Andrew G Clark

Summary

Affiliation: Cornell University
Country: USA

Publications

  1. pmc Genomic scans for selective sweeps using SNP data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1566-75. 2005
  2. pmc Ascertainment bias in studies of human genome-wide polymorphism
    Andrew G Clark
    Molecular Biology and Genetics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1496-502. 2005
  3. pmc Function and evolution of DNA methylation in Nasonia vitripennis
    Xu Wang
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 9:e1003872. 2013
  4. pmc Associations between Variation in X Chromosome Male Reproductive Genes and Sperm Competitive Ability in Drosophila melanogaster
    Leah Greenspan
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 2801, USA
    Int J Evol Biol 2011:214280. 2011
  5. pmc Identification of avian W-linked contigs by short-read sequencing
    Nancy Chen
    Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
    BMC Genomics 13:183. 2012
  6. pmc Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection
    Omer Gokcumen
    Department of Pathology, Brigham and Women s Hospital, 75 Francis Street, Boston, MA 02115, USA
    Genome Biol 12:R52. 2011
  7. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
  8. pmc Simple models of genomic variation in human SNP density
    Raazesh Sainudiin
    Department of Statistics, University of Oxford, Oxford, UK
    BMC Genomics 8:146. 2007
  9. pmc The evolutionary costs of immunological maintenance and deployment
    Kurt A McKean
    Department of Biological Sciences, SUNY at Albany, Albany NY 12222, USA
    BMC Evol Biol 8:76. 2008
  10. pmc Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Am J Hum Genet 73:285-300. 2003

Collaborators

Detail Information

Publications146 found, 100 shown here

  1. pmc Genomic scans for selective sweeps using SNP data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1566-75. 2005
    ..Evidence for selective sweeps is also found in many other regions, including genes known to be associated with disease risk such as DPP10 and COL4A3...
  2. pmc Ascertainment bias in studies of human genome-wide polymorphism
    Andrew G Clark
    Molecular Biology and Genetics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1496-502. 2005
    ....
  3. pmc Function and evolution of DNA methylation in Nasonia vitripennis
    Xu Wang
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 9:e1003872. 2013
    ..We speculate that loss of methylation may result in increased developmental specialization in evolution and acquisition of methylation may lead to broader constitutive expression. ..
  4. pmc Associations between Variation in X Chromosome Male Reproductive Genes and Sperm Competitive Ability in Drosophila melanogaster
    Leah Greenspan
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 2801, USA
    Int J Evol Biol 2011:214280. 2011
    ..This suggests that much of the male reproductive variation lies outside of genes that encode seminal proteins...
  5. pmc Identification of avian W-linked contigs by short-read sequencing
    Nancy Chen
    Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
    BMC Genomics 13:183. 2012
    ..Here, we develop and apply a novel method for identifying sequences that are W-specific...
  6. pmc Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection
    Omer Gokcumen
    Department of Pathology, Brigham and Women s Hospital, 75 Francis Street, Boston, MA 02115, USA
    Genome Biol 12:R52. 2011
    ..Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation...
  7. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
    ....
  8. pmc Simple models of genomic variation in human SNP density
    Raazesh Sainudiin
    Department of Statistics, University of Oxford, Oxford, UK
    BMC Genomics 8:146. 2007
    ..Descriptive hierarchical Poisson models and population-genetic coalescent mixture models are used to describe the observed variation in single-nucleotide polymorphism (SNP) density from samples of size two across the human genome...
  9. pmc The evolutionary costs of immunological maintenance and deployment
    Kurt A McKean
    Department of Biological Sciences, SUNY at Albany, Albany NY 12222, USA
    BMC Evol Biol 8:76. 2008
    ....
  10. pmc Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Am J Hum Genet 73:285-300. 2003
    ..This result is consistent with differences in the genealogical depth of local genomic regions, a finding that has direct bearing on the design and utility of LD mapping and on the National Institutes of Health HapMap project...
  11. ncbi request reprint Genome sequences from extinct relatives
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Cell 134:388-9. 2008
    ..In this issue, Green et al. (2008) exploit this feature to infer the complete mitochondrial genome sequence of one Neanderthal and place bounds on its time of common ancestry with modern humans...
