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For: Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. ACTA ACUST UNITED AC 2009;25:2283-5. [PMID: 19542151 DOI: 10.1093/bioinformatics/btp373] [Citation(s) in RCA: 980] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
851
Shyr D, Liu Q. Next generation sequencing in cancer research and clinical application. Biol Proced Online 2013;15:4. [PMID: 23406336 PMCID: PMC3599179 DOI: 10.1186/1480-9222-15-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 02/09/2013] [Indexed: 01/29/2023]  Open
852
AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications. BMC Genomics 2013;14:101. [PMID: 23405914 PMCID: PMC3583733 DOI: 10.1186/1471-2164-14-101] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/19/2012] [Indexed: 12/02/2022]  Open
853
Kim SC, Jung Y, Park J, Cho S, Seo C, Kim J, Kim P, Park J, Seo J, Kim J, Park S, Jang I, Kim N, Yang JO, Lee B, Rho K, Jung Y, Keum J, Lee J, Han J, Kang S, Bae S, Choi SJ, Kim S, Lee JE, Kim W, Kim J, Lee S. A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers. PLoS One 2013;8:e55596. [PMID: 23405175 PMCID: PMC3566005 DOI: 10.1371/journal.pone.0055596] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/27/2012] [Indexed: 11/18/2022]  Open
854
McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 2013;66:526-38. [DOI: 10.1016/j.ympev.2011.12.007] [Citation(s) in RCA: 370] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 01/09/2023]
855
Hilbers FS, Meijers CM, Laros JFJ, van Galen M, Hoogerbrugge N, Vasen HFA, Nederlof PM, Wijnen JT, van Asperen CJ, Devilee P. Exome sequencing of germline DNA from non-BRCA1/2 familial breast cancer cases selected on the basis of aCGH tumor profiling. PLoS One 2013;8:e55734. [PMID: 23383274 PMCID: PMC3561352 DOI: 10.1371/journal.pone.0055734] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/30/2012] [Indexed: 12/17/2022]  Open
856
Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang WJ, Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol 2013;11:e1001473. [PMID: 23382650 PMCID: PMC3558436 DOI: 10.1371/journal.pbio.1001473] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 12/12/2012] [Indexed: 01/03/2023]  Open
857
Barrett MT, Lenkiewicz E, Evers L, Holley T, Ruiz C, Bubendorf L, Sekulic A, Ramanathan RK, Von Hoff DD. Clonal evolution and therapeutic resistance in solid tumors. Front Pharmacol 2013;4:2. [PMID: 23372550 PMCID: PMC3556559 DOI: 10.3389/fphar.2013.00002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Accepted: 01/07/2013] [Indexed: 01/08/2023]  Open
858
Jan M, Snyder TM, Corces-Zimmerman MR, Vyas P, Weissman IL, Quake SR, Majeti R. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Sci Transl Med 2013;4:149ra118. [PMID: 22932223 DOI: 10.1126/scitranslmed.3004315] [Citation(s) in RCA: 576] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
859
Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing. ScientificWorldJournal 2013;2013:730210. [PMID: 23365548 PMCID: PMC3556895 DOI: 10.1155/2013/730210] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 11/22/2012] [Indexed: 12/28/2022]  Open
860
Wang Y, Lu J, Yu J, Gibbs RA, Yu F. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. Genome Res 2013;23:833-42. [PMID: 23296920 PMCID: PMC3638139 DOI: 10.1101/gr.146084.112] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
861
Chen L, Li Y, Lin CH, Chan THM, Chow RKK, Song Y, Liu M, Yuan YF, Fu L, Kong KL, Qi L, Li Y, Zhang N, Tong AHY, Kwong DLW, Man K, Lo CM, Lok S, Tenen DG, Guan XY. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat Med 2013;19:209-16. [PMID: 23291631 DOI: 10.1038/nm.3043] [Citation(s) in RCA: 412] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 11/21/2012] [Indexed: 01/14/2023]
862
Bohlander SK. ABCs of genomics. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2013;2013:316-323. [PMID: 24319198 DOI: 10.1182/asheducation-2013.1.316] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
863
