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For: Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, Müller-Myhsok B. vipR: variant identification in pooled DNA using R. Bioinformatics 2011;27:i77-84. [PMID: 21685105 PMCID: PMC3117388 DOI: 10.1093/bioinformatics/btr205] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]  Open
Number Cited by Other Article(s)
1
Xie S, Isaacs K, Becker G, Murdoch BM. A computational framework for improving genetic variants identification from 5,061 sheep sequencing data. J Anim Sci Biotechnol 2023;14:127. [PMID: 37779189 PMCID: PMC10544426 DOI: 10.1186/s40104-023-00923-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 08/01/2023] [Indexed: 10/03/2023]  Open
2
Özdemir Özdoğan G, Kaya H. Next-Generation Sequencing Data Analysis on Pool-Seq and Low-Coverage Retinoblastoma Data. Interdiscip Sci 2020;12:302-310. [PMID: 32519123 DOI: 10.1007/s12539-020-00374-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 04/26/2020] [Accepted: 05/22/2020] [Indexed: 12/31/2022]
3
Alzu'bi AA, Zhou L, Watzlaf VJM. Genetic Variations and Precision Medicine. PERSPECTIVES IN HEALTH INFORMATION MANAGEMENT 2019;16:1a. [PMID: 31019429 PMCID: PMC6462879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
4
Approximation of the difference of two Poisson-like counts by Skellam. J Appl Probab 2018. [DOI: 10.1017/jpr.2018.27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
5
Gupta P, Reddaiah B, Salava H, Upadhyaya P, Tyagi K, Sarma S, Datta S, Malhotra B, Thomas S, Sunkum A, Devulapalli S, Till BJ, Sreelakshmi Y, Sharma R. Next-generation sequencing (NGS)-based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum) population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017;92:495-508. [PMID: 28779536 DOI: 10.1111/tpj.13654] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 05/21/2023]
6
Kugelman JR, Wiley MR, Nagle ER, Reyes D, Pfeffer BP, Kuhn JH, Sanchez-Lockhart M, Palacios GF. Error baseline rates of five sample preparation methods used to characterize RNA virus populations. PLoS One 2017;12:e0171333. [PMID: 28182717 PMCID: PMC5300104 DOI: 10.1371/journal.pone.0171333] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 01/18/2017] [Indexed: 11/19/2022]  Open
7
Artigas MS, Wain LV, Shrine N, McKeever TM, UK BiLEVE, Sayers I, Hall IP, Tobin MD. Targeted Sequencing of Lung Function Loci in Chronic Obstructive Pulmonary Disease Cases and Controls. PLoS One 2017;12:e0170222. [PMID: 28114305 PMCID: PMC5256917 DOI: 10.1371/journal.pone.0170222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 01/01/2017] [Indexed: 12/15/2022]  Open
8
Duitama J, Kafuri L, Tello D, Leiva AM, Hofinger B, Datta S, Lentini Z, Aranzales E, Till B, Ceballos H. Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis. Comput Struct Biotechnol J 2017;15:185-194. [PMID: 28179981 PMCID: PMC5295625 DOI: 10.1016/j.csbj.2017.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/26/2016] [Accepted: 01/10/2017] [Indexed: 12/16/2022]  Open
9
Functional Impact of An ADHD-Associated DIRAS2 Promoter Polymorphism. Neuropsychopharmacology 2016;41:3025-3031. [PMID: 27364329 PMCID: PMC5101550 DOI: 10.1038/npp.2016.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/20/2016] [Accepted: 06/24/2016] [Indexed: 12/17/2022]
10
Greenwood JM, Ezquerra AL, Behrens S, Branca A, Mallet L. Current analysis of host–parasite interactions with a focus on next generation sequencing data. ZOOLOGY 2016;119:298-306. [DOI: 10.1016/j.zool.2016.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 01/21/2023]
11
Gao L, Li L, Ye J, Zhu X, Shen N, Zhang X, Wang D, Gao Y, Lin H, Wang Y, Liu Y. Identification of a novel mutation in PLA2G6 gene in a Chinese pedigree with familial cortical myoclonic tremor with epilepsy. Seizure 2016;41:81-5. [PMID: 27513994 DOI: 10.1016/j.seizure.2016.07.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 07/21/2016] [Accepted: 07/21/2016] [Indexed: 11/26/2022]  Open
12
Malde K. Estimating the information value of polymorphic sites using pooled sequences. BMC Genomics 2014;15 Suppl 6:S20. [PMID: 25571927 PMCID: PMC4239578 DOI: 10.1186/1471-2164-15-s6-s20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
13
Shearer A, Eppsteiner R, Booth K, Ephraim S, Gurrola J, Simpson A, Black-Ziegelbein E, Joshi S, Ravi H, Giuffre A, Happe S, Hildebrand M, Azaiez H, Bayazit Y, Erdal M, Lopez-Escamez J, Gazquez I, Tamayo M, Gelvez N, Leal G, Jalas C, Ekstein J, Yang T, Usami SI, Kahrizi K, Bazazzadegan N, Najmabadi H, Scheetz T, Braun T, Casavant T, LeProust E, Smith R. Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants. Am J Hum Genet 2014;95:445-53. [PMID: 25262649 DOI: 10.1016/j.ajhg.2014.09.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 09/08/2014] [Indexed: 10/24/2022]  Open
14
