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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)
801
Valentim CLL, Cioli D, Chevalier FD, Cao X, Taylor AB, Holloway SP, Pica-Mattoccia L, Guidi A, Basso A, Tsai IJ, Berriman M, Carvalho-Queiroz C, Almeida M, Aguilar H, Frantz DE, Hart PJ, LoVerde PT, Anderson TJC. Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites. Science 2013;342:1385-9. [PMID: 24263136 PMCID: PMC4136436 DOI: 10.1126/science.1243106] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
802
Signor S, Seher T, Kopp A. Genomic resources for multiple species in the Drosophila ananassae species group. Fly (Austin) 2013;7:47-57. [PMID: 23639891 DOI: 10.4161/fly.22353] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
803
Berglund EC, Lindqvist CM, Hayat S, Övernäs E, Henriksson N, Nordlund J, Wahlberg P, Forestier E, Lönnerholm G, Syvänen AC. Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment. BMC Genomics 2013;14:856. [PMID: 24314227 PMCID: PMC4046713 DOI: 10.1186/1471-2164-14-856] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 11/25/2013] [Indexed: 01/21/2023]  Open
804
Pyle A, Griffin H, Duff J, Zwolinski S, Smertenko T, Yu-Wai-Man P, Santibanez-Koref M, Horvath R, Chinnery PF. Late-onset sacsinopathy diagnosed by exome sequencing and comparative genomic hybridization. J Neurogenet 2013;27:176-82. [PMID: 24180463 PMCID: PMC4038496 DOI: 10.3109/01677063.2013.831094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
805
Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The next-generation sequencing revolution and its impact on genomics. Cell 2013;155:27-38. [PMID: 24074859 DOI: 10.1016/j.cell.2013.09.006] [Citation(s) in RCA: 645] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Indexed: 02/07/2023]
806
Toonen RJ, Puritz JB, Forsman ZH, Whitney JL, Fernandez-Silva I, Andrews KR, Bird CE. ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ 2013;1:e203. [PMID: 24282669 PMCID: PMC3840413 DOI: 10.7717/peerj.203] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/13/2013] [Indexed: 12/17/2022]  Open
807
Fanciulli M, Di Bonaventura C, Egeo G, Fattouch J, Dazzo E, Radovic S, Spadotto A, Giallonardo AT, Nobile C. Suggestive linkage of familial mesial temporal lobe epilepsy to chromosome 3q26. Epilepsy Res 2013;108:232-40. [PMID: 24315020 DOI: 10.1016/j.eplepsyres.2013.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 09/26/2013] [Accepted: 11/03/2013] [Indexed: 12/01/2022]
808
Konczal M, Koteja P, Stuglik MT, Radwan J, Babik W. Accuracy of allele frequency estimation using pooled RNA-Seq. Mol Ecol Resour 2013;14:381-92. [PMID: 24119300 DOI: 10.1111/1755-0998.12186] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/30/2013] [Accepted: 10/06/2013] [Indexed: 11/28/2022]
809
Lopez-Doriga A, Feliubadaló L, Menéndez M, Lopez-Doriga S, Morón-Duran FD, del Valle J, Tornero E, Montes E, Cuesta R, Campos O, Gómez C, Pineda M, González S, Moreno V, Capellá G, Lázaro C. ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing. Hum Mutat 2013;35:271-7. [PMID: 24227591 DOI: 10.1002/humu.22484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/07/2013] [Indexed: 12/19/2022]
810
Lee YP, Giorgi FM, Lohse M, Kvederaviciute K, Klages S, Usadel B, Meskiene I, Reinhardt R, Hincha DK. Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum). BMC Genomics 2013;14:793. [PMID: 24228715 PMCID: PMC3832907 DOI: 10.1186/1471-2164-14-793] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 11/11/2013] [Indexed: 11/29/2022]  Open
