Click here to view Dr. Clark's Pubmed listing.

 

2007

Hartl, D. L. and A. G. 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, A.M., A.G. Clark, E. Boerwinkle, C.F. Sing, and J.E. Hixson. 2007.  Assessing the accuracy of statistical haplotype inference with sequence data of known phase.   Genet. Epi. 31:659-671.

Jørgensen, F.G., M.H. Schierup and A.G. 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.

Sainudiin, R., A.G. Clark, and R.T. Durrett. 2007.  Simple models of genomic variation in human SNP diversity. BMC Genomics. 8:146.

Fiumera, A., B.L. Dumont, and A.G. Clark. 2007. Associations between sperm competition and natural variation in male reproductive genes on the third chromosome of Drosophila melanogaster.  Genetics 176:1245-1260.

McGraw, L.A., A.C. Fiumera, M. Ramakrishnan, S. Madhavarapu, A. G. Clark and M. F. Wolfner. 2007. Effects of the larval rearing environment on post-copulatory traits in Drosophila melanogaster.  Biol Letters, Aug 21; [Epub ahead of print].

Williamson, S.H., M. J. Hubisz, A. G. Clark, B. A. Payseur, C. D. Bustamante, R. Nielsen. 2007. Localizing recent adaptive evolution in the human genome.  PLoS Genet. 3(6):e90 [Epub ahead of print].

Kininis, M., B.S. Chen, A.G. Diehl, G.D. Isaacs, T. Zhang, A.C. Siepel, A.G. Clark, and W.L. 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.  

Clark, A.G. and J. Li. 2007.  Conjuring SNPs to detect associations.   Nat. Genetics 39:815-816.

Ma, X., Y. Liu, B. B. Gowen, E. A. Graviss, A. G. Clark, and J. M. Musser. 2007.  Full-Exon Sequencing Reveals Toll-like Receptor Variants Contribute to Human Susceptibility to Tuberculosis Disease.  PLoS One, in press.

Schlenke, T.A., J. Morales, S. Govind, and A.G. Clark. 2007. Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster. PLoS Pathogens 3(10):e158 [epub Oct 26].

Huntley, M.A. and A.G. Clark. 2007.   Evolutionary Analysis of Amino Acid Repeats Across the Genomes of 12 Drosophila Species.  Mol Biol Evol.  Jul 19; [Epub ahead of print]

Nielsen, N., I. Hellmann, M. Hubisz, C. Bustamante, and A.G. Clark. 2007.  Recent and ongoing selection in the human genome.  Nat. Reviews Genetics 8:1-12.

Olshen, A.B., B. Gold, K.E. Lohmueller, J.P. Stuewing, J. Satagopan,  S.A. Stefanov, E. Eskin, T. Kirchhoff, J. A. Lautenberger, E. Friedman, L. Norton, N. Ellis, A. Viale, C.S. Lee, P. I. Borgen, A. G. Clark, K. Offit, and J. Boyd. 2007. Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping.  Human Genetics, in press.

Sackton, T.B., B.P. Lazzaro, T.A. Schlenke, J.D. Evans, D. Hultmark and A.G. Clark. 2007.  The evolution of the innate immune system in Drosophila.  Nature Genetics, in press. 

 

Pollard, K.S., D. Serre, X. Wang, T.J. Hudson, A.G. Clark and K. Frazer. 2007 Novel imprinted genes identified through a genome-wide study of differential allelic expression. Human Genetics, in press.

Drosophila 12 Genomes Consortium. 2007a. Evolution of genes and genomes on the Drosophila phylogeny.  Nature, in press.

Drosophila 12 Genomes Consortium. 2007b. Comprehensive discovery of functional elements in 12 fly genomes using evolutionary signatures.  Nature, in press.

2006

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

Fiumera, A.C., B.L. Dumont and A.G. 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.

Bachtrog, D., K. Thornton, A.G. 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, G.M., S. Flibotte, P.I. Missirlis, M.A. Marra, S. Jones, K. Thornton, A.G. Clark and R.A. 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, T.J., A.G. Clark, 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 3:000-000.

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

Brown, C.M., T.J. Rea, S.C. Hamon, J.E. Hixson, E. Boerwinkle, A.G. Clark and C.F. 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, B.A., A.G. Clark, J. Hixson, E. Boerwinkle, and C.F. 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, P.J., B.K. Haerum, and A.G. 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 A.G. Clark. 2006. Membrane lipid physiology and toxin catabolism underlie ethanol and acetic acid tolerance in Drosophila melanogaster. Jour. Exp. Biol. 209: 3837-3850.

