GENCODE

Publications


Reference Publications


  • Creating reference gene annotation for the mouse C57BL6/J genome assembly.

    Mudge JM and Harrow J

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;366-78

  • 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 and Hubbard TJ

    Genome research 2012;22;9;1760-74

  • GENCODE: producing a reference annotation for ENCODE.

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

    Genome biology 2006;7 Suppl 1;S4.1-9


All Publications of Participants


  • 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 and Harrow J

    Nature communications 2016;7;12339

  • Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

    Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS and Harrow J

    Nature communications 2016;7;11778

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

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

    BMC genomics 2015;16 Suppl 8;S2

  • Ensembl 2015.

    Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR and Flicek P

    Nucleic acids research 2015;43;Database issue;D662-9

  • Comparative assembly hubs: web-accessible browsers for comparative genomics.

    Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D and Paten B

    Bioinformatics (Oxford, England) 2014;30;23;3293-301

  • Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.

    Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A and Tress ML

    Human molecular genetics 2014;23;22;5866-78

  • Comparative analysis of pseudogenes across three phyla.

    Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J and Gerstein MB

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;37;13361-6

  • 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 and Waterston R

    Nature 2014;512;7515;445-8

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

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

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;33;E3366

  • Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.

    Deelen J, Beekman M, Uh HW, Broer L, Ayers KL, Tan Q, Kamatani Y, Bennet AM, Tamm R, Trompet S, Guðbjartsson DF, Flachsbart F, Rose G, Viktorin A, Fischer K, Nygaard M, Cordell HJ, Crocco P, van den Akker EB, Böhringer S, Helmer Q, Nelson CP, Saunders GI, Alver M, Andersen-Ranberg K, Breen ME, van der Breggen R, Caliebe A, Capri M, Cevenini E, Collerton JC, Dato S, Davies K, Ford I, Gampe J, Garagnani P, de Geus EJ, Harrow J, van Heemst D, Heijmans BT, Heinsen FA, Hottenga JJ, Hofman A, Jeune B, Jonsson PV, Lathrop M, Lechner D, Martin-Ruiz C, Mcnerlan SE, Mihailov E, Montesanto A, Mooijaart SP, Murphy A, Nohr EA, Paternoster L, Postmus I, Rivadeneira F, Ross OA, Salvioli S, Sattar N, Schreiber S, Stefánsson H, Stott DJ, Tiemeier H, Uitterlinden AG, Westendorp RG, Willemsen G, Samani NJ, Galan P, Sørensen TI, Boomsma DI, Jukema JW, Rea IM, Passarino G, de Craen AJ, Christensen K, Nebel A, Stefánsson K, Metspalu A, Magnusson P, Blanché H, Christiansen L, Kirkwood TB, van Duijn CM, Franceschi C, Houwing-Duistermaat JJ and Slagboom PE

    Human molecular genetics 2014;23;16;4420-32

  • Evidence of efficient stop codon readthrough in four mammalian genes.

    Loughran G, Chou MY, Ivanov IP, Jungreis I, Kellis M, Kiran AM, Baranov PV and Atkins JF

    Nucleic acids research 2014;42;14;8928-38

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

    Johnson R and Guigó R

    RNA (New York, N.Y.) 2014;20;7;959-76

  • Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

    Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT and McVean GA

    Genome biology 2014;15;6;R88

  • Ragout-a reference-assisted assembly tool for bacterial genomes.

    Kolmogorov M, Raney B, Paten B and Pham S

    Bioinformatics (Oxford, England) 2014;30;12;i302-9

  • Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue.

    Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M and Saghatelian A

    Journal of proteome research 2014;13;3;1757-65

  • The Vertebrate Genome Annotation browser 10 years on.

    Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S and Wilming LG

    Nucleic acids research 2014;42;Database issue;D771-9

  • Current status and new features of the Consensus Coding Sequence database.

    Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D and Pruitt KD

    Nucleic acids research 2014;42;Database issue;D865-72

  • Ensembl 2014.

    Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Zerbino DR and Searle SM

    Nucleic acids research 2014;42;Database issue;D749-55

  • Assessment of transcript reconstruction methods for RNA-seq.

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

    Nature methods 2013;10;12;1177-84

  • Functional transcriptomics in the post-ENCODE era.

    Mudge JM, Frankish A and Harrow J

    Genome research 2013;23;12;1961-73

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

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

    Nature methods 2013;10;12;1185-91

  • Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.

    Gonzàlez-Porta M, Frankish A, Rung J, Harrow J and Brazma A

    Genome biology 2013;14;7;R70

  • The UCSC Genome Browser database: extensions and updates 2013.

    Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D and Kent WJ

    Nucleic acids research 2013;41;Database issue;D64-9

  • APPRIS: annotation of principal and alternative splice isoforms.

    Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A and Tress ML

    Nucleic acids research 2013;41;Database issue;D110-7

  • ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

    Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A and Valencia A

    Nucleic acids research 2013;41;Database issue;D142-51

  • ENCODE data in the UCSC Genome Browser: year 5 update.

    Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D and Kent WJ

    Nucleic acids research 2013;41;Database issue;D56-63

  • An integrated map of genetic variation from 1,092 human genomes.

    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT and McVean GA

    Nature 2012;491;7422;56-65

  • The GENCODE pseudogene resource.

    Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J and Gerstein MB

    Genome biology 2012;13;9;R51

  • An integrated encyclopedia of DNA elements in the human genome.

    ENCODE Project Consortium

    Nature 2012;489;7414;57-74

  • Landscape of transcription in human cells.

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

    Nature 2012;489;7414;101-8

  • 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 and Guigó R

    Genome research 2012;22;9;1775-89

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

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

    Genome research 2012;22;9;1698-710

  • Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

    Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A and Tress ML

    Molecular biology and evolution 2012;29;9;2265-83

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

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

    Genome research 2012;22;7;1231-42

  • A systematic survey of loss-of-function variants in human protein-coding genes.

    MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB and Tyler-Smith C

    Science (New York, N.Y.) 2012;335;6070;823-8

  • The importance of identifying alternative splicing in vertebrate genome annotation.

    Frankish A, Mudge JM, Thomas M and Harrow J

    Database : the journal of biological databases and curation 2012;2012;bas014

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

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

    PloS one 2012;7;1;e28213

  • Tracking and coordinating an international curation effort for the CCDS Project.

    Harte RA, Farrell CM, Loveland JE, Suner MM, Wilming L, Aken B, Barrell D, Frankish A, Wallin C, Searle S, Diekhans M, Harrow J and Pruitt KD

    Database : the journal of biological databases and curation 2012;2012;bas008

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

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

    Molecular biology and evolution 2011;28;10;2949-59

  • The GENCODE exome: sequencing the complete human exome.

    Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S, Lehesjoki AE, Turner DJ, Hubbard TJ and Palotie A

    European journal of human genetics : EJHG 2011;19;7;827-31

  • PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.

    Lin MF, Jungreis I and Kellis M

    Bioinformatics (Oxford, England) 2011;27;13;i275-82

  • A user's guide to the encyclopedia of DNA elements (ENCODE).

    ENCODE Project Consortium

    PLoS biology 2011;9;4;e1001046

  • Gene inactivation and its implications for annotation in the era of personal genomics.

    Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J and Gerstein M

    Genes & development 2011;25;1;1-10

  • The UCSC Genome Browser database: update 2011.

    Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D and Kent WJ

    Nucleic acids research 2011;39;Database issue;D876-82

  • ENCODE whole-genome data in the UCSC genome browser (2011 update).

    Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D and Kent WJ

    Nucleic acids research 2011;39;Database issue;D871-5

  • Ensembl 2011.

    Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J and Searle SM

    Nucleic acids research 2011;39;Database issue;D800-6

  • Segmental duplications in the human genome reveal details of pseudogene formation.

    Khurana E, Lam HY, Cheng C, Carriero N, Cayting P and Gerstein MB

    Nucleic acids research 2010;38;20;6997-7007

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

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

    Cell 2010;143;1;46-58

  • A coding-independent function of gene and pseudogene mRNAs regulates tumour biology.

    Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ and Pandolfi PP

    Nature 2010;465;7301;1033-8

  • Ensembl's 10th year.

    Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J and Searle SM

    Nucleic acids research 2010;38;Database issue;D557-62

  • Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.

    Zhang ZD, Frankish A, Hunt T, Harrow J and Gerstein M

    Genome biology 2010;11;3;R26

  • Meeting report: a workshop on Best Practices in Genome Annotation.

    Madupu R, Brinkac LM, Harrow J, Wilming LG, Böhme U, Lamesch P and Hannick LI

    Database : the journal of biological databases and curation 2010;2010;baq001

  • The UCSC Genome Browser database: update 2010.

    Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D and Kent WJ

    Nucleic acids research 2010;38;Database issue;D613-9

  • ENCODE whole-genome data in the UCSC Genome Browser.

    Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D and Kent WJ

    Nucleic acids research 2010;38;Database issue;D620-5

  • AnnoTrack--a tracking system for genome annotation.

    Kokocinski F, Harrow J and Hubbard T

    BMC genomics 2010;11;538

  • Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

    Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G, Hancock RE and Harrow JL

    BMC genomics 2009;10;606

  • Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.

