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Barbour AG, Shao H, Cook VJ, Baldwin-Brown J, Tsao JI, Long AD. Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses. Sci Rep. 2019 Nov 26;9(1):17618. doi: 10.1038/s41598-019-54389-3. PubMed PMID: 31772306; PubMed Central PMCID: PMC6879569.
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. The gene structure and hypervariability of the complete Penaeus monodon Dscam gene. Sci Rep. 2019 Nov 12;9(1):16595. doi: 10.1038/s41598-019-52656-x. PubMed PMID: 31719551; PubMed Central PMCID: PMC6851185.
Chakraborty M, Emerson JJ, Macdonald SJ, Long AD. Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. Nat Commun. 2019 Oct 25;10(1):4872. doi: 10.1038/s41467-019-12884-1. PubMed PMID: 31653862; PubMed Central PMCID: PMC6814777.
Long AD, Baldwin-Brown J, Tao Y, Cook VJ, Balderrama-Gutierrez G, Corbett-Detig R, Mortazavi A, Barbour AG. The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections. Sci Adv. 2019 Jul;5(7):eaaw6441. doi: 10.1126/sciadv.aaw6441. eCollection 2019 Jul. PubMed PMID: 31355335; PubMed Central PMCID: PMC6656541.
Baldwin-Brown JG, Weeks SC, Long AD. A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome. Genome Biol Evol. 2018 Jan 1;10(1):143-156. doi: 10.1093/gbe/evx280. PubMed PMID: 29294012; PubMed Central PMCID: PMC5765565.
Mahdipour-Shirayeh A, Darooneh AH, Long AD, Komarova NL, Kohandel M. Genotype by random environmental interactions gives an advantage to non-favored minor alleles. Sci Rep. 2017 Jul 12;7(1):5193. doi: 10.1038/s41598-017-05375-0. PubMed PMID: 28701726; PubMed Central PMCID: PMC5507875.
King EG, Long AD. The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster. G3 (Bethesda). 2017 Jun 7;7(6):1643-1652. doi: 10.1534/g3.117.041426. PubMed PMID: 28592647; PubMed Central PMCID: PMC5473746.
Sanjak JS, Long AD, Thornton KR. A Model of Compound Heterozygous, Loss-of-Function Alleles Is Broadly Consistent with Observations from Complex-Disease GWAS Datasets. PLoS Genet. 2017 Jan;13(1):e1006573. doi: 10.1371/journal.pgen.1006573. eCollection 2017 Jan. PubMed PMID: 28103232; PubMed Central PMCID: PMC5289629.
Phillips MA, Long AD, Greenspan ZS, Greer LF, Burke MK, Villeponteau B, Matsagas KC, Rizza CL, Mueller LD, Rose MR. Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster. Sci Rep. 2016 Dec 22;6:39281. doi: 10.1038/srep39281. PubMed PMID: 28004838; PubMed Central PMCID: PMC5177908.
Chakraborty M, Baldwin-Brown JG, Long AD, Emerson JJ. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res. 2016 Nov 2;44(19):e147. doi: 10.1093/nar/gkw654. Epub 2016 Jul 25. PubMed PMID: 27458204; PubMed Central PMCID: PMC5100563.
Sanjak JS, Long AD, Thornton KR. Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data. G3 (Bethesda). 2016 Apr 7;6(4):1023-30. doi: 10.1534/g3.115.026013. PubMed PMID: 26865700; PubMed Central PMCID: PMC4825638.
Najarro MA, Hackett JL, Smith BR, Highfill CA, King EG, Long AD, Macdonald SJ. Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila. PLoS Genet. 2015 Nov;11(11):e1005663. doi: 10.1371/journal.pgen.1005663. eCollection 2015 Nov. PubMed PMID: 26619284; PubMed Central PMCID: PMC4664282.
