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GENCODE: the reference human genome annotation for The ENCODE Project.
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The GENCODE pseudogene resource.
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Genome biology 2010;11;11;
PUBMED: 21122162; PMC: 3156947; DOI: 10.1186/gb-2010-11-11-309
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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;
PUBMED: 20210993; PMC: 2864566; DOI: 10.1186/gb-2010-11-3-r26
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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;
PUBMED: 20428316; PMC: 2860899; DOI: 10.1093/database/baq001
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Quantifying the mechanisms of domain gain in animal proteins.
Buljan M, Frankish A and Bateman A
Genome biology 2010;11;7;
PUBMED: 20633280; PMC: 2926785; DOI: 10.1186/gb-2010-11-7-r74
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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;
PUBMED: 20011118; PMC: 2782131; DOI: 10.1371/journal.pgen.1000759
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A novel system of polymorphic and diverse NK cell receptors in primates.
Averdam A, Petersen B, Rosner C, Neff J, Roos C, Eberle M, Aujard F, Münch C, Schempp W, Carrington M, Shiina T, Inoko H, Knaust F, Coggill P, Sehra H, Beck S, Abi-Rached L, Reinhardt R and Walter L
PLoS genetics 2009;5;10;
PUBMED: 19834558; PMC: 2757895; DOI: 10.1371/journal.pgen.1000688
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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;
PUBMED: 19498102; PMC: 2704439; DOI: 10.1101/gr.080531.108
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The genome sequence of taurine cattle: a window to ruminant biology and evolution.
Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, White SN, Wilming LG, Wunderlich KR, Yang J and Zhao FQ
Science (New York, N.Y.) 2009;324;5926;
PUBMED: 19390049; PMC: 2943200; DOI: 10.1126/science.1169588
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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;
PUBMED: 19123937; PMC: 2687790; DOI: 10.1186/gb-2009-10-1-r2
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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;
PUBMED: 19226436; PMC: 2687780; DOI: 10.1186/gb-2009-10-1-201
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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;
PUBMED: 20003482; PMC: 2807441; DOI: 10.1186/1471-2164-10-606
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MHC-linked and un-linked class I genes in the wallaby.
Siddle HV, Deakin JE, Coggill P, Hart E, Cheng Y, Wong ES, Harrow J, Beck S and Belov K
BMC genomics 2009;10;
PUBMED: 19602235; PMC: 2719672; DOI: 10.1186/1471-2164-10-310
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Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians.
Smits G, Mungall AJ, Griffiths-Jones S, Smith P, Beury D, Matthews L, Rogers J, Pask AJ, Shaw G, VandeBerg JL, McCarrey JR, SAVOIR Consortium, Renfree MB, Reik W and Dunham I
Nature genetics 2008;40;8;
PUBMED: 18587395; DOI: 10.1038/ng.168
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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;
PUBMED: 18500348; PMC: 2713501; DOI: 10.1038/nmeth.1216
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The evolution of the DLK1-DIO3 imprinted domain in mammals.
Edwards CA, Mungall AJ, Matthews L, Ryder E, Gray DJ, Pask AJ, Shaw G, Graves JA, Rogers J, SAVOIR consortium, Dunham I, Renfree MB and Ferguson-Smith AC
PLoS biology 2008;6;6;
PUBMED: 18532878; PMC: 2408620; DOI: 10.1371/journal.pbio.0060135
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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;
PUBMED: 18006548; PMC: 2734078; DOI: 10.1093/bioinformatics/btm547
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The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T and Gojobori T
Nucleic acids research 2008;36;Database issue;
PUBMED: 18089548; PMC: 2238988; DOI: 10.1093/nar/gkm999
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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;
PUBMED: 18003653; PMC: 2238886; DOI: 10.1093/nar/gkm987
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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;
PUBMED: 18193213; PMC: 2206249; DOI: 10.1007/s00251-007-0262-2
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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;
PUBMED: 18507838; PMC: 2441477; DOI: 10.1186/gb-2008-9-5-r91
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
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Nature 2007;447;7146;
PUBMED: 17571346; PMC: 2212820; DOI: 10.1038/nature05874
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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;
PUBMED: 17567994; PMC: 1891335; DOI: 10.1101/gr.5660607
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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 and Gerstein MB
Genome research 2007;17;6;
PUBMED: 17568002; PMC: 1891343; DOI: 10.1101/gr.5586307
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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;
PUBMED: 17372197; PMC: 1838448; DOI: 10.1073/pnas.0700800104
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A high utility integrated map of the pig genome.
