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Items: 1 to 20 of 82

1.

Joint genotyping on the fly: identifying variation among a sequenced panel of inbred lines.

Stone EA.

Genome Res. 2012 May;22(5):966-74. doi: 10.1101/gr.129122.111. Epub 2012 Feb 23.

2.

Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains.

Grenier JK, Arguello JR, Moreira MC, Gottipati S, Mohammed J, Hackett SR, Boughton R, Greenberg AJ, Clark AG.

G3 (Bethesda). 2015 Feb 11;5(4):593-603. doi: 10.1534/g3.114.015883.

3.

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

Huang W, Massouras A, Inoue Y, Peiffer J, Ràmia M, Tarone AM, Turlapati L, Zichner T, Zhu D, Lyman RF, Magwire MM, Blankenburg K, Carbone MA, Chang K, Ellis LL, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu L, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu YQ, Yamamoto A, Zhang Y, Zhu Y, Anholt RR, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, Johnston JS, Stone EA, Richards S, Deplancke B, Mackay TF.

Genome Res. 2014 Jul;24(7):1193-208. doi: 10.1101/gr.171546.113. Epub 2014 Apr 8.

4.

Efficiency of selection, as measured by single nucleotide polymorphism variation, is dependent on inbreeding rate in Drosophila melanogaster.

Demontis D, Pertoldi C, Loeschcke V, Mikkelsen K, Axelsson T, Kristensen TN.

Mol Ecol. 2009 Nov;18(22):4551-63. doi: 10.1111/j.1365-294X.2009.04366.x. Epub 2009 Sep 25.

PMID:
19780974
5.

Incorporating sequence quality data into alignment improves DNA read mapping.

Frith MC, Wan R, Horton P.

Nucleic Acids Res. 2010 Apr;38(7):e100. doi: 10.1093/nar/gkq010. Epub 2010 Jan 27.

6.

Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource.

King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ.

Genome Res. 2012 Aug;22(8):1558-66. doi: 10.1101/gr.134031.111. Epub 2012 Apr 10.

7.

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.

8.

A Genomic Reference Panel for Drosophila serrata.

Reddiex AJ, Allen SL, Chenoweth SF.

G3 (Bethesda). 2018 Mar 28;8(4):1335-1346. doi: 10.1534/g3.117.300487.

9.

SNPest: a probabilistic graphical model for estimating genotypes.

Lindgreen S, Krogh A, Pedersen JS.

BMC Res Notes. 2014 Oct 7;7:698. doi: 10.1186/1756-0500-7-698.

10.

Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits.

King EG, Macdonald SJ, Long AD.

Genetics. 2012 Jul;191(3):935-49. doi: 10.1534/genetics.112.138537. Epub 2012 Apr 13.

11.

Development of a high density 600K SNP genotyping array for chicken.

Kranis A, Gheyas AA, Boschiero C, Turner F, Yu L, Smith S, Talbot R, Pirani A, Brew F, Kaiser P, Hocking PM, Fife M, Salmon N, Fulton J, Strom TM, Haberer G, Weigend S, Preisinger R, Gholami M, Qanbari S, Simianer H, Watson KA, Woolliams JA, Burt DW.

BMC Genomics. 2013 Jan 28;14:59. doi: 10.1186/1471-2164-14-59.

12.

Hap-seq: an optimal algorithm for haplotype phasing with imputation using sequencing data.

He D, Han B, Eskin E.

J Comput Biol. 2013 Feb;20(2):80-92. doi: 10.1089/cmb.2012.0091.

13.

Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network.

Gursky VV, Kozlov KN, Kulakovskiy IV, Zubair A, Marjoram P, Lawrie DS, Nuzhdin SV, Samsonova MG.

PLoS One. 2017 Sep 12;12(9):e0184657. doi: 10.1371/journal.pone.0184657. eCollection 2017.

14.

Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout.

Boussaha M, Guyomard R, Cabau C, Esquerré D, Quillet E.

BMC Genomics. 2012 Jun 13;13:238. doi: 10.1186/1471-2164-13-238.

15.

Improved genome inference in the MHC using a population reference graph.

Dilthey A, Cox C, Iqbal Z, Nelson MR, McVean G.

Nat Genet. 2015 Jun;47(6):682-8. doi: 10.1038/ng.3257. Epub 2015 Apr 27.

16.

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome.

Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JD, Varshney RK.

Am J Bot. 2012 Feb;99(2):186-92. doi: 10.3732/ajb.1100419. Epub 2012 Feb 1.

17.

Mutation-selection balance accounting for genetic variation for viability in Drosophila melanogaster as deduced from an inbreeding and artificial selection experiment.

Rodríguez-Ramilo ST, Pérez-Figueroa A, Fernández B, Fernández J, Caballero A.

J Evol Biol. 2004 May;17(3):528-41.

18.

Comparative analysis of haplotype association mapping algorithms.

McClurg P, Pletcher MT, Wiltshire T, Su AI.

BMC Bioinformatics. 2006 Feb 9;7:61.

19.

Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior.

Shorter J, Couch C, Huang W, Carbone MA, Peiffer J, Anholt RR, Mackay TF.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3555-63. doi: 10.1073/pnas.1510104112. Epub 2015 Jun 22.

20.

Design of association studies with pooled or un-pooled next-generation sequencing data.

Kim SY, Li Y, Guo Y, Li R, Holmkvist J, Hansen T, Pedersen O, Wang J, Nielsen R.

Genet Epidemiol. 2010 Jul;34(5):479-91. doi: 10.1002/gepi.20501.

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