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Items: 14

1.

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.

2.

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.

PMID:
23736529
3.

The 1000 Genomes Project: data management and community access.

Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium..

Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974.

4.

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.

5.

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.

6.

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.

7.

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.

8.

Variation in genome-wide mutation rates within and between human families.

Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P; 1000 Genomes Project..

Nat Genet. 2011 Jun 12;43(7):712-4. doi: 10.1038/ng.862.

9.

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.

10.

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.

11.

Diversity of human copy number variation and multicopy genes.

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project., Eichler EE.

Science. 2010 Oct 29;330(6004):641-6. doi: 10.1126/science.1197005.

12.

A map of human genome variation from population-scale sequencing.

1000 Genomes Project Consortium., Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA.

Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534. Erratum in: Nature. 2011 May 26;473(7348):544. Xue, Yali [added]; Cartwright, Reed A [added]; Altshuler, David L [corrected to Altshuler, David]; Kebbel, Andrew [corrected to Keebler, Jonathan]; Koko-Gonzales, Paula [corrected to Kokko-Gonzales, Paula]; Nickerson, Debbie A [corrected to Nickerson, Deborah A].

13.

Rapid whole-genome mutational profiling using next-generation sequencing technologies.

Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM.

Genome Res. 2008 Oct;18(10):1638-42. doi: 10.1101/gr.077776.108.

14.

Pyrobayes: an improved base caller for SNP discovery in pyrosequences.

Quinlan AR, Stewart DA, Strömberg MP, Marth GT.

Nat Methods. 2008 Feb;5(2):179-81. doi: 10.1038/nmeth.1172.

PMID:
18193056

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