  12. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  13. ncbi request reprint The 6th international meeting on single nucleotide polymorphism and complex genome analysis. November 20-23, 2003, Chantilly, VA, USA
    Andrew G Clark
    Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Pharmacogenomics 5:153-6. 2004
  14. pmc A slippery boundary
    Andrew G Clark
    Molecular Biology and Genetics, 107 Biotech Building, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 100:4971-2. 2003
  15. ncbi request reprint Determinants of the success of whole-genome association testing
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1463-7. 2005
  16. ncbi request reprint The role of haplotypes in candidate gene studies
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genet Epidemiol 27:321-33. 2004
    ..Here we examine some of the factors that affect haplotype patterns in genes, how haplotypes may be inferred, and how haplotypes have been useful in the context of testing association between candidate genes and complex traits...
  17. pmc Contrasting methods of quantifying fine structure of human recombination
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Annu Rev Genomics Hum Genet 11:45-64. 2010
    ....
  18. ncbi request reprint Finding genes underlying risk of complex disease by linkage disequilibrium mapping
    Andrew G Clark
    Molecular Biology and Genetics, 107 Biotechnology Building, Cornell University, Ithaca, New York 14853, USA
    Curr Opin Genet Dev 13:296-302. 2003
    ..In this review we consider the latest information regarding the likely efficacy of the linkage disequilibrium mapping approach...
  19. pmc Genetic variation in Drosophila melanogaster resistance to infection: a comparison across bacteria
    Brian P Lazzaro
    Department of Entomology, Field of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
    Genetics 174:1539-54. 2006
    ..lactis and E. faecalis, respectively, most of the molecular polymorphisms tested explain <10% of the total variance in bacterial load sustained after infection...
  20. pmc Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing
    Timothy B Sackton
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    BMC Genomics 10:259. 2009
    ..However, limited functional annotation in non-model systems has hindered understanding of evolutionary novelties in the insect innate immune system...
  21. pmc Assessing the evolutionary impact of amino acid mutations in the human genome
    Adam R Boyko
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Genet 4:e1000083. 2008
    ....
  22. ncbi request reprint Natural selection on protein-coding genes in the human genome
    Carlos D Bustamante
    Department of Biological Statistics and Computational Biology, 101 Biotechnology Building, Cornell University, Ithaca, New York 14853, USA
    Nature 437:1153-7. 2005
    ....
  23. ncbi request reprint Contrasting multi-site genotypic distributions among discordant quantitative phenotypes: the APOA1/C3/A4/A5 gene cluster and cardiovascular disease risk factors
    Bret A Payseur
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
    Genet Epidemiol 30:508-18. 2006
    ..Results indicate that this multi-site test can identify genotype-phenotype associations with reasonable power, including those generated by some simple epistatic models...
  24. pmc Proportionally more deleterious genetic variation in European than in African populations
    Kirk E Lohmueller
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 451:994-7. 2008
    ..Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa...
  25. pmc Folate network genetic variation predicts cardiovascular disease risk in non-Hispanic white males
    Susan M Wernimont
    Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
    J Nutr 142:1272-9. 2012
    ..This work supports a role for SHMT1-related genes and nuclear folate metabolism, including the thymidylate biosynthesis pathway, in mediating CVD risk...
  26. pmc Paternally biased X inactivation in mouse neonatal brain
    Xu Wang
    Deptartment of Molecular Biology and Genetics, Cornell University, 227 Biotechnology Building, Ithaca, NY 14853, USA
    Genome Biol 11:R79. 2010
    ..Methods for scoring allele-specific differential expression with a high degree of accuracy have recently motivated a quantitative reassessment of the randomness of X inactivation...
  27. pmc Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence
    Dara G Torgerson
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
    PLoS Genet 5:e1000592. 2009
    ..Overall we find that natural selection has played an important role in the evolution of candidate cis-regulatory regions throughout hominid evolution...
  28. pmc Strain-dependent differences in several reproductive traits are not accompanied by early postmating transcriptome changes in female Drosophila melanogaster
    Lisa A McGraw
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Genetics 181:1273-80. 2009
    ..melanogaster females are not caused by large modifications of transcript levels. Instead, early postmating phenotypes result from preexisting receptors or pathways that are already in place upon sexual maturity...
  29. pmc Targets of balancing selection in the human genome
    Aida M Andres
    Department of Molecular Biology and Genetics, Cornell University, USA
    Mol Biol Evol 26:2755-64. 2009
    ....
  30. pmc X-linked variation in immune response in Drosophila melanogaster
    Erin M Hill-Burns
    Field of Genetics and Development, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 183:1477-91. 2009
    ..Many of the associations act in a sex-specific or sexually antagonistic manner, supporting the theory that with the selective pressures facing genes on the X chromosome, sexually antagonistic variation may be more easily maintained...
  31. pmc Genotype and gene expression associations with immune function in Drosophila
    Timothy B Sackton
    Field of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 6:e1000797. 2010
    ..These results show that polymorphism in genes near the top of the immune system signaling cascade can have a disproportionate effect on organismal phenotype due to the amplification of minor effects through the cascade...
