsari B, Frankish A, Guigó R

Nucleic Acids Research

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

Bomben, Riccardo; Roisman, Alejandro; D'Agaro, Tiziana; Castellano, Giancarlo; Baumann, Tycho; Delgado, Julio; Lopez-Guillermo, Armando; Zucchetto, Antonella; Dal-Bo, Michele; Bravin, Vanessa; Slavutsky, Irma; Vlasova, Anna; Guigo, Roderic; Martin-Subero, Jose I.; Chapaprieta, Vicente; Beekman, Renee; Martin-Garcia, David; Bea, Silvia; Salaverria, Itziar; Aymerich, Marta; Campo, Elias; Gattei, Valter; Hernandez, Luis;

British Journal Of Haematology

GENCODE reference annotation for the human and mouse genomes

Frankish, Adam; Diekhans, Mark; Ferreira, Anne-Maud; Johnson, Rory; Jungreis, Irwin; Loveland, Jane; Mudge, Jonathan M; Sisu, Cristina; Wright, James; Armstrong, Joel; Barnes, If; Berry, Andrew; Bignell, Alexandra; Sala, Silvia Carbonell; Chrast, Jacqueline; Cunningham, Fiona; Di Domenico, Tomas; Donaldson, Sarah; Fiddes, Ian T; Giron, Carlos Garcia; Gonzalez, Jose Manuel; Grego, Tiago; Hardy, Matthew; Hourlier, Thibaut; Hunt, Toby; Izuogu, Osagie G; Lagarde, Julien; Martin, Fergal J; Martinez, Laura; Mohanan, Shamika; Muir, Paul; Navarro, Fabio C P; Parker, Anne; Pei, Baikang; Pozo, Fernando; Ruffier, Magali; Schmitt, Bianca M; Stapleton, Eloise; Suner, Marie-Marthe; Sycheva, Irina; Uszczynska-Ratajczak, Barbara; Xu, Jinuri; Yates, Andrew; Zerbino, Daniel; Zhang, Yan; Aken, Bronwen; Choudhary, Jyoti S; Gerstein, Mark; Guigo, Roderic; Hubbard, Tim J P; Kellis, Manolis; Paten, Benedict; Reymond, Alexandre; Tress, Michael L; Flicek, Paul

Nucleic Acids Research

SEX DIFFERENCES AT THE MOLECULAR LEVEL: LESSONS FROM THE HUMAN TRANSCRIPTOME

Stranger, Barbara; Oliva, Meritxell; Gamazon, Eric; Reverter, Ferran; Wucher, Valentin; Balliu, Brunilda; Dumitrascu, Bianca; Parsana, Princy; Payne, Anthony; Jo, Brian; Montgomery, Stephen; Battle, Alexis; Ardlie, Kristin; Guigo, Roderic; Engelhardt, Barbara;

European Neuropsychopharmacology

Damage-responsive elements in Drosophila regeneration

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

Genome Research

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Barbeira AN, Dickinson SP, Bonazzola R, Zheng J, Wheeler HE, Torres JM, Torstenson ES, Shah KP, Garcia T, Edwards TL, Stahl EA, Huckins LM,, Nicolae DL, Cox NJ, Im HK GTEx Consortium

Nature Communications

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

Castel SE, Cervera A, Mohammadi P, Aguet F, Reverter F, Wolman A, Guigo R, Iossifov I, Vasileva A, Lappalainen T

Nature Genetics

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

Uszczynska-Ratajczak B, Lagarde J, Frankish A, Guigó R, Johnson R

Nature Reviews Genetics

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

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

Plos Computational Biology

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Ma S, Avanesov AS, Porter E, Lee BC, Mariotti M, Zemskaya N, Guigo R, Moskalev AA, Gladyshev VN

AGING CELL

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia

Beekman, Renee; Chapaprieta, Vicente; Russinol, Nuria; Vilarrasa-Blasi, Roser; Verdaguer-Dot, Nuria; Martens, Joost H. A.; Duran-Ferrer, Marti; Kulis, Marta; Serra, Francois; Javierre, Biola M.; Wingett, Steven W.; Clot, Guillem; Queiros, Ana C.; Castellano, Giancarlo; Blanc, Julie; Gut, Marta; Merkel, Angelika; Heath, Simon; Vlasova, Anna; Ullrich, Sebastian; Palumbo, Emilio; Enjuanes, Anna; Martin-Garcia, David; Bea, Silvia; Pinyol, Magda; Aymerich, Marta; Royo, Romina; Puiggros, Montserrat; Torrents, David; Datta, Avik; Lowy, Ernesto; Kostadima, Myrto; Roller, Masa; Clarke, Laura; Flicek, Paul; Agirre, Xabier; Prosper, Felipe; Baumann, Tycho; Delgado, Julio; Lopez-Guillermo, Armando; Fraser, Peter; Yaspo, Marie-Laure; Guigo, Roderic; Siebert, Reiner; Marti-Renom, Marc A.; Puente, Xose S.; Lopez-Otin, Carlos; Gut, Ivo; Stunnenberg, Hendrik G.; Campo, Elias; Martin-Subero, Jose I.;

Nature Medicine

The molecular basis of the cellular taxonomy of the human body

Breschi, Alessandra; Davis, Carrie; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D.; Vlasova, Anna; Dobin, Alex; Zaleski, Chris; Drenkow, Jorg; Danyko, Cassidy; Scavelli, Alexandra; Munoz, Manuel; Garrido, Diego; Reverter, Ferran; Gingeras, Thomas R.; Guigo, Roderic;

Human Genomics

The discovery potential of RNA processing profiles

Pages, Amadis; Dotu, Ivan; Pallares-Albanell, Joan; Marti, Eulalia; Guigo, Roderic; Eyras, Eduardo

Nucleic Acids Research

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

Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R

Nature Communications

Using geneid to Identify Genes

Alioto T; Blanco E; Parra G; Guigó R

Current Protocols In Bioinformatics

Selenoprofiles: A Computational Pipeline for Annotation of Selenoproteins

Santesmasses D, Mariotti M, Guigó R

Methods In Molecular Biology

The discovery potential of RNA processing profiles

Pagès A, Dotu I, Pallarès-Albanell J, Martí E, Guigó R, Eyras E

Nucleic Acids Research

Recent advances in functional genome analysis

Guigo R, de Hoon M

F1000research

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

Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R

Nature Genetics

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

Yang F, Wang J,, Pierce BL, Chen LS GTEx Consortium

Genome Research

Genetic effects on gene expression across human tissues

, Battle A, Brown CD, Engelhardt BE, Montgomery SB GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lead analysts:, Laboratory, Data Analysis &Coordinating Center (LDACC):, NIH program management:, Biospecimen collection:, Pathology:, eQTL manuscript working group:

Nature

Dynamic landscape and regulation of RNA editing in mammals

Tan MH; Li Q; Shanmugam R; Piskol R; Kohler J; Young AN; Liu KI; Zhang R; Ramaswami G; Ariyoshi K; Gupte A; Keegan LP; George CX; Ramu A; Huang N; Pollina EA; Leeman DS; Rustighi A; Goh YPS; Aguet F; Ardlie KG; Cummings BB; Gelfand ET; Getz G; Hadley K; Handsaker RE; Huang KH; Kashin S; Karczewski KJ; Lek M; Li X; MacArthur DG; Nedzel JL; Nguyen DT; Noble MS; Segrè AV; Trowbridge CA; Tukiainen T; Abell NS; Balliu B; Barshir R; Basha O; Battle A; Bogu GK; Brown A; Brown CD; Castel SE; Chen LS; Chiang C; Conrad DF; Cox NJ; Damani FN; Davis JR; Delaneau O; Dermitzakis ET; Engelhardt BE; Eskin E; Ferreira PG; Frésard L; Gamazon ER; Garrido-Martín D; Gewirtz ADH; Gliner G; Gloudemans MJ; Guigo R; Hall IM; Han B; He Y; Hormozdiari F; Howald C; Im HK; Jo B; Kang EY; Kim Y; Kim-Hellmuth S; Lappalainen T; Li G; Li X; Liu B; Mangul S; McCarthy MI; McDowell IC; Mohammadi P; Monlong J; Montgomery SB; Muñoz-Aguirre M; Ndungu AW; Nicolae DL; Nobel AB; Oliva M; Ongen H; Palowitch JJ; Panousis N; Papasaikas P; Park Y; Parsana P; Payne AJ; Peterson CB; Quan J; Reverter F; Sabatti C; Saha A; Sammeth M; Scott AJ; Shabalin AA; Sodaei R; Stephens M; Stranger BE; Strober BJ; Sul JH; Tsang EK; Urbut S; Van De Bunt M; Wang G; Wen X; Wright FA; Xi HS; Yeger-Lotem E; Zappala Z; Zaugg JB; Zhou Y-H; Akey JM; Bates D; Chan J; Claussnitzer M; Demanelis K; Diegel M; Doherty JA; Feinberg AP; Fernando MS; Halow J; Hansen KD; Haugen E; Hickey PF; Hou L; Jasmine F; Jian R; Jiang L; Johnson A; Kaul R; Kellis M; Kibriya MG; Lee K; Lin J; Lin S; Linder S; Linke C; Liu Y; Maurano MT; Molinie B; Nelson J; Neri FJ; Park Y; Pierce BL; Rinaldi NJ; Rizzardi LF; Sandstrom R; Skol A; Smith KS; Snyder MP; Stamatoyannopoulos J; Tang H; Wang L; Wang M; Van Wittenberghe N; Wu F; Nierras CR; Branton PA; Carithers LJ; Guan P; Moore HM; Rao A; Vaught JB; Gould SE; Lockart NC; Martin C; Struewing JP; Volpi S; Addington AM; Koester SE; Little AR; Brigham LE; Hasz R; Hunter M; Johns C; Johnson M; Kopen G; Leinweber WF; Lonsdale JT; McDonald A; Mestichelli B; Myer K; Roe B; Salvatore M; Shad S; Thomas JA; Walters G; Washington M; Wheeler J; Bridge J; Foster BA; Gillard BM; Karasik E; Kumar R; Miklos M; Moser MT; Jewell SD; Montroy RG; Rohrer DC; Valley DR; Davis DA; Mash DC; Undale AH; Smith AM; Tabor DE; Roche NV; McLean JA; Vatanian N; Robinson KL; Sobin L; Barcus ME; Valentino KM; Qi L; Hunter S; Hariharan P; Singh S; Um KS; Matose T; Tomaszewski MM; Barker LK; Mosavel M; Siminoff LA; Traino HM; Flicek P; Juettemann T; Ruffier M; Sheppard D; Taylor K; Trevanion SJ; Zerbino DR; Craft B; Goldman M; Haeussler M; Kent WJ; Lee CM; Paten B; Rosenbloom KR; Vivian J; Zhu J; Chawla A; Del Sal G; Peltz G; Brunet A; Samuel CE; O'Connell MA; Walkley CR; Nishikura K; Li JB; GTEx Consortium

