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Selfish genetic elements.

Ågren JA, Clark AG.

PLoS Genet. 2018 Nov 15;14(11):e1007700. doi: 10.1371/journal.pgen.1007700. eCollection 2018 Nov.


Allele-specific expression elucidates cis-regulatory logic.

Delbare SYN, Clark AG.

PLoS Genet. 2018 Nov 1;14(11):e1007690. doi: 10.1371/journal.pgen.1007690. eCollection 2018 Nov. No abstract available.


Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix.

Torres MF, Mathew LS, Ahmed I, Al-Azwani IK, Krueger R, Rivera-Nuñez D, Mohamoud YA, Clark AG, Suhre K, Malek JA.

Nat Commun. 2018 Sep 28;9(1):3969. doi: 10.1038/s41467-018-06375-y.


Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes).

Wang X, Pipes L, Trut LN, Herbeck Y, Vladimirova AV, Gulevich RG, Kharlamova AV, Johnson JL, Acland GM, Kukekova AV, Clark AG.

Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):10398-10403. doi: 10.1073/pnas.1800889115. Epub 2018 Sep 18.


3D cell migration in the presence of chemical gradients using microfluidics.

Clark AG, Simon A, Aizel K, Bibette J, Bremond N, Vignjevic DM.

Methods Cell Biol. 2018;147:133-147. doi: 10.1016/bs.mcb.2018.06.007. Epub 2018 Aug 22.


Infrared Thermographic Analysis of Surface Temperature of the Hands During Exposure to Normobaric Hypoxia.

Jones D, Covins SF, Miller GE, Morrison KI, Clark AG, Calcott SD, Anderson AM, Lucas SJE, Imray CHE.

High Alt Med Biol. 2018 Aug 22. doi: 10.1089/ham.2018.0008. [Epub ahead of print]


Author Correction: Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours.

Kukekova AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli KP, Gulevich RG, Vladimirova AV, Hekman JP, Perelman PL, Graphodatsky AS, O'Brien SJ, Wang X, Clark AG, Acland GM, Trut LN, Zhang G.

Nat Ecol Evol. 2018 Sep;2(9):1514. doi: 10.1038/s41559-018-0664-6.


Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours.

Kukekova AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli KP, Gulevich RG, Vladimirova AV, Hekman JP, Perelman PL, Graphodatsky AS, O'Brien SJ, Wang X, Clark AG, Acland GM, Trut LN, Zhang G.

Nat Ecol Evol. 2018 Sep;2(9):1479-1491. doi: 10.1038/s41559-018-0611-6. Epub 2018 Aug 6. Erratum in: Nat Ecol Evol. 2018 Aug 13;:.


Overexpression of a glutathione S-transferase (Mdgst) and a galactosyltransferase-like gene (Mdgt1) is responsible for imidacloprid resistance in house flies.

Reid WR, Sun H, Becnel JJ, Clark AG, Scott JG.

Pest Manag Sci. 2018 Jun 21. doi: 10.1002/ps.5125. [Epub ahead of print]


Rates and Patterns of Mutation in Tandem Repetitive DNA in Six Independent Lineages of Chlamydomonas reinhardtii.

Flynn JM, Lower SE, Barbash DA, Clark AG.

Genome Biol Evol. 2018 Jul 1;10(7):1673-1686. doi: 10.1093/gbe/evy123.


Reducing resistance allele formation in CRISPR gene drive.

Champer J, Liu J, Oh SY, Reeves R, Luthra A, Oakes N, Clark AG, Messer PW.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):5522-5527. doi: 10.1073/pnas.1720354115. Epub 2018 May 7.


Satellite DNA evolution: old ideas, new approaches.

Lower SS, McGurk MP, Clark AG, Barbash DA.

Curr Opin Genet Dev. 2018 Apr;49:70-78. doi: 10.1016/j.gde.2018.03.003. Epub 2018 Mar 23. Review.


Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny.

Wei KH, Lower SE, Caldas IV, Sless TJS, Barbash DA, Clark AG.

Mol Biol Evol. 2018 Apr 1;35(4):925-941. doi: 10.1093/molbev/msy005.


The human microbiome in evolution.

Davenport ER, Sanders JG, Song SJ, Amato KR, Clark AG, Knight R.

BMC Biol. 2017 Dec 27;15(1):127. doi: 10.1186/s12915-017-0454-7. Review.


Altered toll-like receptor responsiveness underlies a dominant heritable defect in B cell tolerance in autoimmune New Zealand Black mice.

Clark AG, Buckley ES, Foster MH.

Eur J Immunol. 2018 Mar;48(3):492-497. doi: 10.1002/eji.201747287. Epub 2018 Jan 19.


Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation.

Clark AG, Naufer MN, Westerlund F, Lincoln P, Rouzina I, Paramanathan T, Williams MC.

Biochemistry. 2018 Feb 6;57(5):614-619. doi: 10.1021/acs.biochem.7b01036. Epub 2018 Jan 5.


Roles of Female and Male Genotype in Post-Mating Responses in Drosophila melanogaster.

Delbare SYN, Chow CY, Wolfner MF, Clark AG.