  32. pmc A scan for positively selected genes in the genomes of humans and chimpanzees
    Rasmus Nielsen
    Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Biol 3:e170. 2005
    ..The polymorphism analysis further supports the presence of positive selection in these genes by showing an excess of high-frequency derived nonsynonymous mutations...
  33. pmc Estimation of fine-scale recombination intensity variation in the white-echinus interval of D. melanogaster
    Nadia D Singh
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    J Mol Evol 69:42-53. 2009
    ..Our results shed light on the relevant physical scale to consider in evolutionary analyses relating to recombination rate and highlight the motivations to increase the resolution of the recombination map in Drosophila...
  34. ncbi request reprint Dynamic evolution of the innate immune system in Drosophila
    Timothy B Sackton
    Field of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
    Nat Genet 39:1461-8. 2007
    ....
  35. pmc Post-mating gene expression profiles of female Drosophila melanogaster in response to time and to four male accessory gland proteins
    Lisa A McGraw
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 179:1395-408. 2008
    ..In contrast, Acp29AB and Acp62F modulated a large number of transcriptional changes shortly after mating...
  36. pmc Localizing recent adaptive evolution in the human genome
    Scott H Williamson
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 3:e90. 2007
    ..In general, we find that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep...
  37. ncbi request reprint Evolution of protein-coding genes in Drosophila
    Amanda M Larracuente
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Trends Genet 24:114-23. 2008
    ....
  38. pmc Neutral genomic regions refine models of recent rapid human population growth
    Elodie Gazave
    Departments of Biological Statistics and Computational Biology and Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
    Proc Natl Acad Sci U S A 111:757-62. 2014
    ..This observation and results also shed light on the discrepancy in demographic estimates among recent studies...
  39. ncbi request reprint Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios
    Andrew G Clark
    Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 302:1960-3. 2003
    ..In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders...
  40. pmc Paternally expressed genes predominate in the placenta
    Xu Wang
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 110:10705-10. 2013
    ..Taken together, these features highlight the plasticity of imprinting in mammals and the central importance of the placenta as a target tissue for genomic imprinting. ..
  41. pmc Gene-based testing of interactions in association studies of quantitative traits
    Li Ma
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Genet 9:e1003321. 2013
    ..We conclude that our GGG tests show improved power to identify gene-level interactions in existing, as well as emerging, association studies...
  42. pmc Recent explosive human population growth has resulted in an excess of rare genetic variants
    Alon Keinan
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    Science 336:740-3. 2012
    ..Hence, the extreme recent human population growth needs to be taken into consideration in studying the genetics of complex diseases and traits...
  43. pmc The genetic basis for male x female interactions underlying variation in reproductive phenotypes of Drosophila
    Clement Y Chow
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 2703, USA
    Genetics 186:1355-65. 2010
    ..The results of this study begin to elucidate the complex genetic architecture of reproductive and sperm competition phenotypes and have significant implications for the evolution of male and female characters...
  44. ncbi request reprint Regulatory changes underlying expression differences within and between Drosophila species
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nat Genet 40:346-50. 2008
    ..Specifically, cis-regulatory changes seem to accumulate preferentially over time...
  45. pmc The effect of recent admixture on inference of ancient human population history
    Kirk E Lohmueller
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 185:611-22. 2010
    ....
  46. pmc Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data
    Kirk E Lohmueller
    Department of Biostatistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genetics 182:217-31. 2009
    ..We have applied our method to data collected by Perlegen Sciences and find evidence for a severe population size reduction in northwestern Europe starting 32,500-47,500 years ago...
  47. pmc Monophyly of Wolbachia pipientis genomes within Drosophila melanogaster: geographic structuring, titre variation and host effects across five populations
    Angela M Early
    Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
    Mol Ecol 22:5765-78. 2013
    ..This demonstration of local phenotypic divergence suggests that intraspecific host genetic variation plays a key role in shaping this model symbiotic system. ..
  48. pmc Large neurological component to genetic differences underlying biased sperm use in Drosophila
    Clement Y Chow
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 2703, USA
    Genetics 193:177-85. 2013
    ..Our results indicate that the study of female control of sperm competition should not be limited to female reproductive tract-specific genes, but should focus also on diverse biological pathways...
  49. pmc Associations between sperm competition and natural variation in male reproductive genes on the third chromosome of Drosophila melanogaster
    Anthony C Fiumera
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 176:1245-60. 2007
    ..Our findings provide evidence that pleiotropy and epistasis are important factors in the genetic architecture of male reproductive success and show that haplotype analyses can identify associations missed in the single-marker approach...