Humphray SJ, Scott CE, Clark R, Marron B, Bender C, Camm N, Davis J, Jenks A, Noon A, Patel M, Sehra H, Yang F, Rogatcheva MB, Milan D, Chardon P, Rohrer G, Nonneman D, de Jong P, Meyers SN, Archibald A, Beever JE, Schook LB and Rogers J
Genome biology 2007;8;7;
PUBMED: 17625002; PMC: 2323232; DOI: 10.1186/gb-2007-8-7-r139
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Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17.
Hart EA, Caccamo M, Harrow JL, Humphray SJ, Gilbert JG, Trevanion S, Hubbard T, Rogers J and Rothschild MF
Genome biology 2007;8;8;
PUBMED: 17705864; PMC: 2374978; DOI: 10.1186/gb-2007-8-8-r168
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The LRC haplotype project: a resource for killer immunoglobulin-like receptor-linked association studies.
Horton R, Coggill P, Miretti MM, Sambrook JG, Traherne JA, Ward R, Sims S, Palmer S, Sehra H, Harrow J, Rogers J, Carrington M, Trowsdale J and Beck S
Tissue antigens 2006;68;5;
PUBMED: 17092261; PMC: 2734079; DOI: 10.1111/j.1399-0039.2006.00697.x
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The genomic sequence and analysis of the swine major histocompatibility complex.
Renard C, Hart E, Sehra H, Beasley H, Coggill P, Howe K, Harrow J, Gilbert J, Sims S, Rogers J, Ando A, Shigenari A, Shiina T, Inoko H, Chardon P and Beck S
Genomics 2006;88;1;
PUBMED: 16515853; DOI: 10.1016/j.ygeno.2006.01.004
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Identification of a single killer immunoglobulin-like receptor (KIR) gene in the porcine leukocyte receptor complex on chromosome 6q.
Sambrook JG, Sehra H, Coggill P, Humphray S, Palmer S, Sims S, Takamatsu HH, Wileman T, Archibald AL and Beck S
Immunogenetics 2006;58;5-6;
PUBMED: 16738944; DOI: 10.1007/s00251-006-0110-9
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The DNA sequence and biological annotation of human chromosome 1.
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Nature 2006;441;7091;
PUBMED: 16710414; DOI: 10.1038/nature04727
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DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.
Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J, Lupski JR, Nicholson C, Searle SM, Wilming L, Young SK, Abouelleil A, Allen NR, Bi W, Bloom T, Borowsky ML, Bugalter BE, Butler J, Chang JL, Chen CK, Cook A, Corum B, Cuomo CA, de Jong PJ, DeCaprio D, Dewar K, FitzGerald M, Gilbert J, Gibson R, Gnerre S, Goldstein S, Grafham DV, Grocock R, Hafez N, Hagopian DS, Hart E, Norman CH, Humphray S, Jaffe DB, Jones M, Kamal M, Khodiyar VK, LaButti K, Laird G, Lehoczky J, Liu X, Lokyitsang T, Loveland J, Lui A, Macdonald P, Major JE, Matthews L, Mauceli E, McCarroll SA, Mihalev AH, Mudge J, Nguyen C, Nicol R, O'Leary SB, Osoegawa K, Schwartz DC, Shaw-Smith C, Stankiewicz P, Steward C, Swarbreck D, Venkataraman V, Whittaker CA, Yang X, Zimmer AR, Bradley A, Hubbard T, Birren BW, Rogers J, Lander ES and Nusbaum C
Nature 2006;440;7087;
PUBMED: 16625196; PMC: 2610434; DOI: 10.1038/nature04689
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Pseudo-messenger RNA: phantoms of the transcriptome.
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PLoS genetics 2006;2;4;
PUBMED: 16683022; PMC: 1449882; DOI: 10.1371/journal.pgen.0020023
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Genomic anatomy of the Tyrp1 (brown) deletion complex.
Smyth IM, Wilming L, Lee AW, Taylor MS, Gautier P, Barlow K, Wallis J, Martin S, Glithero R, Phillimore B, Pelan S, Andrew R, Holt K, Taylor R, McLaren S, Burton J, Bailey J, Sims S, Squares J, Plumb B, Joy A, Gibson R, Gilbert J, Hart E, Laird G, Loveland J, Mudge J, Steward C, Swarbreck D, Harrow J, North P, Leaves N, Greystrong J, Coppola M, Manjunath S, Campbell M, Smith M, Strachan G, Tofts C, Boal E, Cobley V, Hunter G, Kimberley C, Thomas D, Cave-Berry L, Weston P, Botcherby MR, White S, Edgar R, Cross SH, Irvani M, Hummerich H, Simpson EH, Johnson D, Hunsicker PR, Little PF, Hubbard T, Campbell RD, Rogers J and Jackson IJ
Proceedings of the National Academy of Sciences of the United States of America 2006;103;10;
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Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.
