Publications

(Link to Andy’s PubMed list)

2017

Davenport ER, JG Sanders, SJ Song, KR Amato, AG Clark and R Knight.   The human microbiome in evolution.  MBC Biol. 15:127. Doi:10.1186/s12915-017-0454-7.  PMID:  29282061.  PMC5744394.

Chen N, EJ Cosgrove, R Bowman, JW Fitzpatrick and AG Clark.   Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay.  Curr Biol.  26:2974-2979.  PMIC:  27746026.  PMC5102777.

Ahmed-Braimah Y, RL Unckless and AG Clark.  2017.  Evolutionary Dynamics of Male Reproductive Genes in the <i> Drosophila virilis</i> Subgroup.  G3(Bethesda). 7:3145-3155.  PMID:  28739599.  PMC5592939

Champer J, R Reeves, SY Oh, C Liu, et al.  2017.  Novel CRISPR/Cas9 gene drive constructs reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations.  PLoS Genet.  1`3:e1006796.  PMID:  28727785.  PMC5518997.

Flynn JM, I Caldas, ME Cristescu and AG Clark.  2017.  Selection Constrains High Rates of Tandem Repetitive DNA Mutation in <Daphnia pulex>.  Genetics.  doi: 10.1534/genetics.117.300146.  [Epub ahead of print].  PMID:  2811387.  PMC Journal In Process.

Goodrich JK, ER Davenport, AG Clark and RE Ley.  2017.  The Relationship Between the Human Genome and Microbiome Comes into View.  Annu Rev Genet.  doi: 10.1146/annurev-genet-110711-155532. [Epub ahead of print]  PMID:  28934590.  PMCID:  PMC Journal in Process.

Kelsey, KJP and AG Clark.  2017.  Variation in Position Effect Variegation Within a Natural Population.  Genetics.  207:1157-1166.  PMID:  28931559.  PMC5676239.

Delbare SYN, CY Chow, MF Wolfner, et al.  2017. Roles of Female and Male Genotype in Post-Mating Responses in Drosophila melanogaster.  J Hered.  108:740-753.  PMID:  29036644.  PMC Journal In Process.

Aguillon SM, JW Fitzpatrick, R Bowman, et al.  2017.  Deconstructing isolation-by-distance:  the genomic consequences of limited dispersal.  PLoS Genet.  13:e1006911.  PMID:  28771477. PMC5542401.

Ahmed-Braimah Y, RL Unckless and AG Clark.  2017.  Evolutionary Dynamics of Male Reproductive Genes in the <i> Drosophila virilis</i> Subgroup.  G3(Bethesda).  pii: g3.1136.2017. doi: 10.1534/g3.117.1136. [Epub ahead of print]  PMID:  28739599.  PMC5592939.

Champer J, R Reeves, SY Oh, C Liu, et al.  2017.  Novel CRISPR/Cas9 gene drive constructs reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations.  PLoS Genet.  7:3145-3155.  PMID:  28727785.  PMC5518997.

Wei KH, HM Reddy, C Rathnam, J Lee, et al.  2017.  A Pooled Sequencing Approach Identifies a Candidate Meiotic Driver in Drosophila.  Genetics.  206:451-465.  PMID:  28258181.  PMC5419488.

Giardina TJ, AG Clark and AC Fiumera.  2017.  Estimating mating rates in wild Drosophila melanogaster females by decay rates of male reproductive proteins in their reproductive tracts.  Mol Ecol Resour.  17:1202-1209.  PMID:  28213940.  PMC Journal in Process.

Bellott DW, H Skaletsky, TJ Cho, et al.  2017.  Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators.  Nat Genet. 49:387-394.  PMID:  28135246.  PMC5359078.

Early AM, N Shanmugarajah, N Buchon and AG Clark.  2017.  Drosophila Genotype Influences Commensal Bacterial Levels.  PLoS One.  12:E0170332.  doi: 10.1371/journal.pone.0170332.  PMID:  28095502.  PMC5240971.

Sackton TB, BP Lazzaro and AG Clark.  2017.  Rapid expansion of immune-related gene families in the house fly, Musca domestica.  Mol Biol Evol. 34:857-872.  PMID:  28087775.  PMC5400391.

2016

Unckless RL, AG Clark, and PW Messer.  2016.  Evolution of Resistance Against CRISPR/Cas9 Gene Drive.  Genetics. 205:827-841.  PMID:  27941126.  PMC5289854.

Mehrmohamadi M, LK Mentch, AG Clark and JW Locasale.  2016.  Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism.  Nat Commun.  7:13666.  PMID:  27966532.  PMC5171841.

Early AM, JR Arguello, M Cardoso-Moreira, S. Gottipati,, JK Grenier and AG Clark.  2016. Survey of Global Genetic Diversity Within the Drosophila Immune System.  Genetics.  205:353-366.  PMID:  27815361.  PMC5223513.

Slavney A, L Arbiza, AG Clark and A Keinan.  2016.  Strong Constraint on Human Genes Escaping X-Inactivation Is Modulated by their Expression Level and Breadth in Both Sexes.  33:384-393.  PMID:  26494842.  PMC4751236.

Davenport ER, JK Goodrich, JT Bell, TD Spector, RE Ley and AG Clark.  2016.  ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins.  BMC Genomics. 17:941.  PMID:  27871240.  PMC5117602.

Chen N, EJ Cosgrove, R Bowman, JW Fitzpatrick and AG Clark.  2016. Genomic Consequences of Population Decline in the Endangered Florida Scrub-jay.  Curr Biol.  Pii:  26:2974-2979.  PMID:  27746026.  PMC5102777.

Beaumont M, JK Goodrich, MA Jackson, I Yet, et al.  2016.  Heritable components of the human fecal microbiome are associated with visceral fat.  Genome Biol.  17:189.  PMID:  27666579.  PMC5036307.

Guo Y, K Alexander, AG Clark, A Grimson, and H Yu.  2016.  Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs. Cold Spring Harbor Lab. Press for the RNA Society.  22:1663-1672.  PMID:  27604961.  PMC5066619.

Jackson MA, IB Jeffery, M Beaumont, JT Bell, et al.  2016.  Signature of early frailty in the gut microbiota.  Genome Med.  8:8.  PMID:  26822992.  PMC4731918.

Arguello JR, M Cardoso-Moreira, JK Grenier, S Gottipati, et al.  2016.  Extensive local adaptation within the chemosensory system following Drosophila melanogaster’s global expansion.  Nat Commun.  13;7:ncomms11855.  PMID:  27292132.  PMC4910016.

Wang X, JH Werren, and AG Clark.  2016.  Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia.  PLoS Biol. 14:e1002500.  PMID:  27380029.  PMC4933354.

Scott EM, A Halees A, EG Spencer, Y He, et al.  2016.  Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery.  Nat Genet. 48:1071-1076.  PMID:  27428751.  PMC5019950.

Unckless R, PW Messer, T Connallon and AG Clark.  2016.  Modeling the Manipulation of Natural Populations by the Mutagenic Chain Reaction.  Genetics.  201:425-431.  PMID:  2623409.  PMC4596658.

Goodrich JK, ER Davenport, JL Waters , AG Clark, and RE Ley.  2016.  Cross-species comparison of host genetic associations with the microbiome.  Science.  PMID:  27126034.  PMC5116907.

Cardoso-Moreira M, JR Arguello, S Gottipati, LG Harshman, et al.  2016.  Evidence for the fixation of gene duplications by positive selection in Drosophila.  Genome Res. 26:787-798.  PMID:  27197209.  PMC4889967.Goodrich JK, ER Davenport, M Beaumont, MA Jackson, et al. 2016.  Genetic Determinants of the Gut Microbiome in UK Twins.  Cell Host Microb.  19:731-743.  PMID:  27173935.  PMC4915943.

Jackson M, IB Jeffery, M Beaumont, JT Bell, AG Clark, RE Ley, PW O’Toole, TD Spector, CJ Steves. 2016.  Signatures of early frailty in the gut microbiota. Genome Med. 8:8. PMID: 26822992; PMC4731918.

Rodriguez-Flores JL, K Fakhro, F Agosto-Perez, MD Ramstetter, et al. 2016.  Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. Genome Res. 26:151-162. PMID: 26728717; PMC4728368.Chow CY, KJ Kelsey, MF Wolfner and AG Clark.  2016.  Candidate genetic modifiers of retinitis pigmentosa identified by exploiting natural variation in Drosophila.  Hum Mol Genet. 25:651-659.  PMID:  26662796.  PMC4743685.

2015

Clark AG and PW Messer.  2015.  Evolutionary genomics.  Conundrum of jumbled mosquito genomes.  Science.  347:27-28.  PMID:  25554775.

Unckless RL, AM Larraquente and AG Clark.  2015.  Sex-Ratio Meiotic Drive and Y-Linked Resistance in Drosophila affinis.  Genetics.  199:831-840.  PMID:  25571899.  PMC4349075

Dobson AJ, JM Chaston, PD Newell, L Donahoue, et al.  2015.  Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster.  Nat Commun.  6:6312.  PMID:  25692519.  PMC4333721.

Grenier JK, JR Arguello, M Cardoso Moreira, S Gottipati, J Mohammed, SR Hackett, R Boughton, AJ Greenberg and AG Clark.  2015.  Global Diversity Lines – A Five Continent Reference Panel of Sequenced Drosophila melanogaster Strains.  G3 (Bethesda).  5:593-603.  PMID:  25673134.  PMC4390575.

Delaneau O, J Marchini; 1000 Genomes Project Constortium.  2015.  Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.  Nat Comm.  5:3934.   PMID:  25653097.  PMC4338501.

Chow CY, X Wang, D Riccardi, MF Wolfner and AG Clark.  2015.  The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse.  PLoS Genet.  11(2):e1004924.  PMID:  25651210.  PMC4412289.

Yu F, X Liu, E Gazave, D Change, et al.  2015.  Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions.  PLoS One.  10:e0121644.  PMID:  25807536.  PMC4373932.

Chow CY, FW Avila, AG Clark and MF Wolfner.  2015.  Induction of excessive endoplasmic reticulum stress in the Drosophila male accessory gland results in infertility.  10:e0119386.  PMID:  25742606.  PMC4350844.

Connallon T and AG Clark.  2015.  The distribution of fitness effects in an uncertain world.  Evolution.  69:1610-1618.  PMID:  25913128.  PMC4716676.

Henn BM, LR Botigué, CD Bustamante, AG Clark and S Gravel.  2015.  Estimating the mutation load in human genomes.  Nat Rev Genet.  16:333-343.  PMID:  25963372.  PMC4959039.

Ayroles JF, SM Buchanan, C O’Leary, K Skutt-Kakaria, et al.  2015.  Behavioral idiosyncrasy reveals genetic control of phenotypic variability.  Proc Natl Acad Sci USA.  112:6706-6711.  PMID:  25953335.  PMC4450409.

Meisel RP, JG Scott and AG Clark. 2015.  Transcriptome differences between alternative sex determining genotypes in the house fly, Musca domestica.  Genome Biol Evol.  7:2051-2061.  PMID:  26142430.  PMC4524491.