Nature

Landscape of X chromosome inactivation across human tissues

Tukiainen T; Villani A-C; Yen A; Rivas MA; Marshall JL; Satija R; Aguirre M; Gauthier L; Fleharty M; Kirby A; Cummings BB; Castel SE; Karczewski KJ; Aguet F; Byrnes A; Gelfand ET; Getz G; Hadley K; Handsaker RE; Huang KH; Kashin S; Lek M; Li X; Nedzel JL; Nguyen DT; Noble MS; Segrè AV; Trowbridge CA; Abell NS; Balliu B; Barshir R; Basha O; Battle A; Bogu GK; Brown A; Brown CD; Chen LS; Chiang C; Conrad DF; Cox NJ; Damani FN; Davis JR; Delaneau O; Dermitzakis ET; Engelhardt BE; Eskin E; Ferreira PG; Frésard L; Gamazon ER; Garrido-Martín D; Gewirtz ADH; Gliner G; Gloudemans MJ; Guigo R; Hall IM; Han B; He Y; Hormozdiari F; Howald C; Im HK; Jo B; Kang EY; Kim Y; Kim-Hellmuth S; Lappalainen T; Li G; Li X; Liu B; Mangul S; McCarthy MI; McDowell IC; Mohammadi P; Monlong J; Montgomery SB; Muñoz-Aguirre M; Ndungu AW; Nicolae DL; Nobel AB; Oliva M; Ongen H; Palowitch JJ; Panousis N; Papasaikas P; Park Y; Parsana P; Payne AJ; Peterson CB; Quan J; Reverter F; Sabatti C; Saha A; Sammeth M; Scott AJ; Shabalin AA; Sodaei R; Stephens M; Stranger BE; Strober BJ; Sul JH; Tsang EK; Urbut S; Van De Bunt M; Wang G; Wen X; Wright FA; Xi HS; Yeger-Lotem E; Zappala Z; Zaugg JB; Zhou Y-H; Akey JM; Bates D; Chan J; Claussnitzer M; Demanelis K; Diegel M; Doherty JA; Feinberg AP; Fernando MS; Halow J; Hansen KD; Haugen E; Hickey PF; Hou L; Jasmine F; Jian R; Jiang L; Johnson A; Kaul R; Kellis M; Kibriya MG; Lee K; Li JB; Li Q; Lin J; Lin S; Linder S; Linke C; Liu Y; Maurano MT; Molinie B; Nelson J; Neri FJ; Park Y; Pierce BL; Rinaldi NJ; Rizzardi LF; Sandstrom R; Skol A; Smith KS; Snyder MP; Stamatoyannopoulos J; Tang H; Wang L; Wang M; Van Wittenberghe N; Wu F; Zhang R; Nierras CR; Branton PA; Carithers LJ; Guan P; Moore HM; Rao A; Vaught JB; Gould SE; Lockart NC; Martin C; Struewing JP; Volpi S; Addington AM; Koester SE; Little AR; Brigham LE; Hasz R; Hunter M; Johns C; Johnson M; Kopen G; Leinweber WF; Lonsdale JT; McDonald A; Mestichelli B; Myer K; Roe B; Salvatore M; Shad S; Thomas JA; Walters G; Washington M; Wheeler J; Bridge J; Foster BA; Gillard BM; Karasik E; Kumar R; Miklos M; Moser MT; Jewell SD; Montroy RG; Rohrer DC; Valley DR; Davis DA; Mash DC; Undale AH; Smith AM; Tabor DE; Roche NV; McLean JA; Vatanian N; Robinson KL; Sobin L; Barcus ME; Valentino KM; Qi L; Hunter S; Hariharan P; Singh S; Um KS; Matose T; Tomaszewski MM; Barker LK; Mosavel M; Siminoff LA; Traino HM; Flicek P; Juettemann T; Ruffier M; Sheppard D; Taylor K; Trevanion SJ; Zerbino DR; Craft B; Goldman M; Haeussler M; Kent WJ; Lee CM; Paten B; Rosenbloom KR; Vivian J; Zhu J; Regev A; Ardlie KG; Hacohen N; MacArthur DG; GTEx Consortium

Nature

The impact of rare variation on gene expression across tissues

Li X; Kim Y; Tsang EK; Davis JR; Damani FN; Chiang C; Hess GT; Zappala Z; Strober BJ; Scott AJ; Li A; Ganna A; Bassik MC; Merker JD; Aguet F; Ardlie KG; Cummings BB; Gelfand ET; Getz G; Hadley K; Handsaker RE; Huang KH; Kashin S; Karczewski KJ; Lek M; Li X; MacArthur DG; Nedzel JL; Nguyen DT; Noble MS; Segrè AV; Trowbridge CA; Tukiainen T; Abell NS; Balliu B; Barshir R; Basha O; Bogu GK; Brown A; Brown CD; Castel SE; Chen LS; Conrad DF; Cox NJ; Delaneau O; Dermitzakis ET; Engelhardt BE; Eskin E; Ferreira PG; Frésard L; Gamazon ER; Garrido-Martín D; Gewirtz ADH; Gliner G; Gloudemans MJ; Guigo R; Hall IM; Han B; He Y; Hormozdiari F; Howald C; Im HK; Jo B; Kang EY; Kim-Hellmuth S; Lappalainen T; Li G; Liu B; Mangul S; McCarthy MI; McDowell IC; Mohammadi P; Monlong J; Muñoz-Aguirre M; Ndungu AW; Nicolae DL; Nobel AB; Oliva M; Ongen H; Palowitch JJ; Panousis N; Papasaikas P; Park Y; Parsana P; Payne AJ; Peterson CB; Quan J; Reverter F; Sabatti C; Saha A; Sammeth M; Shabalin AA; Sodaei R; Stephens M; Stranger BE; Sul JH; Urbut S; Van De Bunt M; Wang G; Wen X; Wright FA; Xi HS; Yeger-Lotem E; Zaugg JB; Zhou Y-H; Akey JM; Bates D; Chan J; Claussnitzer M; Demanelis K; Diegel M; Doherty JA; Feinberg AP; Fernando MS; Halow J; Hansen KD; Haugen E; Hickey PF; Hou L; Jasmine F; Jian R; Jiang L; Johnson A; Kaul R; Kellis M; Kibriya MG; Lee K; Billy Li J; Li Q; Lin J; Lin S; Linder S; Linke C; Liu Y; Maurano MT; Molinie B; Nelson J; Neri FJ; Park Y; Pierce BL; Rinaldi NJ; Rizzardi LF; Sandstrom R; Skol A; Smith KS; Snyder MP; Stamatoyannopoulos J; Tang H; Wang L; Wang M; Van Wittenberghe N; Wu F; Zhang R; Nierras CR; Branton PA; Carithers LJ; Guan P; Moore HM; Rao A; Vaught JB; Gould SE; Lockart NC; Martin C; Struewing JP; Volpi S; Addington AM; Koester SE; Little AR; Brigham LE; Hasz R; Hunter M; Johns C; Johnson M; Kopen G; Leinweber WF; Lonsdale JT; McDonald A; Mestichelli B; Myer K; Roe B; Salvatore M; Shad S; Thomas JA; Walters G; Washington M; Wheeler J; Bridge J; Foster BA; Gillard BM; Karasik E; Kumar R; Miklos M; Moser MT; Jewell SD; Montroy RG; Rohrer DC; Valley DR; Davis DA; Mash DC; Undale AH; Smith AM; Tabor DE; Roche NV; McLean JA; Vatanian N; Robinson KL; Sobin L; Barcus ME; Valentino KM; Qi L; Hunter S; Hariharan P; Singh S; Sung Um K; Matose T; Tomaszewski MM; Barker LK; Mosavel M; Siminoff LA; Traino HM; Flicek P; Juettemann T; Ruffier M; Sheppard D; Taylor K; Trevanion SJ; Zerbino DR; Craft B; Goldman M; Haeussler M; Kent WJ; Lee CM; Paten B; Rosenbloom KR; Vivian J; Zhu J; Battle A; Montgomery SB; GTEx Consortium

Nature

Comparative transcriptomics in human and mouse

Breschi A, Gingeras TR, Guigó R

Nature Reviews Genetics

LncATLAS database for subcellular localization of long noncoding RNAs

Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido T, Guigo R, Johnson R

Rna

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

Rendon-Anaya, Martha; Montero-Vargas, Josaphat M; Saburido-Alvarez, Soledad; Vlasova, Anna; Capella-Gutierrez, Salvador; Ordaz-Ortiz, Jose Juan; Mario Aguilar, O; Vianello-Brondani, Rosana P; Santalla, Marta; Delaye, Luis; Gabaldon, Toni; Gepts, Paul; Winkler, Robert; Guigo, Roderic; Delgado-Salinas, Alfonso; Herrera-Estrella, Alfredo

Genome Biology

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

Altimiras F, Uszczynska-Ratajczak B, Camara F, Vlasova A, Palumbo E, Newhouse S, Deacon RM, Farias LA, Hurley MJ, Loyola DE, Vásquez RA, Dobson R, Guigó R, Cogram P

Frontiers In Aging Neuroscience

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 Computational Biology

Data Resources for Human Functional Genomics

Ardlie KG, Guigó R

Current Opinion In Systems Biology

Computational identification of the selenocysteine tRNA (tRNASec) in genomes

Santesmasses D, Mariotti M, Guigó R

Plos Computational Biology

Ten Simple Rules on How to Organize a Scientific Retreat

Ponomarenko, Julia; Garrido, Romina; Guigo, Roderic;

PLoS Computational Biology

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

Lanzós A, Carlevaro-Fita J, Mularoni L, Reverter F, Palumbo E, Guigó R, Johnson R

Scientific Reports

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A,, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS BLUEPRINT Consortium

Genome Biology

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

Rodríguez-Martín B, Palumbo E, Marco-Sola S, Griebel T, Ribeca P, Alonso G, Rastrojo A, Aguado B, Guigó R, Djebali S

Bmc Genomics

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC,, Engelhardt BE, Battle A GTEx Consortium

Genome Research

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

Abascal F; Corvelo A; Cruz F; Villanueva-Cañas JL; Vlasova A; Marcet-Houben M; Martínez-Cruz B; Cheng JY; Prieto P; Quesada V; Quilez J; Li G; García F; Rubio-Camarillo M; Frias L; Ribeca P; Capella-Gutiérrez S; Rodríguez JM; Câmara F; Lowy E; Cozzuto L; Erb I; Tress ML; Rodriguez-Ales JL; Ruiz-Orera J; Reverter F; Casas-Marce M; Soriano L; Arango JR; Derdak S; Galán B; Blanc J; Gut M; Lorente-Galdos B; Andrés-Nieto M; López-Otín C; Valencia A; Gut I; García JL; Guigó R; Abascal F; Corvelo A; Cruz F; Villanueva-Cañas JL; Vlasova A; Marcet-Houben M; Martínez-Cruz B; Cheng JY; Prieto P; Quesada V

Genome Biology

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

Astle WJ, Elding H, Jiang T, Allen D, Ruklisa D, Mann AL, Mead D, Bouman H, Riveros-Mckay F, Kostadima MA, Lambourne JJ, Sivapalaratnam S, Downes K, Kundu K, Bomba L, Berentsen K, Bradley JR, Daugherty LC, Delaneau O, Freson K, Garner SF, Grassi L, Guerrero J, Haimel M, Janssen-Megens EM, Kaan A, Kamat M, Kim B, Mandoli A, Marchini J, Martens JHA, Meacham S, Megy K, O'Connell J, Petersen R, Sharifi N, Sheard SM, Staley JR, Tuna S, van der Ent M, Walter K, Wang SY, Wheeler E, Wilder SP, Iotchkova V, Moore C, Sambrook J, Stunnenberg HG, Di Angelantonio E, Kaptoge S, Kuijpers TW, Carrillo-de-Santa-Pau E, Juan D, Rico D, Valencia A, Chen L, Ge B, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yang Y, Guigo R, Beck S, Paul DS, Pastinen T, Bujold D, Bourque G, Frontini M, Danesh J, Roberts DJ, Ouwehand WH, Butterworth AS, Soranzo N

