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For: Collins JE, Goward ME, Cole CG, Smink LJ, Huckle EJ, Knowles S, Bye JM, Beare DM, Dunham I. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res 2003;13:27-36. [PMID: 12529303 PMCID: PMC430954 DOI: 10.1101/gr.695703] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
Youssef SS, Abbas EAER, Elfiky AM, Seif S, Nabeel MM, Shousha HI, Abdelaziz AO. The impact of polymorphism in PNPLA3 and TM6SF2 genes on the susceptibility and survival of hepatitis C-related hepatocellular carcinoma. EGYPTIAN LIVER JOURNAL 2022. [DOI: 10.1186/s43066-022-00212-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
2
Murray JK, Long J, Liu L, Singh S, Pruitt D, Ollmann M, Swearingen E, Hardy M, Homann O, Wu B, Holder JR, Sham K, Herberich B, Lo MC, Dou H, Shkumatov A, Florio M, Rulifson IC. Identification and Optimization of a Minor Allele-Specific Small Interfering RNA to Prevent PNPLA3 I148M-Driven Nonalcoholic Fatty Liver Disease. Nucleic Acid Ther 2021;31:324-340. [PMID: 34297902 DOI: 10.1089/nat.2021.0026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
3
Hatje K, Mühlhausen S, Simm D, Kollmar M. The Protein-Coding Human Genome: Annotating High-Hanging Fruits. Bioessays 2019;41:e1900066. [PMID: 31544971 DOI: 10.1002/bies.201900066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/07/2019] [Indexed: 12/19/2022]
4
Huang Z, Guo X, Zhang G, Liang L, Nong B. Correlation between PNPLA3 rs738409 polymorphism and hepatocellular carcinoma: a meta-analysis of 10,330 subjects. Int J Biol Markers 2019;34:117-122. [PMID: 30852978 DOI: 10.1177/1724600818812471] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
5
Li HG, Liu FF, Zhu HQ, Zhou X, Lu J, Chang H, Hu JH. Significant Association Between Adiponutrin and Hepatocellular Carcinoma Risk. Medicine (Baltimore) 2015;94:e2019. [PMID: 26632699 PMCID: PMC5058968 DOI: 10.1097/md.0000000000002019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]  Open
6
Shi L, Lin YH, Sierant MC, Zhu F, Cui S, Guan Y, Sartor MA, Tanabe O, Lim KC, Engel JD. Developmental transcriptome analysis of human erythropoiesis. Hum Mol Genet 2014;23:4528-42. [PMID: 24781209 DOI: 10.1093/hmg/ddu167] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
7
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. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One 2012;7:e28213. [PMID: 22238572 PMCID: PMC3251577 DOI: 10.1371/journal.pone.0028213] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 11/03/2011] [Indexed: 12/03/2022]  Open
8
Höglund PJ, Nordström KJV, Schiöth HB, Fredriksson R. The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species. Mol Biol Evol 2010;28:1531-41. [PMID: 21186191 PMCID: PMC3058773 DOI: 10.1093/molbev/msq350] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
9
Dunham I, Beare DM, Collins JE. The characteristics of human genes: analysis of human chromosome 22. Comp Funct Genomics 2010;4:635-46. [PMID: 18629020 PMCID: PMC2447302 DOI: 10.1002/cfg.335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Revised: 09/04/2003] [Accepted: 09/08/2003] [Indexed: 11/11/2022]  Open
10
Cole CG, McCann OT, Collins JE, Oliver K, Willey D, Gribble SM, Yang F, McLaren K, Rogers J, Ning Z, Beare DM, Dunham I. Finishing the finished human chromosome 22 sequence. Genome Biol 2008;9:R78. [PMID: 18477386 PMCID: PMC2441464 DOI: 10.1186/gb-2008-9-5-r78] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 04/10/2008] [Accepted: 05/13/2008] [Indexed: 11/25/2022]  Open
11
Buckley NJ. Analysis of transcription, chromatin dynamics and epigenetic changes in neural genes. Prog Neurobiol 2007;83:195-210. [PMID: 17884276 DOI: 10.1016/j.pneurobio.2007.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 06/14/2007] [Accepted: 07/18/2007] [Indexed: 01/08/2023]
12
Frishman D. Protein annotation at genomic scale: the current status. Chem Rev 2007;107:3448-66. [PMID: 17658902 DOI: 10.1021/cr068303k] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
13
Winn VD, Haimov-Kochman R, Paquet AC, Yang YJ, Madhusudhan MS, Gormley M, Feng KTV, Bernlohr DA, McDonagh S, Pereira L, Sali A, Fisher SJ. Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology 2007;148:1059-79. [PMID: 17170095 DOI: 10.1210/en.2006-0683] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
14
Sasaki D, Kondo S, Maeda N, Gingeras TR, Hasegawa Y, Hayashizaki Y. Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: causes of signal variation and false positive signals. Genomics 2007;89:541-51. [PMID: 17292583 DOI: 10.1016/j.ygeno.2006.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 11/14/2006] [Accepted: 12/29/2006] [Indexed: 10/23/2022]
15
Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res 2006;35:D55-60. [PMID: 17099229 PMCID: PMC1669708 DOI: 10.1093/nar/gkl851] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
16