Wang X, JH Werren, and AG Clark.  2015.  Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti.  Proc Natl Acad Sci USA.  112:E3545-3554.  201510338.  26100871.  PMC4500217

Hunter-Zinck H and AG Clark.  2015.  Aberrant time to most recent common ancestor as a signature of natural selection.  Mol Biol Evol.  32:2784-2797.  PMID:  26093129.  PMC454765.

Unckless RL, PW Messer, T Connallon and AG Clark.  2015.  Modeling the Manipulation of Natural Populations by the Mutagenic Chain Reaction.  Genetics.  201:425-431.    PMID:  26232409.  PMC4596658.

Ayroles JF, SM Buchanan, C O’Leary, K Skutt-Kakaria, et al.  2015.  Behavioral idiosyncrasy reveals genetic control of phenotypic variability.  Proc Natl Acad Sci USA.  112:6706-6711.  PMID:  25953335.  PMC4450409.

Slavney A, L Arbiza, AG Clark and A Keinan.  2015.  Strong constraint on human genes escaping X-inactivation is modulated by their expression level and breadth in both sexes.  Mol Biol Evol.  33:384-393.  PMID:  26494842.  PMC4751236.

1000 Genomes Project Consortium.  2015.  A global reference for human genetic variation.  Nature.  526:68-74.  PMID:  26432245.  PMC4750478..

Carvalho AB, B Vicoso, CA Russo, B Swenor, and AG Clark.  2015.  Birth of a new gene on the Y chromosome of Drosophila melanogaster.  Proc Natl Acad Sci.  112:1240-1255.  PMID:  26385968.  PMC4603513.

Blekhman R, JK Goodrich, K Huang, Q Sun, et al.  2015.  Host genetic variation impacts microbiome composition across human body sites.  Genome Biol.  16:191.   PMID:  26374288.  PMC4570153.

Delaneau O, J Marchini, 1000 Genomes Project Consortium.  2015.  Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.  Nat Commun.  5:394.  PMID:  25653097.   PMC4338501.

Gullen Y, N Rius, A Delprat, A Williford, et al.  2015.  Genomics of ecological adaptation in cactophilic Drosophila.  Genome Biol Evol.  7:349-366.  PMID:  25552534.  PMC4316639.

Alexander KA, X Wang, M Shibata, AG Clark and MJ Garcia-Garcia.  2015.  TRIM28 controls genomic imprinting through distinct mechanisms during and after early genome-wide reprogramming.  Cell Rep. 13:1194-1205.  PMID:  26527006.  PMC4644443.

Chow CY, KJ Kelsey, MF Wolfner and AG Clark.  2015.  Candidate genetic modifiers of retinitis pigmentosa identified by exploiting natural variation in Drosophila.  Hum Mol Genet.  Pii:  ddv502. [Epub ahead of print]  PMID:  26662796.  PMC4743685.

2014

Guillen Y, N Rius, A Delprat, A Williford, et al.  2014.  Genomics of ecological adaptation in cactophilic Drosophila.  Genome Biol Evol.  [Epub ahead of print.]  PMID:  25552534.  PMC4316639.

Wei KH, JK Grenier, DA Barbash and AG Clark.  2014.  Correlated variation and population differentiation in satellite DNA abundance among lines of Drosophila melanogaster.  Proc Natl Acad Sci.  111(52):18793-18798.  PMID:  25512552.  PMC4284603.

Ma L, A Keinan, and AG Clark.  2015.  Biological Knowledge-Driven Analysis of Epistasis in Human GWAS with Application to Lipid Traits.  1253:35-45.  Doi:  10.1007/978-1-4939-2155-3_3.  PMID:  25403526.  PMC Exempt – Book Chapter.

Goodrich JK, JL Waters, AC Poole, JL Sutter, et al.  2014.  Human genetics shape the gut microbiome.  Cell.  159(4):789-799.  doi:  10.1016/j.cell.2014.09.053.  PMID:  25417156.  PMC4255478.

Reinhart M, T Carney, AG Clark and AC Fiumera.  2014.  Characterizing male-female interactions using natural genetic variation in Drosophila melanogaster.  J Hered.  Pii:esu076. [Epub ahead of print].  PMID:  25425680.  PMC4261835.

Scott JG, WC Warren, LW Beukeboom, D Bopp, AG Clark, et al.  2014.  Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment.  Genome Biol.  14;15(10):466 [Epub ahead of print]  PMID:  25315136.  PMC4195910.

Chen N, CV Van Hout, S Gottipati and AG Clark.  2014. Using Mendelian inheritance to improve high throughput SNP discovery.  Genetics. 198(3):847-857.  PMID:  25194160.  PMCID:  PMC4224174.

Blekhman R, GH Perry, S Shahbaz, O Fiehn, AG Clark  and Y Gilad.  2014.  Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence.  Sci Rep.  4:5809.  PMID:  25069065.  PMCID:  PMC Journal In Process.

Wang X, KC Douglas, JL Vandeberg, AG Clark and PB Samollow.  2014.  Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica.  Genome Res. 24(1):70-83.  PMID:  24065774.  PMC3875863.

Sing ND, LB Koerich, AB Carvalho and AG Clark.  2014.  Positive and purifying selection on the Drosophila Y chromosome.  Mol Biol Evol. 31(10):2612-2623.   PMID:  24974375.   PMC4166921

Lusk CM, G Dyson, AG Clark, CM Ballantyne, R Frikke-Schmidt, A Tybjaerg-Hansen, E Boerwinkle and CF Sing.  2014.  Validated context-dependent associations of coronary heart disease risk with genotype variation in the chromosome 9p21 region:  the Atherosclerosis Risk in Communities study.  Hum Genet.  [Epub ahead of print]  PMID:  24889828.  PMC4164053.

Unckless, R and AG Clark.  2014.  Sex-ratio meiotic drive and interspecific competition.  J Evol Biol. 27(8):1513-1521..  PMID:  24835887.  PMC4107154.

Connallon T and AG Clark.  2014.  Balancing selection in species with separate sexes:  Insignts from Fisher’s Geometric Model.  Genetics.  197(3):991-1006.  PMID:  24812306.  PMC4096376.

Wang X and AG Clark.  2014.  Using next-generation RNA sequencing to identify imprinted genes.  Heredity.  113(2):156-166..  PMID:  24619182.  PMC4105452.

Spencer HG and AG Clark.  Non-conflict theories for the evolution of genomic imprinting.  2014.  Heredity.  113(2):112-118.  PMID:  24398886.  PMC4105448.

Wei KH, AG Clark and DA Barbash.  2014.  Limited Gene Misregulation Is Exacerbated by Allele-Specific Upregulation in Letal Hybrids between Drosophila melanogaster and Drosophila simulans.  Mol Biol Evol.  31(7);1767-1778.   PMID:  24723419.   PMC24723419.

Clark AG.  2014.  Genetics:  The vital Y chromosome.  Nature.  508(7497):463-465.  PMID:  24759407.  PMCID:  PMC Journal In Process.

Douglas KC, Wang X, Jasti M, Wolff A, VandeBerg JL, Clark AG, and Samaollow PB.  2014.  Genome-wide histone state profiling of bibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene.  BMC Genomics 15:89.  PMID:  24484454.  PMC3912494.

Larracuente AM and AG Clark.  2014.  Recent selection on the Y-to-dot translocation in Drosophila pseudoobscura.  Mol Bol Evol.  31(4):846-856.  PMID:  24390701.   PMC3969560.

Singh ND, EA Stone, CF Aquadro, and AG Clark.  2013.  Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome.  Genetics 194(2):375-387.  PMID: 23410829.  PMC3664848.

Bhaskar A, AG Clark, and YS Song.  2014.  Distortion of genealogical properties when the sample is very large.  Proc Natl Acad Sci. 111(6);2385-2390.   PMID:  24469801.  PMC3926037.

2013

Zhang, R, AG Clark, AC Fiumera.  2013.  Natural genetic variation in male reproductive genes contributes to nontransitivity of sperm competitive ability in Drosophila melanogaster.  Mol Ecol. 22:1400-1415. PMID:  23171073.  PMC Exempt – Not resulting from NIH funding.

Singh, ND, JD Jensen, AG Clark, and CF Aquadro.  2013. Inferences of demography and selection in an African population of Drosophila melanogaster. Genetics 193:215-228. PMID:  23105013.  PMC3527247.

Chow, CY, MF Wolfner, and AG Clark.  2013.  Large neurological component to genetic differences underlying biased sperm use in Drosophila.  Genetics.  193:177-185 PMID:  23105014.  PMC3527244.

Larracuente, AM and AG Clark.  2013.  Surprising differences in the variability of Y chromosomes in African and cosmopolitan populations of Drosophila melanogaster.  Genetics 193:201-214. PMID:  23086221.  PMC3527246.

Ferreira, Z, S Seixas, AM Andres, WW Kretzschmar, et al.  2013.  Reproduction and immunity driven natural selection in the human WFDC locus.  Mol Biol Evol.  30(4):938-950.  PMID:  23292442.  PMC36033151.

Ma, L, AG Clark, and A Keinan.  2013.  Gene-based testing of gene interactions in quantitative trait association studies.  PLoS Genetics.  9(2):e1003321.  PMID:  23468652.  PMC3585009.

Quintana-Murci, L and AG Clark. 2013.   Population genetic dissection of innate immune response in humans and model organisms.   Nat Rev Immunology.  13:280-293.  PMID:  23470320.  PMC Exempt – Invited Review.

Connallon, T and AG Clark. 2013.  Sex-specific selection and the evolution of X inactivation strategies.  PLoS Genet. 67:908-917.  PMID:  23461340.  PMC3590853.

Connallon, T and AG Clark. 2013. Sex-differential selection and the evolution of x inactivation strategies.  PLoS Genet. 9(4):e1003440.  PMID:  23637618.  PMC3630082.

Chow CY, MF Wolfner, and AG Clark. 2013.  Novel ER stress genes in Drosophila discovered from studies of natural variation.  110:913-918.  Proc Natl Acad Sci USA.  PMID:  23667151.  PMC3670321.

Guo Y, X Wei, J Das, A Grimson, SM Lipkin, AG Clark, and H Yu.  2013.  Dissecting disease inheritance modes in a three-dimensional protein network challenges the “Guilt-by-Association” principle.  Am J Hum Genet.  pii: S0002-9297(13) 00235-00238.  PMID:  23791107.  PMC3710751.

Wang X, DC Miller, R Harman, DF Antczak, and AG Clark.  2013.  Paternally expressed genes predominate in the placenta.  Proc Natl Acad Sci.  110(26):10705-10710.  PMID:  23754418.  PMC3696791.

Chow CY, MF Wolfer, and AG Clark.  2013.  Using natural variation in Drosophila to discover previously unknown endoplasmic reticulum stress genes.  Proc Natl Acad Sci.  110(22):9013-9018.  PMID:  23667151.  PMC3670321.

Gazave E, D Chang, AG Clark, and A Keinan.  2013.  Population growth inflates the per-individual number of deleterious mutations and reduces their mean effect.  Genetics. 195(3):969-978.  PMID:  23979573.  PMC3813877.

Carvalo AB and AG Clark.  2013.  Efficient identification of Y chromosome sequences in the human and Drosophila genomes.  Genome Res.  23(11):1894-1907.   PMID:  23921660.  PMC3814889.