Spencer, H.G. and A.G. 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., S. K. Behura, S. H. Berlocher, A. G. Clark, J. S. Johnston, W. S. Sheppard, D. R. Smith, A. V. Suarez, D. Weaver, N. D. Tsutsui. 2006. Thrice out of Africa: Ancient and modern expansions of the honey bee, Apis mellifera. Science 314:642-645.

Weinstock, G., G. 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, B.P., T.B. Sackton, and A.G. Clark. 2006.  Genetic variation in Drosophila melanogaster resistance to infection: a comparison across bacteria.  Genetics 174:1539-1554.

Klos, K.L.E., C.F. Sing, E. Boerwinkle, S. Hamon, T.J. Rea, A.G. Clark, M. Fornage, and J.E. 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

Clark, A.G., M.J. Hubisz, C.D. Bustamante, S. Williamson, and R. Nielsen. 2005. Ascertainment bias in genome-wide human polymorphism studies.  Genome Res. 15:1496-1502.

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

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

Rodin, A, T. H. Mosley., A. G. Clark., C. F. 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.

 

Nielsen, R., A. G. Clark, C. Bustamante, S. Glanowski, M. J. Hubisz, D. M. Tanenbaum, D. Civello, T. J. White, J. J. Sninsky, M. D. Adams, and M. Cargill. 2005.  A scan for positively selected genes in the genomes of humans and chimpanzees. PLOS Biology 3(6):e170 [Epub ahead of print]

Richards, S., Y. Liu, B. R. Bettencourt, P. Hradecky, S. Letovsky, R. Nielsen, K. Thornton, M. J. Todd, et al. 2005.  Comparative sequencing and analysis of Drosophila pseudoobscura.  Genome Res. 15:1-18.

Fiumera, A., B.L. DuMont and A.G. 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, A.G. Clark, and D. Zhang. 2005.  Mapping multiple quantitative trait loci by Bayesian classification.  Genetics   169:2305-2318.

De la Vega, F., H Isaac, A Collins, C R. Scafe, B V. Halldórsson, X Su, R A. Lippert, Y Wang, M Laig-Webster, R. T. Koehler, J S. Ziegle, L T. Wogan, J F. Stevens, K M. Leinen, S J. Olson, K J. Guegler, X You, L H. Xu, H G. Hemken, F Kalush, M Itakura, S J. O’Brien, A. G. Clark, S Istrail, M.W. Hunkapiller, E G. Spier, and D. A. Gilbert. 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, Hamon S, Clark AG, Boerwinkle E, Liu K, Sing CF. 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 A.G. Clark. 2005.  Harvesting medical information from our family tree.  Science 307:1052-1053.

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

Mueller, J.L., K. Ravi Ram, L.A. McGraw, M.C. Bloch Qazi, E.D. Siggia, A.G. Clark, C.F. Aquadro, M.F. Wolfner.  2005.  Cross-species comparison of Drosophila male accessory gland protein genes. Genetics 171:131-143.

Bustamante, C.D., R. Nielsen, A. Fledel-Alon, S. Williamson, M.T. Hubisz, S. Glanowski, D. M. Tanenbaum, T. J. White, J. J. Sninsky, M. D. Adams, M. Cargill, and A.G. Clark.  2005.  Natural selection on protein coding genes in the human genome. Nature 437:1153-1157.

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

Landry, C.R., P.J. Wittkopp, J.M. Ranz, C.H. Taubes, A.G. Clark and D.L. Hartl. 2005.  Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of  Drosophila. Genetics 171:1813-1822

Stranger, B.E., M.S. Forrest, A.G. Clark, S. Deutsch, R. Lyle, S. Hunt, B. Kahl, S.E. Antonarakis, S. Tavaré, P. Deloukas and E.T. Dermitzakis. 2005.  Genome-wide associations of gene expression variation in humans. PLoS Biology ePub 1:e78.

2004

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

Chookajorn, T., A. Kachroo, D. R. Ripoll, A. G. Clark, and J. B. Nasrallah. 2004.  Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand.  Proc. Natl. Acad. Sci. USA 101:911-917.