  50. pmc Larval rearing environment affects several post-copulatory traits in Drosophila melanogaster
    Lisa A McGraw
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Biol Lett 3:607-10. 2007
    ....
  51. pmc A hierarchical Bayesian model for a novel sparse partial diallel crossing design
    Anthony J Greenberg
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Genetics 185:361-73. 2010
    ..We also illustrate how our approach allows the construction of posterior distributions of combinations of parameters by calculating narrow-sense heritability and a genetic correlation between activities of two enzymes...
  52. pmc Association between sex-biased gene expression and mutations with sex-specific phenotypic consequences in Drosophila
    Tim Connallon
    Department of Molecular Biology and Genetics, Cornell University, USA
    Genome Biol Evol 3:151-5. 2011
    ..These results have interesting implications for the evolution of sexual dimorphism and sex-specific adaptation...
  53. ncbi request reprint Evolutionary changes in cis and trans gene regulation
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 430:85-8. 2004
    ..These data indicate that interspecific expression differences are not caused by select trans-regulatory changes with widespread effects, but rather by many cis-acting changes spread throughout the genome...
  54. pmc Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila
    Nadia D Singh
    Department of Molecular Biology and Genetics, Cornell University
    Mol Biol Evol 26:1591-605. 2009
    ....
  55. pmc Detecting directional selection in the presence of recent admixture in African-Americans
    Kirk E Lohmueller
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 187:823-35. 2011
    ..Our results have implications for interpreting recent genome-wide scans for positive selection in human populations...
  56. pmc Linkage disequilibrium as a signature of selective sweeps
    Yuseob Kim
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genetics 167:1513-24. 2004
    ..However, the improvement made by including LD is rather small, suggesting that most of the relevant information regarding selective sweeps is captured by the spatial distribution and marginal allele frequencies of polymorphisms...
  57. pmc Patterns of positive selection in six Mammalian genomes
    Carolin Kosiol
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 4:e1000144. 2008
    ..This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection...
  58. pmc Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations
    Li Ma
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
    PLoS Genet 8:e1002714. 2012
    ..In conclusion, based on a knowledge-driven analysis of epistasis, together with a new locus-based validation method, we successfully identified and validated an interaction affecting a complex trait in multi-ethnic populations...
  59. pmc Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica
    Xu Wang
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 24:70-83. 2014
    ..Our study provides the first comprehensive catalog of parent-of-origin expression status for X-linked genes in a marsupial and sheds light on the regulation and evolution of imprinted XCI in mammals. ..
  60. pmc Population genetic structure of the people of Qatar
    Haley Hunter-Zinck
    Program in Computational Biology and Medicine, Cornell University, Ithaca, NY 14850, USA
    Am J Hum Genet 87:17-25. 2010
    ....
  61. pmc Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping
    Adam B Olshen
    Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BMC Genet 9:14. 2008
    ..435,632 SNPs overlapped and met annotation criteria in the two groups...
  62. ncbi request reprint Genomics of the evolutionary process
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Trends Ecol Evol 21:316-21. 2006
    ..These methods also identify negatively selected genes, providing some clue to genes that are most likely to be mutable to a disease-causing state...
  63. pmc Faster-X evolution of gene expression in Drosophila
    Richard P Meisel
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
    PLoS Genet 8:e1003013. 2012
    ..Finally, we present a conceptional framework to explain faster-X expression evolution, and we use this framework to examine differences in the faster-X effect between Drosophila and mammals...
  64. pmc Impact of genetic architecture on the relative rates of X versus autosomal adaptive substitution
    Tim Connallon
    Department of Molecular Biology and Genetics, Cornell University, USA
    Mol Biol Evol 29:1933-42. 2012
    ....
  65. pmc Disentangling the relationship between sex-biased gene expression and X-linkage
    Richard P Meisel
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 22:1255-65. 2012
    ..However, some taxon-specific patterns remain, and we provide evidence that these are in part a consequence of constraints imposed by the dosage compensation mechanism in Drosophila...
  66. pmc A general population genetic framework for antagonistic selection that accounts for demography and recurrent mutation
    Tim Connallon
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 190:1477-89. 2012
    ..The effects of mutation and demography may generate population differences in overall levels of antagonistic fitness variation, as well as molecular population genetic signatures of balancing selection...
  67. pmc Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain
    Xu Wang
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
    PLoS ONE 3:e3839. 2008
    ....