Long A, Liti G, Luptak A, Tenaillon O. Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nat Rev Genet. 2015 Oct;16(10):567-82. doi: 10.1038/nrg3937. Epub 2015 Sep 8. Review. PubMed PMID: 26347030; PubMed Central PMCID: PMC4733663.
Cridland JM, Thornton KR, Long AD. Gene expression variation in Drosophila melanogaster due to rare transposable element insertion alleles of large effect. Genetics. 2015 Jan;199(1):85-93. doi: 10.1534/genetics.114.170837. Epub 2014 Oct 21. PubMed PMID: 25335504; PubMed Central PMCID: PMC4286695.
Burke MK, Liti G, Long AD. Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae. Mol Biol Evol. 2014 Dec;31(12):3228-39. doi: 10.1093/molbev/msu256. Epub 2014 Aug 28. PubMed PMID: 25172959; PubMed Central PMCID: PMC4245818.
Long AD, Macdonald SJ, King EG. Dissecting complex traits using the Drosophila Synthetic Population Resource. Trends Genet. 2014 Nov;30(11):488-95. doi: 10.1016/j.tig.2014.07.009. Epub 2014 Aug 28. Review. PubMed PMID: 25175100; PubMed Central PMCID: PMC4253597.
Marriage TN, King EG, Long AD, Macdonald SJ. Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation inter-cross population. Genetics. 2014 Sep;198(1):45-57. doi: 10.1534/genetics.114.162107. PubMed PMID: 25236448; PubMed Central PMCID: PMC4174953.
King EG, Kislukhin G, Walters KN, Long AD. Using Drosophila melanogaster to identify chemotherapy toxicity genes. Genetics. 2014 Sep;198(1):31-43. doi: 10.1534/genetics.114.161968. PubMed PMID: 25236447; PubMed Central PMCID: PMC4174942.
King EG, Sanderson BJ, McNeil CL, Long AD, Macdonald SJ. Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity. PLoS Genet. 2014 May;10(5):e1004322. doi: 10.1371/journal.pgen.1004322. eCollection 2014 May. PubMed PMID: 24810915; PubMed Central PMCID: PMC4014434.
Baldwin-Brown JG, Long AD, Thornton KR. The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol Biol Evol. 2014 Apr;31(4):1040-55. doi: 10.1093/molbev/msu048. Epub 2014 Jan 18. PubMed PMID: 24441104; PubMed Central PMCID: PMC3969567.
Burke MK, King EG, Shahrestani P, Rose MR, Long AD. Genome-wide association study of extreme longevity in Drosophila melanogaster. Genome Biol Evol. 2014 Jan;6(1):1-11. doi: 10.1093/gbe/evt180. PubMed PMID: 24259311; PubMed Central PMCID: PMC3914684.
Cridland JM, Macdonald SJ, Long AD, Thornton KR. Abundance and distribution of transposable elements in two Drosophila QTL mapping resources. Mol Biol Evol. 2013 Oct;30(10):2311-27. doi: 10.1093/molbev/mst129. Epub 2013 Jul 24. PubMed PMID: 23883524; PubMed Central PMCID: PMC3773372.
Kislukhin G, King EG, Walters KN, Macdonald SJ, Long AD. The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans. G3 (Bethesda). 2013 Aug 7;3(8):1301-10. doi: 10.1534/g3.113.006619. PubMed PMID: 23733889; PubMed Central PMCID: PMC3737169.
Thornton KR, Foran AJ, Long AD. Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect. PLoS Genet. 2013;9(2):e1003258. doi: 10.1371/journal.pgen.1003258. Epub 2013 Feb 21. PubMed PMID: 23437004; PubMed Central PMCID: PMC3578756.
Burke MK, Long AD. What paths do advantageous alleles take during short-term evolutionary change?. Mol Ecol. 2012 Oct;21(20):4913-6. doi: 10.1111/j.1365-294x.2012.05745.x. PubMed PMID: 23227489.