J Hered. 2017 Oct 30;108(7):740-753. doi: 10.1093/jhered/esx081.


A tuneable microfluidic system for long duration chemotaxis experiments in a 3D collagen matrix.

Aizel K, Clark AG, Simon A, Geraldo S, Funfak A, Vargas P, Bibette J, Vignjevic DM, Bremond N.

Lab Chip. 2017 Nov 7;17(22):3851-3861. doi: 10.1039/c7lc00649g.


The Relationship Between the Human Genome and Microbiome Comes into View.

Goodrich JK, Davenport ER, Clark AG, Ley RE.

Annu Rev Genet. 2017 Nov 27;51:413-433. doi: 10.1146/annurev-genet-110711-155532. Epub 2017 Sep 20. Review.


Variation in Position Effect Variegation Within a Natural Population.

Kelsey KJP, Clark AG.

Genetics. 2017 Nov;207(3):1157-1166. doi: 10.1534/genetics.117.300306. Epub 2017 Sep 20.


Cancer-associated fibroblasts lead tumor invasion through integrin-β3-dependent fibronectin assembly.

Attieh Y, Clark AG, Grass C, Richon S, Pocard M, Mariani P, Elkhatib N, Betz T, Gurchenkov B, Vignjevic DM.

J Cell Biol. 2017 Nov 6;216(11):3509-3520. doi: 10.1083/jcb.201702033. Epub 2017 Sep 20.


A murine Ig light chain transgene reveals IGKV3 gene contributions to anti-collagen types IV and II specificities.

Clark AG, Worni-Schudel IM, Korte FM, Foster MH.

Mol Immunol. 2017 Nov;91:49-56. doi: 10.1016/j.molimm.2017.08.015. Epub 2017 Sep 5.


Selection Constrains High Rates of Tandem Repetitive DNA Mutation in Daphnia pulex.

Flynn JM, Caldas I, Cristescu ME, Clark AG.

Genetics. 2017 Oct;207(2):697-710. doi: 10.1534/genetics.117.300146. Epub 2017 Aug 15.


Deconstructing isolation-by-distance: The genomic consequences of limited dispersal.

Aguillon SM, Fitzpatrick JW, Bowman R, Schoech SJ, Clark AG, Coop G, Chen N.

PLoS Genet. 2017 Aug 3;13(8):e1006911. doi: 10.1371/journal.pgen.1006911. eCollection 2017 Aug.


Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup.

Ahmed-Braimah YH, Unckless RL, Clark AG.

G3 (Bethesda). 2017 Sep 7;7(9):3145-3155. doi: 10.1534/g3.117.1136.


Novel CRISPR/Cas9 gene drive constructs reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations.

Champer J, Reeves R, Oh SY, Liu C, Liu J, Clark AG, Messer PW.

PLoS Genet. 2017 Jul 20;13(7):e1006796. doi: 10.1371/journal.pgen.1006796. eCollection 2017 Jul.


Genomic signatures of local adaptation in the Drosophila immune response.

Early AM, Clark AG.

Fly (Austin). 2017 Oct 2;11(4):277-283. doi: 10.1080/19336934.2017.1337612. Epub 2017 Jun 6.


Actin cortex architecture regulates cell surface tension.

Chugh P, Clark AG, Smith MB, Cassani DAD, Dierkes K, Ragab A, Roux PP, Charras G, Salbreux G, Paluch EK.

Nat Cell Biol. 2017 Jun;19(6):689-697. doi: 10.1038/ncb3525. Epub 2017 May 22.


A Pooled Sequencing Approach Identifies a Candidate Meiotic Driver in Drosophila.

Wei KH, Reddy HM, Rathnam C, Lee J, Lin D, Ji S, Mason JM, Clark AG, Barbash DA.

Genetics. 2017 May;206(1):451-465. doi: 10.1534/genetics.116.197335. Epub 2017 Mar 3.


Estimating mating rates in wild Drosophila melanogaster females by decay rates of male reproductive proteins in their reproductive tracts.

Giardina TJ, Clark AG, Fiumera AC.

Mol Ecol Resour. 2017 Nov;17(6):1202-1209. doi: 10.1111/1755-0998.12661. Epub 2017 Mar 24.


Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators.

Bellott DW, Skaletsky H, Cho TJ, Brown L, Locke D, Chen N, Galkina S, Pyntikova T, Koutseva N, Graves T, Kremitzki C, Warren WC, Clark AG, Gaginskaya E, Wilson RK, Page DC.

Nat Genet. 2017 Mar;49(3):387-394. doi: 10.1038/ng.3778. Epub 2017 Jan 30.


Drosophila Genotype Influences Commensal Bacterial Levels.

Early AM, Shanmugarajah N, Buchon N, Clark AG.

PLoS One. 2017 Jan 17;12(1):e0170332. doi: 10.1371/journal.pone.0170332. eCollection 2017.


Rapid Expansion of Immune-Related Gene Families in the House Fly, Musca domestica.

Sackton TB, Lazzaro BP, Clark AG.