  68. pmc Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster
    Todd A Schlenke
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
    PLoS Pathog 3:1486-501. 2007
    ..However, we uncover the mechanism for one potentially important fitness tradeoff of the generalist's highly immune suppressive infection strategy...
  69. pmc Translocation of Y-linked genes to the dot chromosome in Drosophila pseudoobscura
    Amanda M Larracuente
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
    Mol Biol Evol 27:1612-20. 2010
    ..We postulate that the nascent D. pseudoobscura Y chromosome acquired and amplified copies of the IGS, suggesting a potential mechanism for X-Y pairing in D. pseudoobscura...
  70. pmc Understanding the accuracy of statistical haplotype inference with sequence data of known phase
    Aida M Andres
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
    Genet Epidemiol 31:659-71. 2007
    ..Strategies to improve confidence in reconstructed haplotypes, and realistic alternatives to the analysis of inferred haplotypes, are discussed...
  71. pmc Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genetics 168:2373-82. 2004
    ..Appropriate treatment of SNP ascertainment is vital to our ability to make correct inferences from the data of the International HapMap Project...
  72. pmc Functional regulatory divergence of the innate immune system in interspecific Drosophila hybrids
    Erin M Hill-Burns
    Field of Genetics and Development, Department of Molecular Biology and Genetics, Cornell University
    Mol Biol Evol 27:2596-605. 2010
    ....
  73. pmc Natural variation in male-induced 'cost-of-mating' and allele-specific association with male reproductive genes in Drosophila melanogaster
    Anthony C Fiumera
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Philos Trans R Soc Lond B Biol Sci 361:355-61. 2006
    ..Postcopulatory sexual selection could lead to sexual conflict by favouring males that prevent their mates from mating, even when there is a viability cost to those females...
  74. pmc Mapping multiple Quantitative Trait Loci by Bayesian classification
    Min Zhang
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genetics 169:2305-18. 2005
    ..A simulation study demonstrated the power of this approach across levels of trait heritability and when marker data were sparse...
  75. ncbi request reprint Bayesian and maximum likelihood estimation of genetic maps
    Thomas L York
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
    Genet Res 85:159-68. 2005
    ..We also re-analyse a recently published set of data from the eggplant and show that the use of the MCMC-based method leads to smaller estimates of genetic distances...
  76. ncbi request reprint Bayesian estimation of the number of inversions in the history of two chromosomes
    Thomas L York
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    J Comput Biol 9:805-18. 2002
    ..melanogaster comparison, the lower boundary of a 95% highest posterior density credible interval for the number of inversions is considerably larger than the most parsimonious number of inversions...
  77. pmc Simultaneous inference of selection and population growth from patterns of variation in the human genome
    Scott H Williamson
    Department of Biological Statistics and Computational Biology, 101 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 102:7882-7. 2005
    ....
  78. pmc Random X inactivation in the mule and horse placenta
    Xu Wang
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 22:1855-63. 2012
    ..As the most structurally and morphologically diverse organ in mammals, the placenta also appears to show diverse mechanisms for dosage compensation that may result in differences in conceptus development across species...
  79. pmc Impact of microRNA regulation on variation in human gene expression
    Jian Lu
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 22:1243-54. 2012
    ..A reasonable case can be made that natural selection is driving this pattern of variation...
  80. pmc Environmental and genetic perturbations reveal different networks of metabolic regulation
    Anthony J Greenberg
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Mol Syst Biol 7:563. 2011
    ....
  81. pmc Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 178:1831-5. 2008
    ..The frequency of such independent interactions on a genomic scale is yet to be determined...
  82. pmc Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 173:1817-21. 2006
    ..Offspring from reciprocal crosses exhibit differences in total expression without differences in allelic expression, indicating that other types of maternal and/or paternal effects alter expression...
  83. pmc A survey for novel imprinted genes in the mouse placenta by mRNA-seq
    Xu Wang
    Department of Molecular Biology and Genetics, Cornell Center for Comparative and Population Genomics, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA
    Genetics 189:109-22. 2011
    ..Despite previous appearance that the placenta tends to display an excess of maternally expressed imprinted genes, with the addition of our validated set of placenta-imprinted genes, this maternal bias has disappeared...
  84. pmc Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation
    Richard W Jobson
    Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 101:18064-8. 2004
    ....
  85. pmc Folate network genetic variation, plasma homocysteine, and global genomic methylation content: a genetic association study
    Susan M Wernimont
    Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
    BMC Med Genet 12:150. 2011
    ..Sequence variants in genes functioning in folate-mediated one-carbon metabolism are hypothesized to lead to changes in levels of homocysteine and DNA methylation, which, in turn, are associated with risk of cardiovascular disease...