King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ. Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res. 2012 Aug;22(8):1558-66. doi: 10.1101/gr.134031.111. Epub 2012 Apr 10. PubMed PMID: 22496517; PubMed Central PMCID: PMC3409269.
Martin A, Papa R, Nadeau NJ, Hill RI, Counterman BA, Halder G, Jiggins CD, Kronforst MR, Long AD, McMillan WO, Reed RD. Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand. Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12632-7. doi: 10.1073/pnas.1204800109. Epub 2012 Jul 16. PubMed PMID: 22802635; PubMed Central PMCID: PMC3411988.
King EG, Macdonald SJ, Long AD. Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits. Genetics. 2012 Jul;191(3):935-49. doi: 10.1534/genetics.112.138537. Epub 2012 Apr 13. PubMed PMID: 22505626; PubMed Central PMCID: PMC3389985.
Kislukhin G, Murphy ML, Jafari M, Long AD. Chemotherapy-induced toxicity is highly heritable in Drosophila melanogaster. Pharmacogenet Genomics. 2012 Apr;22(4):285-9. doi: 10.1097/FPC.0b013e3283514395. PubMed PMID: 22336958; PubMed Central PMCID: PMC3303944.
Tenaillon O, Rodríguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, Gaut BS. The molecular diversity of adaptive convergence. Science. 2012 Jan 27;335(6067):457-61. doi: 10.1126/science.1212986. PubMed PMID: 22282810.
Conceição IC, Long AD, Gruber JD, Beldade P. Genomic sequence around butterfly wing development genes: annotation and comparative analysis. PLoS One. 2011;6(8):e23778. doi: 10.1371/journal.pone.0023778. Epub 2011 Aug 31. PubMed PMID: 21909358; PubMed Central PMCID: PMC3166123.
Burke MK, Dunham JP, Shahrestani P, Thornton KR, Rose MR, Long AD. Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature. 2010 Sep 30;467(7315):587-90. doi: 10.1038/nature09352. Epub 2010 Sep 15. PubMed PMID: 20844486.
Beldade P, Van't Hof AE, Jerónimo MA, Long AD. Microsatellite markers associated with genes expressed in developing wings of Bicyclus anynana butterflies. Mol Ecol Resour. 2009 Nov;9(6):1487-92. doi: 10.1111/j.1755-0998.2009.02691.x. Epub 2009 Apr 7. PubMed PMID: 21564941.
Beldade P, Saenko SV, Pul N, Long AD. A gene-based linkage map for Bicyclus anynana butterflies allows for a comprehensive analysis of synteny with the lepidopteran reference genome. PLoS Genet. 2009 Feb;5(2):e1000366. doi: 10.1371/journal.pgen.1000366. Epub 2009 Feb 6. PubMed PMID: 19197358; PubMed Central PMCID: PMC2629579.
Gruber JD, Long AD. Cis-regulatory variation is typically polyallelic in Drosophila. Genetics. 2009 Feb;181(2):661-70. doi: 10.1534/genetics.108.098459. Epub 2008 Dec 8. PubMed PMID: 19064705; PubMed Central PMCID: PMC2644954.
Teotónio H, Chelo IM, Bradić M, Rose MR, Long AD. Experimental evolution reveals natural selection on standing genetic variation. Nat Genet. 2009 Feb;41(2):251-7. doi: 10.1038/ng.289. Epub 2009 Jan 11. PubMed PMID: 19136954.
Macdonald SJ, Long AD. Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics. 2007 Jun;176(2):1261-81. doi: 10.1534/genetics.106.069641. Epub 2007 Apr 15. PubMed PMID: 17435224; PubMed Central PMCID: PMC1894589.
Long AD, Beldade P, Macdonald SJ. Estimation of population heterozygosity and library construction-induced mutation rate from expressed sequence tag collections. Genetics. 2007 May;176(1):711-4. doi: 10.1534/genetics.106.063610. Epub 2006 Dec 18. PubMed PMID: 17179075; PubMed Central PMCID: PMC1893025.