Spencer, H.G., M.W. Feldman, A.G. Clark, and A.E. 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., J.S.F. Barker, J. Frydenberg, and A.G. 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, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR, Flanigan MJ, Edwards NJ, Bolanos R, Fasulo D, Halldorsson BV, Hannenhalli S, Turner R, Yooseph S, Lu F, Nusskern DR, Shue BC, Zheng XH, Zhong F, Delcher AL, Huson DH, Kravitz SA, Mouchard L, Reinert K, Remington KA, Clark AG, Waterman MS, Eichler EE, Adams MD, Hunkapiller MW, Myers EW, Venter JC. 2004.  Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci USA 101:1916-1921.

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

Fullerton, S.M., A. V. Buchanan, V. Sonpar,  J. Stengård,  E. Boerwinkle, K. M. Weiss, A. G. Clark, and D. A. 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, P.J., B.K. Haerum, and A.G. Clark. 2004.  Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.

McGraw, L.A., G.C. Gibson, A. G. Clark, and M. F. Wolfner.  2004.  Genes regulated by mating, sperm or seminal proteins in mated female Drosophila melanogaster.  Current Biology 14:1509-1514

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

Clark, A.G., E.T. 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, S.C., Stengård, J., Clark, A.G., Salomaa, V., Boerwinkle, E. and Sing, C.F. 2004.  Evidence for non-additivity of single nucleotide polymorphism effects within the Apolipoprotein E gene. Ann Hum Genet. 68:521-535.

Nielsen, R., M.J. Hubisz, and A.G. Clark. 2004. Reconstituting the frequency spectrum of ascertained SNP data. Genetics 168:2373-2382.

Gold, B., F. Kalush, J. Bergeron, K. Scott, N. Mitra, K. Wilson, N. Ellis, H. Huang , M. Chen, R. Lippert, B. Halldorson, B. Woodworth, T. White,  A.G. Clark, F. Parl, S. Broder, M. Dean and K. Offit. 2004. Estrogen receptor genotypes and haplotypes associate with breast cancer. Cancer Res. 64:8891-8900.

2003

Clark, A.G., S. Glanowski, R. Nielsen, P. Thomas, A. Kejariwal, M.J. Todd, D.M. Tanenbaum, D. Civello, F. Lu, B. Murphy, S. Ferriera, G. Wang, X. Zheng, T.J. White, J.J. Sninsky, M.D. Adams, and M. Cargill. 2003. Positive selection in the human genome inferred from human-chimp-mouse orthologous gene alignments.  Cold Spr. Harbor Symp. Quant. Biol., 68:471-477.

Carvalho, A.B., M. D. Vibranovski, J. W. Carlson, S. E. Celniker, R. A. Hoskins, G. M. Rubin, G. G. Sutton, E. W. Myers, M. D. Adams and A. G. Clark.  2003.  Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go?  Genetica 117:227-237.

 

Mishmar, D., E. Ruiz-Pesini, P. Golik, V. Macaulay, A.G. Clark, S. Hosseini, M. Brandon, K. Easley, E. Chen, M. D. Brown, R.I. Sukernik, A. Olckers and D. C. Wallace. 2003. Natural selection shaped regional mitochondrial DNA variation in humans. Proc. Natl. Acad. Sci. USA 100:171-176.

 

Dermitzakis, E.T., C.M. Bergman, and A.G. 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, B.P. and A.G. Clark. 2003.  Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster.  Mol. Biol. Evol. 20:914-923.

 

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

Kroetz, D. L., Pauli-Magnus, C., C., C.C. Huang, M. Kawamoto, S.J. Johns, D. Stryke, T.E. Ferrin, J. DeYoung, T. Taylor, E. Carlson, I. Herskowitz, K.M. Giacomini, and A.G. Clark. 2003.  Sequence diversity and haplotype structure in the human MDR1 gene. Pharmacogenetics 13:481-494.

Leabman, M.K., Huang, C.C., DeYoung, J., Carlson, E.J., Taylor, T., de la Cruz, M., Johns, S.J., Stryke, D., Kawamoto, M., Urban, T.J., Kroetz, D.L., Ferrin, T.E., Clark, A.G., Risch, N., Herskowitz, I., Kathleen M., and Giacomini, K.M.  2003.  Natural variation in membrane transporter genes reveals evolutionary constraints.  Proc. Natl. Acad. Sci. USA 100:5896-5901.