  86. pmc Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila
    Jian Lu
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genome Res 20:212-27. 2010
    ....
  87. pmc Sperm competitive ability in Drosophila melanogaster associated with variation in male reproductive proteins
    Anthony C Fiumera
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 169:243-57. 2005
    ..The latter case is consistent with antagonistic pleiotropy and may serve as a mechanism maintaining genetic variation...
  88. pmc The resolution of sexual antagonism by gene duplication
    Tim Connallon
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 2703, USA
    Genetics 187:919-37. 2011
    ..Although this result differs from previous models of sexual antagonism, it is consistent with several findings from the empirical genomics literature...
  89. pmc Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins
    Sergi Castellano
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
    Mol Biol Evol 26:2031-40. 2009
    ..A better understanding of the selenoproteomes and neutral evolutionary patterns in other taxa will be necessary to fully assess the generality of this conclusion...
  90. ncbi request reprint Genetic basis of natural variation in D. melanogaster antibacterial immunity
    Brian P Lazzaro
    Department of Entomology, 4138 Comstock Hall, Cornell University, Ithaca, NY 14853, USA
    Science 303:1873-6. 2004
    ..Variation in these genes, therefore, seems to drive variability in immunocompetence among wild Drosophila...
  91. ncbi request reprint Contrasting the efficacy of selection on the X and autosomes in Drosophila
    Nadia D Singh
    Department of Molecular Biology and Genetics, Cornell University, USA
    Mol Biol Evol 25:454-67. 2008
    ....
  92. pmc Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters
    Miltiadis Kininis
    Department of Molecular Biology and Genetics, Cornell University, 465 Biotechnology Building, Ithaca, NY 14853, USA
    Mol Cell Biol 27:5090-104. 2007
    ..These mechanistic insights are likely to be relevant for understanding gene regulation by a wide variety of nuclear receptors...
  93. pmc Mapping determinants of variation in energy metabolism, respiration and flight in Drosophila
    Kristi L Montooth
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 165:623-35. 2003
    ..This has important consequences for the evolution of performance traits that depend upon these metabolic networks...
  94. ncbi request reprint Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species
    Melanie A Huntley
    Department of Molecular Biology and Genetics Cornell University, USA
    Mol Biol Evol 24:2598-609. 2007
    ..With additional evidence to suggest a corresponding elevation in positive selection we propose that some repeats may be inducing compensatory substitutions in their surrounding sequence...
  95. pmc Gene duplication, gene conversion and the evolution of the Y chromosome
    Tim Connallon
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 2703, USA
    Genetics 186:277-86. 2010
    ..The results may also be applicable to the recently observed pattern of tetraploidy and gene conversion in asexual, bdelloid rotifers...
  96. pmc Sex linkage, sex-specific selection, and the role of recombination in the evolution of sexually dimorphic gene expression
    Tim Connallon
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 2703, USA
    Evolution 64:3417-42. 2010
    ..The theory suggests that sexual selection may strongly influence the architectures of animal genomes, as well as the chromosomal distribution of fixed substitutions underlying sexually dimorphic traits...
  97. pmc Dependence of paracentric inversion rate on tract length
    Thomas L York
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
    BMC Bioinformatics 8:115. 2007
    ..We develop a Bayesian method based on MCMC for estimating the relative rates of pericentric and paracentric inversions from marker data from two species. The method also allows estimation of the distribution of inversion tract lengths...
  98. ncbi request reprint Mapping mutations on phylogenies
    Rasmus Nielsen
    Department of Biological Statistics, Cornell University, 439 Warren Hall, Ithaca, New York 14853 7801, USA
    Syst Biol 51:729-39. 2002
    ..Applications include a method for testing for variation in the substitution rate along the sequence and a method for testing whether the d(N)/d(S) ratio varies among lineages in the phylogeny...
  99. ncbi request reprint Statistical approaches for DNA barcoding
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Center for Bioinformatics, University of Copenhagen Universitetsparken 15, 2100 Copenhagen, Denmark
    Syst Biol 55:162-9. 2006
  100. ncbi request reprint Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system
    Raazesh Sainudiin
    Department of Statistical Science, Cornell University, Ithaca, NY14853, USA
    J Mol Evol 60:315-26. 2005
    ..An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins...
  101. pmc Identification of physicochemical selective pressure on protein encoding nucleotide sequences
    Wendy S W Wong
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    BMC Bioinformatics 7:148. 2006
    ..However, they have been limited by not taking the physiochemical properties of amino acids into account...

