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For: Kent WJ, Haussler D. Assembly of the working draft of the human genome with GigAssembler. Genome Res 2001;11:1541-8. [PMID: 11544197 PMCID: PMC311095 DOI: 10.1101/gr.183201] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Number Cited by Other Article(s)
1
Rood JE, Wynne S, Robson L, Hupalowska A, Randell J, Teichmann SA, Regev A. The Human Cell Atlas from a cell census to a unified foundation model. Nature 2025;637:1065-1071. [PMID: 39566552 DOI: 10.1038/s41586-024-08338-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 11/01/2024] [Indexed: 11/22/2024]
2
Orliaguet L, Ejlalmanesh T, Humbert A, Ballaire R, Diedisheim M, Julla JB, Chokr D, Cuenco J, Michieletto J, Charbit J, Lindén D, Boucher J, Potier C, Hamimi A, Lemoine S, Blugeon C, Legoix P, Lameiras S, Baudrin LG, Baulande S, Soprani A, Castelli FA, Fenaille F, Riveline JP, Dalmas E, Rieusset J, Gautier JF, Venteclef N, Alzaid F. Early macrophage response to obesity encompasses Interferon Regulatory Factor 5 regulated mitochondrial architecture remodelling. Nat Commun 2022;13:5089. [PMID: 36042203 PMCID: PMC9427774 DOI: 10.1038/s41467-022-32813-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/16/2022] [Indexed: 11/29/2022]  Open
3
Badowski C, He B, Garmire LX. Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. NPJ Precis Oncol 2022;6:40. [PMID: 35729321 PMCID: PMC9213432 DOI: 10.1038/s41698-022-00283-7] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022]  Open
4
Eslami Rasekh M, Hernández Y, Drinan SD, Fuxman Bass J, Benson G. Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. Nucleic Acids Res 2021;49:4308-4324. [PMID: 33849068 PMCID: PMC8096271 DOI: 10.1093/nar/gkab224] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/06/2021] [Accepted: 03/18/2021] [Indexed: 11/12/2022]  Open
5
Gavrielatos M, Kyriakidis K, Spandidos DA, Michalopoulos I. Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly. Mol Med Rep 2021;23:251. [PMID: 33537807 PMCID: PMC7893683 DOI: 10.3892/mmr.2021.11890] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/21/2021] [Indexed: 12/30/2022]  Open
6
Kaye AM, Wasserman WW. The genome atlas: navigating a new era of reference genomes. Trends Genet 2021;37:807-818. [PMID: 33419587 DOI: 10.1016/j.tig.2020.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
7
Kumar PS, Dabdoub SM, Ganesan SM. Probing periodontal microbial dark matter using metataxonomics and metagenomics. Periodontol 2000 2020;85:12-27. [PMID: 33226714 DOI: 10.1111/prd.12349] [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]
8
SCOP: a novel scaffolding algorithm based on contig classification and optimization. Bioinformatics 2018;35:1142-1150. [DOI: 10.1093/bioinformatics/bty773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 08/10/2018] [Accepted: 09/01/2018] [Indexed: 12/20/2022]  Open
9
Li M, Tang L, Liao Z, Luo J, Wu F, Pan Y, Wang J. A novel scaffolding algorithm based on contig error correction and path extension. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;16:764-773. [PMID: 30040649 DOI: 10.1109/tcbb.2018.2858267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
10
Gao B, Huang Q, Baudis M. segment_liftover : a Python tool to convert segments between genome assemblies. F1000Res 2018;7:319. [PMID: 29946440 PMCID: PMC5998006 DOI: 10.12688/f1000research.14148.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/01/2018] [Indexed: 11/25/2022]  Open
11
Jäger M, Schubach M, Zemojtel T, Reinert K, Church DM, Robinson PN. Alternate-locus aware variant calling in whole genome sequencing. Genome Med 2016;8:130. [PMID: 27964746 PMCID: PMC5155401 DOI: 10.1186/s13073-016-0383-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/23/2016] [Indexed: 01/09/2023]  Open
12
