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Items: 1 to 50 of 55

1.

Ensembl 2020.

Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Marugán JC, Cummins C, Davidson C, Dodiya K, Fatima R, Gall A, Giron CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Lavidas I, Le T, Lemos D, Martinez JG, Maurel T, McDowall M, McMahon A, Mohanan S, Moore B, Nuhn M, Oheh DN, Parker A, Parton A, Patricio M, Sakthivel MP, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sycheva M, Szuba M, Taylor K, Thormann A, Threadgold G, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Flint B, Frankish A, Hunt SE, IIsley G, Kostadima M, Langridge N, Loveland JE, Martin FJ, Morales J, Mudge JM, Muffato M, Perry E, Ruffier M, Trevanion SJ, Cunningham F, Howe KL, Zerbino DR, Flicek P.

Nucleic Acids Res. 2019 Nov 6. pii: gkz966. doi: 10.1093/nar/gkz966. [Epub ahead of print]

PMID:
31691826
2.

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.

Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright JC, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S, He L, Waterhouse RM, Li Y, Bruford E, Choudhary JS, Frankish A, Kellis M.

Genome Res. 2019 Sep 19. doi: 10.1101/gr.246462.118. [Epub ahead of print]

3.

Getting the Entire Message: Progress in Isoform Sequencing.

Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU.

Front Genet. 2019 Aug 16;10:709. doi: 10.3389/fgene.2019.00709. eCollection 2019. Review.

4.

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

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

Nucleic Acids Res. 2019 Jun 4;47(10):5293-5306. doi: 10.1093/nar/gkz193.

5.

Ensembl 2019.

Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, Cummins C, Davidson C, Dodiya KJ, Gall A, Girón CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Laird MR, Lavidas I, Liu Z, Loveland JE, Marugán JC, Maurel T, McMahon AC, Moore B, Morales J, Mudge JM, Nuhn M, Ogeh D, Parker A, Parton A, Patricio M, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sparrow H, Stapleton E, Szuba M, Taylor K, Threadgold G, Thormann A, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Yates AD, Zerbino DR, Flicek P.

Nucleic Acids Res. 2019 Jan 8;47(D1):D745-D751. doi: 10.1093/nar/gky1113.

6.

GENCODE reference annotation for the human and mouse genomes.

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

Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773. doi: 10.1093/nar/gky955.

7.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM.

Nat Genet. 2018 Nov;50(11):1574-1583. doi: 10.1038/s41588-018-0223-8. Epub 2018 Oct 1.

8.

Genome-wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy.

Schoeler NE, Leu C, Balestrini S, Mudge JM, Steward CA, Frankish A, Leung MA, Mackay M, Scheffer I, Williams R, Sander JW, Cross JH, Sisodiya SM.

Epilepsia. 2018 Aug;59(8):1557-1566. doi: 10.1111/epi.14516. Epub 2018 Jul 16.

9.

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

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

Nat Rev Genet. 2018 Sep;19(9):535-548. doi: 10.1038/s41576-018-0017-y. Review.

10.

Ensembl 2018.

Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P.

Nucleic Acids Res. 2018 Jan 4;46(D1):D754-D761. doi: 10.1093/nar/gkx1098.

11.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D221-D228. doi: 10.1093/nar/gkx1031.

12.

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

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

Nat Genet. 2017 Dec;49(12):1731-1740. doi: 10.1038/ng.3988. Epub 2017 Nov 6.

13.

Genome annotation for clinical genomic diagnostics: strengths and weaknesses.

Steward CA, Parker APJ, Minassian BA, Sisodiya SM, Frankish A, Harrow J.

Genome Med. 2017 May 30;9(1):49. doi: 10.1186/s13073-017-0441-1. Review.

14.

RNAcentral: a comprehensive database of non-coding RNA sequences.

The RNAcentral Consortium, Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME.

Nucleic Acids Res. 2017 Jan 4;45(D1):D128-D134. doi: 10.1093/nar/gkw1008. Epub 2016 Oct 28.

15.

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

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

BMC Genomics. 2015;16 Suppl 8:S2. doi: 10.1186/1471-2164-16-S8-S2. Epub 2015 Jun 18.

16.

Comparative analysis of the transcriptome across distant species.

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

Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.

17.

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, Gerstein MB.

Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13361-6. doi: 10.1073/pnas.1407293111. Epub 2014 Aug 25.

18.

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, Tress ML.

Hum Mol Genet. 2014 Nov 15;23(22):5866-78. doi: 10.1093/hmg/ddu309. Epub 2014 Jun 16.

19.

GENCODE pseudogenes.

Frankish A, Harrow J.

Methods Mol Biol. 2014;1167:129-55. doi: 10.1007/978-1-4939-0835-6_10.

PMID:
24823776
20.

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, Wilming LG.

Nucleic Acids Res. 2014 Jan;42(Database issue):D771-9. doi: 10.1093/nar/gkt1241. Epub 2013 Dec 6.