Connallon T and AG Clark.  2013.  Antagonistic versus non-antagonistic models of balancing selection:  characterizing the relative timescales and hitchhiking effects of partial selective sweeps.   Evolution 67:908-917.  PMID:  23461340.  PMC3590853.

Chakravarti, A, AG Clark, and V Mootha. 2013.  Distilling pathophysiology from complex disease genetics.  Cell.  155(1):21-26.  PMID:  24074858.  PMCID:  PMC4244836.

Scheitz, CJF,  Y Guo, AM Early, LG Harshman, and AG Clark. 2013.  Heritability and inter-population differences in lipid profiles of Drosophila melanogaster.  PLoS ONE  8(8):e72726.  PMID:  24013349.  PMC3754969.

Corbett-Detig RB, J Zhou, AG Clark, DL Hartl, and JF Ayroles.  2013.  Genetic incompatibilities are widespread within species.  Nature  504(7478):135-137.  PMID:  24196712.  PMC4844467.

Wang X, D Wheeler, A Avery, JH Choi, JK Colbourne, AG Clark, and JH Werren.  2013. Function and Evolution of DNA Methylation in Nasonia vitripennis.  PLoS Genet. 9(10):e1003872. doi: 10.1371/journal.pgen.1003872. Epub 2013 Oct 10.  PMID: 24130511.  PMC3794928.

Early AM and AG Clark.  2013.  Monophyly of Wolbachia pipientis genomes within Drosophila melanogaster: geographic structuring, titre variation and host effects across five populations.  Mol.Ecol.  22(23):5765-5778.  PMID:  24118111.  PMC4005148.

Khurana E, Y Fu, V Colonna, et al. , 1000 Genomes Project Consortium.  2013.  Integrative annotation of variants from 1092 humans: application to cancer genomics.  Science.  342(6154):1235587.  PMID:  24092746.  PMC3947637.

Sackton TB, JH Werren, and AG Clark.  2013.  Characterizing the Infection-Induced Transcriptome of <i>Nasonia vitripennis</i> Reveals a Preponderance of Taxonomically-Restricted Immune Genes.  PLoS One 8(12):e83984.  PMID:  24386321.  PMC3873987.

Gazave E, L Ma, D Chang, A Coventry, et al.  2013.  Neutral genomic regions refine models of recent rapid human population growth.  Proc Natl Acad Sci USA.  111(2):757-762.  PMID:  24379384.   PMC3896169.

Ferreira Z, B Hurle, AM Andres, WW Kretzschmar, et al.  2013.  Sequence Diversity of Pan troglodytes Subspecies and the Impact of WFDC6 Selective Contraints in Reproductive Immunity.  Genome Biol Evol.  5(12):2512-2523.  PMID:  24356879.  PMC3879984.

Connallon T and AG Clark.  2013.  Evolutionary inevitability of sexual antagonism.  Proc Biol Sci. 281(1776):20132123.  PMID:  24335980.  PMC3871308.

Singh ND, EA Stone, CF Aquadro, and AG Clark.  2013.  Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome.  Genetics. 194(2):375-387.  PMID: 23410829.  PMC3664848.

2012

Singh ND, EA Stone, CF Aquadro, and AG Clark. 2012.  Fine-scale heterogeneity in crossover rate in the garnetscalloped region of the D. melanogaster X chromosome.  Genetics 194:375-387.  PMID:  23410829.  PMC3664848

Connallon, T, ND Singh, and AG Clark. 2012.  Impact of genetic architecture on the relative rates of X versus autosomal adaptive substitution. Mol Biol Evol.  29:1933-1942. PMID: 22319138.  PMCID:  PMC3408067

Connallon, T and AG Clark. 2012.  A general population genetic framework for antagonistic selection that accounts for demography and recurrent mutation. Genetics 190:1477-1489. PMID:  22298707.  PMC3316657.

Lazzaro, BP and AG Clark. 2012.  Rapid evolution of innate immune response genes. R.A. Singh, Jianping Xu R and R.A. Kulathinal, eds.  Oxford Univ Press. Rapidly Evolving Genes & Genetic Systems.   Chapter 20.   PMC Exempt – Book Chapter.

Garrigan, D, SB Kingan, AJ Geneval, P Andolfatto, AG Clark, KR Thornton and DC Presgraves.  2012.  Genome sequencing reveals complex speciation in the Drosophila simulans clade.  Genome Res.  22:1499-1511. PMID:  22534282.  PMC3409263.

Keinan, A and AG Clark.  2012.  Recent explosive population growth has resulted in a large excess of rare variants in humans.  Science 336:740-743. PMID:  22582263.  PMC3586590.

Gunnar, MR, JA Wenner, KM Thomas, GE Glatt, MC McKenna, and AG Clark.  2012.  The BDNF Val66Met polymorphism moderates early deprivation effects on attention problems. Dev Psycopathol. 24:1215-1223. PMID:  23062292.  PMC3581017.

Lu, J and AG Clark.  2012.  Impact of microRNA regulation on variation in human gene expression.  Genome Res. 22:1243-1254. PMID:  22456605.  PMC3396366.

Bentley, AR, SB Kritchevsky, TB Harris, AB Newman, et al.  2012.  Genetic variation in antioxidant enzymes and lung function.  Free Radic Biol Med.  52:1577-1583. PMID:  22387199.   PMC3390784.

Meisel RP, JH Malone, and AG Clark.  2012.  Disentangling the relationship between sex-biased gene expression and X-linkage.  Genome Res.  22:1255-1265. PMID:  22499666.  PMC3396367.

Ma, L, A Brautbar, E Boerwinkle, CF Sing, AG Clark, and A Keinan.  2012.  Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations.  PLoS Genet. 8(5):e1002714.  PMID:  22654671.  PMC3359971.

Wernimont, SM, AG Clark, PJ Stover, MT Wells, et al.  2012.  Folate network genetic variation predicts cardiovascular disease risk in non-Hispanic white males.  J Nutr.  142:1272-1279. PMID:  22649255.  PMC3374665.

Wang, X, DC Miller, AG Clark, DF Antczak.  2012.  Random X inactivation in the mule and horse placenta.  Genome Res.  22:1855-1863.  PMID:  22645258.  PMC3460181.

Chen, N, DW Bellott, DC Page, and AG Clark.  2012.  Identification of avian W-linked contigs by short-read sequencing.  BMC Genomics   13:183.  PMID:  22583744.  PMCID:  PMC3428670.

Lang, M, S Murat, AG Clark, G Couppil, et al.  2012.  Mutations in the neverland gene turned Drosophila pachea into an obligate specialist species.  Science 337:1658-1661.  PMID 23019649.  PMC Exempt – Not resulting from NIH funding.

Clarke, L, X Zheng-Bradley, R Smith, E Kulesha, et al. The 1000 Genomes Project Consortium.  2012.  The 1000 Genomes Project:  data management and community access.  Nat Methods.  9:459-462.  PMID:  22543379.  PMC3340611.

Meisel, RP, JH Malone, and AG Clark.  2012. Faster-x evolution of gene expression in Drosophila.  PLoS Genet.  8(10):e1003013.  PMID:  23071459.  PMC3469423.

Cunnar, MR, JA Wenner, KM Thomas, CE Glatt, MC McKenna, and AG Clark.  2012.  The brain-derived neurotrophic factor VaI66Met polymorphism moderates early deprivation effects on attention problems.  Dev Psychopathol.  24:1215-1223.  PMID:  23062292.  PMC3581017.

Kidd, JM, S Gravel, J Byrnes, A Moreno-Estrada, et al.  2012.  Population genetic inferences from personal genome data:  impact of ancestry and admixture on human genomic variation.  Am J Hum Genet.  91:660-671. PMID: 23040495.  PMC3484644.

Cardoso-Moreira, M, JR Arguello, and AG Clark.  2012.  Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing.  Genome Biol. 13:R119. PMID:  23259534.  PMCID:  PMC4056370.

1000 Genomes Project Consortium, GR Abecasis, A Auton, LD Brooks, et al.  2012.  An integrated map of genetic variation from 1,092 human genomes.  Nature.  491:56-65.  PMID:  23128226.  PMC3498066.

Chen, N, DW Bellott, DC Page, and AG Clark.  2012.  Identification of avian W-linked contigs by short-read sequencing.  BMC Genomics  13:183. PMID:  22583744. PMC3428670.

2011

Greenberg, AJ, SR Hackett, LG Harshman, and AG Clark.  2011.  Environmental and genetic perturbations reveal networks of metabolic regulation.  Mol Syst Biol.  7:563. PMID:  22186737.  PMC3738848

Cardoso-Moreira, M, JJ Emerson, AG Clark, and M Long.  2011.  Drosophila duplication hotspots are associated with late-replicating regions of the genome.  PLoS Genet. e1002340. PMID:  22072977.  PMC3207856.

Marth, GT, F Yu, AR Indap, K Garimella, et al., 1000 Genomes Project T.  2011.  The functional spectrum of low-frequency coding variation.  Genome Biol. 12:R84. PMID:  21917140.  PMC3308047.

Gottipati, S, L Arbiza, A Siepel, AG Clark, and A Keinan. 2011.  Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing.  Nat Genet. 43:741-743. PMID:  21775991.  PMC3145052.

Gravel, S, BM Henn, RN Gutenkunst, AR Indap, GT Marth, AG Clark, F Yu F, RA Gibbs; The 1000 Genomes Project, and CD Bustamante.  2011.  Demographic history and rare allele sharing among human populations.  Proc Natl Acad Sci USA.  108:11983-11988. PMID:  21730125.  PMC3142009.

Conrad, DF, JE Keebler, MA DePristo, SJ Lindsay, et al.; 1000 Genomes Project.  2011.  Variation in genome-wide mutation rates within and between human families.  Nat Genet.  43:712-714. PMID: 21666693.  PMC3322360.

Greenspan, L and AG Clark.  2011.  Association between variation in X chromosome male reproductive genes and sperm competitive ability in Drosophila melanogaster.  Int J Evol Biol.  2011:214280. PMID:  21716718.  PMC3119407.

Tilley, AE, TP O’Connor TP, NR Hackett, et al.  2011.  Biologic phenotyping of the human small airway epithelial response to cigarette smoking.  PLoS One 6:e22798.  PMID:  21829517.  PMC3145669.

Im, KM, T Kirchhoff, X Wang, B Gold, et al.  2011. Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers.  Hum Genet. 130:685-699. PMID:  21597964.  PMC3196382.

Wang, X, PD Soloway, and AG Clark.  2011. A survey for novel imprinted genes in the mouse placenta by mRNA-seq.  Genetics.  189:109-122. PMID:  21705755.  PMC3176116.

Gokcumen, OO, PL Babb, and R Iskow, et al.  2011.  Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection.  Genome Biol.  12:R52.  PMID:  21627829.  PMC3219974.

Woodard, SH, BJ Fischman, A Venkat, ME Hudson, K Varala, SA Cameron, AG Clark, GE Robinson.  2011.  Genes involved in convergent evolution of eusociality in bees.  Proc Natl Acad Sci USA.  108:7472-7477. PMID:  21482769.   PMC3088614.

