Computational biology of RNA processing group
Roderic Guigo Lab
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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;
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
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;
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
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.;
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;
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
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:
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
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
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
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-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
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
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
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
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
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
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
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
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.;
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
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
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
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
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
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
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
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
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-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
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
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
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
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
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
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
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.;
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
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
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
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
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
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
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
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.;
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
GenePC and ASPIC integrate gene predictions with expressed sequence alignments to predict alternative transcripts
Alioto T; Guigó R; Picardi E; Pesole G
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
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
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
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
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
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
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.;
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.;
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
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
ECCB/JBI 2005
Guigo, R; Moran, F; Valencia, A; Abril, JF;
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
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;
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
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
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
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
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;
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
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;
Sequence similarity based gene prediction
Guigo, R; Burset, M; Agarwal, P; Abril, JF; Smith, RF; Fickett, JW;
Computational gene identification
Guigo, R;
AUTOMATIC EVALUATION OF PROTEIN-SEQUENCE FUNCTIONAL PATTERNS
GUIGO, R; JOHANSSON, A; SMITH, TF;