21.

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, Pruitt KD.

Nucleic Acids Res. 2014 Jan;42(Database issue):D865-72. doi: 10.1093/nar/gkt1059. Epub 2013 Nov 11.

22.

Functional transcriptomics in the post-ENCODE era.

Mudge JM, Frankish A, Harrow J.

Genome Res. 2013 Dec;23(12):1961-73. doi: 10.1101/gr.161315.113. Epub 2013 Oct 30.

23.

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

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

Genome Biol. 2013 Jul 1;14(7):R70. doi: 10.1186/gb-2013-14-7-r70.

24.

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

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

Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111.

25.

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

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

Genome Res. 2012 Sep;22(9):1698-710. doi: 10.1101/gr.134478.111.

26.

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, Gerstein MB.

Genome Biol. 2012 Sep 26;13(9):R51. doi: 10.1186/gb-2012-13-9-r51.

27.

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, Tress ML.

Mol Biol Evol. 2012 Sep;29(9):2265-83. doi: 10.1093/molbev/mss100. Epub 2012 Mar 22.

28.

The importance of identifying alternative splicing in vertebrate genome annotation.

Frankish A, Mudge JM, Thomas M, Harrow J.

Database (Oxford). 2012 Mar 20;2012:bas014. doi: 10.1093/database/bas014. Print 2012.

29.

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, Pruitt KD.

Database (Oxford). 2012 Mar 20;2012:bas008. doi: 10.1093/database/bas008. Print 2012.

30.

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, Tyler-Smith C.

Science. 2012 Feb 17;335(6070):823-8. doi: 10.1126/science.1215040. Erratum in: Science. 2012 Apr 20;336(6079):296.

31.

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

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

PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4.

32.

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

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

Mol Biol Evol. 2011 Oct;28(10):2949-59. doi: 10.1093/molbev/msr127. Epub 2011 May 6.

33.

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T.

Genome Res. 2011 May;21(5):756-67. doi: 10.1101/gr.114272.110. Epub 2011 Apr 1.

34.

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, Gerstein M.

Genes Dev. 2011 Jan 1;25(1):1-10. doi: 10.1101/gad.1968411.

35.

Quantifying the mechanisms of domain gain in animal proteins.

Buljan M, Frankish A, Bateman A.

Genome Biol. 2010;11(7):R74. doi: 10.1186/gb-2010-11-7-r74. Epub 2010 Jul 15.

36.

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

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

Genome Biol. 2010;11(3):R26. doi: 10.1186/gb-2010-11-3-r26. Epub 2010 Mar 8.

37.

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, Lipman D.

Genome Res. 2009 Jul;19(7):1316-23. doi: 10.1101/gr.080531.108. Epub 2009 Jun 4. Erratum in: Genome Res. 2009 Aug;19(8):1506.

38.

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, Gerstein M.

Genome Biol. 2009;10(1):R2. doi: 10.1186/gb-2009-10-1-r2. Epub 2009 Jan 5.

39.

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

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

Nat Methods. 2008 Jul;5(7):629-35. doi: 10.1038/nmeth.1216. Epub 2008 May 25.

40.

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, Valencia A.

Bioinformatics. 2008 Jan 1;24(1):11-7. Epub 2007 Nov 15.

41.

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

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

Nature. 2007 Jun 14;447(7146):799-816.

42.

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

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

Genome Res. 2007 Jun;17(6):839-51.

43.

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

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

Genome Res. 2007 Jun;17(6):746-59.

44.

The implications of alternative splicing in the ENCODE protein complement.

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

Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500. Epub 2007 Mar 19.

45.

GENCODE: producing a reference annotation for ENCODE.

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

Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.

46.

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

Bajic VB, Brent MR, Brown RH, Frankish A, Harrow J, Ohler U, Solovyev VV, Tan SL.

Genome Biol. 2006;7 Suppl 1:S3.1-13. Epub 2006 Aug 7. Review.

47.

The DNA sequence and biological annotation of human chromosome 1.

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Nature. 2006 May 18;441(7091):315-21. Erratum in: Nature. 2006 Oct 26;443(7114):1013. Banerjee, R [added]; Bryant, SP [added]; Burford, DC [added]; Burrill, WDH [added]; Clegg, SM [added]; Dhami, P [added]; Dovey, O [added]; Faulkner, LM [added]; Gribble, SM [added]; Langford, CF [added]; Pandian, RD [added]; Porter, KM [added]; Prigmore, E.

PMID:
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48.

Validation of mRNA/EST-based gene predictions in human Xp11.4 revealed differences to the organization of the orthologous mouse locus.

Wen G, Ramser J, Taudien S, Gausmann U, Blechschmidt K, Frankish A, Ashurst J, Meindl A, Platzer M.

Mamm Genome. 2005 Dec;16(12):934-41. Epub 2005 Dec 8.

PMID:
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The DNA sequence of the human X chromosome.

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