Kryukov K, Imanishi T. Human Contamination in Public Genome Assemblies. PLoS One 2016;11:e0162424. [PMID: 27611326 PMCID: PMC5017631 DOI: 10.1371/journal.pone.0162424] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/31/2016] [Indexed: 01/29/2023]  Open
13
Beier S, Himmelbach A, Schmutzer T, Felder M, Taudien S, Mayer KFX, Platzer M, Stein N, Scholz U, Mascher M. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2016;14:1511-22. [PMID: 26801048 PMCID: PMC5066668 DOI: 10.1111/pbi.12511] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 05/02/2023]
14
Papanicolaou A. The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects. F1000Res 2016;5:18. [PMID: 27006757 PMCID: PMC4798206 DOI: 10.12688/f1000research.7559.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/10/2015] [Indexed: 11/20/2022]  Open
15
Deming Y, Xia J, Cai Y, Lord J, Holmans P, Bertelsen S, Holtzman D, Morris JC, Bales K, Pickering EH, Kauwe J, Goate A, Cruchaga C. A potential endophenotype for Alzheimer's disease: cerebrospinal fluid clusterin. Neurobiol Aging 2016;37:208.e1-208.e9. [PMID: 26545630 PMCID: PMC5118651 DOI: 10.1016/j.neurobiolaging.2015.09.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/12/2015] [Indexed: 12/30/2022]
16
Manel S, Perrier C, Pratlong M, Abi-Rached L, Paganini J, Pontarotti P, Aurelle D. Genomic resources and their influence on the detection of the signal of positive selection in genome scans. Mol Ecol 2015;25:170-84. [DOI: 10.1111/mec.13468] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/06/2015] [Accepted: 11/07/2015] [Indexed: 12/16/2022]
17
Simpson JT, Pop M. The Theory and Practice of Genome Sequence Assembly. Annu Rev Genomics Hum Genet 2015;16:153-72. [PMID: 25939056 DOI: 10.1146/annurev-genom-090314-050032] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
18
Wilks C, Cline MS, Weiler E, Diehkans M, Craft B, Martin C, Murphy D, Pierce H, Black J, Nelson D, Litzinger B, Hatton T, Maltbie L, Ainsworth M, Allen P, Rosewood L, Mitchell E, Smith B, Warner J, Groboske J, Telc H, Wilson D, Sanford B, Schmidt H, Haussler D, Maltbie D. The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014;2014:bau093. [PMID: 25267794 PMCID: PMC4178372 DOI: 10.1093/database/bau093] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
19
Xue W, Li JT, Zhu YP, Hou GY, Kong XF, Kuang YY, Sun XW. L_RNA_scaffolder: scaffolding genomes with transcripts. BMC Genomics 2013;14:604. [PMID: 24010822 PMCID: PMC3846640 DOI: 10.1186/1471-2164-14-604] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 09/03/2013] [Indexed: 11/25/2022]  Open
20
Jorge NAN, Ferreira CG, Passetti F. Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges. Front Genet 2012;3:287. [PMID: 23251139 PMCID: PMC3523245 DOI: 10.3389/fgene.2012.00287] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/22/2012] [Indexed: 12/24/2022]  Open
21
Kuhn RM, Haussler D, Kent WJ. The UCSC genome browser and associated tools. Brief Bioinform 2012;14:144-61. [PMID: 22908213 PMCID: PMC3603215 DOI: 10.1093/bib/bbs038] [Citation(s) in RCA: 607] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
22
Gritsenko AA, Nijkamp JF, Reinders MJT, Ridder DD. GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinformatics 2012;28:1429-37. [DOI: 10.1093/bioinformatics/bts175] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
23
Gao S, Sung WK, Nagarajan N. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol 2011;18:1681-91. [PMID: 21929371 DOI: 10.1089/cmb.2011.0170] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
24
Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GRS, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, Wollam A, Trani L, Fulton L, Fulton R, Matthews L, Whitehead S, Chow W, Torrance J, Dunn M, Harden G, Threadgold G, Wood J, Collins J, Heath P, Griffiths G, Pelan S, Grafham D, Eichler EE, Weinstock G, Mardis ER, Wilson RK, Howe K, Flicek P, Hubbard T. Modernizing reference genome assemblies. PLoS Biol 2011;9:e1001091. [PMID: 21750661 PMCID: PMC3130012 DOI: 10.1371/journal.pbio.1001091] [Citation(s) in RCA: 378] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
