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Items: 1 to 20 of 730

1.

A survey of tools for variant analysis of next-generation genome sequencing data.

Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z.

Brief Bioinform. 2014 Mar;15(2):256-78. doi: 10.1093/bib/bbs086. Epub 2013 Jan 21.

2.

A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders.

Mutarelli M, Marwah V, Rispoli R, Carrella D, Dharmalingam G, Oliva G, di Bernardo D.

BMC Genomics. 2014;15 Suppl 3:S5. doi: 10.1186/1471-2164-15-S3-S5. Epub 2014 May 6.

3.

CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting.

Münz M, Ruark E, Renwick A, Ramsay E, Clarke M, Mahamdallie S, Cloke V, Seal S, Strydom A, Lunter G, Rahman N.

Genome Med. 2015 Jul 28;7:76. doi: 10.1186/s13073-015-0195-6.

4.

NGS for Sequence Variants.

Teng S.

Adv Exp Med Biol. 2016;939:1-20.

PMID:
27807741
5.

From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing.

Laurie S, Fernandez-Callejo M, Marco-Sola S, Trotta JR, Camps J, Chacón A, Espinosa A, Gut M, Gut I, Heath S, Beltran S.

Hum Mutat. 2016 Dec;37(12):1263-1271. doi: 10.1002/humu.23114. Epub 2016 Sep 26.

6.

SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing.

Spinella JF, Mehanna P, Vidal R, Saillour V, Cassart P, Richer C, Ouimet M, Healy J, Sinnett D.

BMC Genomics. 2016 Nov 14;17(1):912.

7.

Analysis and annotation of whole-genome or whole-exome sequencing-derived variants for clinical diagnosis.

Worthey EA.

Curr Protoc Hum Genet. 2013 Oct 18;79:Unit 9.24.. doi: 10.1002/0471142905.hg0924s79.

PMID:
24510652
8.

An evaluation of copy number variation detection tools for cancer using whole exome sequencing data.

Zare F, Dow M, Monteleone N, Hosny A, Nabavi S.

BMC Bioinformatics. 2017 May 31;18(1):286. doi: 10.1186/s12859-017-1705-x.

9.

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data.

Alkodsi A, Louhimo R, Hautaniemi S.

Brief Bioinform. 2015 Mar;16(2):242-54. doi: 10.1093/bib/bbu004. Epub 2014 Mar 5.

PMID:
24599115
10.

Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer.

Katainen R, Donner I, Cajuso T, Kaasinen E, Palin K, Mäkinen V, Aaltonen LA, Pitkänen E.

Nat Protoc. 2018 Nov;13(11):2580-2600. doi: 10.1038/s41596-018-0052-3.

PMID:
30323186
11.

Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing.

Samorodnitsky E, Jewell BM, Hagopian R, Miya J, Wing MR, Lyon E, Damodaran S, Bhatt D, Reeser JW, Datta J, Roychowdhury S.

Hum Mutat. 2015 Sep;36(9):903-14. doi: 10.1002/humu.22825. Epub 2015 Jul 15.

12.

SeqMule: automated pipeline for analysis of human exome/genome sequencing data.

Guo Y, Ding X, Shen Y, Lyon GJ, Wang K.

Sci Rep. 2015 Sep 18;5:14283. doi: 10.1038/srep14283.

13.

An evaluation of copy number variation detection tools from whole-exome sequencing data.

Tan R, Wang Y, Kleinstein SE, Liu Y, Zhu X, Guo H, Jiang Q, Allen AS, Zhu M.

Hum Mutat. 2014 Jul;35(7):899-907. doi: 10.1002/humu.22537. Epub 2014 May 1.

PMID:
24599517
14.

Opportunities and challenges of whole-genome and -exome sequencing.

Petersen BS, Fredrich B, Hoeppner MP, Ellinghaus D, Franke A.

BMC Genet. 2017 Feb 14;18(1):14. doi: 10.1186/s12863-017-0479-5. Review.

15.

Exome versus transcriptome sequencing in identifying coding region variants.

Ku CS, Wu M, Cooper DN, Naidoo N, Pawitan Y, Pang B, Iacopetta B, Soong R.

Expert Rev Mol Diagn. 2012 Apr;12(3):241-51. doi: 10.1586/erm.12.10. Review.

PMID:
22468815
16.

Variant Calling From Next Generation Sequence Data.

Hansen NF.

Methods Mol Biol. 2016;1418:209-24. doi: 10.1007/978-1-4939-3578-9_11.

PMID:
27008017
17.

Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing.

Dolled-Filhart MP, Lee M Jr, Ou-Yang CW, Haraksingh RR, Lin JC.

ScientificWorldJournal. 2013;2013:730210. doi: 10.1155/2013/730210. Epub 2013 Jan 13. Review.

18.

wKGGSeq: A Comprehensive Strategy-Based and Disease-Targeted Online Framework to Facilitate Exome Sequencing Studies of Inherited Disorders.

Li MJ, Deng J, Wang P, Yang W, Ho SL, Sham PC, Wang J, Li M.

Hum Mutat. 2015 May;36(5):496-503. doi: 10.1002/humu.22766. Epub 2015 Apr 4.

PMID:
25676918
19.

CoVaCS: a consensus variant calling system.

Chiara M, Gioiosa S, Chillemi G, D'Antonio M, Flati T, Picardi E, Zambelli F, Horner DS, Pesole G, Castrignanò T.

BMC Genomics. 2018 Feb 5;19(1):120. doi: 10.1186/s12864-018-4508-1.

20.

Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction.

Laehnemann D, Borkhardt A, McHardy AC.

Brief Bioinform. 2016 Jan;17(1):154-79. doi: 10.1093/bib/bbv029. Epub 2015 May 29.

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