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

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

Matise, T.C., R. Sachidanandam, J. Kakol, A.G. Clark, L. Kruglyak, E. Wijsman, S. Buyske, B. Chui, P. Cohen, C. de Toma, M. Ehm, S. Glanowski, C. He, J. Heil, I. McMullen, M. A. Pericak-Vance, L. Stein, M. Wagner, J. Winick, E. S. Winn-Deen, A. F. Wilson, H. M. Cann, E.  Lai, A.  L. Holden. 2003.  A  3.9 cM resolution human SNP linkage map and screening set. Amer. J. Human Genet.73:271-284.

Clark, A.G., R. Nielsen, J. Signorovitch, T. Matise, S. Glanowski, J. Heil, E. Winn-Deen, A. Holden and E. Lai.   2003.  Linkage disequilibrium and inference of population-level recombination at 538 sites across the human genome. Amer. J. Human Genet. 73:285-300.

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

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

Clark, A.G., Glanowski, S., Nielsen, R., Thomas, P.D., Kejariwal, A., Todd, M.A., Tanenbaum, D.M., Civello, D., Lu, F., Murphy, B., Ferriera, S., Wang, G., Zheng, X., White, T.J., Sninsky, J.J., Adams, M.D., and Cargill, M. 2003. Inferring non-neutral evolution from human-chimp-mouse orthologous gene trios. Science 302:1960-1963.

Zhang, J., W.L. Rowe, A.G. Clark and K.H. 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.

2002

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

 

Civetta, A., H. Waldrip-Dail, and A.G. 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, K.M. and A.G. Clark. 2002. Linkage disequilibrium and the mapping of complex human traits.  Trends Genet. 18:19-24.

 

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

 

Fullerton, S.M., K.M. Weiss, A.G. Clark, S.L.  Taylor, J. Stengård, E. Boerwinkle, and D. A. Nickerson. 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, M. K., C. C. Huang, M. Kawamoto, S. J. Johns, D. Stryke, T. E. Ferrin, J. DeYoung, T. Taylor,   A. G. Clark, I. Herskowitz, K. M. Giacomini. 2002.  Leabman, M.K. et al.  2002.  Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics 12:395-405.

 

Stengård, J, A. G. Clark, K. M. Weiss, S. Kardia, D. A. Nickerson, V. Salomaa, C. Ehnholm, E. Boerwinkle and C. F. Sing. 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., A.G. 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, A.G. 2002. Malaria variorum.  Nature  418:283-285.

Holt, R.A., G. Subramanian, A. Halpern, G.G. Sutton, R. Charlab, D.R. Nusskern, P. Wincker, A.G. Clark, et al. 2002. The genome sequence of the malaria mosquito, Anopheles gambiae.  Science 298:129-149.

Lazzaro, B.P., B. K. Sceurman, S. L. Carney, and A.G. Clark. 2002.  fRFLP and fAFLP: A novel method of fluorescently post-labeling restriction digestions for medium-throughput genotyping. Biotechniques 33:539-546.

Clark, A.G. and S.P. Otto. 2002. Genomes and evolution:  Population genetics and molecular evolution of whole genomes.  Curr Opin Genet Dev. 12: 631-633.

2001

Dermitzakis, E.T. and A.G. Clark. 2001. Differential selection after duplication in mammalian developmental genes. Mol. Biol. Evol. 18:557-562.

 

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

 

Swanson, W.J., A. G. Clark, H. M. Waldrip-Dail, M. F. 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, S. M., A. B. Carvalho, and A. G. Clark. 2001. Local rates of recombination are positively correlated with GC content in the human genome. Mol. Biol. Evol. 18:1139-1142.

 

Venter, J. C. et al. 2001. The sequence of the human genome. Science 291:1304-1351.

 

Tishkoff, S.A., R. Varkonyi, N. Cahinhinan, S. Abbes, G. Argyropolous, G. Destro-Bisol, A. Drousiotou, B. Dangerfield, G. Lefranc, J. Loiselet, A. Piro, M. Stoneking, A. Tagarelli, G. Tagarelli, E. Touma, S. M. Williams, A. G. Clark. 2001.  Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance.  Science 293:455-462.

 

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

 

Clark, A.G. 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.