Traherne JA, Horton R, Roberts AN, Miretti MM, Hurles ME, Stewart CA, Ashurst JL, Atrazhev AM, Coggill P, Palmer S, Almeida J, Sims S, Wilming LG, Rogers J, de Jong PJ, Carrington M, Elliott JF, Sawcer S, Todd JA, Trowsdale J and Beck S
PLoS genetics 2006;2;1;
PUBMED: 16440057; PMC: 1331980; DOI: 10.1371/journal.pgen.0020009
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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;
PUBMED: 16925836; PMC: 1810551; DOI: 10.1186/gb-2006-7-s1-s2
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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;
PUBMED: 16925838; PMC: 1810553; DOI: 10.1186/gb-2006-7-s1-s4
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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 and Tan SL
Genome biology 2006;7 Suppl 1;
PUBMED: 16925837; PMC: 1810552; DOI: 10.1186/gb-2006-7-s1-s3
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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 and Platzer M
Mammalian genome : official journal of the International Mammalian Genome Society 2005;16;12;
PUBMED: 16341673; DOI: 10.1007/s00335-005-0090-3
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The transcriptional landscape of the mammalian genome.
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Science (New York, N.Y.) 2005;309;5740;
PUBMED: 16141072; DOI: 10.1126/science.1112014
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VEGA, the genome browser with a difference.
Loveland J
Briefings in bioinformatics 2005;6;2;
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The DNA sequence of the human X chromosome.
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Nature 2005;434;7031;
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The Vertebrate Genome Annotation (Vega) database.
Ashurst JL, Chen CK, Gilbert JG, Jekosch K, Keenan S, Meidl P, Searle SM, Stalker J, Storey R, Trevanion S, Wilming L and Hubbard T
Nucleic acids research 2005;33;Database issue;
PUBMED: 15608237; PMC: 540089; DOI: 10.1093/nar/gki135
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Genomic sequence of the class II region of the canine MHC: comparison with the MHC of other mammalian species.
Debenham SL, Hart EA, Ashurst JL, Howe KL, Quail MA, Ollier WE and Binns MM
Genomics 2005;85;1;
PUBMED: 15607421; DOI: 10.1016/j.ygeno.2004.09.009
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Gene map of the extended human MHC.
Horton R, Wilming L, Rand V, Lovering RC, Bruford EA, Khodiyar VK, Lush MJ, Povey S, Talbot CC, Wright MW, Wain HM, Trowsdale J, Ziegler A and Beck S
Nature reviews. Genetics 2004;5;12;
PUBMED: 15573121; DOI: 10.1038/nrg1489
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The ENCODE (ENCyclopedia Of DNA Elements) Project.
ENCODE Project Consortium
Science (New York, N.Y.) 2004;306;5696;
PUBMED: 15499007; DOI: 10.1126/science.1105136
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Identification of mammalian microRNA host genes and transcription units.
Rodriguez A, Griffiths-Jones S, Ashurst JL and Bradley A
Genome research 2004;14;10A;
PUBMED: 15364901; PMC: 524413; DOI: 10.1101/gr.2722704
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Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse.
Mallon AM, Wilming L, Weekes J, Gilbert JG, Ashurst J, Peyrefitte S, Matthews L, Cadman M, McKeone R, Sellick CA, Arkell R, Botcherby MR, Strivens MA, Campbell RD, Gregory S, Denny P, Hancock JM, Rogers J and Brown SD
Genome research 2004;14;10A;
PUBMED: 15364904; PMC: 524412; DOI: 10.1101/gr.2478604
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Complete MHC haplotype sequencing for common disease gene mapping.
Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, Coggill P, Dunham I, Forbes S, Halls K, Howson JM, Humphray SJ, Hunt S, Mungall AJ, Osoegawa K, Palmer S, Roberts AN, Rogers J, Sims S, Wang Y, Wilming LG, Elliott JF, de Jong PJ, Sawcer S, Todd JA, Trowsdale J and Beck S
Genome research 2004;14;6;
PUBMED: 15140828; PMC: 419796; DOI: 10.1101/gr.2188104
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
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PLoS biology 2004;2;6;
PUBMED: 15103394; PMC: 393292; DOI: 10.1371/journal.pbio.0020162
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The DNA sequence and comparative analysis of human chromosome 10.