Connallon, T and AG Clark.  2011.  Association between sex-biased gene expression and mutations with sex-specific phenotypic consequences in Drosophila.  Genome Biol Evol.  3:151-155. PMID:  21292631.  PMC3048362.

Mills, RE, K Walter, C Stewart, RE Handsaker, et al.  1000 Genomes Project.  2011.  Mapping copy number variation by population-scale genome sequencing.  Nature 470:59-65. PMID:21293372.  PMC3077050.

Connallon, T and AG Clark.  2011.  The resolution of sexual antagonism by gene duplication.  Genetics  187:919-937.  PMID:  21220356.  PMC3063682.

Lohmueller, KE, CD Bustamante, and AG Clark.  2011.  Detecting directional selection in the presence of recent admixture in African Americans.  Genetics 187:823-835.  PMID:  21196524.  PMC3063676.

Wernimont, SM, AG Clark, PJ Stover, MT Wells, et al.  2011.  Folate network genetic variation, plasma homocysteine, and global genomic methylation content:  a genetic association study.  BMC Med Genet.  21:12-150. PMID:  22103680.  PMC3266217.

Giardina, TJ, A Beavis, AG Clark AG, and AC Fiumera.  2011.  Female influence on pre- and post-copulatory sexual selection and its genetic basis in Drosophila melanogaster.  Mol Ecol.  20:4098-4108. PMID:  21902747.  PMC3183161.

Woodard, SH, BJ Fischman, A Venkat, ME Hudson, et al.  2011.  Genes involved in convergent evolution of eusociality in bees.  Proc Natl Acad Sci USA.  108:7472-7477. PMID:  21482769.  PMC3088614.

2010

1000 Genomes Project Consortium, RM Durbin, GR Abecasis, DL Altshuler, A Auton, LD Brooks, RA Gibbs RA, ME Hurles, and GA McVean.  2010.  A map of human genome variation from population-scale sequencing.  Nature 467:1061-1073.  PMID:  20981092.  PMC3042601.

Andres, AM, MY Dennis, WW Kretzschmar, JL Cannons, et al.  2010.  Balancing selection maintains a form of ERAP2 tat undergoes nonsense-mediated decay and affects antigen presentation.  PLoS Genetics.  6:e1001157.  PMID:  20976248.  PMC2954825.

Chow, CY, MF Wolfner, and AG Clark.  2010.  The genetic basis for male x female interactions underlying variation in reproductive phenotypes in Drosophila.  Genetics 186:1355-1365.  PMID:  20876561.  PMC2998317.

Connallon, T and AG Clark.  2010.  Sex linkage, sex-specific selection, and the role of recombination in the evolution of sexually dimorphic gene expression.   Evolution  64:3417-3442.  ,PMID:  20874735.  PMC2998557.

Clark, AG, X Wang, and T Matise.  2010. Contrasting methods of quantifying fine structure of human recombination. Annu Rev Genomics Hum Genet. 11:45-64.  PMID:  20690817.  PMC2980829.

Connallon, T and AG Clark.  2010.  Gene Duplication, Gene Conversion, and the Evolution of the Y Chromosome. Genetics  186:277-286.  PMID:  20551442.  PMC2940292.

Wang, X, PD Soloway, and AG Clark.  2010.  Paternally biased X inactivation in mouse neonatal brain. Genome Biol. 11:R79.  PMID  20663224.  PMC2926790.

Hunter-Zinck, H, S Musharoff, J Salit, KA Al-Ali, L Chouchane, A Gohar, et al.  2010.  Population genetic structure of the people of Qatar. Am J Hum Genet. 87:17-25.   PMID:  20579625.  PMC2896773.

1000 Genomes Project Consortium, PH  Sudamant, JO Kitzman, G Antonacci, C Alkan, et.al.  2010.  Diversity of human copy number variation and multicopy genes.  Science  330:641-646.  PMID:  21030649.  PMC3020103.

Coventry, A, LM Bull-Otterson, X Liu, AG Clark, et.al.  2010.  Deep resequencing reveals excess rare recent variants consistent with explosive population growth.  Nat. Commun. 1:131. PMID:  21119644.  PMC3060603.

Wang, X, PD Soloway, and AG Clark. 2010.  Paternally biased X inactivation in mouse neonatal brain. Genome Biol.  11:R79.  PMID: 20663224.  PMC2926790.

Lohmueller, KE, CD Bustamante, and AG Clark. 2010.  The effect of recent admixture on inference of ancient human population history. Genetics 185:611-622.  PMID:  20382834.  PMC2881141.

Hill-Burns, EM and AG Clark. 2010.  Functional regulatory divergence of the innate immune system in interspecific Drosophila hybrids. Mol Biol Evol.  27:2596-2605.  PMID:  20551040.  PMC3107606.

Royal, CD, J Novembre, SM Fullerton, DB Goldstein, JC  Long, MJ Bamshad, et al.  2010.  Inferring genetic ancestry: opportunities, challenges, and implications. Am J Hum Genet.  86:661-673. PMID:  20466090.  PMC2869013.

Greenberg, AJ, SA Hackett, LG Harshman, and AG Clark.  2010.  A hierarchical Bayesian model for a novel sparse partial diallel crossing design. Genetics 185:361-373.  PMID:  20157001.  PMC2870970.

Larracuente, AM, F Noor, and AG Clark.  2010.  Translocation of Y-linked genes to the dot chromosome in Drosophila pseudoobscura. Mol Biol Evol.  27:1612-1620. PMID:  20147437.  PMC2912472.

Lu, J and AG Clark.  2010.  Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. Genome Res. 20:212-227.  PMID:  19948818.  PMC2813477.

Sackton, TB, BP Lazzaro, and AG Clark.  2010.  Genotype and gene expression associations with immune function in Drosophila. PLoS Genet. 6:e1000797.  PMC2793509.

2009

Manolio, TA, FS Collins, NJ Cox, LA Goldstein, et al.  2009.  Finding the missing heritability of complex diseases.  Nature. 461:747-753.  PMID:  19812666.   PMC2831613.

Hill-Burns, EM and AG Clark.  2009.  X-linked Variation in Immune Response in Drosophila melanogaster. Genetics.  183:1477-1491.  PMID: 19822734.  PMC2787433.

Andrés, AM, MJ Hubisz, A Indap, DG Torgerson, et al.  2009.  Targets of balancing selection in the human genome.  Mol Biol Evol. 26:2755-2764. PMID: 19713326.  PMC2782326.

Torgerson, DG, AR Boyko, RD Hernandez, A Indap, et al.  2009.  Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence.  PLoS Genet.  e10000592. PMID: 19662163.  PMC2714078.

Carvalho, AB, LB Koerich, and AG Clark.  2009.  Origin and evolution of Y chromosomes: Drosophila tales. Trends Genet. 25:270-277. PMID: 19443075.  PMC2921885.

Singh, ND, CF Aquadro, and AG Clark.  2009.  Estimation of fine-scale recombination estimation of recombination intensity variation in the white-echinus interval of D. melanogaster.  J Mol Evol. 69:42-53. PMID:  19504037.  PMC2748731.

Casey, BJ, CE Glatt, N Tottenham, F Soliman, et al.  2009.   Brain-derived neurotrophic factor as a model system for examining gene by environment interactions across development. Neuroscience.  164:108-120.  PMID: 19358879.  PMC2760671.

Sackton, TB and AG Clark.  2009.  Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing. BMC Genomics 10:259. PMID: 19500410.  PMC2701966.

Castellano, S, AM Andrés, E Bosch, M Bayes, R Guigó, and AG Clark.  2009.  Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins.  Mol Biol Evol. 26:2031-2040.  PMID: 19487332.   PMC2734155.

Singh, NS, PF Arndt, AG Clark, and CF Aquadro.  2009. Strong evidence for lineage- and sequence-specificity of substitution rates and patterns in Drosophila.  Mol. Biol. Evol.  26:1591-1605.   PMID: 19351792.  PMC2734147.

Lohmueller, KE, CD Bustamante, and AG Clark. 2009.  Methods for human demographic inference using haplotype patterns from genome-wide single-nucleotide polymorphism data. Genetics. 182:217-231. PMID: 19255370.  PMC2674818.

McGraw, LA, G Gibson, AG Clark AG, and MF Wolfner.  2009.  Strain-dependent differences in several reproductive traits are not accompanied by early post-mating transcriptome changes in female Drosophila melanogaster. Genetics 181:1273-1280.  PMID:19237688.  PMC2666498

Nielsen, R, MJ Hubisz, I Hellmann, D Torgerson, et al, Clark AG.  2009.  Darwinian and demographic forces affecting human protein coding genes. Genome Res. 19:838-849.  PMID: 19279335.  PMC2675972.

Scott, JG, N Liu, M Kristensen, and AG Clark.  2009.  A case for sequencing the genome of the house fly, Musca domestica (Diptera: Muscidae) J. Mol. Entomol.  46:175-182. PMID: 19351068.

Clark, AG.  2009.  Formal Genetics of Humans:  Multifactorial Inheritance and Common Diseases in Human Genetics, in Vogel and Motulsky’s Human Genetics: Problems and Approaches, 4th edition, Vogel, Motulsky, Antonarakis, Speicher, eds., Springer-Verlag.

Turetz, ML, TP O’Connor, AE Tilley, Y Strulovici-Barel, J Salit, D Dang, M Teater, J Mezey, AG Clark, RG Crystal.  2009.  Trachea epithelium as a “canary” for cigarette smoking-induced biologic phenotype of the small airway epithelium.  Clin Transl Sci.  2:260-272. PMID:  20443905.

Singh, ND, AM Larracuente, TB Sackton, and AG Clark.  2009.  Comparative genomics on the Drosophila phylogenetic tree.  Ann. Rev. Ecol. Evol. Syst., 40:459-480.  PMC Exempt – invited review.

Sackton, TB, RJ Kulathinal, CM Bergman, AR Quinlan, E Dopman, GT Marth, E Mardis, DL Hartl, and AG Clark AG.  2009.  Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster.  Genome Biol. Evol., 1:449-465.  PMID:  20333214.  PMC2839279

Dermitzakis, ET and AG Clark.  2009. Genetics. Life after GWA studies. Science 326:239-240.  PMID: 19815762.  PMC2933170.

2008

Olshen, AB, B Gold, KE Lohmueller, JP Struewing, et al.  2008. Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping.  BMC Genet.  9:14. PMID:  18251999.  PMC2259380.

Wang, X, Q Sun, SD McGrath, ER Mardis, PD Soloway, and AG Clark.  2008.  Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One 3:e3839. PMID: 19052635.  PMC2585789.

Hellmann, I,  Z Mang, P Gu, F Li, F de la Vega, AG Clark, and R Nielsen.  2008.  Population genetic analysis shotgun assemblies of genomic sequences from multiple individuals.  Gen Res. 18:1002-1029.  PMID:  18411405.  PMC2493391.

Koerich, LB, X Wang, AG Clark, AB Carvalho AB.  2008.  Low conservation of gene content in the Drosophila Y chromosome. Nature 456:949-951. PMID: 19011613.  PMC2713029.

