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Results: 1 to 20 of 89

1.

Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data.

Jun G, Flickinger M, Hetrick KN, Romm JM, Doheny KF, Abecasis GR, Boehnke M, Kang HM.

Am J Hum Genet. 2012 Nov 2;91(5):839-48. doi: 10.1016/j.ajhg.2012.09.004. Epub 2012 Oct 25.

PMID:
23103226
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Accurate detection and genotyping of SNPs utilizing population sequencing data.

Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA.

Genome Res. 2010 Apr;20(4):537-45. doi: 10.1101/gr.100040.109. Epub 2010 Feb 11.

PMID:
20150320
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

ContEst: estimating cross-contamination of human samples in next-generation sequencing data.

Cibulskis K, McKenna A, Fennell T, Banks E, DePristo M, Getz G.

Bioinformatics. 2011 Sep 15;27(18):2601-2. doi: 10.1093/bioinformatics/btr446. Epub 2011 Jul 29.

PMID:
21803805
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

A tool for RNA sequencing sample identity check.

Huang J, Chen J, Lathrop M, Liang L.

Bioinformatics. 2013 Jun 1;29(11):1463-4. doi: 10.1093/bioinformatics/btt155. Epub 2013 Apr 4.

PMID:
23559639
[PubMed - indexed for MEDLINE]
Free Article
5.

Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing.

Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, Abaan HO, Albert TJ; NISC Comparative Sequencing Program, Margulies EH, Green ED, Collins FS, Mullikin JC, Biesecker LG.

Genome Res. 2010 Oct;20(10):1420-31. doi: 10.1101/gr.106716.110. Epub 2010 Sep 1.

PMID:
20810667
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Fast identification and removal of sequence contamination from genomic and metagenomic datasets.

Schmieder R, Edwards R.

PLoS One. 2011 Mar 9;6(3):e17288. doi: 10.1371/journal.pone.0017288.

PMID:
21408061
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms.

Chen Q, Sun F.

BMC Genomics. 2013;14 Suppl 1:S1. doi: 10.1186/1471-2164-14-S1-S1. Epub 2013 Jan 21.

PMID:
23369070
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies.

Martin ER, Kinnamon DD, Schmidt MA, Powell EH, Zuchner S, Morris RW.

Bioinformatics. 2010 Nov 15;26(22):2803-10. doi: 10.1093/bioinformatics/btq526. Epub 2010 Sep 21.

PMID:
20861027
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Improving ancient DNA read mapping against modern reference genomes.

Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, Krogh A, Orlando L.

BMC Genomics. 2012 May 10;13:178. doi: 10.1186/1471-2164-13-178.

PMID:
22574660
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Exome sequencing of a multigenerational human pedigree.

Hedges DJ, Burges D, Powell E, Almonte C, Huang J, Young S, Boese B, Schmidt M, Pericak-Vance MA, Martin E, Zhang X, Harkins TT, Züchner S.

PLoS One. 2009 Dec 14;4(12):e8232. doi: 10.1371/journal.pone.0008232. Erratum in: PLoS One. 2009;4(12). doi: 10.1371/annotation/b0fe9dd5-16e1-4b50-b590-263518fbd5eb. Hedges, Dale [corrected to Hedges, Dale J].

PMID:
20011588
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Estimation of allele frequency and association mapping using next-generation sequencing data.

Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, Jorgensen T, Hansen T, Pedersen O, Wang J, Nielsen R.

BMC Bioinformatics. 2011 Jun 11;12:231. doi: 10.1186/1471-2105-12-231.

PMID:
21663684
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Comparison of solution-based exome capture methods for next generation sequencing.

Sulonen AM, Ellonen P, Almusa H, Lepistö M, Eldfors S, Hannula S, Miettinen T, Tyynismaa H, Salo P, Heckman C, Joensuu H, Raivio T, Suomalainen A, Saarela J.

Genome Biol. 2011 Sep 28;12(9):R94. doi: 10.1186/gb-2011-12-9-r94.

PMID:
21955854
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data.

Liu Q, Guo Y, Li J, Long J, Zhang B, Shyr Y.

BMC Genomics. 2012;13 Suppl 8:S8. doi: 10.1186/1471-2164-13-S8-S8. Epub 2012 Dec 17.

PMID:
23281772
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Evaluation of next generation sequencing platforms for population targeted sequencing studies.

Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA.

Genome Biol. 2009;10(3):R32. doi: 10.1186/gb-2009-10-3-r32. Epub 2009 Mar 27.

PMID:
19327155
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads.

Duitama J, Kennedy J, Dinakar S, Hernández Y, Wu Y, Măndoiu II.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S53. doi: 10.1186/1471-2105-12-S1-S53.

PMID:
21342586
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Genotype calling from next-generation sequencing data using haplotype information of reads.

Zhi D, Wu J, Liu N, Zhang K.

Bioinformatics. 2012 Apr 1;28(7):938-46. doi: 10.1093/bioinformatics/bts047. Epub 2012 Jan 27.

PMID:
22285565
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A statistical method for the detection of variants from next-generation resequencing of DNA pools.

Bansal V.

Bioinformatics. 2010 Jun 15;26(12):i318-24. doi: 10.1093/bioinformatics/btq214.

PMID:
20529923
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Efficiency and power as a function of sequence coverage, SNP array density, and imputation.

Flannick J, Korn JM, Fontanillas P, Grant GB, Banks E, Depristo MA, Altshuler D.

PLoS Comput Biol. 2012;8(7):e1002604. doi: 10.1371/journal.pcbi.1002604. Epub 2012 Jul 12.

PMID:
22807667
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold.

Menelaou A, Marchini J.

Bioinformatics. 2013 Jan 1;29(1):84-91. doi: 10.1093/bioinformatics/bts632. Epub 2012 Oct 23.

PMID:
23093610
[PubMed - indexed for MEDLINE]
Free Article
20.

QC-Chain: fast and holistic quality control method for next-generation sequencing data.

Zhou Q, Su X, Wang A, Xu J, Ning K.

PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.

PMID:
23565205
[PubMed - indexed for MEDLINE]
Free PMC Article

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