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Results: 1 to 20 of 35

1.

Toolbox for mobile-element insertion detection on cancer genomes.

Lee WP, Wu J, Marth GT.

Cancer Inform. 2015 Feb 12;14(Suppl 1):37-44. doi: 10.4137/CIN.S24657. eCollection 2015.

2.

Extending reference assembly models.

Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P.

Genome Biol. 2015 Jan 24;16:13. doi: 10.1186/s13059-015-0587-3.

3.

Toolbox for mobile-element insertion detection on cancer genomes.

Lee WP, Wu J, Marth GT.

Cancer Inform. 2014 Oct 15;13(Suppl 4):45-52. doi: 10.4137/CIN.S13979. eCollection 2014.

4.

bam.iobio: a web-based, real-time, sequence alignment file inspector.

Miller CA, Qiao Y, DiSera T, D'Astous B, Marth GT.

Nat Methods. 2014 Dec;11(12):1189. doi: 10.1038/nmeth.3174. No abstract available.

5.

Tangram: a comprehensive toolbox for mobile element insertion detection.

Wu J, Lee WP, Ward A, Walker JA, Konkel MK, Batzer MA, Marth GT.

BMC Genomics. 2014 Sep 16;15:795. doi: 10.1186/1471-2164-15-795.

6.

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

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

Genome Biol. 2014 Aug 26;15(8):443. doi: 10.1186/s13059-014-0443-x.

7.

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Genome Biol. 2014 Jun 30;15(6):R88. doi: 10.1186/gb-2014-15-6-r88.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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