Greenberg, AJ, SR Stockwell, and AG Clark. 2008.  Evolutionary constraint and adaptation in the metabolic network of Drosophila. Mol Biol Evol. 25:2537-2546. PMID: 18799713.   PMC2721553.

Clark, AG.  2008.  Genome sequences from extinct relatives. Cell 134:388-389.  PMID: 18692462.

McKean, KA, CP Yourth, BP Lazzaro, and AG Clark.  2008.  The evolutionary costs of immunological maintenance and deployment. BMC Evol Biol.  8:76. PMID: 18315877.  PMC2292698.

Lohmueller, KE, AR Indap, S Schmidt, AR Boyko, et al.  2008.  Proportionally more deleterious genetic variation in European than in African populations. Nature 451:994-997.  PMID: 18288194.  PMC2923434.

Wittkopp, PJ, BK Haerum, and AG Clark.  2008.  Regulatory changes underlying expression differences within and between Drosophila species. Nat Genet. 40:346-350. PMID: 18278046.

Larracuente, AM, TB Sackton, A Greenberg , A Wong, ND Singh, D Sturgill, Y  Zhang , B Oliver, and AG Clark.  2008.  Evolution of protein-coding genes in Drosophila.  Trends Genetics 24:114-123.  PMID: 18249460.

Wittkopp, PJ, BK Haerum, and AG Clark.  2008. Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster. Genetics.  178:1831-1835.  PMID: 18245838.   PMC2278090.

Pollard, KS, D Serre, X Wang, TJ Hudson, AG Clark, and K Frazer.  2008. Novel imprinted genes identified through a genome-wide study of differential allelic expression. Human Genetics.  122:625-634.  PMID:  17955261.

Gold, B, T Kirchhoff, S Stefanov, J Lautenberger, et al.  2008.  Genome-wide association study provides evidence for a breast cancer risk locus at 6Q2233.  Proc Natl Acad Sci USA.  105:4340-4345. PMID  18326623.  PMC2393811.

Boyko, AR, SH Williamson, AR Indap, JD Degenhardt, et al.  2008.  Assessing the evolutionary impact of amino acid mutations in the human genome.  PLoS Genet.  4:e1000083.  PMID:  18516229.  PMC2377339.

McGraw, LA, AG Clark, and MF Wolfner.  2008.  Post-mating gene expression profiles of female Drosophila melanogaster in response to time and to four male accessory gland proteins.  Genetics.  179:1395-1408. PMID:  18562649.  PMC2475742.

2007

Hartl, DL and AG Clark.  2007.  Principles of Population Genetics, Fourth edition, Sinauer Associates, Sunderland, MA.

Rhesus Macaque Genome Sequencing and Analysis Consortium.  2007.  Evolutionary and biomedical insights from the rhesus macaque genome.  Science 316:222-234.

Andrés, AM, AG Clark, E Boerwinkle, CF Sing, and JE Hixson.  2007.  Assessing the accuracy of statistical haplotype inference with sequence data of known phase.   Genet. Epi. 31:659-671.

Jørgensen, FG, MH Schierup, and AG Clark.  2007.   Heterogeneity in regional GC content and differential usage of codons and amino acids in GC-poor and GC-rich regions of the genome of Apis mellifera.   Mol. Biol. Evol.  24:611-619.

Ma X, Y Liu, BB Gowen, EA Graviss, AG Clark, and JM Musser.  2007.  Full-exon resequencing reveals toll-like receptor variants contribute to human susceptibility to tuberculosis disease. PLoS One 2:e1318.  PMID: 18091991.  PMC2117342.

Singh, ND, AM Larracuente, and AG Clark.  2007.  Contrasting the efficacy of selection on the X and autosomes in Drosophila. Mol Biol Evol. 25:454-467.  PMID: 18083702.

Rhesus Macaque Genome Sequencing and Analysis Consortium.  2007.  Evolutionary and biomedical insights from the rhesus macaque genome.  Science 316:222-234.  PMID:  17431167.

Andrés, AM, AG Clark, L Shimm, E Boerwinkle, CF Sing, and JE Hixson.  2007.  Understanding the accuracy of statistical haplotype inference with sequence data of known phase.   Genet. Epi. 31;659-671.  PMID:  17922479.  PMC2291540.

Jørgensen, FG, MH Schierup, and AG Clark.  2007.  Heterogeneity in regional GC content and differential usage of codons and amino acids in GC-poor and GC-rich regions of the genome of Apis mellifera.   Mol. Biol. Evol.  24:611-619. PMID:  17150976.

Sainudiin, R, AG Clark, and RT Durrett.  2007.  Simple models of genomic variation in human SNP diversity. BMC Genomics 8:146.  PMID:  17553150.  PMC1919371.

Fiumera, A, BL Dumont, and AG Clark.  2007. Associations between sperm competition and natural variation in male reproductive genes on the third chromosome of Drosophila melanogaster.  Genetics 176:1245-1260.  PMID:  17435238.  PMC1894588.

McGraw, LA, AC Fiumera, M Ramakrishnan, S Madhavarapu, AG Clark and MF Wolfner.  2007.  Effects of the larval rearing environment on post-copulatory traits in Drosophila melanogaster.  Biol Letters, 3:607-610.  PMID:  17711815.  PMC2391209.

Williamson, SH, MJ Hubisz, AG Clark, BA Payseur, CD Bustamante, and R Nielsen.  2007.  Localizing recent adaptive evolution in the human genome.  PLoS Genet. e90.  PMID:  17542651.  PMC1885279.

Kininis, M, BS Chen, AG Diehl, GD Isaacs, T Zhang, AC Siepel, AG Clark, and WL Kraus.  2007.  Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol.  27:5090-5104. PMID:  17515612.  PMC1951957.

Clark, AG and J Li.  2007.  Conjuring SNPs to detect associations.   Nat. Genetics. 39:815-816.  PMID:  17597769.

Ma X, Y Liu, BB Gowen, EA Graviss, AG Clark, and JM Musser.  2007.  Full-exon sequencing reveals Toll-like receptor variants contribute to human susceptibility to tuberculosis disease.  PLoS One 2:e1318.  PMID:  18091991.  PMC2117342.

Schlenke, TA, J Morales, S Govind, and AG Clark.  2007.  Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster.  PLoS Pathog.  3:1486-1501. PMID:  17967061.  PMC2042021.

Huntley, MA and AG Clark.  2007.  Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species.  Mol Biol Evol.  24:2598-2609. PMID:  17602168.

Nielsen, N, I Hellmann, M Hubisz, CD Bustamante, and AG Clark.  2007.  Recent and ongoing selection in the human genome.  Nat. Reviews Genetics 8:857-868.  PMID:  17943193.  PMC2933187.

Sackton, TB, BP Lazzaro, TA Schlenke, JD Evans, D Hultmark, and AG Clark.  2007.  Dynamic evolution of the innate immune system in Drosophila.  Nat Genet. 39:1461-1468. PMID:  17987029.

Drosophila 12 Genomes Consortium.  2007a. Evolution of genes and genomes on the Drosophila phylogeny.  Nature 450:203-218.  PMID:  17994087.

Drosophila 12 Genomes Consortium.  2007b. Discovery of functional elements in 12 fly genomes using evolutionary signatures.  Nature 450:219-232.  PMID:  17994088.  PMC2474711.

2006

Bachtrog, D, K Thornton, AG Clark, and P Andolfatto.  2006.  Extensive introgression of mitochondrial DNA in the absence of nuclear gene flow in the Drosophila yakuba subgroup. Evolution 60:292-302.

Wilson, GM, S Flibotte, PI Missirlis, MA Marra, S Jones, K Thornton, AG Clark and RA Holt.  2006. Identification by full coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res. 16:173-181.
White, TJ, AG Clark, and S. Broder.  2006. Genome-based biomarkers for adverse drug effects, patient enrichment and prediction of drug response, and their incorporation into clinical trial design. Pers. Medicine 3:177-185.

Fiumera, AC, BL Dumont, and AG Clark.  2006.  Natural variation in male-induced ‘cost-of-mating’ and allele-specific association with male reproductive genes in Drosophila melanogaster.  Phil. Trans. Roy. Soc. B, 361:355-361.

Hamon, SC, SL Kardia, E Boerwinkle, K Liu, KL Klos, AG Clark, and CF Sing. 2006. Evidence for consistent intragenic and intergenic interactions between SNP effects in the APOA1/C3/A4/A5 gene cluster. Hum Hered. 61:87-96.

Clark, AG.  2006.  Genomics of the evolutionary process.   Trend Ecol. Evolution 21:316-321.

Brown, CM, TJ Rea, SC Hamon, JE Hixson, E Boerwinkle, AG Clark, and CF Sing.  2006.  The contribution of individual and pairwise combinations of SNPs in the APOA1 and APOC3 genes to interindividual HDL-C variability.  Jour. Mol. Med 84:561-572.

Payseur, BA, AG Clark, J Hixson, E Boerwinkle, and CF Sing.  2006.    Contrasting multi-site genotypic distributions among discordant quantitative phenotypes: the APOA1/C3/A4/A5 gene cluster and cardiovascular disease risk factors.  Genet. Epi. 30:508-518.

Wittkopp, PJ, BK Haerum, and AG Clark.  2006.  Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting. Genetics 173:1817-1821.

Montooth, K, K Siebenthal, and AG Clark.  2006. Membrane lipid physiology and toxin catabolism underlie ethanol and acetic acid tolerance in Drosophila melanogaster. Jour. Exp. Biol. 209: 3837-3850.

Spencer HG and AG Clark.  2006.   A Chip off the Old Block: A model for the evolution of genomic imprinting via selection for parental similarity.  Genetics 174:931-935.

Whitfield, C, SK Behura, SH Berlocher, AG Clark, et al.  2006. Thrice out of Africa: Ancient and modern expansions of the honey bee, Apis mellifera. Science 314:642-645.

Weinstock, GG, E Robinson, and The Honeybee Genome Sequencing Consortium.  2006. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443:931-949.

Lazzaro, BP, TB Sackton, and AG Clark.  2006.  Genetic variation in Drosophila melanogaster resistance to infection: a comparison across bacteria.  Genetics 174:1539-1554.

Klos, KLE, CF Sing, E Boerwinkle, S Hamon, TJ Rea, AG Clark, M Fornage, and JE Hixson.  2006. Consistent effects of genes involved in reverse cholesterol transport on plasma lipid and apolipoprotein levels in CARDIA participants.   ATVB 26:1828-36.

2005

Rodin, A, TH Mosley, AG Clark, CF Sing and E Boerwinkle.  2005.  Mining genetic epidemiology data with Bayesian networks II. Application to ApoE gene variation and plasma lipid levels.   J Comput Biol.12:1-11.

Carvalho, AB and AG Clark.  2005.  The Y chromosome of D. pseudoobscura is not homologous to the ancestral Drosophila Y.  Science 307:108-110.

Nielsen, R, AG Clark, C Bustamante, S Glanowski, et al.  2005.  A scan for positively selected genes in the genomes of humans and chimpanzees. PLOS Biology 3(6):e170

Richards, S, Y Liu, BR Bettencourt, P Hradecky, et al.  2005.  Comparative sequencing and analysis of Drosophila pseudoobscura.  Genome Res. 15:1-18.

