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Items: 20

1.

The Drosophila melanogaster Genetic Reference Panel.

Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF, Zhu D, Casillas S, Han Y, Magwire MM, Cridland JM, Richardson MF, Anholt RR, Barrón M, Bess C, Blankenburg KP, Carbone MA, Castellano D, Chaboub L, Duncan L, Harris Z, Javaid M, Jayaseelan JC, Jhangiani SN, Jordan KW, Lara F, Lawrence F, Lee SL, Librado P, Linheiro RS, Lyman RF, Mackey AJ, Munidasa M, Muzny DM, Nazareth L, Newsham I, Perales L, Pu LL, Qu C, Ràmia M, Reid JG, Rollmann SM, Rozas J, Saada N, Turlapati L, Worley KC, Wu YQ, Yamamoto A, Zhu Y, Bergman CM, Thornton KR, Mittelman D, Gibbs RA.

Nature. 2012 Feb 8;482(7384):173-8. doi: 10.1038/nature10811.

2.
3.

Whole-genome sequencing of multiple Arabidopsis thaliana populations.

Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D.

Nat Genet. 2011 Aug 28;43(10):956-63. doi: 10.1038/ng.911.

PMID:
21874002
4.

Genotype and SNP calling from next-generation sequencing data.

Nielsen R, Paul JS, Albrechtsen A, Song YS.

Nat Rev Genet. 2011 Jun;12(6):443-51. doi: 10.1038/nrg2986. Review.

5.

A framework for variation discovery and genotyping using next-generation DNA sequencing data.

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.

Nat Genet. 2011 May;43(5):491-8. doi: 10.1038/ng.806. Epub 2011 Apr 10.

6.

Genetic analysis of complex traits in the emerging Collaborative Cross.

Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SN, Collins FS, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R, Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D, de Villena FP, Churchill GA.

Genome Res. 2011 Aug;21(8):1213-22. doi: 10.1101/gr.111310.110. Epub 2011 Mar 15.

7.

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].

8.

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples.

Le SQ, Durbin R.

Genome Res. 2011 Jun;21(6):952-60. doi: 10.1101/gr.113084.110. Epub 2010 Oct 27.

9.

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants.

Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, Grarup N, Guo Y, Hellman I, Jin X, Li Q, Liu J, Liu X, Sparsø T, Tang M, Wu H, Wu R, Yu C, Zheng H, Astrup A, Bolund L, Holmkvist J, Jørgensen T, Kristiansen K, Schmitz O, Schwartz TW, Zhang X, Li R, Yang H, Wang J, Hansen T, Pedersen O, Nielsen R, Wang J.

Nat Genet. 2010 Nov;42(11):969-72. doi: 10.1038/ng.680. Epub 2010 Oct 3.

PMID:
20890277
10.

Natural variation, functional pleiotropy and transcriptional contexts of odorant binding protein genes in Drosophila melanogaster.

Arya GH, Weber AL, Wang P, Magwire MM, Negron YL, Mackay TF, Anholt RR.

Genetics. 2010 Dec;186(4):1475-85. doi: 10.1534/genetics.110.123166. Epub 2010 Sep 24.

11.

Analysis of next-generation genomic data in cancer: accomplishments and challenges.

Ding L, Wendl MC, Koboldt DC, Mardis ER.

Hum Mol Genet. 2010 Oct 15;19(R2):R188-96. doi: 10.1093/hmg/ddq391. Epub 2010 Sep 15. Review.

12.

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA.

Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19.

13.

Sequencing of 50 human exomes reveals adaptation to high altitude.

Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZX, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, Nie X, Wu H, Zhao M, Cao H, Zou J, Shan Y, Li S, Yang Q, Asan, Ni P, Tian G, Xu J, Liu X, Jiang T, Wu R, Zhou G, Tang M, Qin J, Wang T, Feng S, Li G, Huasang, Luosang J, Wang W, Chen F, Wang Y, Zheng X, Li Z, Bianba Z, Yang G, Wang X, Tang S, Gao G, Chen Y, Luo Z, Gusang L, Cao Z, Zhang Q, Ouyang W, Ren X, Liang H, Zheng H, Huang Y, Li J, Bolund L, Kristiansen K, Li Y, Zhang Y, Zhang X, Li R, Li S, Yang H, Nielsen R, Wang J, Wang J.

Science. 2010 Jul 2;329(5987):75-8. doi: 10.1126/science.1190371.

14.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.

Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3.

15.

A SNP discovery method to assess variant allele probability from next-generation resequencing data.

Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F.

Genome Res. 2010 Feb;20(2):273-80. doi: 10.1101/gr.096388.109. Epub 2009 Dec 17.

16.

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.

17.

Fast and accurate short read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.

18.

Estimation of allele frequencies from high-coverage genome-sequencing projects.

Lynch M.

Genetics. 2009 May;182(1):295-301. doi: 10.1534/genetics.109.100479. Epub 2009 Mar 16.

19.

The Effect of Inbreeding on the Variation Due to Recessive Genes.

Robertson A.

Genetics. 1952 Mar;37(2):189-207. No abstract available.

20.

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