Damaraju S, Murray D, Dufour J, Carandang D, Myrehaug S, Fallone G, Field C, Greiner R, Hanson J, Cass CE, Parliament M. Association of DNA repair and steroid metabolism gene polymorphisms with clinical late toxicity in patients treated with conformal radiotherapy for prostate cancer. Clin Cancer Res 2006;12:2545-54. [PMID: 16638864 DOI: 10.1158/1078-0432.ccr-05-2703] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
17
Wu J, Haussler D. Coding exon detection using comparative sequences. J Comput Biol 2006;13:1148-64. [PMID: 16901234 DOI: 10.1089/cmb.2006.13.1148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
18
Flicek P, Brent MR. Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts. Genome Biol 2006;7 Suppl 1:S8.1-9. [PMID: 16925842 PMCID: PMC1810557 DOI: 10.1186/gb-2006-7-s1-s8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
19
Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol 2006;7 Suppl 1:S2.1-31. [PMID: 16925836 PMCID: PMC1810551 DOI: 10.1186/gb-2006-7-s1-s2] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
20
Stanke M, Schöffmann O, Morgenstern B, Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 2006;7:62. [PMID: 16469098 PMCID: PMC1409804 DOI: 10.1186/1471-2105-7-62] [Citation(s) in RCA: 766] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Accepted: 02/09/2006] [Indexed: 11/10/2022]  Open
21
Narang V, Sung WK, Mittal A. Computational modeling of oligonucleotide positional densities for human promoter prediction. Artif Intell Med 2005;35:107-19. [PMID: 16076553 DOI: 10.1016/j.artmed.2005.02.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2004] [Revised: 01/31/2005] [Accepted: 02/22/2005] [Indexed: 11/18/2022]
22
Lipovich L, King MC. Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. Genome Res 2005;16:45-54. [PMID: 16344557 PMCID: PMC1356128 DOI: 10.1101/gr.3883606] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
23
Seng TJ, Ichimura K, Liu L, Tingby O, Pearson DM, Collins VP. Complex chromosome 22 rearrangements in astrocytic tumors identified using microsatellite and chromosome 22 tile path array analysis. Genes Chromosomes Cancer 2005;43:181-93. [PMID: 15770670 DOI: 10.1002/gcc.20181] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
24
Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol 2005;349:27-45. [PMID: 15876366 DOI: 10.1016/j.jmb.2005.02.072] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Revised: 02/16/2005] [Accepted: 02/23/2005] [Indexed: 02/06/2023]
25
Nelson DR, Nebert DW. The truth about mouse, human, worms and yeast. Hum Genomics 2005;1:146-9. [PMID: 15601543 PMCID: PMC3525071 DOI: 10.1186/1479-7364-1-2-146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
26
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 duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004;431:946-57. [PMID: 15496914 DOI: 10.1038/nature03025] [Citation(s) in RCA: 1406] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Accepted: 09/08/2004] [Indexed: 12/16/2022]
27
Finishing the euchromatic sequence of the human genome. Nature 2004;431:931-45. [PMID: 15496913 DOI: 10.1038/nature03001] [Citation(s) in RCA: 2806] [Impact Index Per Article: 140.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Accepted: 09/07/2004] [Indexed: 12/13/2022]
28
Arcand SL, Mes-Masson AM, Provencher D, Hudson TJ, Tonin PN. Gene expression microarray analysis and genome databases facilitate the characterization of a chromosome 22 derived homogeneously staining region. Mol Carcinog 2004;41:17-38. [PMID: 15352123 DOI: 10.1002/mc.20038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
29
Lipovich L, King MC. Novel transcriptional units and unconventional gene pairs in the human genome: toward a sequence-level basis for primate-specific phenotypes? COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004;68:461-70. [PMID: 15338649 DOI: 10.1101/sqb.2003.68.461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
30
Collins JE, Wright CL, Edwards CA, Davis MP, Grinham JA, Cole CG, Goward ME, Aguado B, Mallya M, Mokrab Y, Huckle EJ, Beare DM, Dunham I. A genome annotation-driven approach to cloning the human ORFeome. Genome Biol 2004;5:R84. [PMID: 15461802 PMCID: PMC545604 DOI: 10.1186/gb-2004-5-10-r84] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2004] [Revised: 07/16/2004] [Accepted: 08/11/2004] [Indexed: 11/10/2022]  Open
31
Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, Svetnik V, Leonardson A, Hart KW, Russell A, Li G, Cavet G, Castle J, McDonagh P, Kan Z, Chen R, Kasarskis A, Margarint M, Caceres RM, Johnson JM, Armour CD, Garrett-Engele PW, Tsinoremas NF, Shoemaker DD. A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol 2004;5:R73. [PMID: 15461792 PMCID: PMC545593 DOI: 10.1186/gb-2004-5-10-r73] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 07/07/2004] [Accepted: 08/16/2004] [Indexed: 12/13/2022]  Open
32
Down TA, Hubbard TJP. What can we learn from noncoding regions of similarity between genomes? BMC Bioinformatics 2004;5:131. [PMID: 15369604 PMCID: PMC523850 DOI: 10.1186/1471-2105-5-131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Accepted: 09/15/2004] [Indexed: 11/10/2022]  Open