Fiumera, A, BL DuMont and AG. Clark.  2005. Associations between variation in second chromosome male reproductive proteins and sperm competitive ability in Drosophila melanogaster.  Genetics 169:243-257.

Zhang, M, K Montooth, M Wells, AG Clark, and D Zhang.  2005.  Mapping multiple quantitative trait loci by Bayesian classification.  Genetics.  169:2305-2318.  PMID:  15520261.  PMC1449613.

De la Vega, F, H Isaac, A Collins, CR Scafe, et al. 2005.  The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Res., 15:454-462.

Klos KL, S Hamon, AG Clark, E Boerwinkle, K Liu, and CF Sing . 2005.  APOA5 polymorphisms influence plasma triglycerides in young, healthy African Americans and whites of the CARDIA Study.  J Lipid Res. 46:564-571.

Altshuler, D and AG Clark.  2005.  Harvesting medical information from our family tree.  Science 307:1052-1053.

Clark, AG. 2005.  Hotspots unglued.    Nature Genetics 37:563-564.

Mueller, JL, K Ravi Ram, LA McGraw, MC Bloch Qazi, ED Siggia, AG Clark, CF Aquadro, MF Wolfner.  2005.  Cross-species comparison of Drosophila male accessory gland protein genes. Genetics 171:131-143.

Bustamante, CD, R Nielsen, A Fledel-Alon, S Williamson, et al. and AG Clark.  2005.  Natural selection on protein coding genes in the human genome. Nature 437:1153-1157.

Clark, AG, E Boerwinkle, J Hixson, and CF Sing.  2005.  Determinants of the success of whole genome association testing. Genome Res. 15:1463-1467.

Nielsen, R, S Williamson, Y Kim, MJ Hubisz, AG Clark and C Bustamante.  2005. Genomic scans for selective sweeps using SNP data. Genome Res. 15:1566-1575.

Clark, AG, MJ Hubisz, CD Bustamante, S Williamson, and R Nielsen.  2005. Ascertainment bias in genome-wide human polymorphism studies.  Genome Res. 15:1496-1502.

Landry, CR, PJ Wittkopp, JM Ranz, CH Taubes, AG Clark and DL Hartl.  2005.  Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171:1813-1822

Stranger, BE, MS Forrest, AG Clark, S Deutsch, et al.  2005.  Genome-wide associations of gene expression variation in humans. PLoS Biology ePub 1:e78.

2004

Chookajorn, T, A Kachroo, DR Ripoll, AG Clark, and JB Nasrallah.  2004.  Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand.  Proc. Natl. Acad. Sci. USA 101:911-917.

Spencer, HG, MW Feldman, AG Clark, and AE Weisstein.  2004.  The effect of genetic conflict on genomic imprinting and modification of expression at a sex-linked locus.  Genetics 166: 565-579.

Bundgaard, J, JSF Barker, J Frydenberg, and AG Clark.  2004.  Remating and sperm displacement in a natural population of Drosophila buzzatii inferred from mother-offspring analysis of microsatellite loci.  J. Evol. Biol. 17:376-381.

Clark AG.  2004.  The 6th international meeting on single nucleotide polymorphism and complex genome analysis.  Pharmacogenomics.  5:153-156.

Istrail S, Sutton GG, Florea L, Halpern AL, et al.  2004.  Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci USA 101:1916-1921.

Lazzaro, BP, B. K Sceurman and AG Clark.  2004.  The genetic basis of natural variation in D. melanogaster antibacterial immunity. Science 303:1873-1876.

Fullerton, SM, AV Buchanan, V Sonpar,  J Stengård,  E Boerwinkle, KM Weiss, AG Clark, and DA Nickerson.  2004.  The effects of scale: variation in the APOA1/C3/A4/A5 gene cluster.   Human Genet. 115:36-56.

Ohashi J, Naka I, Patarapotikul J, Hananantachai H, Brittenham G, Looareesuwan S, Clark AG, Tokunaga K.  2004.  Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection.  Am J Hum Genet. 74:1198-1208

Wittkopp, PJ, BK Haerum, and AG Clark.  2004.  Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.

McGraw, LA, GC Gibson, AG Clark, and MF Wolfner.  2004.  Genes regulated by mating, sperm or seminal proteins in mated female Drosophila melanogaster.  Current Biology 14:1509-1514

Halldórsson, BV, V Bafna, R Schwartz, AG Clark, S Istrail.  2004.  Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Res. 14:1633-1640.

Clark, AG, ET Dermitzakis, and S Antonarakis. 2004.  Trisomic phase inference. Pp. 1-8 in  S. Istrail et al. (eds.): SNPs and Haplotype Inference, Lecture Notes in Bioinformatics 2983, Springer-Verlag, Heidelberg.

Hamon, SC, Stengård, J, Clark, AG, Salomaa, V, Boerwinkle, E and Sing, CF.  2004.  Evidence for non-additivity of single nucleotide polymorphism effects within the Apolipoprotein E gene.  Ann Hum Genet. 68:521-535.

Nielsen, R, MJ Hubisz, and AG Clark.  2004. Reconstituting the frequency spectrum of ascertained SNP data. Genetics 168:2373-2382.

Clark, AG.  2004. The role of haplotypes in candidate gene studies.  Genet. Epid. 27:321-333.

Gold, B, F Kalush, J Bergeron, K Scott, et al.  2004. Estrogen receptor genotypes and haplotypes associate with breast cancer. Cancer Res. 64:8891-8900.

2003

Mishmar, D, E Ruiz-Pesini, P Golik, V Macaulay, AG Clark, et al.  2003. Natural selection shaped regional mitochondrial DNA variation in humans. Proc. Natl. Acad. Sci. USA 100:171-176.

Dermitzakis, ET, CM Bergman, and AG Clark.  2003.  Tracing the Evolutionary History of Drosophila Regulatory Regions with Models that Identify Transcription Factor Binding Sites. Mol Biol Evol.  20:703-714.

Lazzaro, BP and AG Clark.  2003.  Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster.  Mol. Biol. Evol. 20:914-923.

Carvalho, AB, MD Vibranovski, JW Carlson, SE Celniker, et al.  2003.  Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go?  Genetica 117:227-237.

Jones, B and AG Clark.  2003. Bayesian sperm competition estimates. Genetics 163:1193-1199.

Kroetz, DL, C Pauli-Magnus, CC Huang, M. Kawamoto, et al.  2003.  Sequence diversity and haplotype structure in the human MDR1 gene. Pharmacogenetics 13:481-494.

Leabman, MK, Huang, CC, DeYoung, J, Carlson, EJ, et al.  2003.  Natural variation in membrane transporter genes reveals evolutionary constraints.  Proc. Natl. Acad. Sci. USA 100:5896-5901.

Montooth, K, JH Marden and AG Clark.  2003. Mapping determinants of variation in energy metabolism, respiration and flight in Drosophila. Genetics 165:623-635.

Schwartz, R, Halldórsson, BV, Bafna, V, AG Clark, and S Istrail.  2003. Robustness of inference of haplotype block structure.  Jour. Comp. Biol. 10:13-19.

Matise, TC, R. Sachidanandam, J Kakol, AG Clark, et al.  2003.  A 3.9 cM resolution human SNP linkage map and screening set. Amer. J. Human Genet.73:271-284.

Clark, AG, R Nielsen, J Signorovitch, T Matise, et al.   2003.  Linkage disequilibrium and inference of population-level recombination at 538 sites across the human genome. Amer. J. Human Genet. 73:285-300.

Clark, AG.  2003. A slippery boundary.  Proc. Natl. Acad. Sci. USA 100:4971-4972.

Clark, AG.  2003. Finding genes underlying risk of complex disease by linkage disequilibrium mapping. Curr. Op. Genet. Devel. 13:296-302.

Clark, AG, Glanowski, S, Nielsen, R, Thomas, et al.  2003. Inferring non-neutral evolution from human-chimp-mouse orthologous gene trios. Science 302:1960-1963.

Zhang, J, WL Rowe, AG Clark and KH Buetow.  2003.  Genome-wide distribution of high frequency, completely mismatching SNP haplotype pairs observed to be common across human populations. Am. J. Hum. Genet. 73:1073-1081.

Clark, AG, S Glanowski, R Nielsen, P Thomas, et al.  2003. Positive selection in the human genome inferred from human-chimp-mouse orthologous gene alignments.  Cold Spr. Harbor Symp. Quant. Biol., 68:471-477.

2002

Civetta, A, H Waldrip-Dail, and AG Clark.  2002.  An introgression approach to mapping differences in mating success and sperm competitive ability in Drosophila simulans and D. sechellia.  Genet. Res. 79:65-74.

Weiss, KM and AG Clark.  2002. Linkage disequilibrium and the mapping of complex human traits.  Trends Genet. 18:19-24.

Dermitzakis, EM and AG Clark.  2002.  Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 19: 1114-1121.

Clark, AG. 2002.  Sperm competition and the maintenance of polymorphism. Heredity 88:148-153.

Fullerton, SM, KM Weiss, AG Clark, SL Taylor, et al.  2002.  Sequence polymorphism at the human Apolipoprotein AII gene (APOA2):  Unexpected deficit of variation in an African-American sample.  Human Genetics 111:75-87.

Leabman, MK, CC Huang, M Kawamoto, SJ Johns, et al.  2002.  Leabman, M.K. et al.  2002.  Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics 12:395-405.

Stengård, J, AG Clark, KM Weiss, S Kardia, et al.  2002.  Contributions of 18 additional DNA sequence variations in the gene coding for apolipoprotein E to explaining variation in quantitative measures of lipid metabolism.  Am. J. Hum. Genet. 71:501-517.

Schwartz, R, AG Clark, and S Istrail.  2002. Methods for inferring block-wise ancestral history from haploid sequences. Pp. 44-59 in Guigo, R. and Gusfield, D., eds., Algorithms in Bioinformatics: Lecture Notes in Computer Science 2452. Springer, Berlin.

Clark, AG.  2002. Malaria variorum.  Nature  418:283-285.

Holt, RA, G Subramanian, A Halpern, GG Sutton, et al. 2002. The genome sequence of the malaria mosquito, Anopheles gambiae.  Science 298:129-149.

Lazzaro, BP, BK Sceurman, SL Carney, and AG Clark.  2002.  fRFLP and fAFLP: A novel method of fluorescently post-labeling restriction digestions for medium-throughput genotyping. Biotechniques 33:539-546.

Clark, AG and SP Otto.  2002. Genomes and evolution:  Population genetics and molecular evolution of whole genomes.  Curr Opin Genet Dev. 12: 631-633.

2001

Dermitzakis, ET and AG Clark.  2001. Differential selection after duplication in mammalian developmental genes. Mol. Biol. Evol. 18:557-562.

Swanson, WJ, AG Clark, HM Waldrip-Dail, MF Wolfner and C F Aquadro.  2001.  Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc. Natl. Acad. Sci. 98:7375-7379.

Fullerton, SM, AB Carvalho, and AG Clark.  2001. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18:1139-1142.

Venter, JC, MD Adams, EW Myers, PW Li, et al.  2001. The sequence of the human genome. Science 291:1304-1351.