811
Kukimoto I, Maehama T, Sekizuka T, Ogasawara Y, Kondo K, Kusumoto-Matsuo R, Mori S, Ishii Y, Takeuchi T, Yamaji T, Takeuchi F, Hanada K, Kuroda M. Genetic variation of human papillomavirus type 16 in individual clinical specimens revealed by deep sequencing. PLoS One 2013;8:e80583. [PMID: 24236186 PMCID: PMC3827439 DOI: 10.1371/journal.pone.0080583] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/04/2013] [Indexed: 01/10/2023]  Open
812
Pritchard CC, Salipante SJ, Koehler K, Smith C, Scroggins S, Wood B, Wu D, Lee MK, Dintzis S, Adey A, Liu Y, Eaton KD, Martins R, Stricker K, Margolin KA, Hoffman N, Churpek JE, Tait JF, King MC, Walsh T. Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. J Mol Diagn 2013;16:56-67. [PMID: 24189654 DOI: 10.1016/j.jmoldx.2013.08.004] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/25/2013] [Accepted: 08/07/2013] [Indexed: 11/15/2022]  Open
813
Dutton-Regester K, Kakavand H, Aoude LG, Stark MS, Gartside MG, Johansson P, O'Connor L, Lanagan C, Tembe V, Pupo GM, Haydu LE, Schmidt CW, Mann GJ, Thompson JF, Scolyer RA, Hayward NK. Melanomas of unknown primary have a mutation profile consistent with cutaneous sun-exposed melanoma. Pigment Cell Melanoma Res 2013;26:852-60. [PMID: 23890154 DOI: 10.1111/pcmr.12153] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/19/2013] [Indexed: 11/29/2022]
814
Zheng Z, Geng J, Yao RE, Li C, Ying D, Shen Y, Ying L, Yu Y, Fu Q. Molecular defects identified by whole exome sequencing in a child with Fanconi anemia. Gene 2013;530:295-300. [DOI: 10.1016/j.gene.2013.08.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 08/01/2013] [Accepted: 08/09/2013] [Indexed: 01/25/2023]
815
Ferretti L, Ramos-Onsins SE, Pérez-Enciso M. Population genomics from pool sequencing. Mol Ecol 2013;22:5561-76. [DOI: 10.1111/mec.12522] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 08/03/2013] [Accepted: 09/06/2013] [Indexed: 11/30/2022]
816
Worthey EA. Analysis and annotation of whole-genome or whole-exome sequencing-derived variants for clinical diagnosis. CURRENT PROTOCOLS IN HUMAN GENETICS 2013;79:9.24.1-9.24.24. [PMID: 24510652 DOI: 10.1002/0471142905.hg0924s79] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
817
Barturen G, Rueda A, Oliver JL, Hackenberg M. MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data. F1000Res 2013;2:217. [PMID: 24627790 PMCID: PMC3938178 DOI: 10.12688/f1000research.2-217.v2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2014] [Indexed: 01/10/2023]  Open
818
Barturen G, Rueda A, Oliver JL, Hackenberg M. MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data. F1000Res 2013;2:217. [PMID: 24627790 DOI: 10.12688/f1000research.2-217.v1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/09/2013] [Indexed: 01/30/2023]  Open
819
Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nat Genet 2013;45:1459-63. [PMID: 24121792 DOI: 10.1038/ng.2798] [Citation(s) in RCA: 369] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 09/16/2013] [Indexed: 12/15/2022]
820
Kosugi S, Natsume S, Yoshida K, MacLean D, Cano L, Kamoun S, Terauchi R. Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data. PLoS One 2013;8:e75402. [PMID: 24116042 PMCID: PMC3792961 DOI: 10.1371/journal.pone.0075402] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 08/14/2013] [Indexed: 11/26/2022]  Open
821