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Nature 2004;429;6990;
PUBMED: 15164054; DOI: 10.1038/nature02462
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DNA sequence and analysis of human chromosome 9.
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Nature 2004;429;6990;
PUBMED: 15164053; PMC: 2734081; DOI: 10.1038/nature02465
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The DNA sequence and analysis of human chromosome 13.
Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL, Ashcroft KJ, Beare DM, Burford DC, Hunt SE, Griffiths-Jones S, Jones MC, Keenan SJ, Oliver K, Scott CE, Ainscough R, Almeida JP, Ambrose KD, Andrews DT, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Bannerjee R, Barlow KF, Bates K, Beasley H, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burrill W, Carder C, Carter NP, Chapman JC, Clamp ME, Clark SY, Clarke G, Clee CM, Clegg SC, Cobley V, Collins JE, Corby N, Coville GJ, Deloukas P, Dhami P, Dunham I, Dunn M, Earthrowl ME, Ellington AG, Faulkner L, Frankish AG, Frankland J, French L, Garner P, Garnett J, Gilbert JG, Gilson CJ, Ghori J, Grafham DV, Gribble SM, Griffiths C, Hall RE, Hammond S, Harley JL, Hart EA, Heath PD, Howden PJ, Huckle EJ, Hunt PJ, Hunt AR, Johnson C, Johnson D, Kay M, Kimberley AM, King A, Laird GK, Langford CJ, Lawlor S, Leongamornlert DA, Lloyd DM, Lloyd C, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, McLaren SJ, McMurray A, Milne S, Moore MJ, Nickerson T, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter KM, Rice CM, Searle S, Sehra HK, Shownkeen R, Skuce CD, Smith M, Steward CA, Sycamore N, Tester J, Thomas DW, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Wilming L, Wray PW, Wright MW, Young L, Coulson A, Durbin R, Hubbard T, Sulston JE, Beck S, Bentley DR, Rogers J and Ross MT
Nature 2004;428;6982;
PUBMED: 15057823; PMC: 2665288; DOI: 10.1038/nature02379
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Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.
Taudien S, Galgoczy P, Huse K, Reichwald K, Schilhabel M, Szafranski K, Shimizu A, Asakawa S, Frankish A, Loncarevic IF, Shimizu N, Siddiqui R and Platzer M
BMC genomics 2004;5;1;
PUBMED: 15588320; PMC: 544879; DOI: 10.1186/1471-2164-5-92
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The DNA sequence and analysis of human chromosome 6.
Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JG, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJ, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd CR, Lloyd DM, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen GL, Matthews L, McCann OT, McLaren SJ, McLay K, McMurray A, Moore MJ, Mullikin JC, Niblett D, Nickerson T, Novik KL, Oliver K, Overton-Larty EK, Parker A, Patel R, Pearce AV, Peck AI, Phillimore B, Phillips S, Plumb RW, Porter KM, Ramsey Y, Ranby SA, Rice CM, Ross MT, Searle SM, Sehra HK, Sheridan E, Skuce CD, Smith S, Smith M, Spraggon L, Squares SL, Steward CA, Sycamore N, Tamlyn-Hall G, Tester J, Theaker AJ, Thomas DW, Thorpe A, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, White SS, Whitehead SL, Whittaker H, Wild A, Willey DJ, Wilmer TE, Wood JM, Wray PW, Wyatt JC, Young L, Younger RM, Bentley DR, Coulson A, Durbin R, Hubbard T, Sulston JE, Dunham I, Rogers J and Beck S
Nature 2003;425;6960;
PUBMED: 14574404; DOI: 10.1038/nature02055
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Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.
Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M, RIKEN GER Group and GSL Members
Genome research 2003;13;6B;
PUBMED: 12819127; PMC: 403720; DOI: 10.1101/gr.1011603
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Gene annotation: prediction and testing.
Ashurst JL and Collins JE
Annual review of genomics and human genetics 2003;4;
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Meeting highlights: genome informatics.
Wixon J and Ashurst J
Comparative and functional genomics 2003;4;5;
PUBMED: 18629014; PMC: 2447296; DOI: 10.1002/cfg.300
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Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
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Nature 2001;414;6866;
PUBMED: 11780052; DOI: 10.1038/414865a
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Initial sequencing and analysis of the human genome.
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Nature 2001;409;6822;
PUBMED: 11237011; DOI: 10.1038/35057062
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The DNA sequence of human chromosome 22.
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PUBMED: 10591208; DOI: 10.1038/990031