Michaeli M, Noga H, Tabibian-Keissar H, Barshack I, Mehr R. Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing. Front Immunol 2012;3:386. [PMID: 23293637 PMCID: PMC3531709 DOI: 10.3389/fimmu.2012.00386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/30/2012] [Indexed: 01/10/2023]  Open
864
Bioinformatic perspectives in the neuronal ceroid lipofuscinoses. Biochim Biophys Acta Mol Basis Dis 2012;1832:1831-41. [PMID: 23274885 DOI: 10.1016/j.bbadis.2012.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/16/2012] [Accepted: 12/19/2012] [Indexed: 02/06/2023]
865
Genotyping of fanconi anemia patients by whole exome sequencing: advantages and challenges. PLoS One 2012;7:e52648. [PMID: 23285130 PMCID: PMC3527584 DOI: 10.1371/journal.pone.0052648] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 11/20/2012] [Indexed: 11/19/2022]  Open
866
Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing. BMC Genomics 2012;13:692. [PMID: 23231371 PMCID: PMC3539923 DOI: 10.1186/1471-2164-13-692] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 11/22/2012] [Indexed: 01/07/2023]  Open
867
Holley T, Lenkiewicz E, Evers L, Tembe W, Ruiz C, Gsponer JR, Rentsch CA, Bubendorf L, Stapleton M, Amorese D, Legendre C, Cunliffe HE, McCullough AE, Pockaj B, Craig D, Carpten J, Von Hoff D, Iacobuzio-Donahue C, Barrett MT. Deep clonal profiling of formalin fixed paraffin embedded clinical samples. PLoS One 2012;7:e50586. [PMID: 23226320 PMCID: PMC3511535 DOI: 10.1371/journal.pone.0050586] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/23/2012] [Indexed: 01/15/2023]  Open
868
Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, Doherty R, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Hu S, Iodice J, Kissinger JC, Kraemer ET, Li W, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ, Wang H, Warrenfeltz S. EuPathDB: the eukaryotic pathogen database. Nucleic Acids Res 2012;41:D684-91. [PMID: 23175615 PMCID: PMC3531183 DOI: 10.1093/nar/gks1113] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
869
Xuan J, Yu Y, Qing T, Guo L, Shi L. Next-generation sequencing in the clinic: promises and challenges. Cancer Lett 2012;340:284-95. [PMID: 23174106 DOI: 10.1016/j.canlet.2012.11.025] [Citation(s) in RCA: 215] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/13/2012] [Accepted: 11/13/2012] [Indexed: 02/06/2023]
870
Yang X, Todd JA, Clayton D, Wallace C. Extra-binomial variation approach for analysis of pooled DNA sequencing data. Bioinformatics 2012;28:2898-904. [PMID: 22976083 PMCID: PMC3496343 DOI: 10.1093/bioinformatics/bts553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 08/03/2012] [Accepted: 09/05/2012] [Indexed: 11/25/2022]  Open
871
Liu X, Wang J, Chen L. Whole-exome sequencing reveals recurrent somatic mutation networks in cancer. Cancer Lett 2012;340:270-6. [PMID: 23153794 DOI: 10.1016/j.canlet.2012.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/30/2012] [Accepted: 11/02/2012] [Indexed: 11/26/2022]
872
Systems genetics in "-omics" era: current and future development. Theory Biosci 2012;132:1-16. [PMID: 23138757 DOI: 10.1007/s12064-012-0168-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 10/25/2012] [Indexed: 02/06/2023]
873
Gullapalli RR, Desai KV, Santana-Santos L, Kant JA, Becich MJ. Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics. J Pathol Inform 2012;3:40. [PMID: 23248761 PMCID: PMC3519097 DOI: 10.4103/2153-3539.103013] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 07/19/2012] [Indexed: 11/25/2022]  Open
874
Wilm A, Aw PPK, Bertrand D, Yeo GHT, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res 2012;40:11189-201. [PMID: 23066108 PMCID: PMC3526318 DOI: 10.1093/nar/gks918] [Citation(s) in RCA: 962] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
875
Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O'Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, Hundal J, Cook LL, Swift GW, Reed JP, Alldredge PA, Wylie TN, Walker JR, Watson MA, Heath SE, Shannon WD, Varghese N, Nagarajan R, Payton JE, Baty JD, Kulkarni S, Klco JM, Tomasson MH, Westervelt P, Walter MJ, Graubert TA, DiPersio JF, Ding L, Mardis ER, Wilson RK. The origin and evolution of mutations in acute myeloid leukemia. Cell 2012;150:264-78. [PMID: 22817890 DOI: 10.1016/j.cell.2012.06.023] [Citation(s) in RCA: 1248] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 04/27/2012] [Accepted: 06/24/2012] [Indexed: 10/28/2022]