Tishkoff, SA, R Varkonyi, N Cahinhinan, S Abbes, et al.  2001.  Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance.  Science 293:455-462.

Subrahmanyan, L, MA Eberle, AG Clark, L Kruglyak, and DA Nickerson.  2001. Sequence Variation and Linkage Disequilibrium in the Human T-cell receptor beta (TCRB) Locus. Am. J. Hum. Genet.  69:381-395.

Clark, AG.  2001.  A lifetime’s struggle with the meaning of variation.  Review of Evolutionary Genetics: From Molecules to Morphology, R.S. Singh and C. Krimbas, eds.   Evolution 55:1492-1495.

Clark, AG.  2001.  The search for meaning in noncoding DNA.  Genome Res. 11:1319-1320.

Carvalho, AB, BA Dobo, MD Vibranovski, and AG Clark.  2001.  Identification of five new genes on the Y chromosome of Drosophila melanogaster.  Proc. Natl. Acad. Sci, USA 98: 13225-13230.

Lazzaro, BP and AG Clark.  2001.  Evidence for recurrent paralogous gene conversion and exceptional allelic divergence in the Attacin genes of Drosophila melanogaster.  Genetics 159: 659-671.

Rand, DM, AG Clark, and LM Kann. 2001. Sexually antagonistic cytonuclear fitness interactions in Drosophila melanogaster.  Genetics 159:173-187.

2000

Clark, AG.  2000.  Limits to prediction of phenotypes from knowledge of genotypes.  Evol. Biol. 32: 205-224.

Dermitzakis, ET, JP Masly, and AG Clark. 2000.  Non-Mendelian segregation of sex chromosomes in heterospecific Drosophila males.  Genetics 154:687-694.

Civetta, A and AG Clark. 2000.  Chromosomal effects on male and female components of sperm precedence in Drosophila.  Genet. Res. 75:143-151.

Templeton, AR, AG Clark, KM Weiss, DA Nickerson, et al. 2000. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am. J. Hum. Genet.  66:69-83.

Clark, AG, ET Dermitzakis, and A Civetta. 2000. Non-transitivity of sperm precedence in Drosophila. Evolution 54:1030-1035.

Prout, T and AG Clark.  2000.  Seminal fluid causes temporarily reduced egg hatch in previously-mated females. Proc. Roy. Soc. Lond. Series B. 267:201-203.

Clark, AG and A Civetta.  2000.  Protamine wars.  Nature 401:261-263.

Begun, DJ, P Whitley, B Todd, H Waldrip-Dail, and AG Clark.  2000. Molecular population genetics of male accessory gland proteins in Drosophila. Genetics 156:1879-1888.

Tishkoff, SA, AJ Pakstis, M Stoneking, JR Kidd, et al.  2000.  Microsatellite-Alu haplotype variation at the PLAT locus. Am. J. Hum. Genet.  67:901-925.

Nickerson, DA, SL Taylor, SM Fullerton, KM Weiss, AG Clark, et al.  2000.  Sequence Diversity and Large-scale Typing of SNPs in the Human Apolipoprotein E Gene. Genomic Research 10:1532-1545.

Fullerton, SM, AG Clark, KM Weiss, DA Nickerson, et al.  2000. Apolipoprotein E variation at the sequence haplotype level: Implications  for the origin and maintenance of a major human polymorphism. Am. J. Hum. Genet. 67:881-900.

Carvalho, AB, BP Lazzaro, and AG Clark.  2000.  Y chromosomal fertility factors kl-2 and kl-3 of D. melanogaster encode dynein heavy chain polypeptides. Proc. Natl. Acad. Sci. USA 97:13239-13244.

Civetta, A and AG Clark.  2000.  Correlated effects of sperm competition and post-mating female mortality. Proc. Natl. Acad. Sci. USA 97:13162-13165.

1999

Spencer, HG, AG Clark and MW Feldman. 1999.  Genetic conflicts and the evolutionary origin of genomic imprinting.  Trends Ecol. Evol. 14:197-201.

Harshman, LG, AA Hoffmann, and AG Clark. 1999. Selection for starvation resistance in Drosophila melanogaster: physiological correlates, enzyme activities and multiple stress responses. J. Evol. Biol. 12: 370-379.

Clark, AG, DJ Begun, and T Prout. 1999.  Female × male interactions in Drosophila sperm competition. Science 283:217-220.

Destro-Bisol, G, R Maviglia, A Caglià, I Boschi, et al. 1999.  Estimating European admixture in an African-Americans by using microsatellites and a microsatellite haplotype (CD4/Alu). Hum. Genet.104:149-157.

Rieder, M J, S Taylor, AG Clark, and DA Nickerson. 1999. Sequence variation in the human angiotensin converting enzyme.  Nature Genetics 22:59-62.

Carvalho, AB and AG Clark. 1999. Intron size and natural selection. Nature 401:344.

Clark, AG.  1999. Chips for chimps. Nature Genetics 22:119-120.

Clark, AG.  1999. The size distribution of homozygous segments in the human genome.  Am. J. Hum. Genet 65:1489-1492.

1998

Clark, AG.  1998. Inference of heterosis and epistasis in transposon-tagged Drosophila. Crop Sci. Soc. Pub. 25:89-97.

Clark, AG.  1998.  Mutation-selection balance with multiple alleles. Genetica 102:41-47.

Harshman, LG and AG Clark. 1998.  Inference of sperm competition from broods of field-caught Drosophila.  Evolution 52:1334-1341.

Spencer, H, MW Feldman, and AG Clark. 1998.  Genetic conflicts, multiple paternity and the evolution of genomic imprinting.  Genetics 148:893-904.

Tishkoff, S, KK Kidd, and AG Clark 1998.  Inferences of modern human origins from variation in CD4 haplotypes.  Proc. Trinational Workshop on Mol. Evol., Duke Univ. Publ., pp. 181-198.

Karafet, T, P de Knijff, E Wood, J Ragland, AG Clark, and MF Hammer. 1998.  Different patterns of variation at the X- and Y-linked microsatellite loci DXYS156X and DXYS156Y in human populations.  Hum. Biol. 70:979-992.

Clark, AG and DJ Begun. 1998.  Female genotypes affect sperm displacement in Drosophila. Genetics 149:1487-1493.

Clark, AG and CD Fucito. 1998.  Stress tolerance and metabolic response to stress in Drosophila melanogaster.  Heredity 81:514-527.

Dermitzakis, ET, AG Clark, C Batargias, A Magoulas, and E Zouros. 1998.  Negative covariance suggests mutation bias in a two-locus microsatellite system in the fish Sparus aurata. Genetics 150:1567-1575.

Nickerson, DA, SL Taylor, KM Weiss, AG Clark, et al.  1998.  DNA sequence diversity in a 9.7 kb region of the human lipoprotein lipase gene.  Natur. Genet. 19:233-240.

Clark, AG, KM Weiss, DA Nickerson, SL Taylor, et al. 1998.  Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63:595-612.

1997

Clark, AG.  1997.  Theory and Applications of RAPD-PCR: Mispriming.  pp. 221-229.  In:  Progress in Population Genetics and Human Evolution, IMA Symposium, ed. by S. Tavaré and P. Donnelly.

Clark, AG.  1997.  Estimating nucleotide divergence with RAPD data.  pp. 219-226 In Fingerprinting Methods Based on Arbitrarily Primed PCR, M.R. Micheli and R. Bova, eds., Springer-Verlag, Heidelberg.

Muse, SV, AG Clark, and GH Thomas. 1997. Comparisons of the nucleotide substitution process among repetitive segments of the alpha and beta spectrin genes.  J. Mol. Evol. 44:492-500.

Clark, AG and Y Zheng 1997. Dynamics of linkage disequilibrium in bacterial genomes undergoing transformation and/or conjugation. J. Evol. Biol. 10:663-676.

Clark, AG and L Wang. 1997.  Epistasis in measured genotypes: Drosophila P-element insertions. Genetics 147:157-163.

Thomas, GH, C Newbern, CC Korte, MA Bales, SV Muse, AG Clark, and DP Kiehart. 1997.  Intragenic duplication and divergence in the spectrin superfamily of proteins. Mol. Biol. Evol. 14:1285-1295.

Clark, AG.  1997. Stress and metabolic regulation in Drosophila. Pp. 117-132 in Environmental Stress, Adaptation and Evolution, R, Bijlsma and V. Loeschcke, eds., Birkhauser Verlag, Basel.

Clark, AG  and L Wang. 1997.  Molecular population genetics of Drosophila immune system genes. Genetics 147:713-724.

Clark, AG.  1997. Neutral behavior of shared polymorphism. Proc. Natl. Acad. Sci. USA 94:7730-7734.

Hartl, DL and AG Clark. 1997.  Principles of Population Genetics, third edition, Sinauer Associates, Sunderland, MA.

1996

Prout, T and AG Clark. 1996. Polymorphism in genes that influence sperm displacement. Genetics 144:401-408.

Clark, AG.  1996.  Population genetic aspects of gametophytic self-incompatibility.  Plant Species Biol. 11:13-22.

1995

Leicht, BG, SV Muse, M Hanczyc, and AG Clark. 1995.  Constraints on intron evolution in the gene encoding the myosin alkali light chain in Drosophila. Genetics 139:299-308.

Clark, AG, M Aguadé, T Prout, LG Harshman, and CH Langley. 1995.  Variation in sperm displacement and its association with accessory gland protein loci in Drosophila melanogaster. Genetics 139:189-201.

Clark, AG, L Wang, and T Hulleberg. 1995. P-element-induced variation in metabolic regulation in Drosophila.  Genetics 139:337-348.

Clark, AG, L Wang, and T Hulleberg. 1995.  Spontaneous mutation rate of modifiers of metabolism in Drosophila. Genetics 139:767-779.

Clark, AG and R Guadalupe. 1995.  Probing the evolution of senescence in Drosophila melanogaster with P-element tagging.  Genetica 96:225-234.

Wang, L and AG Clark. 1995. Physiological genetics of response to a high-sucrose diet by Drosophila melanogaster.  Biochem. Genet. 33:149-164.

Goldstein, DB and AG Clark. 1995.  Microsatellite variation in North American populations of Drosophila melanogaster.  Nuc. Acids. Res. 23:3882-3886.

Clark, AG, BG Leicht, and SV Muse. 1995.  Length variation and secondary structure of introns in the Mlc1 gene in six species of Drosophila. Mol. Biol. Evol. 13:471-482.

Clark, AG, JF Hamilton, and GK Chambers. 1995.  Inference of population subdivision from the VNTR distributions of New Zealanders. Genetica 96:37-49.

1994

Clark, AG and TH Kao.  1994.  Self‑incompatibility: theoretical concepts and evolution. In: Genetic Control of Self‑Incompatibility and Reproductive Development in Flowering Plants, pp. 220-242, EG Williams, AE Clarke and RB Knox, eds. Kluwer Academic Publishers, Dordrecht, Netherlands.

Clark, AG, S Silveria, W Meyers, and CH Langley. 1994.  Nature Screen: An efficient method for screening natural populations of Drosophila for targeted P-element insertions.  Proc. Natl. Acad. Sci. USA 91:719-722.

