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For: Neuman JA, Isakov O, Shomron N. Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Brief Bioinform 2012;14:46-55. [PMID: 22707752 DOI: 10.1093/bib/bbs013] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
Number Cited by Other Article(s)
1
Koh GCC, Nanda AS, Rinaldi G, Boushaki S, Degasperi A, Badja C, Pregnall AM, Zhao SJ, Chmelova L, Black D, Heskin L, Dias J, Young J, Memari Y, Shooter S, Czarnecki J, Brown MA, Davies HR, Zou X, Nik-Zainal S. A redefined InDel taxonomy provides insights into mutational signatures. Nat Genet 2025;57:1132-1141. [PMID: 40210680 DOI: 10.1038/s41588-025-02152-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/04/2025] [Indexed: 04/12/2025]
2
Sealock JM, Ivankovic F, Liao C, Chen S, Churchhouse C, Karczewski KJ, Howrigan DP, Neale BM. Tutorial: guidelines for quality filtering of whole-exome and whole-genome sequencing data for population-scale association analyses. Nat Protoc 2025:10.1038/s41596-025-01169-1. [PMID: 40155705 DOI: 10.1038/s41596-025-01169-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 03/04/2025] [Indexed: 04/01/2025]
3
Zhou X, Li J, Chen L, Guo M, Liang R, Pan Y. The genomic pattern of insertion/deletion variations during rice improvement. BMC Genomics 2024;25:1263. [PMID: 39741238 DOI: 10.1186/s12864-024-11178-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Accepted: 12/20/2024] [Indexed: 01/02/2025]  Open
4
Sarwal V, Niehus S, Ayyala R, Kim M, Sarkar A, Chang S, Lu A, Rajkumar N, Darci-Maher N, Littman R, Chhugani K, Soylev A, Comarova Z, Wesel E, Castellanos J, Chikka R, Distler MG, Eskin E, Flint J, Mangul S. A comprehensive benchmarking of WGS-based deletion structural variant callers. Brief Bioinform 2022;23:bbac221. [PMID: 35753701 PMCID: PMC9294411 DOI: 10.1093/bib/bbac221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/30/2022] [Accepted: 05/11/2022] [Indexed: 01/10/2023]  Open
5
Kubicová Z, Roussel S, Félix B, Cabanová L. Genomic Diversity of Listeria monocytogenes Isolates From Slovakia (2010 to 2020). Front Microbiol 2021;12:729050. [PMID: 34795648 PMCID: PMC8593459 DOI: 10.3389/fmicb.2021.729050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022]  Open
6
Zanti M, Michailidou K, Loizidou MA, Machattou C, Pirpa P, Christodoulou K, Spyrou GM, Kyriacou K, Hadjisavvas A. Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels. BMC Bioinformatics 2021;22:218. [PMID: 33910496 PMCID: PMC8080428 DOI: 10.1186/s12859-021-04144-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/15/2021] [Indexed: 11/10/2022]  Open
7
Zhang W, Ghosh D. A general approach to sensitivity analysis for Mendelian randomization. STATISTICS IN BIOSCIENCES 2021;13:34-55. [PMID: 33737984 DOI: 10.1007/s12561-020-09280-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
8
Hashimoto S, Noguchi E, Bando H, Miyadera H, Morii W, Nakamura T, Hara H. Neoantigen prediction in human breast cancer using RNA sequencing data. Cancer Sci 2021;112:465-475. [PMID: 33155341 PMCID: PMC7780012 DOI: 10.1111/cas.14720] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/08/2020] [Accepted: 11/02/2020] [Indexed: 12/30/2022]  Open
9
Skuza L, Filip E, Szućko I, Bocianowski J. SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species. Int J Mol Sci 2020;21:ijms21249421. [PMID: 33321948 PMCID: PMC7762986 DOI: 10.3390/ijms21249421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 01/09/2023]  Open
10
Rabinowitz T, Shomron N. Genome-wide noninvasive prenatal diagnosis of monogenic disorders: Current and future trends. Comput Struct Biotechnol J 2020;18:2463-2470. [PMID: 33005308 PMCID: PMC7509788 DOI: 10.1016/j.csbj.2020.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/17/2020] [Accepted: 09/01/2020] [Indexed: 02/09/2023]  Open
11
Li M, Tang L, Wu FX, Pan Y, Wang J. CSA: a web service for the complete process of ChIP-Seq analysis. BMC Bioinformatics 2019;20:515. [PMID: 31874601 PMCID: PMC6929326 DOI: 10.1186/s12859-019-3090-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 09/10/2019] [Indexed: 01/10/2023]  Open