876
Sifrim A, Van Houdt JKJ, Tranchevent LC, Nowakowska B, Sakai R, Pavlopoulos GA, Devriendt K, Vermeesch JR, Moreau Y, Aerts J. Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. Genome Med 2012;4:73. [PMID: 23013645 PMCID: PMC3580443 DOI: 10.1186/gm374] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 09/14/2012] [Accepted: 09/26/2012] [Indexed: 12/18/2022]  Open
877
Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S, Pérez-Enciso M. SNP calling by sequencing pooled samples. BMC Bioinformatics 2012;13:239. [PMID: 22992255 PMCID: PMC3475117 DOI: 10.1186/1471-2105-13-239] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 09/06/2012] [Indexed: 12/21/2022]  Open
878
High throughput sequencing approaches to mutation discovery in the mouse. Mamm Genome 2012;23:499-513. [PMID: 22991087 DOI: 10.1007/s00335-012-9424-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/19/2012] [Indexed: 12/19/2022]
879
Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR. De novo assembly of highly diverse viral populations. BMC Genomics 2012;13:475. [PMID: 22974120 PMCID: PMC3469330 DOI: 10.1186/1471-2164-13-475] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 09/06/2012] [Indexed: 01/14/2023]  Open
880
High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic. BMC Genomics 2012;13:468. [PMID: 22963323 PMCID: PMC3473251 DOI: 10.1186/1471-2164-13-468] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/28/2012] [Indexed: 11/16/2022]  Open
881
Forster M, Forster P, Elsharawy A, Hemmrich G, Kreck B, Wittig M, Thomsen I, Stade B, Barann M, Ellinghaus D, Petersen BS, May S, Melum E, Schilhabel MB, Keller A, Schreiber S, Rosenstiel P, Franke A. From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software. Nucleic Acids Res 2012;41:e16. [PMID: 22965131 PMCID: PMC3592472 DOI: 10.1093/nar/gks836] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
882
Ma S, Bao JYJ, Kwan PS, Chan YP, Tong CM, Fu L, Zhang N, Tong AHY, Qin YR, Tsao SW, Chan KW, Lok S, Guan XY. Identification of PTK6, via RNA sequencing analysis, as a suppressor of esophageal squamous cell carcinoma. Gastroenterology 2012;143:675-686.e12. [PMID: 22705009 DOI: 10.1053/j.gastro.2012.06.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Revised: 05/31/2012] [Accepted: 06/04/2012] [Indexed: 12/20/2022]
883
Spans L, Atak ZK, Van Nieuwerburgh F, Deforce D, Lerut E, Aerts S, Claessens F. Variations in the exome of the LNCaP prostate cancer cell line. Prostate 2012;72:1317-27. [PMID: 22213130 DOI: 10.1002/pros.22480] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/04/2011] [Indexed: 11/09/2022]
884
Vidal RO, do Nascimento LC, Mondego JMC, Pereira GAG, Carazzolle MF. Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance. Genet Mol Biol 2012;35:331-4. [PMID: 22802718 PMCID: PMC3392885 DOI: 10.1590/s1415-47572012000200014] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
885
Huang J, Deng Q, Wang Q, Li KY, Dai JH, Li N, Zhu ZD, Zhou B, Liu XY, Liu RF, Fei QL, Chen H, Cai B, Zhou B, Xiao HS, Qin LX, Han ZG. Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat Genet 2012;44:1117-21. [PMID: 22922871 DOI: 10.1038/ng.2391] [Citation(s) in RCA: 307] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 08/01/2012] [Indexed: 02/07/2023]
886
Zhou B. An empirical Bayes mixture model for SNP detection in pooled sequencing data. Bioinformatics 2012;28:2569-75. [PMID: 22914221 DOI: 10.1093/bioinformatics/bts501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
887
Aguilar C, Escalante A, Flores N, de Anda R, Riveros-McKay F, Gosset G, Morett E, Bolívar F. Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system. BMC Genomics 2012;13:385. [PMID: 22884033 PMCID: PMC3469383 DOI: 10.1186/1471-2164-13-385] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 08/02/2012] [Indexed: 01/15/2023]  Open
888