25
Mortazavi A, Schwarz EM, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW. Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res 2010;20:1740-7. [PMID: 20980554 PMCID: PMC2990000 DOI: 10.1101/gr.111021.110] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 08/24/2010] [Indexed: 11/25/2022]
26
Narzisi G, Mishra B. Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons. ACTA ACUST UNITED AC 2010;27:153-60. [PMID: 21088026 DOI: 10.1093/bioinformatics/btq646] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
27
Homer N, Nelson SF. Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol 2010;11:R99. [PMID: 20932289 PMCID: PMC3218665 DOI: 10.1186/gb-2010-11-10-r99] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 08/25/2010] [Accepted: 10/08/2010] [Indexed: 11/10/2022]  Open
28
Next-generation gap. Nat Methods 2009;6:S2-5. [PMID: 19844227 DOI: 10.1038/nmeth.f.268] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
29
Nelson W, Soderlund C. Integrating sequence with FPC fingerprint maps. Nucleic Acids Res 2009;37:e36. [PMID: 19181701 PMCID: PMC2655663 DOI: 10.1093/nar/gkp034] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
30
Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, Tommerup N, Gilchrist MJ, Nygård AB, Cirera S, Jørgensen CB, Fredholm M, Gorodkin J. Sequence assembly. Comput Biol Chem 2008;33:121-36. [PMID: 19152793 DOI: 10.1016/j.compbiolchem.2008.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 11/28/2008] [Accepted: 11/28/2008] [Indexed: 01/20/2023]
31
Profile of David Haussler. Proc Natl Acad Sci U S A 2008;105:14251-3. [DOI: 10.1073/pnas.0808284105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
32
Rouchka EC, Phatak AW, Singh AV. Effect of single nucleotide polymorphisms on Affymetrix match-mismatch probe pairs. Bioinformation 2008;2:405-11. [PMID: 18795114 PMCID: PMC2533060 DOI: 10.6026/97320630002405] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Revised: 06/17/2008] [Accepted: 07/03/2008] [Indexed: 11/23/2022]  Open
33
A scaffold analysis tool using mate-pair information in genome sequencing. J Biomed Biotechnol 2008;2008:675741. [PMID: 18414585 PMCID: PMC2291285 DOI: 10.1155/2008/675741] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Accepted: 12/24/2007] [Indexed: 11/27/2022]  Open
34
Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G. Consensus generation and variant detection by Celera Assembler. Bioinformatics 2008;24:1035-40. [PMID: 18321888 DOI: 10.1093/bioinformatics/btn074] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
35
Tang H. Genome assembly, rearrangement, and repeats. Chem Rev 2007;107:3391-406. [PMID: 17636888 DOI: 10.1021/cr0683008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
36
Sugino H. Comparative genomic analysis of the mouse and rat amylase multigene family. FEBS Lett 2007;581:355-60. [PMID: 17223109 DOI: 10.1016/j.febslet.2006.12.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 12/21/2006] [Accepted: 12/22/2006] [Indexed: 11/21/2022]
37
Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang SP, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AS, Marra MA, Wilson RK, Jones SJ. Physical map-assisted whole-genome shotgun sequence assemblies. Genes Dev 2006;16:768-75. [PMID: 16741162 PMCID: PMC1473187 DOI: 10.1101/gr.5090606] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Accepted: 04/11/2006] [Indexed: 01/15/2023]
38
Loraine AE, Helt GA, Cline MS, Siani-Rose MA. Exploring alternative transcript structure in the human genome using blocks and InterPro. J Bioinform Comput Biol 2005;1:289-306. [PMID: 15290774 DOI: 10.1142/s0219720003000113] [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] [Received: 09/15/2002] [Revised: 12/07/2002] [Accepted: 01/15/2003] [Indexed: 11/18/2022]
39