CELL

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N

Cell

Selenoprotein Gene Nomenclature

Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Sandeep Prabhu K, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonovi? M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y

JOURNAL OF BIOLOGICAL CHEMISTRY

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 Biology

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,, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M GEUVADIS Consortium

Scientific Reports

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

Molecular Biology And Evolution

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

Nature Communications

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 Biology

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 J; Gómez-Garrido J; Carreté L; Bello X; Gut M; Gut I; Marcet-Houben M; Forn-Cuní G; Galán B; García J; Abal-Fabeiro J; Pardo B; Taboada X; Fernández C; Vlasova A; Hermoso-Pulido A; Guigó R; Álvarez-Dios J; Gómez-Tato A; Viñas A; Maside X; Gabaldón T; Novoa B; Bouza C; Alioto T; Martínez P

Dna Research

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

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

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

Genome Biology

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

Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection (vol 112, pg 14936, 2015)

Mesquita, Rafael D.; Vionette-Amaral, Raquel J.; Lowenberger, Carl; Rivera-Pomar, Rolando; Monteiro, Fernando A.; Minx, Patrick; Spieth, John; Carvalho, A. Bernardo; Panzera, Francisco; Lawson, Daniel; Torres, Andre Q.; Ribeiro, Jose M. C.; Sorgine, Marcos H. F.; Waterhouse, Robert M.; Montague, Michael J.; Abad-Franch, Fernando; Alves-Bezerra, Michele; Amaral, Laurence R.; Araujo, HelenaM.; Araujo, Ricardo N.; Aravind, L.; Atella, Georgia C.; Azambuja, Patricia; Berni, Mateus; Bittencourt-Cunha, Paula R.; Braz, Gloria R. C.; Calderon-Fernandez, Gustavo; Carareto, Claudia M. A.; Christensen, Mikkel B.; Costa, Igor R.; Costa, Samara G.; Dansa, Marilvia; Daumas-Filho, Carlos R. O.; De-Paula, Iron F.; Dias, Felipe A.; Dimopoulos, George; Emrich, Scott J.; Esponda-Behrens, Natalia; Fampa, Patricia; Fernandez-Medina, Rita D.; da Fonseca, Rodrigo N.; Fontenele, Marcio; Fronick, Catrina; Fulton, Lucinda A.; Gandara, Ana Caroline; Garcia, Eloi S.; Genta, Fernando A.; Giraldo-Calderon, Gloria I.; Gomes, Bruno; Gondim, Katia C.; Granzotto, Adriana; Guarneri, Alessandra A.; Guigo, Roderic; Harry, Myriam; Hughes, Daniel S. T.; Jablonka, Willy; Jacquin-Joly, Emmanuelle; Juarez, M. Patricia; Koerich, Leonardo B.; Lange, Angela B.; Latorre-Estivalis, Jose Manuel; Lavore, Andres; Lawrence, Gena G.; Lazoski, Cristiano; Lazzari, Claudio R.; Lopes, Raphael R.; Lorenzo, Marcelo G.; Lugon, Magda D.; Majerowicz, David; Marcet, Paula L.; Mariotti, Marco; Masuda, Hatisaburo; Megy, Karine; Melo, Ana C. A.; Missirlis, Fanis; Mota, Theo; Noriega, Fernando G.; Nouzova, Marcela; Nunes, Rodrigo D.; Oliveir, Raquel L. L.; Oliveira-Silveira, Gilbert; Ons, Sheila; Orchard, Ian; Pagola, Lucia; Paiva-Silva, Gabriela O.; Pascual, Agustina; Pavan, Marcio G.; Pedrini, Nicolas; Peixoto, Alexandre A.; Pereira, Marcos H.; Pike, Andrew; Polycarpo, Carla; Prosdocimi, Francisco; Ribeiro-Rodrigues, Rodrigo; Robertson, Hugh M.; Salerno, Ana Paula; Salmon, Didier; Santesmasses, Didac; Schama, Renata; Seabra-Junior, Eloy S.; Silva-Cardoso, Livia; Silva-Neto, Mario A. C.; Souza-Gomes, Matheus; Sterkel, Marcos; Taracena, Mabel L.; Tojo, Marta; Tu, Zhijian Jake; Tubio, Jose M. C.; Ursic-Bedoya, Raul; Venancio, Thiago M.; Walter-Nuno, Ana Beatriz; Wilson, Derek; Warren, Wesley C.; Wilson, Richard K.; Huebner, Erwin; Dotson, Ellen M.; Oliveira, Pedro L.;

Proceedings Of The National Academy Of Sciences Of The United States Of America

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

Vlasova, Anna; Capella-Gutierrez, Salvador; Rendon-Anaya, Martha; Hernandez-Onate, Miguel; Minoche, Andre E; Erb, Ionas; Camara, Francisco; Prieto-Barja, Pablo; Corvelo, Andre; Sanseverino, Walter; Westergaard, Gaston; Dohm, Juliane C; Pappas, Georgios J, Jr; Saburido-Alvarez, Soledad; Kedra, Darek; Gonzalez, Irene; Cozzuto, Luca; Gomez-Garrido, Jessica; Aguilar-Moron, Maria A; Andreu, Nuria; Mario Aguilar, O; Garcia-Mas, Jordi; Zehnsdorf, Maik; Vazquezi, Martin P; Delgado-Salinas, Alfonso; Delaye, Luis; Lowy, Ernesto; Mentaberry, Alejandro; Vianello-Brondani, Rosana P; Luis Garcia, Jose; Alioto, Tyler; Sanchez, Federico; Himmelbauer, Heinz; Santalla, Marta; Notredame, Cedric; Gabaldon, Toni; Herrera-Estrella, Alfredo; Guigo, Roderic

Genome Biology

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

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

Cell Reports

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 Biochemistry And Molecular Biology

Evolution of selenophosphate synthetase

Mariotti M; Santesmasses D; Guigó R

Selenium: Its Molecular Biology And Role In Human Health, Fourth Edition

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

Journal Of Molecular And Cellular Cardiology

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

Proceedings Of The National Academy Of Sciences Of The United States Of America

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

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

Proceedings Of The National Academy Of Sciences Of The United States Of America

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

Nature Genetics

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

Carithers, Latarsha J.; Ardlie, Kristin; Barcus, Mary; Branton, Philip A.; Britton, Angela; Buia, Stephen A.; Compton, Carolyn C.; DeLuca, David S.; Peter-Demchok, Joanne; Gelfand, Ellen T.; Guan, Ping; Korzeniewski, Greg E.; Lockhart, Nicole C.; Rabiner, Chana A.; Rao, Abhi K.; Robinson, Karna L.; Roche, Nancy V.; Sawyer, Sherilyn J.; Segre, Ayellet V.; Shive, Charles E.; Smith, Anna M.; Sobin, Leslie H.; Undale, Anita H.; Valentino, Kimberly M.; Vaught, Jim; Young, Taylor R.; Moore, Helen M.;GTEx Consortium

Biopreservation and Biobanking

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

Mariotti, Marco; Santesmasses, Didac; Capella-Gutierrez, Salvador; Mateo, Andrea; Arnan, Carme; Johnson, Rory; D'Aniello, Salvatore; Yim, Sun Hee; Gladyshev, Vadim N; Serras, Florenci; Corominas, Montserrat; Gabaldon, Toni; Guigo, Roderic

Genome Research

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

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

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,, Wright FA, Lappalainen T, Calvo M, Getz G, Dermitzakis ET, Ardlie KG, Guigó R GTEx Consortium

Science

Human genomics

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,, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG GTEx Consortium, Geuvadis Consortium

SCIENCE

Human genomics

GTEx Consortium

Science

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

Pierson, Emma; Koller, Daphne; Battle, Alexis; Mostafavi, Sara;GTEx Consortium

PLoS Computational Biology

The genomes of two key bumblebee species with primitive eusocial organization

Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJ, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MM, Blaxter ML, Bourke AF, Brown MJ, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FC, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HM, Leask M, Lockett GA, Mallon EB, Antonio DS, Marxer M, Meeus I, Moritz RF, Nair A, Näpflin K, Nissen I, Niu J, Nunes FM, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZL, Soares MP, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KK, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC

Genome Biology

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

Molecular Ecology

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

European Heart Journal

Prescribing splicing

Guigo, Roderic; Valcarcel, Juan;

Science

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

Nature Communications

Principles of regulatory information conservation between mouse and human

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B,, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP mouse ENCODE Consortium

Nature

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

The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

Chipman, Ariel D; Ferrier, David E K; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S T; Schroeder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C; Alonso, Claudio R; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C J; Blankenburg, Kerstin P; Brites, Daniela; Capella-Gutierrez, Salvador; Coyle, Marcus; Dearden, Peter K; Du Pasquier, Louis; Duncan, Elizabeth J; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D; Extavour, Cassandra G; Francisco, Liezl; Gabaldon, Toni; Gillis, William J; Goodwin-Horn, Elizabeth A; Green, Jack E; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J P; Gubbala, Sai; Guigo, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H L; Hunn, Julia P; Hunnekuhl, Vera S; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N; Jiggins, Francis M; Jones, Tamsin E; Kaiser, Tobias S; Kalra, Divya; Kenny, Nathan J; Korchina, Viktoriya; Kovar, Christie L; Kraus, F Bernhard; Lapraz, Francois; Lee, Sandra L; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C; Robertson, Helen E; Robertson, Hugh M; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sanchez-Gracia, Alejandro; Scherer, Steven E; Schurko, Andrew M; Siggens, Kenneth W; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M; Willis, Judith H; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M; Worley, Kim C; Gibbs, Richard A; Akam, Michael; Richards, Stephen

Plos Biology

Transcriptional Signatures of Viral Control in HIV-1 Infected South African Women

Gentle, Nikki L.; Djebali, Sarah; Martinson, Neil A.; Spencer, David; Guigo, Roderic; Tiemessen, Caroline T.;

Aids Research And Human Retroviruses

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

Nature Communications

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

Kellis, Manolis; Wold, Barbara; Snyder, Michael P.; Bernstein, Bradley E.; Kundaje, Anshul; Marinov, Georgi K.; Ward, Lucas D.; Birney, Ewan; Crawford, Gregory E.; Dekker, Job; Dunham, Ian; Elnitski, Laura L.; Farnham, Peggy J.; Feingold, Elise A.; Gerstein, Mark; Giddings, Morgan C.; Gilbert, David M.; Gingeras, Thomas R.; Green, Eric D.; Guigo, Roderic; Hubbard, Tim; Kent, Jim; Lieb, Jason D.; Myers, Richard M.; Pazin, Michael J.; Ren, Bing; Stamatoyannopoulos, John; Weng, Zhiping; White, Kevin P.; Hardison, Ross C.;

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants

Greger L, Su J, Rung J, Ferreira PG,, Lappalainen T, Dermitzakis ET, Brazma A Geuvadis consortium