12
Li D, Kim W, Wang L, Yoon KA, Park B, Park C, Kong SY, Hwang Y, Baek D, Lee ES, Won S. Comparison of INDEL Calling Tools with Simulation Data and Real Short-Read Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:1635-1644. [PMID: 30004886 DOI: 10.1109/tcbb.2018.2854793] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
13
Crespo-Piazuelo D, Criado-Mesas L, Revilla M, Castelló A, Fernández AI, Folch JM, Ballester M. Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs. PLoS One 2019;14:e0218862. [PMID: 31246983 PMCID: PMC6597088 DOI: 10.1371/journal.pone.0218862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/11/2019] [Indexed: 12/15/2022]  Open
14
Kumaran M, Subramanian U, Devarajan B. Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data. BMC Bioinformatics 2019;20:342. [PMID: 31208315 PMCID: PMC6580603 DOI: 10.1186/s12859-019-2928-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 05/31/2019] [Indexed: 12/30/2022]  Open
15
Rabinowitz T, Polsky A, Golan D, Danilevsky A, Shapira G, Raff C, Basel-Salmon L, Matar RT, Shomron N. Bayesian-based noninvasive prenatal diagnosis of single-gene disorders. Genome Res 2019;29:428-438. [PMID: 30787035 PMCID: PMC6396420 DOI: 10.1101/gr.235796.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 01/23/2019] [Indexed: 12/04/2022]
16
Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher JPA. Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. Brief Bioinform 2018;18:973-983. [PMID: 27473065 PMCID: PMC5862335 DOI: 10.1093/bib/bbw069] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Indexed: 11/29/2022]  Open
17
Kotelnikova EA, Pyatnitskiy M, Paleeva A, Kremenetskaya O, Vinogradov D. Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. Oncotarget 2018;7:52493-52516. [PMID: 27191992 PMCID: PMC5239569 DOI: 10.18632/oncotarget.9370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 04/18/2016] [Indexed: 12/17/2022]  Open
18
Wadapurkar RM, Vyas R. Computational analysis of next generation sequencing data and its applications in clinical oncology. INFORMATICS IN MEDICINE UNLOCKED 2018. [DOI: 10.1016/j.imu.2018.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
19
Felten A, Vila Nova M, Durimel K, Guillier L, Mistou MY, Radomski N. First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts. BMC Microbiol 2017;17:222. [PMID: 29183286 PMCID: PMC5706153 DOI: 10.1186/s12866-017-1132-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/16/2017] [Indexed: 12/13/2022]  Open
20
UPS-indel: a Universal Positioning System for Indels. Sci Rep 2017;7:14106. [PMID: 29074871 PMCID: PMC5658412 DOI: 10.1038/s41598-017-14400-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]  Open
21
Song X, Haghighi A, Iliuta IA, Pei Y. Molecular diagnosis of autosomal dominant polycystic kidney disease. Expert Rev Mol Diagn 2017;17:885-895. [PMID: 28724316 DOI: 10.1080/14737159.2017.1358088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
22
Kim BY, Park JH, Jo HY, Koo SK, Park MH. Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. PLoS One 2017;12:e0182272. [PMID: 28792971 PMCID: PMC5549930 DOI: 10.1371/journal.pone.0182272] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/14/2017] [Indexed: 12/22/2022]  Open
23
Chintalapati M, Dannemann M, Prüfer K. Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans. BMC Evol Biol 2017;17:179. [PMID: 28778150 PMCID: PMC5543596 DOI: 10.1186/s12862-017-1018-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/19/2017] [Indexed: 12/24/2022]  Open
24
Replication Errors Made During Oogenesis Lead to Detectable De Novo mtDNA Mutations in Zebrafish Oocytes with a Low mtDNA Copy Number. Genetics 2016;204:1423-1431. [PMID: 27770035 DOI: 10.1534/genetics.116.194035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/13/2016] [Indexed: 01/30/2023]  Open
25
