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Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses.

Barbour AG, Shao H, Cook VJ, Baldwin-Brown J, Tsao JI, Long AD.

Sci Rep. 2019 Nov 26;9(1):17618. doi: 10.1038/s41598-019-54389-3.


The gene structure and hypervariability of the complete Penaeus monodon Dscam gene.

Apitanyasai K, Huang SW, Ng TH, He ST, Huang YH, Chiu SP, Tseng KC, Lin SS, Chang WC, Baldwin-Brown JG, Long AD, Lo CF, Yu HT, Wang HC.

Sci Rep. 2019 Nov 12;9(1):16595. doi: 10.1038/s41598-019-52656-x.


Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits.

Chakraborty M, Emerson JJ, Macdonald SJ, Long AD.

Nat Commun. 2019 Oct 25;10(1):4872. doi: 10.1038/s41467-019-12884-1.


The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections.

Long AD, Baldwin-Brown J, Tao Y, Cook VJ, Balderrama-Gutierrez G, Corbett-Detig R, Mortazavi A, Barbour AG.

Sci Adv. 2019 Jul 24;5(7):eaaw6441. doi: 10.1126/sciadv.aaw6441. eCollection 2019 Jul.


Machine learning concepts, concerns and opportunities for a pediatric radiologist.

Moore MM, Slonimsky E, Long AD, Sze RW, Iyer RS.

Pediatr Radiol. 2019 Apr;49(4):509-516. doi: 10.1007/s00247-018-4277-7. Epub 2019 Mar 29. Review.


Genotype by random environmental interactions gives an advantage to non-favored minor alleles.

Mahdipour-Shirayeh A, Darooneh AH, Long AD, Komarova NL, Kohandel M.

Sci Rep. 2017 Jul 12;7(1):5193. doi: 10.1038/s41598-017-05375-0.


The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster.

King EG, Long AD.

G3 (Bethesda). 2017 Jun 7;7(6):1643-1652. doi: 10.1534/g3.117.041426.


A Model of Compound Heterozygous, Loss-of-Function Alleles Is Broadly Consistent with Observations from Complex-Disease GWAS Datasets.

Sanjak JS, Long AD, Thornton KR.

PLoS Genet. 2017 Jan 19;13(1):e1006573. doi: 10.1371/journal.pgen.1006573. eCollection 2017 Jan.


Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster.

Phillips MA, Long AD, Greenspan ZS, Greer LF, Burke MK, Villeponteau B, Matsagas KC, Rizza CL, Mueller LD, Rose MR.

Sci Rep. 2016 Dec 22;6:39281. doi: 10.1038/srep39281.


Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage.

Chakraborty M, Baldwin-Brown JG, Long AD, Emerson JJ.

Nucleic Acids Res. 2016 Nov 2;44(19):e147. Epub 2016 Jul 25.


Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data.

Sanjak JS, Long AD, Thornton KR.

G3 (Bethesda). 2016 Apr 7;6(4):1023-30. doi: 10.1534/g3.115.026013.


Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila.

Najarro MA, Hackett JL, Smith BR, Highfill CA, King EG, Long AD, Macdonald SJ.

PLoS Genet. 2015 Nov 30;11(11):e1005663. doi: 10.1371/journal.pgen.1005663. eCollection 2015 Nov. Erratum in: PLoS Genet. 2016 Jan;12(1):e1005830.


Gene expression variation in Drosophila melanogaster due to rare transposable element insertion alleles of large effect.

Cridland JM, Thornton KR, Long AD.

Genetics. 2015 Jan;199(1):85-93. doi: 10.1534/genetics.114.170837. Epub 2014 Oct 21.


Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation inter-cross population.

Marriage TN, King EG, Long AD, Macdonald SJ.

Genetics. 2014 Sep;198(1):45-57. doi: 10.1534/genetics.114.162107.


Using Drosophila melanogaster to identify chemotherapy toxicity genes.

King EG, Kislukhin G, Walters KN, Long AD.

Genetics. 2014 Sep;198(1):31-43. doi: 10.1534/genetics.114.161968.


Dissecting complex traits using the Drosophila Synthetic Population Resource.

Long AD, Macdonald SJ, King EG.

Trends Genet. 2014 Nov;30(11):488-95. doi: 10.1016/j.tig.2014.07.009. Epub 2014 Aug 28. Review.


Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae.

Burke MK, Liti G, Long AD.

Mol Biol Evol. 2014 Dec;31(12):3228-39. doi: 10.1093/molbev/msu256. Epub 2014 Aug 28.


Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity.

King EG, Sanderson BJ, McNeil CL, Long AD, Macdonald SJ.

PLoS Genet. 2014 May 8;10(5):e1004322. doi: 10.1371/journal.pgen.1004322. eCollection 2014 May.


The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms.

Baldwin-Brown JG, Long AD, Thornton KR.

Mol Biol Evol. 2014 Apr;31(4):1040-55. doi: 10.1093/molbev/msu048. Epub 2014 Jan 18.


Genome-wide association study of extreme longevity in Drosophila melanogaster.

Burke MK, King EG, Shahrestani P, Rose MR, Long AD.

Genome Biol Evol. 2014 Jan;6(1):1-11. doi: 10.1093/gbe/evt180.


Abundance and distribution of transposable elements in two Drosophila QTL mapping resources.

Cridland JM, Macdonald SJ, Long AD, Thornton KR.

Mol Biol Evol. 2013 Oct;30(10):2311-27. doi: 10.1093/molbev/mst129. Epub 2013 Jul 24.