Plos One

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

Johnson R, Guigó R

Rna

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

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Ferreira, Pedro G; Jares, Pedro; Rico, Daniel; Gomez-Lopez, Gonzalo; Villamor, Neus; Ecker, Simone; Gonzalez-Perez, Abel; Knowles, David G; Monlong, Jean; Johnson, Rory; Quesada, Victor; Djebali, Sarah; Papasaikas, Panagiotis; Lopez-Guerra, Monica; Colomer, Dolors; Royo, Cristina; Cazorla, Maite; Pinyol, Magda; Clot, Guillem; Aymerich, Marta; Rozman, Maria; Kulis, Marta; Tamborero, David; Gouin, Anais; Blanc, Julie; Gut, Marta; Gut, Ivo; Puente, Xose S; Pisano, David G; Ignacio Martin-Subero, Jose; Lopez-Bigas, Nuria; Lopez-Guillermo, Armando; Valencia, Alfonso; Lopez-Otin, Carlos; Campo, Elias; Guigo, Roderic

Genome Research

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,, 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 HGSC production teams, Honey Bee Genome Sequencing Consortium

Bmc Genomics

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

Romagne, Frederic; Santesmasses, Didac; White, Louise; Sarangi, Gaurab K; Mariotti, Marco; Huebler, Ron; Weihmann, Antje; Parra, Genis; Gladyshev, Vadim N; Guigo, Roderic; Castellano, Sergi

Nucleic Acids Research

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

Alioto T; Picardi E; Guigó R; Pesole G

Biomed Research International

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

Nature Methods

Assessment of transcript reconstruction methods for RNA-seq

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

Nature Methods

Topoisomerase II regulates yeast genes with singular chromatin architectures

Nikolaou, Christoforos; Bermudez, Ignacio; Manichanh, Chaysavanh; Garcia-Martinez, Jose; Guigo, Roderic; Perez-Ortin, Jose E; Roca, Joaquim

NUCLEIC ACIDS RESEARCH

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

't Hoen, Peter A. C.; Friedlaender, Marc R.; Almloef, Jonas; Sammeth, Michael; Pulyakhina, Irina; Anvar, Seyed Yahya; Laros, Jeroen F. J.; Buermans, Henk P. J.; Karlberg, Olof; Brannvall, Mathias; den Dunnen, Johan T.; van Ommen, Gert-Jan B.; Gut, Ivo G.; Guigo, Roderic; Estivill, Xavier; Syvanen, Ann-Christine; Dermitzakis, Emmanouil T.; Lappalainen, Tuuli;GEUVADIS Consortium

Nature Biotechnology

Improving data and knowledge management to better integrate health care and research

Cases, M; Furlong, L I; Albanell, J; Altman, R B; Bellazzi, R; Boyer, S; Brand, A; Brookes, A J; Brunak, S; Clark, T W; Gea, J; Ghazal, P; Graf, N; Guigo, R; Klein, T E; Lopez-Bigas, N; Maojo, V; Mons, B; Musen, M; Oliveira, J L; Rowe, A; Ruch, P; Shabo, A; Shortliffe, E H; Valencia, A; van der Lei, J; Mayer, M A; Sanz, F

Journal Of Internal Medicine

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,, 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 Geuvadis Consortium

Nature

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

Duran, Elisa; Djebali, Sarah; Gonzalez, Santi; Flores, Oscar; Mercader, Josep Maria; Guigo, Roderic; Torrents, David; Soler-Lopez, Montserrat; Orozco, Modesto

Nucleic Acids Research

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

Mariotti M, Lobanov AV, Guigo R, Gladyshev VN

NUCLEIC ACIDS RESEARCH

The Genotype-Tissue Expression (GTEx) project

Lonsdale, John; Thomas, Jeffrey; Salvatore, Mike; Phillips, Rebecca; Lo, Edmund; Shad, Saboor; Hasz, Richard; Walters, Gary; Garcia, Fernando; Young, Nancy; Foster, Barbara; Moser, Mike; Karasik, Ellen; Gillard, Bryan; Ramsey, Kimberley; Sullivan, Susan; Bridge, Jason; Magazine, Harold; Syron, John; Fleming, Johnelle; Siminoff, Laura; Traino, Heather; Mosavel, Maghboeba; Barker, Laura; Jewell, Scott; Rohrer, Dan; Maxim, Dan; Filkins, Dana; Harbach, Philip; Cortadillo, Eddie; Berghuis, Bree; Turner, Lisa; Hudson, Eric; Feenstra, Kristin; Sobin, Leslie; Robb, James; Branton, Phillip; Korzeniewski, Greg; Shive, Charles; Tabor, David; Qi, Liqun; Groch, Kevin; Nampally, Sreenath; Buia, Steve; Zimmerman, Angela; Smith, Anna; Burges, Robin; Robinson, Karna; Valentino, Kim; Bradbury, Deborah; Cosentino, Mark; Diaz-Mayoral, Norma; Kennedy, Mary; Engel, Theresa; Williams, Penelope; Erickson, Kenyon; Ardlie, Kristin; Winckler, Wendy; Getz, Gad; DeLuca, David; MacArthur, Daniel; Kellis, Manolis; Thomson, Alexander; Young, Taylor; Gelfand, Ellen; Donovan, Molly; Meng, Yan; Grant, George; Mash, Deborah; Marcus, Yvonne; Basile, Margaret; Liu, Jun; Zhu, Jun; Tu, Zhidong; Cox, Nancy J.; Nicolae, Dan L.; Gamazon, Eric R.; Im, Hae Kyung; Konkashbaev, Anuar; Pritchard, Jonathan; Stevens, Matthew; Flutre, Timothee; Wen, Xiaoquan; Dermitzakis, Emmanouil T.; Lappalainen, Tuuli; Guigo, Roderic; Monlong, Jean; Sammeth, Michael; Koller, Daphne; Battle, Alexis; Mostafavi, Sara; McCarthy, Mark; Rivas, Manual; Maller, Julian; Rusyn, Ivan; Nobel, Andrew; Wright, Fred; Shabalin, Andrey; Feolo, Mike; Sharopova, Nataliya; Sturcke, Anne; Paschal, Justin; Anderson, James M.; Wilder, Elizabeth L.; Derr, Leslie K.; Green, Eric D.; Struewing, Jeffery P.; Temple, Gary; Volpi, Simona; Boyer, Joy T.; Thomson, Elizabeth J.; Guyer, Mark S.; Cathy Ng; Abdallah, Assya; Colantuoni, Deborah; Insel, Thomas R.; Koester, Susan E.; Little, A. Roger; Bender, Patrick K.; Lehner, Thomas; Yao, Yin; Compton, Carolyn C.; Vaught, Jimmie B.; Sawyer, Sherilyn; Lockhart, Nicole C.; Demchok, Joanne; Moore, Helen F.;

NATURE GENETICS

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

Bava, Felice-Alessio; Eliscovich, Carolina; Ferreira, Pedro G; Minana, Belen; Ben-Dov, Claudia; Guigo, Roderic; Valcarcel, Juan; Mendez, Raul

Nature

Grape RNA-Seq analysis pipeline environment

Knowles DG, Röder M, Merkel A, Guigó R

Bioinformatics

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

Ferreira, Pedro G; Patalano, Solenn; Chauhan, Ritika; Ffrench-Constant, Richard; Gabaldon, Toni; Guigo, Roderic; Sumner, Seirian

Genome Biology

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

Pervouchine DD, Knowles DG, Guigó R

Bioinformatics

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

Derrien T, Guigó R, Johnson R

Frontiers In Genetics

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

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

NATURE 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 Research

Landscape of transcription in human cells

Djebali S; Davis C; Merkel A; Dobin A; Lassmann T; Mortazavi A; Tanzer A; Lagarde J; Lin W; Schlesinger F; Xue C; Marinov G; Khatun J; Williams B; Zaleski C; Rozowsky J; Röder M; Kokocinski F; Abdelhamid R; Alioto T; Antoshechkin I; Baer M; Bar N; 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; Djebali S; Davis C; Merkel A; Dobin A; Lassmann T; Mortazavi A; Tanzer A; Lagarde J; Lin W; Schlesinger F; Xue C; Marinov G; Khatun J; Williams B; Zaleski C; Rozowsky J; Röder M; Kokocinski F; Abdelhamid R; Alioto T; Antoshechkin I; Baer M; Bar N; 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; Djebali S; Davis C; Merkel A; Dobin A; Lassmann T

Nature

An integrated encyclopedia of DNA elements in the human genome

ENCODE Project Consortium

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 Biology

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 Research

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 Research

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 Research

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 Research

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 Research

An encyclopedia of mouse DNA elements (Mouse ENCODE)

Stamatoyannopoulos, John A.; Snyder, Michael; Hardison, Ross; Ren, Bing; Gingeras, Thomas; Gilbert, David M.; Groudine, Mark; Bender, Michael; Kaul, Rajinder; Canfield, Theresa; Giste, Erica; Johnson, Audra; Zhang, Mia; Balasundaram, Gayathri; Byron, Rachel; Roach, Vaughan; Sabo, Peter J.; Sandstrom, Richard; Stehling, A. Sandra; Thurman, Robert E.; Weissman, Sherman M.; Cayting, Philip; Hariharan, Manoj; Lian, Jin; Cheng, Yong; Landt, Stephen G.; Ma, Zhihai; Wold, Barbara J.; Dekker, Job; Crawford, Gregory E.; Keller, Cheryl A.; Wu, Weisheng; Morrissey, Christopher; Kumar, Swathi A.; Mishra, Tejaswini; Jain, Deepti; Byrska-Bishop, Marta; Blankenberg, Daniel; Lajoie, Bryan R.; Jain, Gaurav; Sanyal, Amartya; Chen, Kaun-Bei; Denas, Olgert; Taylor, James; Blobel, Gerd A.; Weiss, Mitchell J.; Pimkin, Max; Deng, Wulan; Marinov, Georgi K.; Williams, Brian A.; Fisher-Aylor, Katherine I.; Desalvo, Gilberto; Kiralusha, Anthony; Trout, Diane; Amrhein, Henry; Mortazavi, Ali; Edsall, Lee; McCleary, David; Kuan, Samantha; Shen, Yin; Yue, Feng; Ye, Zhen; Davis, Carrie A.; Zaleski, Chris; Jha, Sonali; Xue, Chenghai; Dobin, Alex; Lin, Wei; Fastuca, Meagan; Wang, Huaien; Guigo, Roderic; Djebali, Sarah; Lagarde, Julien; Ryba, Tyrone; Sasaki, Takayo; Malladi, Venkat S.; Cline, Melissa S.; Kirkup, Vanessa M.; Learned, Katrina; Rosenbloom, Kate R.; Kent, W. James; Feingold, Elise A.; Good, Peter J.; Pazin, Michael; Lowdon, Rebecca F.; Adams, Leslie B.;Mouse ENCODE Consortium

Genome Biology

The genome of melon (Cucumis melo L.)