From next-generation resequencing reads to a high-quality variant data set. Heredity (Edinb) 2016;118:111-124. [PMID: 27759079 DOI: 10.1038/hdy.2016.102] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 09/03/2016] [Accepted: 09/06/2016] [Indexed: 12/11/2022]  Open
26
Piccolo SR, Frampton MB. Tools and techniques for computational reproducibility. Gigascience 2016;5:30. [PMID: 27401684 PMCID: PMC4940747 DOI: 10.1186/s13742-016-0135-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
27
Deng X, den Bakker HC, Hendriksen RS. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens. Annu Rev Food Sci Technol 2016;7:353-74. [PMID: 26772415 DOI: 10.1146/annurev-food-041715-033259] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
28
Next Generation Sequencing Data and Proteogenomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016;926:11-19. [DOI: 10.1007/978-3-319-42316-6_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
29
Yang R, Nelson AC, Henzler C, Thyagarajan B, Silverstein KAT. ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly. Genome Med 2015;7:127. [PMID: 26643039 PMCID: PMC4671222 DOI: 10.1186/s13073-015-0251-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/18/2015] [Indexed: 12/30/2022]  Open
30
Gézsi A, Bolgár B, Marx P, Sarkozy P, Szalai C, Antal P. VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering. BMC Genomics 2015;16:875. [PMID: 26510841 PMCID: PMC4625715 DOI: 10.1186/s12864-015-2050-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/06/2015] [Indexed: 11/10/2022]  Open
31
Hasan MS, Wu X, Zhang L. Performance evaluation of indel calling tools using real short-read data. Hum Genomics 2015;9:20. [PMID: 26286629 PMCID: PMC4545535 DOI: 10.1186/s40246-015-0042-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/20/2015] [Indexed: 12/16/2022]  Open
32
Liu J, Qu J, Yang C, Tang D, Li J, Lan H, Rong T. Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data. BMC Genomics 2015;16:601. [PMID: 26269146 PMCID: PMC4535256 DOI: 10.1186/s12864-015-1797-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 07/24/2015] [Indexed: 12/11/2022]  Open
33
Boschiero C, Gheyas AA, Ralph HK, Eory L, Paton B, Kuo R, Fulton J, Preisinger R, Kaiser P, Burt DW. Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes. BMC Genomics 2015;16:562. [PMID: 26227840 PMCID: PMC4563830 DOI: 10.1186/s12864-015-1711-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 06/22/2015] [Indexed: 01/17/2023]  Open
34
Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, et alSchmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015;145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Show More Authors] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
35
Jiang Y, Turinsky AL, Brudno M. The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection. Nucleic Acids Res 2015;43:7217-28. [PMID: 26130710 PMCID: PMC4551921 DOI: 10.1093/nar/gkv677] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/19/2015] [Indexed: 12/22/2022]  Open
36
Bianco E, Nevado B, Ramos-Onsins SE, Pérez-Enciso M. A deep catalog of autosomal single nucleotide variation in the pig. PLoS One 2015;10:e0118867. [PMID: 25789620 PMCID: PMC4366260 DOI: 10.1371/journal.pone.0118867] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/27/2014] [Indexed: 12/31/2022]  Open
37
Challis D, Antunes L, Garrison E, Banks E, Evani US, Muzny D, Poplin R, Gibbs RA, Marth G, Yu F. The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes. BMC Genomics 2015;16:143. [PMID: 25765891 PMCID: PMC4352271 DOI: 10.1186/s12864-015-1333-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 02/09/2015] [Indexed: 12/30/2022]  Open
38
Godoy TF, Moreira GCM, Boschiero C, Gheyas AA, Gasparin G, Paduan M, Andrade SCS, Montenegro H, Burt DW, Ledur MC, Coutinho LL. SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition. Anim Genet 2015;46:158-63. [PMID: 25690762 DOI: 10.1111/age.12271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2014] [Indexed: 11/28/2022]