Research Grants40

  1. POLYMORPHISM/DIVERGENCE IN DROSOPHILA PATHOGEN DEFENSES
    Andrew Clark; Fiscal Year: 2000
    ....
  2. Modeling DNA Diversity in Reverse Cholestrol Transport
    Andrew Clark; Fiscal Year: 2009
    ..This research not only considers the individual effects of variation in each gene, but their interactions with other genes and with the environment. ..
  3. Functional and Comparative Genomic of Drosophila immunity
    Andrew Clark; Fiscal Year: 2009
    ..Through our modeling efforts, data from all four aims will provide an integrated, quantitative picture of variation in Drosophila innate immune function and its control by its underlying gene regulatory network. ..
  4. Inferring Multiple-SNP Disease Association with DNA Resequence Data
    Andrew Clark; Fiscal Year: 2008
    ..These methods will also be extended to include prior information about molecular mechanisms of gene function, where available, as well as environmental contributions to disease risk. ..
  5. Dimension Reduction Approaches for Genome-wide Association Testing
    Andrew Clark; Fiscal Year: 2008
    ..Of particular interest will be the tuning model parameters to optimize the balance of false positive and false negative inferences. [unreadable] [unreadable] [unreadable] [unreadable]..
  6. Functional and Comparative Genomic of Drosophila immunity
    Andrew Clark; Fiscal Year: 2008
    ..Through our modeling efforts, data from all four aims will provide an integrated, quantitative picture of variation in Drosophila innate immune function and its control by its underlying gene regulatory network. ..
  7. Comparative Functional Genomics of Drosophila Obesity
    Andrew Clark; Fiscal Year: 2008
    ..which particular genes and pathways are most relevant to variation in fat storage homeostasis, and by developing a systems biology approach to make inferences from data that span cellular, endocrine, and whole-organism attributes ..
  8. Population genetic inferences from dense genotype data
    Andrew Clark; Fiscal Year: 2008
    ..These inferences can provide vital clues to identifying genes that are associated with risk of complex genetic disorders. ..
  9. Modeling DNA Diversity in Reverse Cholestrol Transport
    Andrew Clark; Fiscal Year: 2008
    ..This research not only considers the individual effects of variation in each gene, but their interactions with other genes and with the environment. ..
  10. Comparative Functional Genomics of Drosophila Obesity
    Andrew Clark; Fiscal Year: 2009
    ..which particular genes and pathways are most relevant to variation in fat storage homeostasis, and by developing a systems biology approach to make inferences from data that span cellular, endocrine, and whole-organism attributes ..
  11. Drosophila genes causing male x female interaction in reproduction
    Andrew Clark; Fiscal Year: 2009
    ..abstract_text> ..
  12. Molecular Evolution of Drosophila Y Chromosome
    ANDREW G contact CLARK; Fiscal Year: 2010
    ..The proposed study entails primary discovery of most of the Y- linked genes across a group of 12 species and a detailed study of their evolutionary divergence. ..
  13. Population genetic inferences from dense genotype data
    Andrew Clark; Fiscal Year: 2009
    ..These inferences can provide vital clues to identifying genes that are associated with risk of complex genetic disorders. ..
  14. Drosophila genes causing male x female interaction in reproduction
    MARIANA FEDERICA WOLFNER; Fiscal Year: 2010
    ..abstract_text> ..
  15. Population genetic inferences from dense genotype data
    Rasmus Nielsen; Fiscal Year: 2010
    ..These inferences can provide vital clues to identifying genes that are associated with risk of complex genetic disorders. ..
  16. Modeling DNA Diversity in Reverse Cholestrol Transport
    Andrew G Clark; Fiscal Year: 2010
    ..This research not only considers the individual effects of variation in each gene, but their interactions with other genes and with the environment. ..
  17. Inferring Multiple-SNP Disease Association with DNA Resequence Data
    Andrew Clark; Fiscal Year: 2009
    ..These methods will also be extended to include prior information about molecular mechanisms of gene function, where available, as well as environmental contributions to disease risk. ..
  18. Population genetic inferences from dense genotype data
    Andrew Clark; Fiscal Year: 2009
    ..These inferences can provide vital clues to identifying genes that are associated with risk of complex genetic disorders. ..
  19. Molecular Evolution of Drosophila Y Chromosome
    Andrew Clark; Fiscal Year: 2009
    ..The proposed study entails primary discovery of most of the Y- linked genes across a group of 12 species and a detailed study of their evolutionary divergence. ..
  20. Dimension Reduction Approaches for Genome-wide Association Testing
    Andrew Clark; Fiscal Year: 2007
    ..Of particular interest will be the tuning model parameters to optimize the balance of false positive and false negative inferences. [unreadable] [unreadable] [unreadable] [unreadable]..