Cruceanu C, Ambalavanan A, Spiegelman D, Gauthier J, Lafrenière RG, Dion PA, Alda M, Turecki G, Rouleau GA. Family-based exome-sequencing approach identifies rare susceptibility variants for lithium-responsive bipolar disorder. Genome 2013;56:634-40. [DOI: 10.1139/gen-2013-0081] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
822
Cabanski CR, Wilkerson MD, Soloway M, Parker JS, Liu J, Prins JF, Marron JS, Perou CM, Hayes DN. BlackOPs: increasing confidence in variant detection through mappability filtering. Nucleic Acids Res 2013;41:e178. [PMID: 23935067 PMCID: PMC3799449 DOI: 10.1093/nar/gkt692] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/24/2013] [Accepted: 07/16/2013] [Indexed: 01/05/2023]  Open
823
Yu X, Sun S. Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC Bioinformatics 2013;14:274. [PMID: 24044377 PMCID: PMC3848615 DOI: 10.1186/1471-2105-14-274] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/12/2013] [Indexed: 11/10/2022]  Open
824
Liu G, Zhang L, Qin Y, Zou G, Li Z, Yan X, Wei X, Chen M, Chen L, Zheng K, Zhang J, Ma L, Li J, Liu R, Xu H, Bao X, Fang X, Wang L, Zhong Y, Liu W, Zheng H, Wang S, Wang C, Xun L, Zhao GP, Wang T, Zhou Z, Qu Y. Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes. Sci Rep 2013;3:1569. [PMID: 23535838 PMCID: PMC3610096 DOI: 10.1038/srep01569] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 03/13/2013] [Indexed: 12/12/2022]  Open
825
Peralta M, Combes MC, Cenci A, Lashermes P, Dereeper A. SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2013;2013:890123. [PMID: 24163691 PMCID: PMC3791807 DOI: 10.1155/2013/890123] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/26/2013] [Accepted: 07/30/2013] [Indexed: 05/18/2023]
826
Strino F, Parisi F, Micsinai M, Kluger Y. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res 2013;41:e165. [PMID: 23892400 PMCID: PMC3783191 DOI: 10.1093/nar/gkt641] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 06/11/2013] [Accepted: 07/02/2013] [Indexed: 01/01/2023]  Open
827
Kim S, Jeong K, Bhutani K, Lee JH, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol 2013;14:R90. [PMID: 23987214 PMCID: PMC4054681 DOI: 10.1186/gb-2013-14-8-r90] [Citation(s) in RCA: 51] [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: 04/30/2013] [Revised: 07/17/2013] [Accepted: 08/29/2013] [Indexed: 11/10/2022]  Open
828
de Miranda NFCC, Peng R, Georgiou K, Wu C, Falk Sörqvist E, Berglund M, Chen L, Gao Z, Lagerstedt K, Lisboa S, Roos F, van Wezel T, Teixeira MR, Rosenquist R, Sundström C, Enblad G, Nilsson M, Zeng Y, Kipling D, Pan-Hammarström Q. DNA repair genes are selectively mutated in diffuse large B cell lymphomas. ACTA ACUST UNITED AC 2013;210:1729-42. [PMID: 23960188 PMCID: PMC3754869 DOI: 10.1084/jem.20122842] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
829
Wang K, Kim C, Bradfield J, Guo Y, Toskala E, Otieno FG, Hou C, Thomas K, Cardinale C, Lyon GJ, Golhar R, Hakonarson H. Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement. Genome Med 2013;5:67. [PMID: 23889995 PMCID: PMC3971341 DOI: 10.1186/gm471] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 07/15/2013] [Accepted: 07/26/2013] [Indexed: 12/19/2022]  Open
830
Pavlopoulos GA, Oulas A, Iacucci E, Sifrim A, Moreau Y, Schneider R, Aerts J, Iliopoulos I. Unraveling genomic variation from next generation sequencing data. BioData Min 2013;6:13. [PMID: 23885890 PMCID: PMC3726446 DOI: 10.1186/1756-0381-6-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 07/18/2013] [Indexed: 12/29/2022]  Open
831