Thumma BR, Sharma N, Southerton SG. Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection. BMC Genomics 2012;13:364. [PMID: 22853646 PMCID: PMC3472208 DOI: 10.1186/1471-2164-13-364] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 07/20/2012] [Indexed: 12/03/2022]  Open
889
Fischer M, Snajder R, Pabinger S, Dander A, Schossig A, Zschocke J, Trajanoski Z, Stocker G. SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. PLoS One 2012;7:e41948. [PMID: 22870267 PMCID: PMC3411592 DOI: 10.1371/journal.pone.0041948] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 06/28/2012] [Indexed: 01/24/2023]  Open
890
Furney SJ, Turajlic S, Fenwick K, Lambros MB, MacKay A, Ricken G, Mitsopoulos C, Kozarewa I, Hakas J, Zvelebil M, Lord CJ, Ashworth A, Reis-Filho JS, Herlyn M, Murata H, Marais R. Genomic characterisation of acral melanoma cell lines. Pigment Cell Melanoma Res 2012;25:488-92. [PMID: 22578220 DOI: 10.1111/j.1755-148x.2012.01016.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
891
Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data. STATISTICS IN BIOSCIENCES 2012;5:3-25. [PMID: 24489615 DOI: 10.1007/s12561-012-9067-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
892
Medugorac I, Seichter D, Graf A, Russ I, Blum H, Göpel KH, Rothammer S, Förster M, Krebs S. Bovine polledness--an autosomal dominant trait with allelic heterogeneity. PLoS One 2012;7:e39477. [PMID: 22737241 PMCID: PMC3380827 DOI: 10.1371/journal.pone.0039477] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/25/2012] [Indexed: 11/18/2022]  Open
893
Xiong D, Li G, Li K, Xu Q, Pan Z, Ding F, Vedell P, Liu P, Cui P, Hua X, Jiang H, Yin Y, Zhu Z, Li X, Zhang B, Ma D, Wang Y, You M. Exome sequencing identifies MXRA5 as a novel cancer gene frequently mutated in non-small cell lung carcinoma from Chinese patients. Carcinogenesis 2012;33:1797-805. [PMID: 22696596 DOI: 10.1093/carcin/bgs210] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
894
Kalender Atak Z, De Keersmaecker K, Gianfelici V, Geerdens E, Vandepoel R, Pauwels D, Porcu M, Lahortiga I, Brys V, Dirks WG, Quentmeier H, Cloos J, Cuppens H, Uyttebroeck A, Vandenberghe P, Cools J, Aerts S. High accuracy mutation detection in leukemia on a selected panel of cancer genes. PLoS One 2012;7:e38463. [PMID: 22675565 PMCID: PMC3366948 DOI: 10.1371/journal.pone.0038463] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 05/05/2012] [Indexed: 01/12/2023]  Open
895
Diagnosis of fanconi anemia: mutation analysis by next-generation sequencing. Anemia 2012;2012:132856. [PMID: 22720145 PMCID: PMC3374947 DOI: 10.1155/2012/132856] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 03/21/2012] [Indexed: 12/31/2022]  Open
896
Systems genetics: challenges and developing strategies. Biologia (Bratisl) 2012. [DOI: 10.2478/s11756-012-0026-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
897
GATA2 zinc finger 1 mutations associated with biallelic CEBPA mutations define a unique genetic entity of acute myeloid leukemia. Blood 2012;120:395-403. [PMID: 22649106 DOI: 10.1182/blood-2012-01-403220] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
898
Li M, Stoneking M. A new approach for detecting low-level mutations in next-generation sequence data. Genome Biol 2012;13:R34. [PMID: 22621726 PMCID: PMC3446287 DOI: 10.1186/gb-2012-13-5-r34] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 05/14/2012] [Accepted: 05/23/2012] [Indexed: 01/01/2023]  Open
899
Kwok H, Tong AHY, Lin CH, Lok S, Farrell PJ, Kwong DLW, Chiang AKS. Genomic sequencing and comparative analysis of Epstein-Barr virus genome isolated from primary nasopharyngeal carcinoma biopsy. PLoS One 2012;7:e36939. [PMID: 22590638 PMCID: PMC3349645 DOI: 10.1371/journal.pone.0036939] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 04/16/2012] [Indexed: 12/15/2022]  Open
900
Saunders CT, Wong WSW, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. ACTA ACUST UNITED AC 2012;28:1811-7. [PMID: 22581179 DOI: 10.1093/bioinformatics/bts271] [Citation(s) in RCA: 1207] [Impact Index Per Article: 92.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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