 

Carvalho, A. B., B. A. Dobo, M. D. Vibranovski, and A. G. Clark. 2001.  Identification of five new genes on the Y chromosome of Drosophila melanogaster.  Proc. Natl. Acad. Sci, USA 98: 13225-13230.

 

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

 

Rand, D.M., A.G. Clark, and L.M. Kann. 2001. Sexually antagonistic cytonuclear fitness interactions in Drosophila melanogaster.  Genetics 159:173-187.

 

2000

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

 

Dermitzakis, E. T., J. P. Masly, and A. G. Clark. 2000.  Non-Mendelian segregation of sex chromosomes in heterospecific Drosophila males.  Genetics  154:687-694.

 

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

 

Templeton, A. R., A. G. Clark, K. M. Weiss, D. A. Nickerson, J. Stengård, E. Boerwinkle, and C.F. Sing. 2000. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am. J. Hum. Genet 66:69-83.

 

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

 

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

 

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

 

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

 

Tishkoff, S.A., A.J. Pakstis, M. Stoneking, J.R. Kidd, G. Destro-Bisol, A. Sanjantilla, A. Deinard, G. Sirugo, T. Jenkins, K.K. Kidd, and A.G. Clark. 2000.  Microsatellite-Alu haplotype variation at the PLAT locus. Am. J. Hum. Genet. 67:901-925.

 

Nickerson, D.A., S. L.Taylor, S. M. Fullerton, K. M. Weiss, A. G. Clark, J. Stengård, E. Boerwinkle, and C. F. Sing^.   2000.  Sequence Diversity and Large-scale Typing of SNPs in the Human Apolipoprotein E Gene. Genomic Research 10:1532-1545.

 

Fullerton, S.M., A.G. Clark, K.M. Weiss, D. A. Nickerson, S. L. Taylor, J. Stengård, V. Salomaa, E. Vartiainen, M. Perola, E. Boerwinkle and C. F. Sing. 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, A.B., B.P. Lazzaro, and A.G. 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 A.G. Clark. 2000.  Correlated effects of sperm competition and post-mating female mortality. Proc. Natl. Acad. Sci. USA 97:13162-13165.

 

1999

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

 

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

 

Spencer, H.G., A.G. Clark and M.W. Feldman. 1999.  Genetic conflicts and the evolutionary origin of genomic imprinting.  Trends Ecol. Evol. 14:197-201.

 

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

 

Clark, A.G., D.J. 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, G. Spedini, V. Pascali , A. Clark, and S. Tishkoff.  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, A. G. Clark, and D. A. Nickerson. 1999. Sequence variation in the human angiotensin converting enzyme.  Nature Genetics 22:59-62.

 

Carvalho, A.B. and A.G. Clark. 1999. Intron size and natural selection. Nature 401:344.

 

1998

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

 

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

 

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

 

Spencer, H., M. W. Feldman, and A. G. Clark. 1998.  Genetic conflicts, multiple paternity and the evolution of genomic imprinting.  Genetics 148:893-904.

 

Tishkoff, S., K. K. Kidd, and A. G. 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, A. G. Clark, and M. F. 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, A. G. and D. J. Begun. 1998.  Female genotypes affect sperm displacement in Drosophila. Genetics 149:1487-1493.

 

Clark, A.G. and C.D. Fucito. 1998.  Stress tolerance and metabolic response to stress in Drosophila melanogaster.  Heredity 81:514-527.

 

Dermitzakis, E.T., A.G. 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, D.A., S.L. Taylor, K.M. Weiss, A.G. Clark, T.G. Hutchinson, J. Stengård, V. Salomaa, E. Vartiainen, E. Boerwinkle, & C.F. Sing.  1998.  DNA sequence diversity in a 9.7 kb region of the human lipoprotein lipase gene.  Natur. Genet. 19:233-240.

 

Clark, A.G., K.M. Weiss, D.A. Nickerson, S.L. Taylor, A. Buchanan, J. Stengård, V. Salomaa, E. Vartiainen, M. Perola, E. Boerwinkle and C. F. Sing. 1998.  Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63:595-612.

 

1997

Hartl, D.L. and A.G. Clark 1997.   Principles of Population Genetics.    Third edition.  Sinauer and Associates, Sunderland, MA.

 

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

 

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

 

Thomas, G. H., C. Newbern, C. C. Korte, M.A. Bales, S.V. Muse, A.G. Clark, and D.P. Kiehart. 1997.  Intragenic duplication and divergence in the spectrin superfamily of proteins. Mol. Biol. Evol. 14:1285-1295.