Clark, AG.  1994.  Invasion and maintenance of a gene duplication.  Proc. Natl. Acad. Sci. USA. 91:2950-2954.

Clark, AG. 1994.  A neutrality test for continuous characters based on levels of intraspecific variation and interspecific divergence.  pp. 101-111, In: Non-Neutral Evolution: Theories and Molecular Data, B. Golding, ed., Chapman Hall.

Clark, AG  and L Wang. 1994.  Comparative evolutionary analysis of metabolism in nine species of Drosophila.  Evolution 48:1230-1243.

Clark, AG.  1994. Mutation-selection balance and the evolution of senescence. In: Genetics and Evolution of Aging.  MR Rose and CE Finch, eds. Kluwer Academic.

Clark, AG.  1994.  Molecular population genetics of gametophytic self-incompatibility alleles. Cur. Topics Plant Phys. 12:193-211.

1993

Leicht, BG, EMS Lyckegaard, CM Benedict, and AG Clark. 1993.  Conservation of alternative splicing and genomic organization of the myosin light chain (Mlc1) gene among Drosophila species.  Mol. Biol. Evol. 10:769-790.

Clark, AG and CMS Lanigan. 1993.  Prospects for estimating nucleotide divergence with RAPDs. Mol. Biol. Evol. 10:1096-1111.

1992

Clark, AG and TS Whittam.  1992.  Sequencing errors and molecular evolutionary analysis.  Mol. Biol. Evol. 9:744-752.

Clark, AG.  1992.  Evolutionary inferences from molecular characterization of self‑incompatibility alleles.  In Mechanisms of Molecular Evolution. N Takahata and AG  Clark, eds., Japan Society Press/ Sinauer Associates, Sunderland, MA.

1991

Clark, AG, FM Szumski, and EMS Lyckegaard.  1991.  Population genetics of the Y chromosome of Drosophila melanogaster:  rDNA variation and phenotypic correlates.  Genet. Res. 58:7-13.

Lyckegaard, EMS and AG Clark.  1991.  Evolution of ribosomal RNA gene copy number on the sex chromosomes of Drosophila melanogaster.  Mol. Biol. Evol. 8:458-474.

Clark, AG. 1991.  Mutation-selection balance and metabolic control theory.  Genetics 129:909-923.

Clark, AG and TH Kao.  1991.  Excess nonsynonymous substitution at shared polymorphic sites among self-incompatibility alleles of Solanaceae.  Proc. Natl. Acad. Sci. USA, 88:9823-9827.

Merriwether, DA, AG Clark, SW Ballinger, TG Schurr, H Soodyall, T Jenkins, ST Sherry and DC Wallace.  1991.  The structure of human mitochondrial DNA variation.  Jour. Mol. Evol. 33:543-555.

Clark, AG and RK Koehn.  1991.  Enzymes and Adaptation. pp. 193-228, in Genes in  Ecology, R.J. Berry, T.J. Crawford, and G.M. Hewett, eds., Blackwell Scientific Publications, Oxford.

1990

Barton, NH and AG Clark.  1990.  Population structure and process in evolution.  Pp. 115-173.  In: Population Biology:  Ecological and Evolutionary Viewpoints, K. Wöhrmann and S. Jain, editors, Springer-Verlag, Berlin.

Clark, AG.  1990.  Genetic components of variation in energy storage in Drosophila melanogaster.  Evolution  44:637-650.

Clark, AG.  1990.  Inference of haplotypes from PCR amplified samples of diploid populations.  Mol. Biol. Evol. 7:111-122.

Clark, AG.  1990.  Two tests of Y chromosomal variation in male fertility of Drosophila melanogaster.  Genetics 125:527-534.

Clark, AG, FM Szumski, KA Bell, LE Keith, S Houtz, and DA Merriwether.  1990.  Direct and correlated responses to artificial selection on lipid and glycogen contents in Drosophila melanogaster.  Genetical Research 56:49-56.

Clark, AG and EMS Lyckegaard.  1990.  Two neutrality tests of Y-linked rDNA variation in Drosophila melanogaster.  Evolution 44:2106-2112.

Selander, RK, AG Clark, and TS Whittam.  1990.  Evolution at the Molecular Level, (eds.) Sinauer Associates, Inc. Sunderland, MA.

Krane, DE, AG. Clark, JF Cheng, and RC Hardison.  1990.  Subfamily relationships and clustering of rabbit C repeats.  Mol. Biol. Evol. 8:1-30.

Ioerger, TR, AG Clark, and TH Kao.  1990.  Polymorphism at the self-incompatibility locus in Solanaceae predates speciation.  Proc. Natl. Acad. Sci.  USA, 87:9732-9735.

Clark, AG.  1990.  Review of Population Biology of Genes and Molecules.  edited by N. Takahata and J. Crow, Baifukan Press, Tokyo.  Mol. Biol. Evol. 8:392-395.

1989

Hartl, DL and AG Clark.  1989.  Principles of Population Genetics, Second edition, Sinauer Associates, Sunderland, MA.

Lyckegaard, EMS and AG Clark.  1989.  Ribosomal DNA and Stellate gene copy number variation on the Y chromosome of Drosophila melanogaster.  Proc. Natl. Acad. Sci. USA 86:1944-1948.

Clark, AG and LE Keith.  1989.  Rapid enzyme kinetic assays of individual Drosophila and comparisons of field-caught Drosophila melanogaster and Drosophila simulans.  Biochem. Genet. 27:263-278.

Clark, AG.  1989.  Causes and consequences of variation in lipid and carbohydrate storage in Drosophila.  Genetics 123:131-144.

1988

Clark, AG and EMS Lyckegaard.  1988.  Natural selection with nuclear and cytoplasmic transmission.  III.  Mitochondrial DNA variation and analyses of segregation and mtDNA in Drosophila melanogaster.  Genetics 118:471-482.

Clark, AG.  1988.  Review of Nei’s Molecular Evolutionary Genetics.  Mol. Biol. Evol. 5:109.112.

Clark, AG.  1988.  Deterministic theory of  heteroplasmy.  Evolution 42:621-626.

Clark, AG  1988.  The evolution of the Y chromosome with X-Y recombination.  Genetics 119:711-720.

Clark, AG and LE Keith.  1988.  Variation among extracted lines of Drosophila melanogaster in triacylglycerol and carbohydrate storage.  Genetics 119:595-607.

Hughes, D and AG Clark.  1988.  Analysis of the genetic structure of life history of Drosophila melanogaster using recombinant extracted lines.  Evolution 42:1309-1320.

1987

Clark, AG.  1987.  Variation in Y chromosome segregation in natural populations of Drosophila melanogaster.  Genetics 115:143-151.

Clark, AG.  1987.  A test of multilocus interaction in Drosophila melanogaster.  Am. Nat. 130:283-299.

Clark, AG.  1987.  The use of multiple restriction fragment length polymorphisms in prenatal risk estimation.  II.  Conditional risk distribution.  Human Heredity 37:41-53.

Clark, AG.  1987.  Senescence and the genetic correlation hang-up.  Am. Nat. 127:932-940.

Clark, AG.  1987.  Natural selection and Y-linked polymorphism.  Genetics 115:569-577.

Clark, AG.  1987.  Genetic correlation;  The quantitative genetic basis of an evolutionary constraint.  pp. 25-45.  In: Genetic Constraints on Adaptive Evolution, edited by V. Loeschcke.  (ed.) Springer-Verlag, Berlin.

Clark, AG.  1987.   Neutrality tests of highly polymorphic RFLPs.  Am. J. Hum. Genetics 41:948-958.

1986

Clark, AG.  1986.  Partitioning genetic variation in viability among lines of Drosophila.  Am. Nat. 128:263-271.

Clark, AG and MW Feldman.  1986.  A numerical simulation of the one locus multiple allele fertility model.  Genetics 113:161-176.

Teague, MD, AG Clark, and WW Doane.  1986.  Developmental analysis of lipids from wild-type and adipose-60 mutants of Drosophila melanogaster.  Jour. Exp. Zool. 240:95-104.

Whittam, TS, AG Clark, M Stoneking, R Cann and AC Wilson.  1986.  Allelic variation in human mitochondrial genes based on patterns of restriction site polymorphisms.  Proc. Nat. Acad. Sci. USA 83:9611-9615.

1985

Clark, AG.  1985.  The use of multiple restriction fragment length polymorphisms in prenatal risk estimation.  I.  X-linked diseases.  Am. Jour. Human Genetics 37:60-72

Clark, AG and W Gellman.  1985.  A rapid spectrophotometric assay of triglycerides in Drosophila.  Dros. Inf. Serv. 61:190.

Clark, AG.  1985.  Natural selection with nuclear and cytoplasmic transmission:  II.  Experimental assessment with Drosophila.  Genetics 111:97-112.

1984

Clark, AG and WW Doane.  1984.  Interactions between the Amylase and adipose chromosomal regions of Drosophila melanogaster.  Evolution 38:957-982.

Turelli, M, AG Clark and JB Spofford.  1984.  Linkage data supporting a mathematical explanation for some empirical cis-trans effects.  Heredity 52:145-147.

Doane, WW and AG Clark.  1984.  A revised map location for the narrow locus of Drosophila melanogaster.  Dros. Inf. Serv. 60:234.

Markow, TA and AG Clark.  1984.  Correlated responses to phototactic selection.  Behavior Genetics 14:279-293.

Clark, AG and J Bundgaard.  1984.  Selection components in background replacement lines of Drosophila melanogaster.  Genetics 108:181-200.

Clark, AG.  1984.  Natural selection with nuclear and cytoplasmic selection.  I.  A deterministic model.  Genetics 107:679-701.

Pre-1984

Clark, AG and WW Doane.  1983.  Desiccation tolerance of the adipose-60 mutant of Drosophila melanogaster.  Hereditas 99:165-175.

Clark, AG, MW Feldman, and FB Christiansen.  1981.  The estimation of epistasis in components of fitness in experimental populations of Drosophila melanogaster.  I.  A two-stage maximum likelihood model.  Heredity 46:25-50.

Clark, AG and MW Feldman.  1981.  The estimation of epistasis in components of fitness in experimental populations of Drosophila melanogaster.  II. Assessment of meiotic drive, viability, fecundity and sexual selection.  Heredity 46:51-81.

Clark, AG and MW Feldman.  1981.  Disequilibrium between linked inversions:  An alternative hypothesis.  Heredity 46:83-94.

Clark, AG and MW Feldman.  1981.  Density dependent fertility selection in experimental populations of Drosophila melanogaster.  Genetics 98:849-869.

Clark, AG.  1979.  The effects of interspecific competition on the dynamics of a polymorphism in an experimental population of Drosophila melanogaster.  Genetics 92:1315-1328.

DeAngelis, DL, SW Christensen and AG Clark.  1977.  Responses of a fish population model to young-of-the-year mortality.  Jour. Fish. Res. Board Canada 34:2124-2132.

Christensen, SW, DL DeAngelis, and AG Clark.  1977.  Development of a stock-progeny model for assessing power-plant effects on fish populations.  In: Assessing Power-Plant Induced Mortality of Fish Populations, Oak Ridge National Lab, Pergamon Press, New York.  pp. 196-226.