Abdel-Rahman MH, Craig EL, Davidorf FH, Eng C. Expression of Vascular Endothelial Growth Factor in Uveal Melanoma Is Independent of 6p21-Region Copy Number. Clin Cancer Res 2005. [DOI: 10.1158/1078-0432.73.11.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
40
Gladyshev VN, Kryukov GV, Fomenko DE, Hatfield DL. IDENTIFICATION OF TRACE ELEMENT–CONTAINING PROTEINS IN GENOMIC DATABASES. Annu Rev Nutr 2004;24:579-96. [PMID: 15189132 DOI: 10.1146/annurev.nutr.24.012003.132241] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
41
Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Girn N, Lee D, Masson A, Mayo M, Olson T, Pandoh P, Prabhu AL, Schoenmakers E, Tsai M, Albertson D, Lam W, Choy CO, Osoegawa K, Zhao S, de Jong PJ, Schein J, Jones S, Marra MA. A set of BAC clones spanning the human genome. Nucleic Acids Res 2004;32:3651-60. [PMID: 15247347 PMCID: PMC484185 DOI: 10.1093/nar/gkh700] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Revised: 06/22/2004] [Accepted: 06/22/2004] [Indexed: 11/15/2022]  Open
42
Havlak P, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Weinstock GM, Gibbs RA. The Atlas genome assembly system. Genome Res 2004;14:721-32. [PMID: 15060016 PMCID: PMC383319 DOI: 10.1101/gr.2264004] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
43
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo MDF, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R. Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, et alImanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo MDF, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R. Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2004;2:e162. [PMID: 15103394 PMCID: PMC393292 DOI: 10.1371/journal.pbio.0020162] [Show More Authors] [Citation(s) in RCA: 234] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Accepted: 04/01/2004] [Indexed: 01/08/2023]  Open
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Pop M, Kosack DS, Salzberg SL. Hierarchical scaffolding with Bambus. Genome Res 2004;14:149-59. [PMID: 14707177 PMCID: PMC314292 DOI: 10.1101/gr.1536204] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Zou A, Lin Z, Humble M, Creech CD, Wagoner PK, Krafte D, Jegla TJ, Wickenden AD. Distribution and functional properties of human KCNH8 (Elk1) potassium channels. Am J Physiol Cell Physiol 2003;285:C1356-66. [PMID: 12890647 DOI: 10.1152/ajpcell.00179.2003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Choi V, Farach-Colton M. Barnacle: an assembly algorithm for clone-based sequences of whole genomes. Gene 2003;320:165-76. [PMID: 14597400 DOI: 10.1016/s0378-1119(03)00825-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, Okada N. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol 2003;4:R74. [PMID: 14611660 PMCID: PMC329124 DOI: 10.1186/gb-2003-4-11-r74] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2003] [Revised: 09/02/2003] [Accepted: 09/25/2003] [Indexed: 01/26/2023]  Open
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Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer K, Graner A. Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Genet Genomics 2003;270:24-33. [PMID: 12938038 DOI: 10.1007/s00438-003-0891-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2003] [Accepted: 06/01/2003] [Indexed: 11/27/2022]
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Engler FW, Hatfield J, Nelson W, Soderlund CA. Locating sequence on FPC maps and selecting a minimal tiling path. Genome Res 2003;13:2152-63. [PMID: 12915486 PMCID: PMC403717 DOI: 10.1101/gr.1068603] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Huntley D, Hummerich H, Smedley D, Kittivoravitkul S, McCarthy M, Little P, Sergot M. GANESH: software for customized annotation of genome regions. Genome Res 2003;13:2195-202. [PMID: 12952886 PMCID: PMC403729 DOI: 10.1101/gr.698103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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