Mol Biol Evol. 2017 Apr 1;34(4):857-872. doi: 10.1093/molbev/msw285.


Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism.

Mehrmohamadi M, Mentch LK, Clark AG, Locasale JW.

Nat Commun. 2016 Dec 14;7:13666. doi: 10.1038/ncomms13666.


Evolution of Resistance Against CRISPR/Cas9 Gene Drive.

Unckless RL, Clark AG, Messer PW.

Genetics. 2017 Feb;205(2):827-841. doi: 10.1534/genetics.116.197285. Epub 2016 Dec 10.


ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins.

Davenport ER, Goodrich JK, Bell JT, Spector TD, Ley RE, Clark AG.

BMC Genomics. 2016 Nov 21;17(1):941.


Survey of Global Genetic Diversity Within the Drosophila Immune System.

Early AM, Arguello JR, Cardoso-Moreira M, Gottipati S, Grenier JK, Clark AG.

Genetics. 2017 Jan;205(1):353-366. doi: 10.1534/genetics.116.195016. Epub 2016 Nov 4.


Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay.

Chen N, Cosgrove EJ, Bowman R, Fitzpatrick JW, Clark AG.

Curr Biol. 2016 Nov 7;26(21):2974-2979. doi: 10.1016/j.cub.2016.08.062. Epub 2016 Oct 13.


Heritable components of the human fecal microbiome are associated with visceral fat.

Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD, Bell JT.

Genome Biol. 2016 Sep 26;17(1):189.


Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs.

Guo Y, Alexander K, Clark AG, Grimson A, Yu H.

RNA. 2016 Nov;22(11):1663-1672. Epub 2016 Sep 7.


Uncommon structural motifs dominate the antigen binding site in human autoantibodies reactive with basement membrane collagen.

Foster MH, Buckley ES, Chen BJ, Hwang KK, Clark AG.

Mol Immunol. 2016 Aug;76:123-33. doi: 10.1016/j.molimm.2016.07.004. Epub 2016 Jul 20.


Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery.

Scott EM, Halees A, Itan Y, Spencer EG, He Y, Azab MA, Gabriel SB, Belkadi A, Boisson B, Abel L, Clark AG; Greater Middle East Variome Consortium, Alkuraya FS, Casanova JL, Gleeson JG.

Nat Genet. 2016 Sep;48(9):1071-6. doi: 10.1038/ng.3592. Epub 2016 Jul 18.


Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia.

Wang X, Werren JH, Clark AG.

PLoS Biol. 2016 Jul 5;14(7):e1002500. doi: 10.1371/journal.pbio.1002500. eCollection 2016 Jul.


Extensive local adaptation within the chemosensory system following Drosophila melanogaster's global expansion.

Arguello JR, Cardoso-Moreira M, Grenier JK, Gottipati S, Clark AG, Benton R.

Nat Commun. 2016 Jun 13;7:ncomms11855. doi: 10.1038/ncomms11855.


Evidence for the fixation of gene duplications by positive selection in Drosophila.

Cardoso-Moreira M, Arguello JR, Gottipati S, Harshman LG, Grenier JK, Clark AG.

Genome Res. 2016 Jun;26(6):787-98. doi: 10.1101/gr.199323.115. Epub 2016 Apr 12.


Genetic Determinants of the Gut Microbiome in UK Twins.

Goodrich JK, Davenport ER, Beaumont M, Jackson MA, Knight R, Ober C, Spector TD, Bell JT, Clark AG, Ley RE.

Cell Host Microbe. 2016 May 11;19(5):731-43. doi: 10.1016/j.chom.2016.04.017.


Cross-species comparisons of host genetic associations with the microbiome.

Goodrich JK, Davenport ER, Waters JL, Clark AG, Ley RE.

Science. 2016 Apr 29;352(6285):532-5. doi: 10.1126/science.aad9379. Review.


Erratum to: signatures of early frailty in the gut microbiota.

Jackson MA, Jeffery IB, Beaumont M, Bell JT, Clark AG, Ley RE, O'Toole PW, Spector TD, Steves CJ.

Genome Med. 2016 Feb 17;8(1):21. doi: 10.1186/s13073-016-0275-2. No abstract available.


Signatures of early frailty in the gut microbiota.

Jackson MA, Jeffery IB, Beaumont M, Bell JT, Clark AG, Ley RE, O'Toole PW, Spector TD, Steves CJ.

Genome Med. 2016 Jan 29;8(1):8. doi: 10.1186/s13073-016-0262-7. Erratum in: Genome Med. 2016;8(1):21. Jackson, Matt [corrected to Jackson, Matthew A].


Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations.

Rodriguez-Flores JL, Fakhro K, Agosto-Perez F, Ramstetter MD, Arbiza L, Vincent TL, Robay A, Malek JA, Suhre K, Chouchane L, Badii R, Al-Nabet Al-Marri A, Abi Khalil C, Zirie M, Jayyousi A, Salit J, Keinan A, Clark AG, Crystal RG, Mezey JG.

Genome Res. 2016 Feb;26(2):151-62. doi: 10.1101/gr.191478.115. Epub 2016 Jan 4.

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