 

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

 

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

 

1996

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

 

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

 

1995

Leicht, B.G., S.V. Muse, M. Hanczyc, and A.G. Clark. 1995.  Constraints on intron evolution in the gene encoding the myosin alkali light chain in Drosophila. Genetics 139:299-308.

 

Clark, A.G., M. Aguadé, T. Prout, L.G. Harshman, and C.H. Langley. 1995.  Variation in sperm displacement and its association with accessory gland protein loci in Drosophila melanogaster. Genetics 139:189-201.

 

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

 

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

 

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

 

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

 

Goldstein, D.B. and A.G. Clark. 1995.  Microsatellite variation in North American populations of Drosophila melanogaster.  Nuc. Acids. Res. 23:3882-3886.

 

Clark, A.G., B.G. Leicht, and S.V. 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, A.G., J.F. Hamilton, and G.K. Chambers. 1995.  Inference of population subdivision from the VNTR distributions of New Zealanders. Genetica 96:37-49.

 

1994

Clark, A.G. and T.‑h. Kao.  1994.  Self‑incompatibility: theoretical concepts and evolution. In: Genetic Control of Self‑Incompatibility and Reproductive Development in Flowering Plants, pp. 220-242, E.G. Williams, A.E. Clarke and R.B. Knox, eds. Kluwer Academic Publishers, Dordrecht, Netherlands.  

 

Clark, A.G., S. Silveria, W. Meyers, and C.H. 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, A.G.  1994.  Invasion and maintenance of a gene duplication.  Proc. Natl. Acad. Sci. USA. 91:2950-2954.

 

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

 

Clark, A.G. 1994. Mutation-selection balance and the evolution of senescence. In: Genetics and Evolution of Aging, M.R. Rose and C.E. Finch, eds. Kluwer Academic.

 

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

 

1993

Leicht, B.G., E.M.S. Lyckegaard, C.M. Benedict, and A.G. 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, A.G. and C.M.S. Lanigan. 1993.  Prospects for estimating nucleotide divergence with RAPDs. Mol. Biol. Evol. 10:1096-1111.

 

1992

Clark, A.G., and T.S. Whittam.  1992.  Sequencing errors and molecular evolutionary analysis.  Mol. Biol. Evol. 9:744-752.

 

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

 

1991

Clark, A. G., F. M. Szumski, and E. M. S. Lyckegaard.  1991.  Population genetics of the Y chromosome of Drosophila melanogaster:  rDNA variation and phenotypic correlates.  Genet. Res. 58:7-13.

 

Lyckegaard, E. M. S. and A. G. Clark.  1991.  Evolution of ribosomal RNA gene copy number on the sex chromosomes of Drosophila melanogaster.  Mol. Biol. Evol. 8:458-474.

 

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

 

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

 

Merriwether, D. A., A. G. Clark, S. W. Ballinger, T. G. Schurr, H. Soodyall, T. Jenkins, S. T. Sherry and D. C. Wallace.  1991.  The structure of human mitochondrial DNA variation.  Jour. Mol. Evol. 33:543-555.

 

Clark, A.G. and R.K. 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, N. H. and A. G. 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, A. G.  1990.  Genetic components of variation in energy storage in Drosophila melanogaster.  Evolution  44:637-650.

 

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

 

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

 

Clark, A. G., F. M. Szumski, K. A. Bell, L. E. Keith, S. Houtz, and D. A. Merriwether.  1990.  Direct and correlated responses to artificial selection on lipid and glycogen contents in Drosophila melanogaster.  Genetical Research 56:49-56.

 

Clark, A. G. and E. M. S. Lyckegaard.  1990.  Two neutrality tests of Y-linked rDNA variation in Drosophila melanogaster.  Evolution 44:2106-2112.

 

Selander, R. K., A. G. Clark, and T. S. Whittam.  1990.  Evolution at the Molecular Level, (eds.) Sinauer Associates, Inc. Sunderland, MA.

 

Krane, D. E., A. G. Clark, J.-F. Cheng, and R. C. Hardison.  1990.  Subfamily relationships and clustering of rabbit C repeats.  Mol. Biol. Evol. 8:1-30.

 

Ioerger, T. R., A. G. Clark, and T.-H. Kao.  1990.  Polymorphism at the self-incompatibility locus in Solanaceae predates speciation.  Proc. Natl. Acad. Sci.  USA, 87:9732-9735.