McElroy K, Zagordi O, Bull R, Luciani F, Beerenwinkel N. Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias. BMC Genomics 2013;14:501. [PMID: 23879730 PMCID: PMC3848937 DOI: 10.1186/1471-2164-14-501] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/15/2013] [Indexed: 11/10/2022]  Open
832
Bian J, Liu C, Wang H, Xing J, Kachroo P, Zhou X. SNVHMM: predicting single nucleotide variants from next generation sequencing. BMC Bioinformatics 2013;14:225. [PMID: 23855743 PMCID: PMC3718670 DOI: 10.1186/1471-2105-14-225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/03/2013] [Indexed: 02/04/2023]  Open
833
Badouin H, Belkhir K, Gregson E, Galindo J, Sundström L, Martin SJ, Butlin RK, Smadja CM. Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera. PLoS One 2013;8:e68200. [PMID: 23874539 PMCID: PMC3709892 DOI: 10.1371/journal.pone.0068200] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/28/2013] [Indexed: 11/19/2022]  Open
834
Roberts ND, Kortschak RD, Parker WT, Schreiber AW, Branford S, Scott HS, Glonek G, Adelson DL. A comparative analysis of algorithms for somatic SNV detection in cancer. ACTA ACUST UNITED AC 2013;29:2223-30. [PMID: 23842810 PMCID: PMC3753564 DOI: 10.1093/bioinformatics/btt375] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
835
Nocq J, Celton M, Gendron P, Lemieux S, Wilhelm BT. Harnessing virtual machines to simplify next-generation DNA sequencing analysis. Bioinformatics 2013;29:2075-83. [PMID: 23786767 DOI: 10.1093/bioinformatics/btt352] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
836
Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6. Eur J Hum Genet 2013;22:208-15. [PMID: 23714752 DOI: 10.1038/ejhg.2013.108] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 04/08/2013] [Accepted: 04/19/2013] [Indexed: 12/16/2022]  Open
837
Víquez-Zamora M, Vosman B, van de Geest H, Bovy A, Visser RGF, Finkers R, van Heusden AW. Tomato breeding in the genomics era: insights from a SNP array. BMC Genomics 2013;14:354. [PMID: 23711327 PMCID: PMC3680325 DOI: 10.1186/1471-2164-14-354] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/20/2013] [Indexed: 02/01/2023]  Open
838
Warshauer DH, Lin D, Hari K, Jain R, Davis C, Larue B, King JL, Budowle B. STRait Razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data. Forensic Sci Int Genet 2013;7:409-17. [PMID: 23768312 DOI: 10.1016/j.fsigen.2013.04.005] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/04/2013] [Accepted: 04/15/2013] [Indexed: 12/31/2022]
839
Simons C, Wolf N, McNeil N, Caldovic L, Devaney J, Takanohashi A, Crawford J, Ru K, Grimmond S, Miller D, Tonduti D, Schmidt J, Chudnow R, van Coster R, Lagae L, Kisler J, Sperner J, van der Knaap M, Schiffmann R, Taft R, Vanderver A. A de novo mutation in the β-tubulin gene TUBB4A results in the leukoencephalopathy hypomyelination with atrophy of the basal ganglia and cerebellum. Am J Hum Genet 2013;92:767-73. [PMID: 23582646 DOI: 10.1016/j.ajhg.2013.03.018] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 02/12/2013] [Accepted: 03/19/2013] [Indexed: 01/06/2023]  Open
840
Solomon O, Oren S, Safran M, Deshet-Unger N, Akiva P, Jacob-Hirsch J, Cesarkas K, Kabesa R, Amariglio N, Unger R, Rechavi G, Eyal E. Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). RNA (NEW YORK, N.Y.) 2013;19:591-604. [PMID: 23474544 PMCID: PMC3677275 DOI: 10.1261/rna.038042.112] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
841
