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Results: 1 to 20 of 29

1.

SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.

Qiao Y, Quinlan AR, Jazaeri AA, Verhaak R, Wheeler DA, Marth GT.

Genome Biol. 2014 Aug 26;15(8):443. [Epub ahead of print]

PMID:
25160522
[PubMed - as supplied by publisher]
2.

Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii.

Farrell A, Coleman BI, Benenati B, Brown KM, Blader IJ, Marth GT, Gubbels MJ.

BMC Genomics. 2014 May 10;15:354. doi: 10.1186/1471-2164-15-354.

PMID:
24885922
[PubMed - in process]
Free PMC Article
3.

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT.

PLoS One. 2014 Mar 5;9(3):e90581. doi: 10.1371/journal.pone.0090581. eCollection 2014.

PMID:
24599324
[PubMed - in process]
Free PMC Article
4.

SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications.

Zhao M, Lee WP, Garrison EP, Marth GT.

PLoS One. 2013 Dec 4;8(12):e82138. doi: 10.1371/journal.pone.0082138. eCollection 2013.

PMID:
24324759
[PubMed - in process]
Free PMC Article
5.

Variant discovery in targeted resequencing using whole genome amplified DNA.

Indap AR, Cole R, Runge CL, Marth GT, Olivier M.

BMC Genomics. 2013 Jul 10;14:468. doi: 10.1186/1471-2164-14-468.

PMID:
23837845
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains.

Yang N, Farrell A, Niedelman W, Melo M, Lu D, Julien L, Marth GT, Gubbels MJ, Saeij JP.

BMC Genomics. 2013 Jul 10;14:467. doi: 10.1186/1471-2164-14-467.

PMID:
23837824
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.

Busby MA, Stewart C, Miller CA, Grzeda KR, Marth GT.

Bioinformatics. 2013 Mar 1;29(5):656-7. doi: 10.1093/bioinformatics/btt015. Epub 2013 Jan 12.

PMID:
23314327
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data.

Wu J, Grzeda KR, Stewart C, Grubert F, Urban AE, Snyder MP, Marth GT.

BMC Bioinformatics. 2012 Nov 17;13:305. doi: 10.1186/1471-2105-13-305.

PMID:
23157288
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

An integrated map of genetic variation from 1,092 human genomes.

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632.

PMID:
23128226
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Targeted proteomic dissection of Toxoplasma cytoskeleton sub-compartments using MORN1.

Lorestani A, Ivey FD, Thirugnanam S, Busby MA, Marth GT, Cheeseman IM, Gubbels MJ.

Cytoskeleton (Hoboken). 2012 Dec;69(12):1069-85. doi: 10.1002/cm.21077. Epub 2012 Oct 11.

PMID:
23027733
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A DOC2 protein identified by mutational profiling is essential for apicomplexan parasite exocytosis.

Farrell A, Thirugnanam S, Lorestani A, Dvorin JD, Eidell KP, Ferguson DJ, Anderson-White BR, Duraisingh MT, Marth GT, Gubbels MJ.

Science. 2012 Jan 13;335(6065):218-21. doi: 10.1126/science.1210829. Erratum in: Science. 2012 Apr 13;336(6078):155.

PMID:
22246776
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Expression divergence measured by transcriptome sequencing of four yeast species.

Busby MA, Gray JM, Costa AM, Stewart C, Stromberg MP, Barnett D, Chuang JH, Springer M, Marth GT.

BMC Genomics. 2011 Dec 29;12:635. doi: 10.1186/1471-2164-12-635.

PMID:
22206443
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

ART: a next-generation sequencing read simulator.

Huang W, Li L, Myers JR, Marth GT.

Bioinformatics. 2012 Feb 15;28(4):593-4. doi: 10.1093/bioinformatics/btr708. Epub 2011 Dec 23.

PMID:
22199392
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The functional spectrum of low-frequency coding variation.

Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R; 1000 Genomes Project.

Genome Biol. 2011 Sep 14;12(9):R84. doi: 10.1186/gb-2011-12-9-r84.

PMID:
21917140
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A comprehensive map of mobile element insertion polymorphisms in humans.

Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT; 1000 Genomes Project.

PLoS Genet. 2011 Aug;7(8):e1002236. doi: 10.1371/journal.pgen.1002236. Epub 2011 Aug 18.

PMID:
21876680
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Demographic history and rare allele sharing among human populations.

Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA; 1000 Genomes Project, Bustamante CD.

Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-8. doi: 10.1073/pnas.1019276108. Epub 2011 Jul 5.

PMID:
21730125
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group.

Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.

PMID:
21653522
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT.

Bioinformatics. 2011 Jun 15;27(12):1691-2. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14.

PMID:
21493652
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Mapping copy number variation by population-scale genome sequencing.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.

PMID:
21293372
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A standard variation file format for human genome sequences.

Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K.

Genome Biol. 2010;11(8):R88. doi: 10.1186/gb-2010-11-8-r88. Epub 2010 Aug 26.

PMID:
20796305
[PubMed - indexed for MEDLINE]
Free PMC Article

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