    Boles MK, Wilkinson BM, Wilming LG, Liu B, Probst FJ, Harrow J, Grafham D, Hentges KE, Woodward LP, Maxwell A, Mitchell K, Risley MD, Johnson R, Hirschi K, Lupski JR, Funato Y, Miki H, Marin-Garcia P, Matthews L, Coffey AJ, Parker A, Hubbard TJ, Rogers J, Bradley A, Adams DJ and Justice MJ

    PLoS genetics 2009;5;12;e1000759

  • Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.

    Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R and Gerstein MB

    BMC genomics 2009;10;480

  • The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

    Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R and Lipman D

    Genome research 2009;19;7;1316-23

  • Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

    Lu DV, Brown RH, Arumugam M and Brent MR

    Bioinformatics (Oxford, England) 2009;25;13;1587-93

  • Small RNAs originated from pseudogenes: cis- or trans-acting?

    Guo X, Zhang Z, Gerstein MB and Zheng D

    PLoS computational biology 2009;5;7;e1000449

  • The UCSC Genome Browser Database: update 2009.

    Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D and Kent WJ

    Nucleic acids research 2009;37;Database issue;D755-61

  • Pseudofam: the pseudogene families database.

    Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH and Gerstein MB

    Nucleic acids research 2009;37;Database issue;D738-43

  • Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.

    Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P and Gerstein M

    Genome biology 2009;10;1;R2

  • Identifying protein-coding genes in genomic sequences.

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

    Genome biology 2009;10;1;201

  • Retrocopy contributions to the evolution of the human genome.

    Baertsch R, Diekhans M, Kent WJ, Haussler D and Brosius J

    BMC genomics 2008;9;466

  • 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 and Guigó R

    Nature methods 2008;5;7;629-35

  • An endogenous small interfering RNA pathway in Drosophila.

    Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R, Hannon GJ and Brennecke J

    Nature 2008;453;7196;798-802

  • Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

    Stanke M, Diekhans M, Baertsch R and Haussler D

    Bioinformatics (Oxford, England) 2008;24;5;637-44

  • The vertebrate genome annotation (Vega) database.

    Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T and Harrow JL

    Nucleic acids research 2008;36;Database issue;D753-60

  • Determination and validation of principal gene products.

    Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J and Valencia A

    Bioinformatics (Oxford, England) 2008;24;1;11-7

  • Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice.

    Mudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL, Nicholson C, Robertson DH, Wilming LG and Harrow JL

    Genome biology 2008;9;5;R91

  • The UCSC Genome Browser Database: 2008 update.

    Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D and Kent WJ

    Nucleic acids research 2008;36;Database issue;D773-9

  • Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.

    Zhang ZD, Cayting P, Weinstock G and Gerstein M

    Molecular biology and evolution 2008;25;1;131-43

  • Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

    Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JG, Halls K, Harrow JL, Hart E, Howe K, Jackson DK, Palmer S, Roberts AN, Sims S, Stewart CA, Traherne JA, Trevanion S, Wilming L, Rogers J, de Jong PJ, Elliott JF, Sawcer S, Todd JA, Trowsdale J and Beck S

    Immunogenetics 2008;60;1;1-18

  • Proteomics studies confirm the presence of alternative protein isoforms on a large scale.

    Tress ML, Bodenmiller B, Aebersold R and Valencia A

    Genome biology 2008;9;11;R162

  • 28-way vertebrate alignment and conservation track in the UCSC Genome Browser.

    Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D and Kent WJ

    Genome research 2007;17;12;1797-808

  • Targeted discovery of novel human exons by comparative genomics.

    Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C, Yu HC, Li J, Roe BA, Green P, Gerhard DS, Temple G, Haussler D and Brent MR

    Genome research 2007;17;12;1763-73

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

    ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenb 10f8 aum 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, 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, 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, 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, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B and de Jong PJ

    Nature 2007;447;7146;799-816

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

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

    Genome research 2007;17;6;746-59

  • 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 and Valencia A

    Proceedings of the National Academy of Sciences of the United States of America 2007;104;13;5495-500

  • The ENCODE Project at UC Santa Cruz.

    Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J, Kuhn RM, Rhead BL, Smith KE, Thakkapallayil A, Zweig AS, ENCODE Project Consortium, Haussler D and Kent WJ

    Nucleic acids research 2007;35;Database issue;D663-7

  • The UCSC genome browser database: update 2007.

    Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D and Kent WJ

    Nucleic acids research 2007;35;Database issue;D668-73

  • EGASP: the human ENCODE Genome Annotation Assessment Project.

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

    Genome biology 2006;7 Suppl 1;S2.1-31

 
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