Garcia-Mas, Jordi; Benjak, Andrej; Sanseverino, Walter; Bourgeois, Michael; Mir, Gisela; Gonzalez, Victor M; Henaff, Elizabeth; Camara, Francisco; Cozzuto, Luca; Lowy, Ernesto; Alioto, Tyler; Capella-Gutierrez, Salvador; Blanca, Jose; Canizares, Joaquin; Ziarsolo, Pello; Gonzalez-Ibeas, Daniel; Rodriguez-Moreno, Luis; Droege, Marcus; Du, Lei; Alvarez-Tejado, Miguel; Lorente-Galdos, Belen; Mele, Marta; Yang, Luming; Weng, Yiqun; Navarro, Arcadi; Marques-Bonet, Tomas; Aranda, Miguel A; Nuez, Fernando; Pico, Belen; Gabaldon, Toni; Roma, Guglielmo; Guigo, Roderic; Casacuberta, Josep M; Arus, Pere; Puigdomenech, Pere

Proceedings Of The National Academy Of Sciences Of The United States Of America

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 Research

The tomato genome sequence provides insights into fleshy fruit evolution

Tomato Genome Consortium

Nature

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

Estimation of alternative splicing variability in human populations

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

GENOME RESEARCH

SPIn: model selection for phylogenetic mixtures via linear invariants

Kedzierska AM, Drton M, Guigó R, Casanellas M

Molecular Biology And Evolution

BLUEPRINT to decode the epigenetic signature written in blood

Adams, David; Altucci, Lucia; Antonarakis, Stylianos E.; Ballesteros, Juan; Beck, Stephan; Bird, Adrian; Bock, Christoph; Boehm, Bernhard; Campo, Elias; Caricasole, Andrea; Dahl, Fredrik; Dermitzakis, Emmanouil T.; Enver, Tariq; Esteller, Manel; Estivill, Xavier; Ferguson-Smith, Anne; Fitzgibbon, Jude; Flicek, Paul; Giehl, Claudia; Graf, Thomas; Grosveld, Frank; Guigo, Roderic; Gut, Ivo; Helin, Kristian; Jarvius, Jonas; Kueppers, Ralf; Lehrach, Hans; Lengauer, Thomas; Lernmark, Ake; Leslie, David; Loeffler, Markus; Macintyre, Elizabeth; Mai, Antonello; Martens, Joost H. A.; Minucci, Saverio; Ouwehand, Willem H.; Pelicci, Pier Giuseppe; Pendeville, Helene; Porse, Bo; Rakyan, Vardhman; Reik, Wolf; Schrappe, Martin; Schuebeler, Dirk; Seifert, Martin; Siebert, Reiner; Simmons, David; Soranzo, Nicole; Spicuglia, Salvatore; Stratton, Michael; Stunnenberg, Hendrik G.; Tanay, Amos; Torrents, David; Valencia, Alfonso; Vellenga, Edo; Vingron, Martin; Walter, Joern; Willcocks, Spike;BLUEPRINT Consortium

Nature Biotechnology

Analysis of RNA Transcripts by High-Throughput RNA Sequencing

Ribeca P; Lacroix V; Sammeth M; Guigó R

Alternative Pre-Mrna Splicing: Theory And Protocols

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 J; Howald C; Foissac S; Ucla C; Chrast J; Ribeca P; Martin D; Murray R; Yang X; Ghamsari L; Lin C; Bell I; Dumais E; Drenkow J; Tress M; Gelpí J; Orozco M; Valencia A; van Berkum N; Lajoie B; Vidal M; Stamatoyannopoulos J; Batut P; Dobin A; Harrow J; Hubbard T; Dekker J; Frankish A; Salehi-Ashtiani K; Reymond A; Antonarakis S; Guigó R; Gingeras T

Plos One

Interplay between BRCA1 and RHAMM Regulates Epithelial Apicobasal Polarization and May Influence Risk of Breast Cancer

Maxwell, Christopher A; Benitez, Javier; Gomez-Baldo, Laia; Osorio, Ana; Bonifaci, Nuria; Fernandez-Ramires, Ricardo; Costes, Sylvain V; Guino, Elisabet; Chen, Helen; Evans, Gareth J R; Mohan, Pooja; Catala, Isabel; Petit, Anna; Aguilar, Helena; Villanueva, Alberto; Aytes, Alvaro; Serra-Musach, Jordi; Rennert, Gad; Lejbkowicz, Flavio; Peterlongo, Paolo; Manoukian, Siranoush; Peissel, Bernard; Ripamonti, Carla B; Bonanni, Bernardo; Viel, Alessandra; Allavena, Anna; Bernard, Loris; Radice, Paolo; Friedman, Eitan; Kaufman, Bella; Laitman, Yael; Dubrovsky, Maya; Milgrom, Roni; Jakubowska, Anna; Cybulski, Cezary; Gorski, Bohdan; Jaworska, Katarzyna; Durda, Katarzyna; Sukiennicki, Grzegorz; Lubinski, Jan; Shugart, Yin Yao; Domchek, Susan M; Letrero, Richard; Weber, Barbara L; Hogervorst, Frans B L; Rookus, Matti A; Collee, J Margriet; Devilee, Peter; Ligtenberg, Marjolijn J; van der Luijt, Rob B; Aalfs, Cora M; Waisfisz, Quinten; Wijnen, Juul; van Roozendaal, Cornelis E P; Easton, Douglas F; Peock, Susan; Cook, Margaret; Oliver, Clare; Frost, Debra; Harrington, Patricia; Evans, D Gareth; Lalloo, Fiona; Eeles, Rosalind; Izatt, Louise; Chu, Carol; Eccles, Diana; Douglas, Fiona; Brewer, Carole; Nevanlinna, Heli; Heikkinen, Tuomas; Couch, Fergus J; Lindor, Noralane M; Wang, Xianshu; Godwin, Andrew K; Caligo, Maria A; Lombardi, Grazia; Loman, Niklas; Karlsson, Per; Ehrencrona, Hans; von Wachenfeldt, Anna; Barkardottir, Rosa Bjork; Hamann, Ute; Rashid, Muhammad U; Lasa, Adriana; Caldes, Trinidad; Andres, Raquel; Schmitt, Michael; Assmann, Volker; Stevens, Kristen; Offit, Kenneth; Curado, Joao; Tilgner, Hagen; Guigo, Roderic; Aiza, Gemma; Brunet, Joan; Castellsague, Joan; Martrat, Griselda; Urruticoechea, Ander; Blanco, Ignacio; Tihomirova, Laima; Goldgar, David E; Buys, Saundra; John, Esther M; Miron, Alexander; Southey, Melissa; Daly, Mary B; Schmutzler, Rita K; Wappenschmidt, Barbara; Meindl, Alfons; Arnold, Norbert; Deissler, Helmut; Varon-Mateeva, Raymonda; Sutter, Christian; Niederacher, Dieter; Imyamitov, Evgeny; Sinilnikova, Olga M; Stoppa-Lyonne, Dominique; Mazoyer, Sylvie; Verny-Pierre, Carole; Castera, Laurent; de Pauw, Antoine; Bignon, Yves-Jean; Uhrhammer, Nancy; Peyrat, Jean-Philippe; Vennin, Philippe; Ferrer, Sandra Fert; Collonge-Rame, Marie-Agnes; Mortemousque, Isabelle; Spurdle, Amanda B; Beesley, Jonathan; Chen, Xiaoqing; Healey, Sue; Barcellos-Hoff, Mary Helen; Vidal, Marc; Gruber, Stephen B; Lazaro, Conxi; Capella, Gabriel; McGuffog, Lesley; Nathanson, Katherine L; Antoniou, Antonis C; Chenevix-Trench, Georgia; Fleisch, Markus C; Moreno, Victor; Angel Pujana, Miguel;HEBON; EMBRACE; SWE-BRCA; BCFR; GEMO Study Collaborators; kConFab

Plos Biology

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

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

Molecular Biology And Evolution

Erratum: Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes (Nature Structural and Molecular Biology (2011) 18 (708-714))

Martin D; Pantoja C; Miñán A; Valdes-Quezada C; Moltó E; Matesanz F; Bogdanovi? O; De La Calle-Mustienes E; Domínguez O; Taher L; Furlan-Magaril M; Alcina A; Cañón S; Fedetz M; Blasco M; Pereira P; Ovcharenko I; Recillas-Targa F; Montoliu L; Manzanares M; Guigó R; Serrano M; Casares F; Gómez-Skarmeta J

Nature Structural & Molecular Biology

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

Pinyol M; Conde, Laura; Villamor, Neus; Jares, Pedro; Bea, Silvia; Juan, Manel; Lopez-Guerra, Monica; Colomer, Dolors; Navarro, Alba; Aymerich, Marta; Rozman, Maria; Hernandez, Jesus M; Hernandez L; Yaguee, Jordi; de Sanjose, Silvia; Lopez-Guillermo, Armando; Montserrat, Emili; Campo, Elias

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, Bogdanovi? 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

Nature Structural & Molecular Biology

A user's guide to the Encyclopedia of DNA elements (ENCODE)

ENCODE Project Consortium

Plos Biology

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

Derrien, Thomas; Guigo, Roderic;

M S-MEDECINE SCIENCES

Long noncoding RNAs as enhancers of gene expression

Ørom UA, Derrien T, Guigo R, Shiekhattar R

Cold Spring Harbor Symposia On Quantitative Biology

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

Nikolaou, Christoforos; Althammer, Sonja; Beato, Miguel; Guigo, Roderic

Epigenetics & Chromatin

Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes

Mariotti M, Guigó R

BIOINFORMATICS

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

Arensburger P; Megy K; Waterhouse RM; Abrudan J; Amedeo P; Antelo B; Bartholomay L; Bidwell S; Caler E; Camara F; Campbell CL; Campbell KS; Casola C; Castro MT; Chandramouliswaran I; Chapman SB; Christley S; Costas J; Eisenstadt E; Feschotte C; Fraser-Liggett C; Guigo R; Haas B; Hammond M; Hansson BS; Hemingway J; Hill SR; Howarth C; Ignell R; Kennedy RC; Kodira CD; Lobo NF; Mao C; Mayhew G; Michel K; Mori A; Liu N; Naveira H; Nene V; Nguyen N; Pearson MD; Pritham EJ; Puiu D; Qi Y; Ranson H; Ribeiro JMC; Roberston HM; Severson DW; Shumway M; Stanke M; Strausberg RL; Sun C; Sutton G; Tu Z; Tubio JMC; Unger MF; Vanlandingham DL; Vilella AJ; White O; White JR; Wondji CS; Wortman J; Zdobnov EM; Birren B; Christensen BM; Collins FH; Cornel A; Dimopoulos G; Hannick LI; Higgs S; Lanzaro GC; Lawson D; Lee NH; Muskavitch MAT; Raikhel AS; Atkinson PW

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, Chaysavanh; Reeder, Jens; Gibert, Prudence; Varela, Encarna; Llopis, Marta; Antolin, Maria; Guigo, Roderic; Knight, Rob; Guarner, Francisco;

