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Results: 1 to 20 of 117

1.

BlackOPs: increasing confidence in variant detection through mappability filtering.

Cabanski CR, Wilkerson MD, Soloway M, Parker JS, Liu J, Prins JF, Marron JS, Perou CM, Hayes DN.

Nucleic Acids Res. 2013 Oct;41(19):e178. doi: 10.1093/nar/gkt692. Epub 2013 Aug 8.

PMID:
23935067
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A novel multi-alignment pipeline for high-throughput sequencing data.

Huang S, Holt J, Kao CY, McMillan L, Wang W.

Database (Oxford). 2014 Jun 18;2014. pii: bau057. doi: 10.1093/database/bau057. Print 2014.

PMID:
24948510
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

WEP: a high-performance analysis pipeline for whole-exome data.

D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, Pallocca M, Sanna N, Picardi E, Pesole G, Castrignanò T.

BMC Bioinformatics. 2013;14 Suppl 7:S11. doi: 10.1186/1471-2105-14-S7-S11. Epub 2013 Apr 22.

PMID:
23815231
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

Ramos E, Levinson BT, Chasnoff S, Hughes A, Young AL, Thornton K, Li A, Vallania FL, Province M, Druley TE.

BMC Genomics. 2012 Dec 6;13:683. doi: 10.1186/1471-2164-13-683.

PMID:
23216810
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis.

Guo Y, Li J, Li CI, Shyr Y, Samuels DC.

Bioinformatics. 2013 May 1;29(9):1210-1. doi: 10.1093/bioinformatics/btt118. Epub 2013 Mar 6.

PMID:
23471301
[PubMed - indexed for MEDLINE]
Free Article
6.

FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets.

Pope BJ, Nguyen-Dumont T, Odefrey F, Hammet F, Bell R, Tao K, Tavtigian SV, Goldgar DE, Lonie A, Southey MC, Park DJ.

BMC Bioinformatics. 2013 Feb 25;14:65. doi: 10.1186/1471-2105-14-65.

PMID:
23441864
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

VarBin, a novel method for classifying true and false positive variants in NGS data.

Durtschi J, Margraf RL, Coonrod EM, Mallempati KC, Voelkerding KV.

BMC Bioinformatics. 2013;14 Suppl 13:S2. doi: 10.1186/1471-2105-14-S13-S2. Epub 2013 Oct 1.

PMID:
24266885
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.

Rubio-Camarillo M, Gómez-López G, Fernández JM, Valencia A, Pisano DG.

Bioinformatics. 2013 Jul 1;29(13):1687-9. doi: 10.1093/bioinformatics/btt203. Epub 2013 Apr 28.

PMID:
23630175
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.

Raczy C, Petrovski R, Saunders CT, Chorny I, Kruglyak S, Margulies EH, Chuang HY, Källberg M, Kumar SA, Liao A, Little KM, Strömberg MP, Tanner SW.

Bioinformatics. 2013 Aug 15;29(16):2041-3. doi: 10.1093/bioinformatics/btt314. Epub 2013 Jun 4.

PMID:
23736529
[PubMed - indexed for MEDLINE]
Free Article
10.

Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing.

Elsharawy A, Forster M, Schracke N, Keller A, Thomsen I, Petersen BS, Stade B, Stähler P, Schreiber S, Rosenstiel P, Franke A.

BMC Genomics. 2012 Aug 22;13:417. doi: 10.1186/1471-2164-13-417.

PMID:
22913592
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Visualization and probability-based scoring of structural variants within repetitive sequences.

Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA.

Bioinformatics. 2014 Jun 1;30(11):1514-21. doi: 10.1093/bioinformatics/btu054. Epub 2014 Feb 4.

PMID:
24501098
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A framework for variation discovery and genotyping using next-generation DNA sequencing data.

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.

Nat Genet. 2011 May;43(5):491-8. doi: 10.1038/ng.806. Epub 2011 Apr 10.

PMID:
21478889
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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
[PubMed - indexed for MEDLINE]
14.

Detection and quantification of alternative splicing variants using RNA-seq.

Bryant DW Jr, Priest HD, Mockler TC.

Methods Mol Biol. 2012;883:97-110. doi: 10.1007/978-1-61779-839-9_7.

PMID:
22589127
[PubMed - indexed for MEDLINE]
15.

SNP calling by sequencing pooled samples.

Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S, Pérez-Enciso M.

BMC Bioinformatics. 2012 Sep 20;13:239. doi: 10.1186/1471-2105-13-239.

PMID:
22992255
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

OSA: a fast and accurate alignment tool for RNA-Seq.

Hu J, Ge H, Newman M, Liu K.

Bioinformatics. 2012 Jul 15;28(14):1933-4. doi: 10.1093/bioinformatics/bts294. Epub 2012 May 15.

PMID:
22592379
[PubMed - indexed for MEDLINE]
Free Article
17.

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.

Cirulli ET, Singh A, Shianna KV, Ge D, Smith JP, Maia JM, Heinzen EL, Goedert JJ, Goldstein DB; Center for HIV/AIDS Vaccine Immunology (CHAVI).

Genome Biol. 2010;11(5):R57. doi: 10.1186/gb-2010-11-5-r57. Epub 2010 May 28.

PMID:
20598109
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.

PMID:
21989248
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Effective filtering strategies to improve data quality from population-based whole exome sequencing studies.

Carson AR, Smith EN, Matsui H, Brækkan SK, Jepsen K, Hansen JB, Frazer KA.

BMC Bioinformatics. 2014 May 2;15:125. doi: 10.1186/1471-2105-15-125.

PMID:
24884706
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models.

Andrews TD, Whittle B, Field MA, Balakishnan B, Zhang Y, Shao Y, Cho V, Kirk M, Singh M, Xia Y, Hager J, Winslade S, Sjollema G, Beutler B, Enders A, Goodnow CC.

Open Biol. 2012 May;2(5):120061. doi: 10.1098/rsob.120061.

PMID:
22724066
[PubMed - indexed for MEDLINE]
Free PMC Article

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