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Results: 1 to 20 of 101

1.

High-throughput discovery of rare insertions and deletions in large cohorts.

Vallania FL, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD.

Genome Res. 2010 Dec;20(12):1711-8. doi: 10.1101/gr.109157.110. Epub 2010 Nov 1.

PMID:
21041413
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Detection of rare genomic variants from pooled sequencing using SPLINTER.

Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE.

J Vis Exp. 2012 Jun 23;(64). pii: 3943. doi: 10.3791/3943.

PMID:
22760212
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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
4.

A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.

Bansal V, Libiger O.

Bioinformatics. 2011 Aug 1;27(15):2047-53. doi: 10.1093/bioinformatics/btr344. Epub 2011 Jun 7.

PMID:
21653520
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Dindel: accurate indel calls from short-read data.

Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R.

Genome Res. 2011 Jun;21(6):961-73. doi: 10.1101/gr.112326.110. Epub 2010 Oct 27.

PMID:
20980555
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster.

Santoni FA, Makrythanasis P, Nikolaev S, Guipponi M, Robyr D, Bottani A, Antonarakis SE.

Genome Res. 2014 Feb;24(2):349-55. doi: 10.1101/gr.163832.113. Epub 2014 Jan 3.

PMID:
24389049
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

Pattnaik S, Gupta S, Rao AA, Panda B.

BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40.

PMID:
24495296
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Efficient and cost effective population resequencing by pooling and in-solution hybridization.

Bansal V, Tewhey R, Leproust EM, Schork NJ.

PLoS One. 2011 Mar 30;6(3):e18353. doi: 10.1371/journal.pone.0018353.

PMID:
21479135
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population.

Pelleymounter LL, Moon I, Johnson JA, Laederach A, Halvorsen M, Eckloff B, Abo R, Rossetti S.

Mol Genet Metab. 2011 Dec;104(4):457-69. doi: 10.1016/j.ymgme.2011.08.019. Epub 2011 Aug 24.

PMID:
21917492
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Predicting the functional effect of amino acid substitutions and indels.

Choi Y, Sims GE, Murphy S, Miller JR, Chan AP.

PLoS One. 2012;7(10):e46688. doi: 10.1371/journal.pone.0046688. Epub 2012 Oct 8.

PMID:
23056405
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits.

Zaboli G, Ameur A, Igl W, Johansson Å, Hayward C, Vitart V, Campbell S, Zgaga L, Polasek O, Schmitz G, van Duijn C, Oostra B, Pramstaller P, Hicks A, Meitinger T, Rudan I, Wright A, Wilson JF, Campbell H, Gyllensten U; EUROSPAN Consortium.

Eur J Hum Genet. 2012 Jan;20(1):77-83. doi: 10.1038/ejhg.2011.138. Epub 2011 Aug 3.

PMID:
21811304
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Sensitive and accurate detection of copy number variants using read depth of coverage.

Yoon S, Xuan Z, Makarov V, Ye K, Sebat J.

Genome Res. 2009 Sep;19(9):1586-92. doi: 10.1101/gr.092981.109. Epub 2009 Aug 5.

PMID:
19657104
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.

Marschall T, Hajirasouliha I, Schönhuth A.

Bioinformatics. 2013 Dec 15;29(24):3143-50. doi: 10.1093/bioinformatics/btt556. Epub 2013 Sep 25.

PMID:
24072733
[PubMed - indexed for MEDLINE]
14.

VarScan: variant detection in massively parallel sequencing of individual and pooled samples.

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.

Bioinformatics. 2009 Sep 1;25(17):2283-5. doi: 10.1093/bioinformatics/btp373. Epub 2009 Jun 19.

PMID:
19542151
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis.

Niranjan TS, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R, Wang T.

Genome Biol. 2011 Sep 28;12(9):R93. doi: 10.1186/gb-2011-12-9-r93.

PMID:
21955804
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.

Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.

BMC Bioinformatics. 2011 May 5;12:134. doi: 10.1186/1471-2105-12-134.

PMID:
21545712
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Identification of genomic indels and structural variations using split reads.

Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M.

BMC Genomics. 2011 Jul 25;12:375. doi: 10.1186/1471-2164-12-375.

PMID:
21787423
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage.

Jansen S, Aigner B, Pausch H, Wysocki M, Eck S, Benet-Pagès A, Graf E, Wieland T, Strom TM, Meitinger T, Fries R.

BMC Genomics. 2013 Jul 4;14:446. doi: 10.1186/1471-2164-14-446.

PMID:
23826801
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A method for discovery of genome-wide SNP between any two genotypes from whole-genome re-sequencing data.

Krishnan SG, Waters DL, Henry RJ.

Methods Mol Biol. 2014;1099:287-94. doi: 10.1007/978-1-62703-715-0_24.

PMID:
24243213
[PubMed - indexed for MEDLINE]
20.

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.

Bioinformatics. 2009 Nov 1;25(21):2865-71. doi: 10.1093/bioinformatics/btp394. Epub 2009 Jun 26.

PMID:
19561018
[PubMed - indexed for MEDLINE]
Free PMC Article

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