Gruber JD, Genissel A, Macdonald SJ, Long AD. How repeatable are associations between polymorphisms in achaete-scute and bristle number variation in Drosophila?. Genetics. 2007 Apr;175(4):1987-97. doi: 10.1534/genetics.106.067108. Epub 2007 Feb 4. PubMed PMID: 17277365; PubMed Central PMCID: PMC1855119.
Jafari M, Long AD, Mueller LD, Rose MR. The pharmacology of ageing in Drosophila. Curr Drug Targets. 2006 Nov;7(11):1479-83. doi: 10.2174/1389450110607011479. Review. PubMed PMID: 17100588.
Beldade P, Rudd S, Gruber JD, Long AD. A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model. BMC Genomics. 2006 May 31;7:130. doi: 10.1186/1471-2164-7-130. PubMed PMID: 16737530; PubMed Central PMCID: PMC1534037.
Drapeau MD, Cyran SA, Viering MM, Geyer PK, Long AD. A cis-regulatory sequence within the yellow locus of Drosophila melanogaster required for normal male mating success. Genetics. 2006 Feb;172(2):1009-30. doi: 10.1534/genetics.105.045666. Epub 2005 Nov 4. PubMed PMID: 16272418; PubMed Central PMCID: PMC1456202.
Macdonald SJ, Long AD. Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura. Genome Biol. 2006;7(7):R67. doi: 10.1186/gb-2006-7-7-R67. PubMed PMID: 16872532; PubMed Central PMCID: PMC1779558.
Macdonald SJ, Pastinen T, Genissel A, Cornforth TW, Long AD. A low-cost open-source SNP genotyping platform for association mapping applications. Genome Biol. 2005;6(12):R105. doi: 10.1186/gb-2005-6-12-r105. Epub 2005 Dec 2. PubMed PMID: 16356268; PubMed Central PMCID: PMC1414086.
Macdonald SJ, Pastinen T, Long AD. The effect of polymorphisms in the enhancer of split gene complex on bristle number variation in a large wild-caught cohort of Drosophila melanogaster. Genetics. 2005 Dec;171(4):1741-56. doi: 10.1534/genetics.105.045344. Epub 2005 Sep 2. PubMed PMID: 16143618; PubMed Central PMCID: PMC1456100.
Riehle MM, Bennett AF, Long AD. Differential Patterns of Gene Expression and Gene Complement in Laboratory-Evolved Lines of E. coli. Integr Comp Biol. 2005 Jun;45(3):532-8. doi: 10.1093/icb/45.3.532. PubMed PMID: 21676798.
Macdonald SJ, Long AD. Prospects for identifying functional variation across the genome. Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6614-21. doi: 10.1073/pnas.0501990102. Epub 2005 Apr 25. PubMed PMID: 15851675; PubMed Central PMCID: PMC1131871.
Riehle MM, Bennett AF, Long AD. Changes in gene expression following high-temperature adaptation in experimentally evolved populations of E. coli. Physiol Biochem Zool. 2005 May-Jun;78(3):299-315. doi: 10.1086/430035. Epub 2005 May 3. PubMed PMID: 15887077.
Macdonald SJ, Long AD. Identifying signatures of selection at the enhancer of split neurogenic gene complex in Drosophila. Mol Biol Evol. 2005 Mar;22(3):607-19. doi: 10.1093/molbev/msi046. Epub 2004 Nov 10. PubMed PMID: 15537803.
Beldade P, Brakefield PM, Long AD. Generating phenotypic variation: prospects from "evo-devo" research on Bicyclus anynana wing patterns. Evol Dev. 2005 Mar-Apr;7(2):101-7. doi: 10.1111/j.1525-142X.2005.05011.x. PubMed PMID: 15733307.
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