The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans.

Kislukhin G, King EG, Walters KN, Macdonald SJ, Long AD.

G3 (Bethesda). 2013 Aug 7;3(8):1301-10. doi: 10.1534/g3.113.006619.


Controlled synthesis and transfer of large-area WS2 sheets: from single layer to few layers.

Elías AL, Perea-López N, Castro-Beltrán A, Berkdemir A, Lv R, Feng S, Long AD, Hayashi T, Kim YA, Endo M, Gutiérrez HR, Pradhan NR, Balicas L, Mallouk TE, López-Urías F, Terrones H, Terrones M.

ACS Nano. 2013 Jun 25;7(6):5235-42. doi: 10.1021/nn400971k. Epub 2013 May 15.


Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect.

Thornton KR, Foran AJ, Long AD.

PLoS Genet. 2013;9(2):e1003258. doi: 10.1371/journal.pgen.1003258. Epub 2013 Feb 21.


What paths do advantageous alleles take during short-term evolutionary change?

Burke MK, Long AD.

Mol Ecol. 2012 Oct;21(20):4913-6.


Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.

Martin A, Papa R, Nadeau NJ, Hill RI, Counterman BA, Halder G, Jiggins CD, Kronforst MR, Long AD, McMillan WO, Reed RD.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12632-7. doi: 10.1073/pnas.1204800109. Epub 2012 Jul 16.


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.


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.


Chemotherapy-induced toxicity is highly heritable in Drosophila melanogaster.

Kislukhin G, Murphy ML, Jafari M, Long AD.

Pharmacogenet Genomics. 2012 Apr;22(4):285-9. doi: 10.1097/FPC.0b013e3283514395.


The molecular diversity of adaptive convergence.

Tenaillon O, Rodríguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, Gaut BS.

Science. 2012 Jan 27;335(6067):457-61. doi: 10.1126/science.1212986.


Genomic sequence around butterfly wing development genes: annotation and comparative analysis.

Conceição IC, Long AD, Gruber JD, Beldade P.

PLoS One. 2011;6(8):e23778. doi: 10.1371/journal.pone.0023778. Epub 2011 Aug 31.


Genome-wide analysis of a long-term evolution experiment with Drosophila.

Burke MK, Dunham JP, Shahrestani P, Thornton KR, Rose MR, Long AD.

Nature. 2010 Sep 30;467(7315):587-90. doi: 10.1038/nature09352. Epub 2010 Sep 15.


Microsatellite markers associated with genes expressed in developing wings of Bicyclus anynana butterflies.

Beldade P, Van't Hof AE, Jerónimo MA, Long AD.

Mol Ecol Resour. 2009 Nov;9(6):1487-92. doi: 10.1111/j.1755-0998.2009.02691.x. Epub 2009 Apr 7.


A gene-based linkage map for Bicyclus anynana butterflies allows for a comprehensive analysis of synteny with the lepidopteran reference genome.

Beldade P, Saenko SV, Pul N, Long AD.

PLoS Genet. 2009 Feb;5(2):e1000366. doi: 10.1371/journal.pgen.1000366. Epub 2009 Feb 6.


Experimental evolution reveals natural selection on standing genetic variation.

Teotónio H, Chelo IM, Bradić M, Rose MR, Long AD.

Nat Genet. 2009 Feb;41(2):251-7. doi: 10.1038/ng.289. Epub 2009 Jan 11.


Cis-regulatory variation is typically polyallelic in Drosophila.

Gruber JD, Long AD.

Genetics. 2009 Feb;181(2):661-70. doi: 10.1534/genetics.108.098459. Epub 2008 Dec 8.


How repeatable are associations between polymorphisms in achaete-scute and bristle number variation in Drosophila?

Gruber JD, Genissel A, Macdonald SJ, Long AD.

Genetics. 2007 Apr;175(4):1987-97. Epub 2007 Feb 4.


The pharmacology of ageing in Drosophila.

Jafari M, Long AD, Mueller LD, Rose MR.

Curr Drug Targets. 2006 Nov;7(11):1479-83. Review.


A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model.

Beldade P, Rudd S, Gruber JD, Long AD.

BMC Genomics. 2006 May 31;7:130.


A low-cost open-source SNP genotyping platform for association mapping applications.

Macdonald SJ, Pastinen T, Genissel A, Cornforth TW, Long AD.

Genome Biol. 2005;6(12):R105. Epub 2005 Dec 2.


A cis-regulatory sequence within the yellow locus of Drosophila melanogaster required for normal male mating success.

Drapeau MD, Cyran SA, Viering MM, Geyer PK, Long AD.

Genetics. 2006 Feb;172(2):1009-30. Epub 2005 Nov 4.


Differential Patterns of Gene Expression and Gene Complement in Laboratory-Evolved Lines of E. coli.

Riehle MM, Bennett AF, Long AD.

Integr Comp Biol. 2005 Jun;45(3):532-8. doi: 10.1093/icb/45.3.532.


Changes in gene expression following high-temperature adaptation in experimentally evolved populations of E. coli.

Riehle MM, Bennett AF, Long AD.

Physiol Biochem Zool. 2005 May-Jun;78(3):299-315. Epub 2005 May 3.


Prospects for identifying functional variation across the genome.

Macdonald SJ, Long AD.

Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6614-21. Epub 2005 Apr 25.


Generating phenotypic variation: prospects from "evo-devo" research on Bicyclus anynana wing patterns.

Beldade P, Brakefield PM, Long AD.

Evol Dev. 2005 Mar-Apr;7(2):101-7.


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