GENOME RESEARCH

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

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

International network of cancer genome projects

Decaens, Thomas; Campo, Elias; de Sanjose, Silvia; Bea, Silvia

Nature

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

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

Tilgner H, Guigó R

Epigenetics

Genome sequence of the pea aphid Acyrthosiphon pisum

Richards S; Gibbs RA; Gerardo NM; Moran N; Nakabachi A; Stern D; Tagu D; Wilson ACC; Muzny D; Kovar C; Cree A; Chacko J; Chandrabose MN; Dao MD; Dinh HH; Gabisi RA; Hines S; Hume J; Jhangian SN; Joshi V; Lewis LR; Liu YS; Lopez J; Morgan MB; Nguyen NB; Okwuonu GO; Ruiz SJ; Santibanez J; Wright RA; Fowler GR; Hitchens ME; Lozado RJ; Moen C; Steffen D; Warren JT; Zhang J; Nazareth LV; Chavez D; Davis C; Lee SL; Richards S; Gibbs RA; Gerardo NM; Moran N; Nakabachi A; Stern D; Tagu D; Wilson ACC; Muzny D; Kovar C; Cree A; Chacko J; Chandrabose MN; Dao MD; Dinh HH; Gabisi RA; Hines S; Hume J; Jhangian SN; Joshi V; Lewis LR; Liu YS; Lopez J; Morgan MB; Nguyen NB; Okwuonu GO; Ruiz SJ; Santibanez J; Wright RA; Fowler GR; Hitchens ME; Lozado RJ; Moen C; Steffen D; Warren JT; Zhang J; Nazareth LV; Chavez D; Davis C; Lee SL; Richards S; Gibbs RA; Gerardo NM; Moran N; Nakabachi A; Stern D; Tagu D; Wilson ACC; Muzny D; Kovar C; Cree A; Chacko J; Chandrabose MN; Dao MD; Dinh HH; Gabisi RA; Hines S; Hume J; Jhangian SN; Joshi V

Plos Biology

From identification to validation to gene count

Amid, Clara; Frankish, Adam; Havana; Aken, Bronwen; Ezkurdia, Iakes; Kokocinsk, Felix; Gilbert, James; White, Simon; Carninci, Piero; Gingeras, Thomas; Guigo, Roderic; Searle, Steve; Tress, Michael L.; Harrow, Jennifer; Hubbard, Tim;

GENOME BIOLOGY

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

Buschbeck, Marcus; Uribesalgo, Iris; Wibowo, Indra; Rue, Pau; Martin, David; Gutierrez, Arantxa; Morey, Lluis; Guigo, Roderic; Lopez-Schier, Hernan; Di Croce, Luciano

Nature Structural & Molecular Biology

Nucleosome positioning as a determinant of exon recognition

Tilgner, Hagen; Nikolaou, Christoforos; Althammer, Sonja; Sammeth, Michael; Beato, Miguel; Valcarcel, Juan; Guigo, Roderic

Nature Structural & Molecular Biology

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

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

MOLECULAR BIOLOGY AND EVOLUTION

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

HUMAN MUTATION

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

Arman, Monica; Aguilera-Montilla, Noemi; Mas, Virginia; Puig-Kroeger, Amaya; Pignatelli, Miguel; Guigo, Roderic; Corbi, Angel-Luis; Lozano, Francisco;

MOLECULAR IMMUNOLOGY

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, Joan-Marc; Pignatelli, Miguel; Maestro, Miguel Angel; Cardalda, Carina; Boj, Sylvia F; Lozano, Juanjo; Blanco, Enrique; Lafuente, Amalia; Mccarthy, Mark I; Sumoy, Lauro; Guigo, Roderic; Ferrer, Jorge

Molecular And Cellular Biology

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 Research

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

Boj, Sylvia F; Servitja, Joan Marc; Martin, David; Rios, Martin; Talianidis, Iannis; Guigo, Roderic; Ferrer, Jorge

Diabetes

A Snapshot of the Emerging Tomato Genome Sequence

Mueller, Lukas A; Lankhorst, Rene Klein; Tanksley, Steven D; Giovannoni, James J; White, Ruth; Vrebalov, Julia; Fei, Zhangjun; van Eck, Joyce; Buels, Robert; Mills, Adri A; Menda, Naama; Tecle, Isaak Y; Bombarely, Aureliano; Stack, Stephen; Royer, Suzanne M; Chang, Song-Bin; Shearer, Lindsay A; Kim, Byung Dong; Jo, Sung-Hwan; Hur, Cheol-Goo; Choi, Doil; Li, Chang-Bao; Zhao, Jiuhai; Jiang, Hongling; Geng, Yu; Dai, Yuanyuan; Fan, Huajie; Chen, Jinfeng; Lu, Fei; Shi, Jinfeng; Sun, Shouhong; Chen, Jianjun; Yang, Xiaohua; Lu, Chen; Chen, Mingsheng; Cheng, Zhukuan; Li, Chuanyou; Ling, Hongqing; Xue, Yongbiao; Wang, Ying; Seymour, Graham B; Bishop, Gerard J; Bryan, Glenn; Rogers, Jane; Sims, Sarah; Butcher, Sarah; Buchan, Daniel; Abbott, James; Beasley, Helen; Nicholson, Christine; Riddle, Clare; Humphray, Sean; McLaren, Karen; Mathur, Saloni; Vyas, Shailendra; Solanke, Amolkumar U; Kumar, Rahul; Gupta, Vikrant; Sharma, Arun K; Khurana, Paramjit; Khurana, Jitendra P; Tyagi, Akhilesh; Sarita; Chowdhury, Parul; Shridhar, Smriti; Chattopadhyay, Debasis; Pandit, Awadhesh; Singh, Pradeep; Kumar, Ajay; Dixit, Rekha; Singh, Archana; Praveen, Sumera; Dalal, Vivek; Yadav, Mahavir; Ghazi, Irfan Ahmad; Gaikwad, Kishor; Sharma, Tilak Raj; Mohapatra, Trilochan; Singh, Nagendra Kumar; Szinay, Dora; de Jong, Hans; Peters, Sander; van Staveren, Marjo; Datema, Erwin; Fiers, Mark W E J; van Ham, Roeland C H J; Lindhout, P; Philippot, Murielle; Frasse, Pierre; Regad, Farid; Zouine, Mohamed; Bouzayen, Mondher; Asamizu, Erika; Sato, Shusei; Fukuoka, Hiroyuki; Tabata, Satoshi; Shibata, Daisuke; Botella, Miguel A; Perez-Alonso, M; Fernandez-Pedrosa, V; Osorio, Sonia; Mico, Amparo; Granell, Antonio; Zhang, Zhonghua; He, Jun; Huang, Sanwen; Du, Yongchen; Qu, Dongyu; Liu, Longfei; Liu, Dongyuan; Wang, Jun; Ye, Zhibiao; Yang, Wencai; Wang, Guoping; Vezzi, Alessandro; Todesco, Sara; Valle, Giorgio; Falcone, Giulia; Pietrella, Marco; Giuliano, Giovanni; Grandillo, Silvana; Traini, Alessandra; D'Agostino, Nunzio; Chiusano, Maria Luisa; Ercolano, Mara; Barone, Amalia; Frusciante, Luigi; Schoof, Heiko; Joecker, Anika; Bruggmann, Remy; Spannagl, Manuel; Mayer, Klaus X F; Guigo, Roderic; Camara, Francisco; Rombauts, Stephane; Fawcett, Jeffrey A; Van de Peer, Yves; Knapp, Sandra; Zamir, Dani; Stiekema, Willem

Plant Genome

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

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; Chappie 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; 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; Chappie 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; 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

Science

ASTD: The Alternative Splicing and Transcript Diversity database

Koscielny, Gautier; Le Texier, Vincent; Gopalakrishnan, Chellappa; Kumanduri, Vasudev; Riethoven, Jean-Jack; Nardone, Francesco; Stanley, Eleanor; Fallsehr, Christine; Hofmann, Oliver; Kull, Meelis; Harrington, Eoghan; Boue, Stephanie; Eyras, Eduardo; Plass, Mireya; Lopez, Fabrice; Ritchie, William; Moucadel, Virginie; Ara, Takeshi; Pospisil, Heike; Herrmann, Alexander; Reich, Jens G; Guigo, Roderic; Bork, Peer; Doeberitz, Magnus von Knebel; Vilo, Jaak; Hide, Winston; Apweiler, Rolf; Thanaraj, Thangavel Alphonse; Gautheret, Daniel

Genomics

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

Chapple CE, Guigó R, Krol A

Bioinformatics

Identifying protein-coding genes in genomic sequences

Harrow; Jennifer Nagy; Alinda Reymond; Alexandre Alioto; Tyler Patthy; Laszlo Antonarakis; Stylianos E Guigo; Roderic

Genome Biology

GenePC and ASPIC integrate gene predictions with expressed sequence alignments to predict alternative transcripts

Alioto T; Guigó R; Picardi E; Pesole G

Series On Advances In Bioinformatics And Computational Biology

Exact transcriptome reconstruction from short sequence reads

Lacroix V; Sammeth M; Guigo R; Bergeron A

Lecture Notes In Computer Science

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 Research

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 Biology

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 Computational Biology

Bubbles: Alternative splicing events of arbitrary dimension in splicing graphs

Sammeth M; Valiente G; Guigó R

Lecture Notes In Computer Science

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

Nature Methods

Interoperability with Moby 1.0 - Its better than sharing your toothbrush

Wilkinson, Mark D; Senger, Martin; Kawas, Edward; Bruskiewich, Richard; Gouzy, Jerome; Noirot, Celine; Bardou, Philippe; Ng, Ambrose; Haase, Dirk; Saiz, Enrique de Andres; Wang, Dennis; Gibbons, Frank; Gordon, Paul M K; Sensen, Christoph W; Carrasco, Jose Manuel Rodriguez; Fernandez, Jose M; Shen, Lixin; Links, Matthew; Ng, Michael; Opushneva, Nina; Neerincx, Pieter B T; Leunissen, Jack A M; Ernst, Rebecca; Twigger, Simon; Usadel, Bjorn; Good, Benjamin; Wong, Yan; Stein, Lincoln; Crosby, William; Karlsson, Johan; Royo, Romina; Parraga, Ivan; Ramirez, Sergio; Gelpi, Josep Lluis; Trelles, Oswaldo; Pisano, David G; Jimenez, Natalia; Kerhornou, Arnaud; Rosset, Roman; Zamacola, Leire; Tarraga, Joaquin; Huerta-Cepas, Jaime; Carazo, Jose Maria; Dopazo, Joaquin; Guigo, Roderic; Navarro, Arcadi; Orozco, Modesto; Valencia, Alfonso; Claros, M Gonzalo; Perez, Antonio J; Aldana, Jose; Rojano, M Mar; Cruz, Raul Fernandez-Santa; Navas, Ismael; Schiltz, Gary; Farmer, Andrew; Gessler, Damian; Schoof, Heiko; Groscurth, Andreas;BioMoby Consortium

Briefings In Bioinformatics

SNP and haplotype mapping for genetic analysis in the rat

, 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 STAR Consortium

Nature Genetics

In silico meets in vivo

Weng, Zhiping; Guigo, Roderic;

GENOME BIOLOGY

A Combinatorial Code for CPE-Mediated Translational Control

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

Cell

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

Castellano, Sergi; Gladyshev, Vadim N; Guigo, Roderic; Berry, Marla J

NUCLEIC ACIDS RESEARCH

State of the art in eukaryotic gene prediction

Alioto T; Guigó R

Modern Genome Annotation: The Biosapiens Network

Evolution of genes and genomes on the Drosophila phylogeny

Abad Lorenzo, Jose Pascual

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 Research

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

Kerhornou A, Guigó R

BIOINFORMATICS

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

, 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, 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, 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, Xu M, Haidar JN, Yu 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 ENCODE Project Consortium, 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