Nijveen H, van Kaauwen M, Esselink DG, Hoegen B, Vosman B. QualitySNPng: a user-friendly SNP detection and visualization tool. Nucleic Acids Res 2013;41:W587-90. [PMID: 23632165 PMCID: PMC3692117 DOI: 10.1093/nar/gkt333] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
842
Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nat Biotechnol 2013;31:458-64. [PMID: 23604283 PMCID: PMC3791587 DOI: 10.1038/nbt.2566] [Citation(s) in RCA: 359] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 04/02/2013] [Indexed: 12/24/2022]
843
Bareke E, Saillour V, Spinella JF, Vidal R, Healy J, Sinnett D, Csűrös M. Joint genotype inference with germline and somatic mutations. BMC Bioinformatics 2013;14 Suppl 5:S3. [PMID: 23734724 PMCID: PMC3622648 DOI: 10.1186/1471-2105-14-s5-s3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
844
Nota B, Struys E, Pop A, Jansen E, Fernandez Ojeda M, Kanhai W, Kranendijk M, van Dooren S, Bevova M, Sistermans E, Nieuwint A, Barth M, Ben-Omran T, Hoffmann G, de Lonlay P, McDonald M, Meberg A, Muntau A, Nuoffer JM, Parini R, Read MH, Renneberg A, Santer R, Strahleck T, van Schaftingen E, van der Knaap M, Jakobs C, Salomons G. Deficiency in SLC25A1, encoding the mitochondrial citrate carrier, causes combined D-2- and L-2-hydroxyglutaric aciduria. Am J Hum Genet 2013;92:627-31. [PMID: 23561848 DOI: 10.1016/j.ajhg.2013.03.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 01/02/2013] [Accepted: 03/13/2013] [Indexed: 12/17/2022]  Open
845
Ophir R. Bioinformatics Tools for Marker Discovery in Plant Breeding. Isr J Chem 2013. [DOI: 10.1002/ijch.201200090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
846
Bettencourt C, López-Sendón JL, García-Caldentey J, Rizzu P, Bakker IMC, Shomroni O, Quintáns B, Dávila JR, Bevova MR, Sobrido MJ, Heutink P, de Yébenes JG. Exome sequencing is a useful diagnostic tool for complicated forms of hereditary spastic paraplegia. Clin Genet 2013;85:154-8. [PMID: 23438842 DOI: 10.1111/cge.12133] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/20/2013] [Accepted: 02/20/2013] [Indexed: 01/02/2023]
847
Kevelam SH, Bugiani M, Salomons GS, Feigenbaum A, Blaser S, Prasad C, Häberle J, Barić I, Bakker IMC, Postma NL, Kanhai WA, Wolf NI, Abbink TEM, Waisfisz Q, Heutink P, van der Knaap MS. Exome sequencing reveals mutated SLC19A3 in patients with an early-infantile, lethal encephalopathy. Brain 2013;136:1534-43. [DOI: 10.1093/brain/awt054] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
848
Zhu S, Dai YM, Zhang XY, Ye JR, Wang MX, Huang MR. Untangling the transcriptome from fungus-infected plant tissues. Gene 2013;519:238-44. [PMID: 23466979 DOI: 10.1016/j.gene.2013.02.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 01/29/2013] [Accepted: 02/13/2013] [Indexed: 12/31/2022]
849
Singhal S. De novo transcriptomic analyses for non‐model organisms: an evaluation of methods across a multi‐species data set. Mol Ecol Resour 2013;13:403-16. [DOI: 10.1111/1755-0998.12077] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/13/2012] [Accepted: 12/22/2012] [Indexed: 01/09/2023]
850
Yost SE, Pastorino S, Rozenzhak S, Smith EN, Chao YS, Jiang P, Kesari S, Frazer KA, Harismendy O. High-resolution mutational profiling suggests the genetic validity of glioblastoma patient-derived pre-clinical models. PLoS One 2013;8:e56185. [PMID: 23441165 PMCID: PMC3575368 DOI: 10.1371/journal.pone.0056185] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/07/2013] [Indexed: 11/19/2022]  Open
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