33
Taylor TD. After 'completion': the changing face of human chromosomes 21 and 22. Genome Biol 2004;5:111. [PMID: 15239819 PMCID: PMC463270 DOI: 10.1186/gb-2004-5-7-111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
34
Bentley DR. Genomes for medicine. Nature 2004;429:440-5. [PMID: 15164068 DOI: 10.1038/nature02622] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
35
Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol 2004;24:3804-14. [PMID: 15082775 PMCID: PMC387762 DOI: 10.1128/mcb.24.9.3804-3814.2004] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
36
Eichler EE, Clark RA, She X. An assessment of the sequence gaps: Unfinished business in a finished human genome. Nat Rev Genet 2004;5:345-54. [PMID: 15143317 DOI: 10.1038/nrg1322] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
37
Searle SMJ, Gilbert J, Iyer V, Clamp M. The otter annotation system. Genome Res 2004;14:963-70. [PMID: 15123593 PMCID: PMC479127 DOI: 10.1101/gr.1864804] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Accepted: 03/04/2004] [Indexed: 11/25/2022]
38
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 RIS, 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 SCM, 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 JGR, 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 MJF, 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, Ross MT. The DNA sequence and analysis of human chromosome 13. Nature 2004;428:522-8. [PMID: 15057823 PMCID: PMC2665288 DOI: 10.1038/nature02379] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Accepted: 01/27/2004] [Indexed: 12/14/2022]
39
Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, Gingeras TR. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 2004;14:331-42. [PMID: 14993201 PMCID: PMC353210 DOI: 10.1101/gr.2094104] [Citation(s) in RCA: 417] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
40
Porcel BM, Delfour O, Castelli V, De Berardinis V, Friedlander L, Cruaud C, Ureta-Vidal A, Scarpelli C, Wincker P, Schächter V, Saurin W, Gyapay G, Salanoubat M, Weissenbach J. Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection. Genome Res 2004;14:463-71. [PMID: 14962985 PMCID: PMC353234 DOI: 10.1101/gr.1481104] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Babcock M, Pavlicek A, Spiteri E, Kashork CD, Ioshikhes I, Shaffer LG, Jurka J, Morrow BE. Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. Genome Res 2004;13:2519-32. [PMID: 14656960 PMCID: PMC403794 DOI: 10.1101/gr.1549503] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Res 2004;13:2559-67. [PMID: 14656963 PMCID: PMC403797 DOI: 10.1101/gr.1455503] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Thomas S, Porteous D, Visscher PM. Power of direct vs. indirect haplotyping in association studies. Genet Epidemiol 2004;26:116-24. [PMID: 14748011 DOI: 10.1002/gepi.10300] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD, Debernardi S, Mott R, Dunham I, Carter NP. Replication timing of the human genome. Hum Mol Genet 2003;13:191-202. [PMID: 14645202 DOI: 10.1093/hmg/ddh016] [Citation(s) in RCA: 242] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JGR, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RIS, 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 MJR, 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 MJF, 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, Beck S. The DNA sequence and analysis of human chromosome 6. Nature 2003;425:805-11. [PMID: 14574404 DOI: 10.1038/nature02055] [Citation(s) in RCA: 235] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2003] [Accepted: 09/11/2003] [Indexed: 01/17/2023]
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Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A 2003;100:12247-52. [PMID: 14527995 PMCID: PMC218744 DOI: 10.1073/pnas.2135255100] [Citation(s) in RCA: 266] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 2003;100:11484-9. [PMID: 14500911 PMCID: PMC208784 DOI: 10.1073/pnas.1932072100] [Citation(s) in RCA: 603] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2003] [Indexed: 11/18/2022]  Open
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Ashurst JL, Collins JE. GENEANNOTATION: PREDICTION ANDTESTING. Annu Rev Genomics Hum Genet 2003;4:69-88. [PMID: 14527297 DOI: 10.1146/annurev.genom.4.070802.110300] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wang J, Li S, Zhang Y, Zheng H, Xu Z, Ye J, Yu J, Wong GKS. Vertebrate gene predictions and the problem of large genes. Nat Rev Genet 2003;4:741-9. [PMID: 12951575 DOI: 10.1038/nrg1160] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Chong A, Zhang G, Bajic VB. FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes. Nucleic Acids Res 2003;31:3546-53. [PMID: 12824363 PMCID: PMC169010 DOI: 10.1093/nar/gkg604] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
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