Nature

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 C; Holroyd N; Dickson M; Taylor R; Hance Z; Foissac S; Myers R; Rogers J; Hubbard T; Harrow J; Guigó R; Gingeras T; Antonarakis S; Reymond A

Genome Research

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 RESEARCH

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

Rozowsky, Joel S.; Newburger, Daniel; Sayward, Fred; Wu, Jiaqian; Jordan, Greg; Korbel, Jan O.; Nagalakshmi, Ugrappa; Yang, Jin; Zheng, Deyou; Guigo, Roderic; Gingeras, Thomas R.; Weissman, Sherman; Miller, Perry; Snyder, Michael; Gerstein, Mark B.;

GENOME RESEARCH

Structured RNAs in the ENCODE selected regions of the human genome

Washietl, Stefan; Pedersen, Jakob S.; Korbel, Jan O.; Stocsits, Claudia; Gruber, Andreas R.; Hackermueller, Joerg; Hertel, Jana; Lindemeyer, Manja; Reiche, Kristin; Tanzer, Andrea; Ucla, Catherine; Wyss, Carine; Antonarakis, Stylianos E.; Denoeud, France; Lagarde, Julien; Drenkow, Jorg; Kapranov, Philipp; Gingeras, Thomas R.; Guigo, Roderic; Snyder, Michael; Gerstein, Mark B.; Reymond, Alexandre; Hofacker, Ivo L.; Stadler, Peter F.;

GENOME RESEARCH

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

Proceedings Of The National Academy Of Sciences Of The United States Of America

Improving gene annotation using peptide mass spectrometry

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

GENOME RESEARCH

Using geneid to identify genes

Blanco E, Parra G, Guigó R

Current Protocols In Bioinformatics

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

Unweaving the meanings of messenger RNA sequences

Guigo, Roderic; Valcarcel, Juan;

Molecular Cell

Transcription factor map alignment of promoter regions

Blanco E, Messeguer X, Smith TF, Guigó R

PLoS Computational Biology

Mutation patterns of amino acid tandem repeats in the human proteome

Mularoni L, Guigó R, Albà MM

GENOME BIOLOGY

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 Research

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 Biology

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 BIOLOGY

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

Blanco, Enrique; Farre, Domenec; Alba, M Mar; Messeguer, Xavier; Guigo, Roderic

Nucleic Acids Research

EGASP: Introduction

Reese, Martin G.; Guigo, Roderic;

Genome Biology

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 Research

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

Proceedings Of The National Academy Of Sciences Of The United States Of America

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 Research

ECCB/JBI 2005

Guigo, R; Moran, F; Valencia, A; Abril, JF;

BIOINFORMATICS

BioSapiens: a European network for integrated genome annotation

Thornton, J; Tramontano, A; Roma, U; Valencia, A; Brunak, R; Antonarakis, S; Bork, P; Casadio, R; Danchin, A; Durbin, R; Frishman, D; Guigo, R; von Heijne, G; van Helden, J; Lengauer, T; Linial, M; Mott, R; Orengo, C; Jones, D; Patthy, L; Rychlewski, L; Schachter, V; Schomburg, D; Ukkonen, E; Veuthey, AL; Vingron, M; Vriend, G; Nyberg, K;BioSapiens Network Excellence

EUROPEAN JOURNAL OF HUMAN GENETICS

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

Molecular Cell

EGASP: collaboration through competition to find human genes

Guigo, R; Reese, MG;

NATURE 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

Are splicing mutations the most frequent cause of hereditary disease?

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

Febs Letters

Comparison of splice sites in mammals and chicken

Abril JF, Castelo R, Guigó R

Genome Research

Gene organization features in A/T-rich organisms

Szafranski, K; Lehmann, R; Parra, G; Guigo, R; Glockner, G;

Journal Of Molecular Evolution

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Hillier, LW; Miller, W; Birney, E; Warren, W; Hardison, RC; Ponting, CP; Bork, P; Burt, DW; Groenen, MAM; Delany, ME; Dodgson, JB; Chinwalla, AT; Cliften, PF; Clifton, SW; Delehaunty, KD; Fronick, C; Fulton, RS; Graves, TA; Kremitzki, C; Layman, D; Magrini, V; McPherson, JD; Miner, TL; Minx, P; Nash, WE; Nhan, MN; Nelson, JO; Oddy, LG; Pohl, CS; Randall-Maher, J; Smith, SM; Wallis, JW; Yang, SP; Romanov, MN; Rondelli, CM; Paton, B; Smith, J; Morrice, D; Daniels, L; Tempest, HG; Robertson, L; Masabanda, JS; Griffin, DK; Vignal, A; Fillon, V; Jacobbson, L; Kerje, S; Andersson, L; Crooijmans, RPM; Aerts, J; van der Poel, JJ; Ellegren, H; Caldwell, RB; Hubbard, SJ; Grafham, DV; Kierzek, AM; McLaren, SR; Overton, IM; Arakawa, H; Beattie, KJ; Bezzubov, Y; Boardman, PE; Bonfield, JK; Croning, MDR; Davies, RM; Francis, MD; Humphray, SJ; Scott, CE; Taylor, RG; Tickle, C; Brown, WRA; Rogers, J; Buerstedde, JM; Wilson, SA; Stubbs, L; Ovcharenko, I; Gordon, L; Lucas, S; Miller, MM; Inoko, H; Shiina, T; Kaufman, J; Salomonsen, J; Skjoedt, K; Wong, GKS; Wang, J; Liu, B; Wang, J; Yu, J; Yang, HM; Nefedov, M; Koriabine, M; deJong, PJ; Goodstadt, L; Webber, C; Dickens, NJ; Letunic, I; Suyama, M; Torrents, D; von Mering, C; Zdobnov, EM; Makova, K; Nekrutenko, A; Elnitski, L; Eswara, P; King, DC; Yang, S; Tyekucheva, S; Radakrishnan, A; Harris, RS; Chiaromonte, F; Taylor, J; He, JB; Rijnkels, M; Griffiths-Jones, S; Ureta-Vidal, A; Hoffman, MM; Severin, J; Searle, SMJ; Law, AS; Speed, D; Waddington, D; Cheng, Z; Tuzun, E; Eichler, E; Bao, ZR; Flicek, P; Shteynberg, DD; Brent, MR; Bye, JM; Huckle, EJ; Chatterji, S; Dewey, C; Pachter, L; Kouranov, A; Mourelatos, Z; Hatzigeorgiou, AG; Paterson, AH; Ivarie, R; Brandstrom, M; Axelsson, E; Backstrom, N; Berlin, S; Webster, MT; Pourquie, O; Reymond, A; Ucla, C; Antonarakis, SE; Long, MY; Emerson, JJ; Betran, E; Dupanloup, I; Kaessmann, H; Hinrichs, AS; Bejerano, G; Furey, TS; Harte, RA; Raney, B; Siepel, A; Kent, WJ; Haussler, D; Eyras, E; Castelo, R; Abril, JF; Castellano, S; Camara, F; Parra, G; Guigo, R; Bourque, G; Tesler, G; Pevzner, PA; Smit, A; Fulton, LA; Mardis, ER; Wilson, RK;

NATURE

Splice site identification by idlBNs

Castelo R, Guigó R

Bioinformatics

The ENCODE (ENCyclopedia of DNA elements) Project

Feingold, EA; Good, PJ; Guyer, MS; Kamholz, S; Liefer, L; Wetterstrand, K; Collins, FS; Gingeras, TR; Kampa, D; Sekinger, EA; Cheng, J; Hirsch, H; Ghosh, S; Zhu, Z; Pate, S; Piccolboni, A; Yang, A; Tammana, H; Bekiranov, S; Kapranov, P; Harrison, R; Church, G; Struhl, K; Ren, B; Kim, TH; Barrera, LO; Qu, C; Van Calcar, S; Luna, R; Glass, CK; Rosenfeld, MG; Guigo, R; Antonarakis, SE; Birney, E; Brent, M; Pachter, L; Reymond, A; Dermitzakis, ET; Dewey, C; Keefe, D; Denoeud, F; Lagarde, J; Ashurst, J; Hubbard, T; Wesselink, JJ; Castelo, R; Eyras, E; Myers, RM; Sidow, A; Batzoglou, S; Trinklein, ND; Hartman, SJ; Aldred, SF; Anton, E; Schroeder, DI; Marticke, SS; Nguyen, L; Schmutz, J; Grimwood, J; Dickson, M; Cooper, GM; Stone, EA; Asimenos, G; Brudno, M; Dutta, A; Karnani, N; Taylor, CM; Kim, HK; Robins, G; Stamatoyannopoulos, G; Stamatoyannopoulos, JA; Dorschner, M; Sabo, P; Hawrytycz, M; Humbert, R; Wallace, J; Yu, M; Navas, PA; McArthur, M; Noble, WS; Dunham, I; Koch, CM; Andrews, RM; Clelland, GK; Wilcox, S; Fowler, JC; James, KD; Groth, P; Dovey, OM; Ellis, PD; Wraight, VL; Mungall, AJ; Dhami, P; Fiegler, H; Langford, CF; Carter, NP; Vetrie, D; Snyder, M; Euskirchen, G; Urban, AE; Nagalakshmi, U; Rinn, J; Popescu, G; Bertone, P; Hartman, S; Rozowsky, J; Emanuelsson, O; Royce, T; Chung, S; Gerstein, M; Lian, Z; Lian, J; Nakayama, Y; Weissman, S; Stoic, V; Tongprasit, W; Sethi, H; Jones, S; Marra, M; Shin, H; Schein, J; Clamp, M; Lindblad-Toh, K; Chang, J; Jaffe, DB; Kamal, ES; Lander, ES; Mikkelsen, TS; Vinson, J; Zody, MC; de Jong, PJ; Osoegawa, K; Nefedov, M; Zhu, B; Baxevanis, AD; Wolfsberg, TG; Collins, FS; Crawford, GE; Holt, E; Vasicek, TJ; Zhou, D; Luo, S; Green, ED; Bouffard, GG; Margulies, EH; Portnoy, ME; Hansen, NF; Thomas, PJ; Mcdowell, JC; Maskeri, B; Young, AC; Idol, JR; Blakesley, RW; Schuler, G; Miller, W; Hardison, R; Elnitski, L; Shah, P; Salzberg, SL; Pertea, M; Majoros, WH; Haussler, D; Thomas, D; Rosenbloom, KR; Clawson, H; Siepe, A; Kent, WJ; Weng, Z; Jin, S; Halees, A; Burden, H; Karaoz, U; Fu, Y; Yu, Y; Ding, C; Cantor, CR; Kingston, RE; Dennis, J; Green, RD; Singer, MA; Richmond, TA; Norton, JE; Farnham, PJ; Oberley, MJ; Inman, DR; McCormick, MR; Kim, H; Middle, CL; Pirrung, MC; Fu, XD; Kwon, YS; Ye, Z; Dekker, J; Tabuchi, TM; Gheldof, N; Dostie, J; Harvey, SC;ENCODE Project Consortium

SCIENCE

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

Journal Of Molecular Evolution

Recent advances in gene structure prediction

Brent MR, Guigó R

CURRENT OPINION IN STRUCTURAL BIOLOGY

Comparative analysis of amino acid repeats in rodents and humans

Albà MM, Guigó R

GENOME RESEARCH

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, 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, 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 REPORTS