 

Clark, A. G. 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, D. L. and A. G. Clark.  1989.  Principles of Population Genetics, Second edition, Sinauer Associates, Sunderland, MA.

 

Lyckegaard, E. M. S. and A. G. 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, A. G. and L. E. 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, A. G.  1989.  Causes and consequences of variation in lipid and carbohydrate storage in Drosophila.  Genetics 123:131-144.

 

 

1988

Clark, A. G. and E. 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, A. G.  1988.  Review of Nei's Molecular Evolutionary Genetics.  Mol. Biol. Evol. 5:109.112.

 

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

 

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

 

Clark, A. G. and L. E. Keith.  1988.  Variation among extracted lines of Drosophila melanogaster in triacylglycerol and carbohydrate storage.  Genetics 119:595-607.

 

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

 

1987

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

 

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

 

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

 

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

 

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

 

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

 

1986

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

 

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

 

Teague, M. D., A. G. Clark, and W. W. Doane.  1986.  Developmental analysis of lipids from wild-type and adipose-60 mutants of Drosophila melanogaster.  Jour. Exp. Zool. 240:95-104.

 

Whittam, T., A. G. Clark, M. Stoneking, R. Cann and A. C. 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, A. G.  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, A. G. and W. Gellman.  1985.  A rapid spectrophotometric assay of triglycerides in Drosophila.  Dros. Inf. Serv. 61:190.

 

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

 

 

1984

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

 

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

 

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

 

Markow, T. A. and A. G. Clark.  1984.  Correlated responses to phototactic selection.  Behavior Genetics 14:279-293.

 

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

 

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

 

Pre-1983

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

 

Clark, A. G., M. W. Feldman, and F. B. 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, A. G. and M. W. 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, A. G. and M. W. Feldman.  1981.  Disequilibrium between linked inversions:  An alternative hypothesis.  Heredity 46:83-94.

 

Clark, A. G. and M. W. Feldman.  1981.  Density dependent fertility selection in experimental populations of Drosophila melanogaster.  Genetics 98:849-869.

 

Clark, A. G.  1981.  Estimation of linkage in the presence of multiplicative viability effects.  Genetics 99:157-168.

 

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

 

Papers in Review

Wittkopp, P.J., B.K. Haerum and A.G. Clark. 2007.  Genetic basis of regulatory variation within and between species. Natur. Genetics, submitted.

Lohmueller, K.E., A.R. Indap, S. Schmidt, A.R. Boyko, R.D. Hernandez, M.J. Hubisz, J.J. Sninsky, T.J. White, S. Sunyaev, R. Nielsen, A.G. Clark, and C.D. Bustamante. 2007.   Proportionally More Deleterious Variation in European than African  Populations. Nature, submitted.   

Boyko, A.R., S.H. Williamson, A.R. Indap, J.D. Degenhardt, R.D. Hernandez, K.E. Lohmueller, M.D. Adams, M. Cargill, A. Eyre-Wakler, S. Schmidt, S.R. Sunyaev, T. J. White, J.J. Sninsky, R. Nielsen, A.G. Clark and C.D. Bustamante. 2007  Quantifying the distribution of selective effects among newly arising amino acid mutations in the human genome. PLoS Biology, submitted.  

Quinlan, AR, Clark AG, Fewell G, Mardis ER, and Marth GT. 2007  Whole-genome polymorphism discovery with light-shotgun, single-coverage 454 pyrosequences.  Nature Genetics, submitted.

 

McKean, K.A., C.P. Yourth, B.P. Lazzaro and A.G. Clark. 2007.  The evolutionary costs of immunological maintenance and deployment.  Evolution, submitted.

 

Singh, N, A. Larracuente, and A.G. Clark.  2007.  Contrasting the efficacy of selection on the X and autosomes in Drosophila.  Mol. Biol. Evol., submitted.

 

Larracuente, A.M., T. B. Sackton, A. Greenberg, A. Wong, N. D. Singh, D. Sturgill, Y. Zhang, B. Oliver, and A. G. Clark. 2007.  Rates and patterns of molecular evolution of protein-coding genes in Drosophila.  Trends Genetics, submitted.

 

Wittkopp. P.J., B.K. Haerum, A.G. Clark. 2007.  Independ