Sequencing pools of individuals — mining genome-wide polymorphism data without big funding. Nat Rev Genet 2014;15:749-63. [DOI: 10.1038/nrg3803] [Citation(s) in RCA: 512] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
15
Zhao Z, Wang W, Wei Z. An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data. Ann Appl Stat 2013. [DOI: 10.1214/13-aoas660] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
16
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]
17
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]
18
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
19
Morata J, Béjar S, Talavera D, Riera C, Lois S, de Xaxars GM, de la Cruz X. The relationship between gene isoform multiplicity, number of exons and protein divergence. PLoS One 2013;8:e72742. [PMID: 24023641 PMCID: PMC3758341 DOI: 10.1371/journal.pone.0072742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/14/2013] [Indexed: 11/18/2022]  Open
20
Miyagawa M, Naito T, Nishio SY, Kamatani N, Usami SI. Targeted exon sequencing successfully discovers rare causative genes and clarifies the molecular epidemiology of Japanese deafness patients. PLoS One 2013;8:e71381. [PMID: 23967202 PMCID: PMC3742761 DOI: 10.1371/journal.pone.0071381] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 06/30/2013] [Indexed: 11/19/2022]  Open
21
Quast C, Cuboni S, Bader D, Altmann A, Weber P, Arloth J, Röh S, Brückl T, Ising M, Kopczak A, Erhardt A, Hausch F, Lucae S, Binder EB. Functional coding variants in SLC6A15, a possible risk gene for major depression. PLoS One 2013;8:e68645. [PMID: 23874702 PMCID: PMC3712998 DOI: 10.1371/journal.pone.0068645] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 05/30/2013] [Indexed: 11/18/2022]  Open
22
Chen Q, Sun F. A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms. BMC Genomics 2013;14 Suppl 1:S1. [PMID: 23369070 PMCID: PMC3549804 DOI: 10.1186/1471-2164-14-s1-s1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
23
Altmann A, Quast C, Weber P. Detecting rare variants for psychiatric disorders using next generation sequencing: a methods primer. Curr Psychiatry Rep 2013;15:333. [PMID: 23250814 DOI: 10.1007/s11920-012-0333-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
24
Quast C, Altmann A, Weber P, Arloth J, Bader D, Heck A, Pfister H, Müller-Myhsok B, Erhardt A, Binder EB. Rare variants in TMEM132D in a case-control sample for panic disorder. Am J Med Genet B Neuropsychiatr Genet 2012;159B:896-907. [PMID: 22911938 DOI: 10.1002/ajmg.b.32096] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 08/03/2012] [Indexed: 11/06/2022]
25
Shearer AE, Hildebrand MS, Ravi H, Joshi S, Guiffre AC, Novak B, Happe S, LeProust EM, Smith RJH. Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment. BMC Genomics 2012;13:618. [PMID: 23148716 PMCID: PMC3534602 DOI: 10.1186/1471-2164-13-618] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 11/09/2012] [Indexed: 01/19/2023]  Open
26
Beerenwinkel N, Günthard HF, Roth V, Metzner KJ. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front Microbiol 2012;3:329. [PMID: 22973268 PMCID: PMC3438994 DOI: 10.3389/fmicb.2012.00329] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/24/2012] [Indexed: 12/17/2022]  Open
27
Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N. Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nat Commun 2012;3:811. [PMID: 22549840 DOI: 10.1038/ncomms1814] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 03/30/2012] [Indexed: 01/06/2023]  Open
28
Izawa K, Hijikata A, Tanaka N, Kawai T, Saito MK, Goldbach-Mansky R, Aksentijevich I, Yasumi T, Nakahata T, Heike T, Nishikomori R, Ohara O. Detection of base substitution-type somatic mosaicism of the NLRP3 gene with >99.9% statistical confidence by massively parallel sequencing. DNA Res 2012;19:143-52. [PMID: 22279087 PMCID: PMC3325078 DOI: 10.1093/dnares/dsr047] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
29
Mullen MP, Creevey CJ, Berry DP, McCabe MS, Magee DA, Howard DJ, Killeen AP, Park SD, McGettigan PA, Lucy MC, Machugh DE, Waters SM. Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples. BMC Genomics 2012;13:16. [PMID: 22235840 PMCID: PMC3315736 DOI: 10.1186/1471-2164-13-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 01/11/2012] [Indexed: 11/10/2022]  Open
30
Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, Haffari G, Hirst M, Marra MA, Condon A, Aparicio S, Shah SP. Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. ACTA ACUST UNITED AC 2011;28:167-75. [PMID: 22084253 PMCID: PMC3259434 DOI: 10.1093/bioinformatics/btr629] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
31
Wittler R, Chauve C. Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. BMC Bioinformatics 2011;12 Suppl 9:S21. [PMID: 22152084 PMCID: PMC3283309 DOI: 10.1186/1471-2105-12-s9-s21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
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