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

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Proceedings Of The National Academy Of Sciences Of The United States Of America

Comparative gene prediction in human and mouse

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

Genome Research

Initial sequencing and comparative analysis of the mouse genome

, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES Mouse Genome Sequencing Consortium

Nature

The genome sequence of the malaria mosquito Anopheles gambiae

Holt, RA; Subramanian, GM; Halpern, A; Sutton, GG; Charlab, R; Nusskern, DR; Wincker, P; Clark, AG; Ribeiro, JMC; Wides, R; Salzberg, SL; Loftus, B; Yandell, M; Majoros, WH; Rusch, DB; Lai, ZW; Kraft, CL; Abril, JF; Anthouard, V; Arensburger, P; Atkinson, PW; Baden, H; de Berardinis, V; Baldwin, D; Benes, V; Biedler, J; Blass, C; Bolanos, R; Boscus, D; Barnstead, M; Cai, S; Center, A; Chatuverdi, K; Christophides, GK; Chrystal, MA; Clamp, M; Cravchik, A; Curwen, V; Dana, A; Delcher, A; Dew, I; Evans, CA; Flanigan, M; Grundschober-Freimoser, A; Friedli, L; Gu, ZP; Guan, P; Guigo, R; Hillenmeyer, ME; Hladun, SL; Hogan, JR; Hong, YS; Hoover, J; Jaillon, O; Ke, ZX; Kodira, C; Kokoza, E; Koutsos, A; Letunic, I; Levitsky, A; Liang, Y; Lin, JJ; Lobo, NF; Lopez, JR; Malek, JA; McIntosh, TC; Meister, S; Miller, J; Mobarry, C; Mongin, E; Murphy, SD; O'Brochta, DA; Pfannkoch, C; Qi, R; Regier, MA; Remington, K; Shao, HG; Sharakhova, MV; Sitter, CD; Shetty, J; Smith, TJ; Strong, R; Sun, JT; Thomasova, D; Ton, LQ; Topalis, P; Tu, ZJ; Unger, MF; Walenz, B; Wang, AH; Wang, J; Wang, M; Wang, XL; Woodford, KJ; Wortman, JR; Wu, M; Yao, A; Zdobnov, EM; Zhang, HY; Zhao, Q; Zhao, SY; Zhu, SPC; Zhimulev, I; Coluzzi, M; della Torre, A; Roth, CW; Louis, C; Kalush, F; Mural, RJ; Myers, EW; Adams, MD; Smith, HO; Broder, S; Gardner, MJ; Fraser, CM; Birney, E; Bork, P; Brey, PT; Venter, JC; Weissenbach, J; Kafatos, FC; Collins, FH; Hoffman, SL;

SCIENCE

Sequence and analysis of chromosome 2 of Dictyostelium discoideum

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

Nature

Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution?

Betts, MJ; Guigo, R; Agarwal, P; Russell, RB;

EMBO JOURNAL

SGP-1: Prediction and validation of homologous genes based on sequence alignments

Wiehe, T; Gebauer-Jung, S; Mitchell-Olds, T; Guigo, R;

GENOME RESEARCH

In silico identification of novel selenoproteins in the Drosophila melanogaster genome

Castellano, S; Morozova, N; Morey, M; Berry, MJ; Serras, F; Corominas, M; Guigo, R;

EMBO REPORTS

The sequence of the human genome

Venter, JC; Adams, MD; Myers, EW; Li, PW; Mural, RJ; Sutton, GG; Smith, HO; Yandell, M; Evans, CA; Holt, RA; Gocayne, JD; Amanatides, P; Ballew, RM; Huson, DH; Wortman, JR; Zhang, Q; Kodira, CD; Zheng, XQH; Chen, L; Skupski, M; Subramanian, G; Thomas, PD; Zhang, JH; Miklos, GLG; Nelson, C; Broder, S; Clark, AG; Nadeau, C; McKusick, VA; Zinder, N; Levine, AJ; Roberts, RJ; Simon, M; Slayman, C; Hunkapiller, M; Bolanos, R; Delcher, A; Dew, I; Fasulo, D; Flanigan, M; Florea, L; Halpern, A; Hannenhalli, S; Kravitz, S; Levy, S; Mobarry, C; Reinert, K; Remington, K; Abu-Threideh, J; Beasley, E; Biddick, K; Bonazzi, V; Brandon, R; Cargill, M; Chandramouliswaran, I; Charlab, R; Chaturvedi, K; Deng, ZM; Di Francesco, V; Dunn, P; Eilbeck, K; Evangelista, C; Gabrielian, AE; Gan, W; Ge, WM; Gong, FC; Gu, ZP; Guan, P; Heiman, TJ; Higgins, ME; Ji, RR; Ke, ZX; Ketchum, KA; Lai, ZW; Lei, YD; Li, ZY; Li, JY; Liang, Y; Lin, XY; Lu, F; Merkulov, GV; Milshina, N; Moore, HM; Naik, AK; Narayan, VA; Neelam, B; Nusskern, D; Rusch, DB; Salzberg, S; Shao, W; Shue, BX; Sun, JT; Wang, ZY; Wang, AH; Wang, X; Wang, J; Wei, MH; Wides, R; Xiao, CL; Yan, CH; Yao, A; Ye, J; Zhan, M; Zhang, WQ; Zhang, HY; Zhao, Q; Zheng, LS; Zhong, F; Zhong, WY; Zhu, SPC; Zhao, SY; Gilbert, D; Baumhueter, S; Spier, G; Carter, C; Cravchik, A; Woodage, T; Ali, F; An, HJ; Awe, A; Baldwin, D; Baden, H; Barnstead, M; Barrow, I; Beeson, K; Busam, D; Carver, A; Center, A; Cheng, ML; Curry, L; Danaher, S; Davenport, L; Desilets, R; Dietz, S; Dodson, K; Doup, L; Ferriera, S; Garg, N; Gluecksmann, A; Hart, B; Haynes, J; Haynes, C; Heiner, C; Hladun, S; Hostin, D; Houck, J; Howland, T; Ibegwam, C; Johnson, J; Kalush, F; Kline, L; Koduru, S; Love, A; Mann, F; May, D; McCawley, S; McIntosh, T; McMullen, I; Moy, M; Moy, L; Murphy, B; Nelson, K; Pfannkoch, C; Pratts, E; Puri, V; Qureshi, H; Reardon, M; Rodriguez, R; Rogers, YH; Romblad, D; Ruhfel, B; Scott, R; Sitter, C; Smallwood, M; Stewart, E; Strong, R; Suh, E; Thomas, R; Tint, NN; Tse, S; Vech, C; Wang, G; Wetter, J; Williams, S; Williams, M; Windsor, S; Winn-Deen, E; Wolfe, K; Zaveri, J; Zaveri, K; Abril, JF; Guigo, R; Campbell, MJ; Sjolander, KV; Karlak, B; Kejariwal, A; Mi, HY; Lazareva, B; Hatton, T; Narechania, A; Diemer, K; Muruganujan, A; Guo, N; Sato, S; Bafna, V; Istrail, S; Lippert, R; Schwartz, R; Walenz, B; Yooseph, S; Allen, D; Basu, A; Baxendale, J; Blick, L; Caminha, M; Carnes-Stine, J; Caulk, P; Chiang, YH; Coyne, M; Dahlke, C; Mays, AD; Dombroski, M; Donnelly, M; Ely, D; Esparham, S; Fosler, C; Gire, H; Glanowski, S; Glasser, K; Glodek, A; Gorokhov, M; Graham, K; Gropman, B; Harris, M; Heil, J; Henderson, S; Hoover, J; Jennings, D; Jordan, C; Jordan, J; Kasha, J; Kagan, L; Kraft, C; Levitsky, A; Lewis, M; Liu, XJ; Lopez, J; Ma, D; Majoros, W; McDaniel, J; Murphy, S; Newman, M; Nguyen, T; Nguyen, N; Nodell, M; Pan, S; Peck, J; Peterson, M; Rowe, W; Sanders, R; Scott, J; Simpson, M; Smith, T; Sprague, A; Stockwell, T; Turner, R; Venter, E; Wang, M; Wen, MY; Wu, D; Wu, M; Xia, A; Zandieh, A; Zhu, XH;

SCIENCE

Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene

Thomson, TM; Lozano, JJ; Loukili, N; Carrio, R; Serras, F; Cormand, B; Valeri, M; Diaz, VM; Abril, J; Burset, M; Merino, J; Macaya, A; Corominas, M; Guigo, R;

GENOME RESEARCH

An assessment of gene prediction accuracy in large DNA sequences

Guigo, R; Agarwal, P; Abril, JF; Burset, M; Fickett, JW;

GENOME RESEARCH

gff2ps: visualizing genomic annotations

Abril, JF; Guigo, R;

BIOINFORMATICS

GeneID in Drosophila

Parra, G; Blanco, E; Guigo, R;

GENOME RESEARCH

Sequence similarity based gene prediction

Guigo, R; Burset, M; Agarwal, P; Abril, JF; Smith, RF; Fickett, JW;

GENOMICS AND PROTEOMICS

Assembling genes from predicted exons in linear time with dynamic programming

Guigo, R;

JOURNAL OF COMPUTATIONAL BIOLOGY

Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ

Lozano, JJ; LopezdeBrinas, E; Centeno, NB; Guigo, R; Sanz, F;

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Computational gene identification

Guigo, R;

JOURNAL OF MOLECULAR MEDICINE-JMM

Computational gene identification: an open problem

Guigo, R;

Computers & Chemistry

Reconstruction of ancient molecular phylogeny

Guigo, R; Muchnik, I; Smith, TF;

MOLECULAR PHYLOGENETICS AND EVOLUTION

Evaluation of gene structure prediction programs

Burset, M; Guigo, R;

GENOMICS

DISTINCTIVE SEQUENCE FEATURES IN PROTEIN-CODING GENIC NONCODING, AND INTERGENIC HUMAN DNA

GUIGO, R; FICKETT, JW;

JOURNAL OF MOLECULAR BIOLOGY

INFERRING CORRELATION BETWEEN DATABASE QUERIES - ANALYSIS OF PROTEIN-SEQUENCE PATTERNS

GUIGO, R; SMITH, TF;

Ieee Transactions On Pattern Analysis And Machine Intelligence

ESTIMATION OF PROTEIN-CODING DENSITY IN A CORPUS OF DNA-SEQUENCE DATA

FICKETT, JW; GUIGO, R;

NUCLEIC ACIDS RESEARCH

PREDICTION OF GENE STRUCTURE

GUIGO, R; KNUDSEN, S; DRAKE, N; SMITH, T;

JOURNAL OF MOLECULAR BIOLOGY

A COMMON PATTERN BETWEEN THE TGF-BETA FAMILY AND GLUTAREDOXIN

GUIGO, R; SMITH, TF;

BIOCHEMICAL JOURNAL

AUTOMATIC EVALUATION OF PROTEIN-SEQUENCE FUNCTIONAL PATTERNS

GUIGO, R; JOHANSSON, A; SMITH, TF;

COMPUTER APPLICATIONS IN THE BIOSCIENCES

AUTOIMMUNE-RESPONSE IN AIDS

VEGA, MA; GUIGO, R; SMITH, TF;

NATURE

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