39
Chen W, Zhang L. The pattern of DNA cleavage intensity around indels. Sci Rep 2015;5:8333. [PMID: 25660536 PMCID: PMC4321175 DOI: 10.1038/srep08333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022]  Open
40
Moreira GCM, Godoy TF, Boschiero C, Gheyas A, Gasparin G, Andrade SCS, Paduan M, Montenegro H, Burt DW, Ledur MC, Coutinho LL. Variant discovery in a QTL region on chromosome 3 associated with fatness in chickens. Anim Genet 2015;46:141-7. [PMID: 25643900 DOI: 10.1111/age.12263] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2014] [Indexed: 12/17/2022]
41
Ghoneim DH, Myers JR, Tuttle E, Paciorkowski AR. Comparison of insertion/deletion calling algorithms on human next-generation sequencing data. BMC Res Notes 2014;7:864. [PMID: 25435282 PMCID: PMC4265454 DOI: 10.1186/1756-0500-7-864] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/21/2014] [Indexed: 11/10/2022]  Open
42
Abo RP, Ducar M, Garcia EP, Thorner AR, Rojas-Rudilla V, Lin L, Sholl LM, Hahn WC, Meyerson M, Lindeman NI, Van Hummelen P, MacConaill LE. BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers. Nucleic Acids Res 2014;43:e19. [PMID: 25428359 PMCID: PMC4330340 DOI: 10.1093/nar/gku1211] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
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Ward RM, Schmieder R, Highnam G, Mittelman D. Big data challenges and opportunities in high-throughput sequencing. ACTA ACUST UNITED AC 2014. [DOI: 10.4161/sysb.24470] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Yan Y, Yi G, Sun C, Qu L, Yang N. Genome-wide characterization of insertion and deletion variation in chicken using next generation sequencing. PLoS One 2014;9:e104652. [PMID: 25133774 PMCID: PMC4136736 DOI: 10.1371/journal.pone.0104652] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/10/2014] [Indexed: 12/30/2022]  Open
45
Chambers JC, Abbott J, Zhang W, Turro E, Scott WR, Tan ST, Afzal U, Afaq S, Loh M, Lehne B, O'Reilly P, Gaulton KJ, Pearson RD, Li X, Lavery A, Vandrovcova J, Wass MN, Miller K, Sehmi J, Oozageer L, Kooner IK, Al-Hussaini A, Mills R, Grewal J, Panoulas V, Lewin AM, Northwood K, Wander GS, Geoghegan F, Li Y, Wang J, Aitman TJ, McCarthy MI, Scott J, Butcher S, Elliott P, Kooner JS. The South Asian genome. PLoS One 2014;9:e102645. [PMID: 25115870 PMCID: PMC4130493 DOI: 10.1371/journal.pone.0102645] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 06/21/2014] [Indexed: 12/15/2022]  Open
46
Van Geystelen A, Wenseleers T, Decorte R, Caspers MJL, Larmuseau MHD. In silico detection of phylogenetic informative Y-chromosomal single nucleotide polymorphisms from whole genome sequencing data. Electrophoresis 2014;35:3102-10. [DOI: 10.1002/elps.201300459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/03/2013] [Accepted: 01/07/2014] [Indexed: 12/25/2022]
47
Cao MD, Tasker E, Willadsen K, Imelfort M, Vishwanathan S, Sureshkumar S, Balasubramanian S, Bodén M. Inferring short tandem repeat variation from paired-end short reads. Nucleic Acids Res 2013;42:e16. [PMID: 24353318 PMCID: PMC3919575 DOI: 10.1093/nar/gkt1313] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
48
Dorn C, Grunert M, Sperling SR. Application of high-throughput sequencing for studying genomic variations in congenital heart disease. Brief Funct Genomics 2013;13:51-65. [PMID: 24095982 DOI: 10.1093/bfgp/elt040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
49
Chong Z, Zhai W, Li C, Gao M, Gong Q, Ruan J, Li J, Jiang L, Lv X, Hungate E, Wu CI. The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster. Mol Biol Evol 2013;30:2699-708. [PMID: 24077769 DOI: 10.1093/molbev/mst167] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]  Open
50
Rogan PK, Zou GY. Best Practices for Evaluating Mutation Prediction Methods. Hum Mutat 2013;34:1581-2. [DOI: 10.1002/humu.22401] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 08/13/2013] [Indexed: 01/07/2023]
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