  21. Functional and Comparative Genomic of Drosophila immunity
    Andrew Clark; Fiscal Year: 2007
    ..Through our modeling efforts, data from all four aims will provide an integrated, quantitative picture of variation in Drosophila innate immune function and its control by its underlying gene regulatory network. ..
  22. Modeling DNA Diversity in Reverse Cholesterol Transport
    Andrew Clark; Fiscal Year: 2004
    ..Novel approaches to genotype-phenotype associations will be pursued, in close collaboration with Component 3, by testing the fit of the neutral site frequency spectrum to data stratified by phenotypic measures. ..
  23. Molecular Evolution of Drosophila Y Chromosome
    Andrew Clark; Fiscal Year: 2004
    ..These studies will establish D. melanogaster as a key experimental system for analysis of Y chromosome polymorphism and molecular evolution. ..
  24. Molecular Evolution of Drosophila Y Chromosome
    Andrew Clark; Fiscal Year: 2003
    ..These studies will establish D. melanogaster as a key experimental system for analysis of Y chromosome polymorphism and molecular evolution. ..
  25. Molecular Evolution of Drosophila Y Chromosome
    Andrew Clark; Fiscal Year: 2002
    ..These studies will establish D. melanogaster as a key experimental system for analysis of Y chromosome polymorphism and molecular evolution. ..
  26. Modeling DNA Diversity in Reverse Cholesterol Transport
    Andrew Clark; Fiscal Year: 2003
    ..Novel approaches to genotype-phenotype associations will be pursued, in close collaboration with Component 3, by testing the fit of the neutral site frequency spectrum to data stratified by phenotypic measures. ..
  27. POLYMORPHISM/DIVERGENCE IN DROSOPHILA PATHOGEN DEFENSES
    Andrew Clark; Fiscal Year: 2002
    ....
  28. Molecular Evolution of Drosophila Y Chromosome
    Andrew Clark; Fiscal Year: 2002
    ..These studies will establish D. melanogaster as a key experimental system for analysis of Y chromosome polymorphism and molecular evolution. ..
  29. POLYMORPHISM/DIVERGENCE IN DROSOPHILA PATHOGEN DEFENSES
    Andrew Clark; Fiscal Year: 2001
    ....
  30. Population genetic inferences from dense genotype data
    Andrew Clark; Fiscal Year: 2004
    ..These tests will help identify the attributes of local LD that best predict the power of association tests, and will serve as additional guidance to identify regions requiring more dense SNP coverage. ..
  31. Molecular Evolution of Drosophila Y Chromosome
    Andrew Clark; Fiscal Year: 2005
    ..These studies will establish D. melanogaster as a key experimental system for analysis of Y chromosome polymorphism and molecular evolution. ..
  32. Comparative Functional Genomics of Drosophila Obesity
    Andrew Clark; Fiscal Year: 2007
    ..which particular genes and pathways are most relevant to variation in fat storage homeostasis, and by developing a systems biology approach to make inferences from data that span cellular, endocrine, and whole-organism attributes ..
  33. Population genetic inferences from dense genotype data
    Andrew Clark; Fiscal Year: 2006
    ..These tests will help identify the attributes of local LD that best predict the power of association tests, and will serve as additional guidance to identify regions requiring more dense SNP coverage. ..
  34. Modeling DNA Diversity in Reverse Cholesterol Transport
    Andrew Clark; Fiscal Year: 2006
    ..Novel approaches to genotype-phenotype associations will be pursued, in close collaboration with Component 3, by testing the fit of the neutral site frequency spectrum to data stratified by phenotypic measures. ..
  35. Comparative Functional Genomics of Drosophila Obesity
    Andrew Clark; Fiscal Year: 2006
    ..which particular genes and pathways are most relevant to variation in fat storage homeostasis, and by developing a systems biology approach to make inferences from data that span cellular, endocrine, and whole-organism attributes ..
  36. Functional and Comparative Genomic of Drosphila immunity
    Andrew Clark; Fiscal Year: 2006
    ..Through our modeling efforts, data from all four aims will provide an integrated, quantitative picture of variation in Drosophila innate immune function and its control by its underlying gene regulatory network. ..
  37. Functional /Comparative Genomic of Drosophila immunity
    Andrew Clark; Fiscal Year: 2005
    ..Through our modeling efforts, data from all four aims will provide an integrated, quantitative picture of variation in Drosophila innate immune function and its control by its underlying gene regulatory network. ..
  38. Population genetic inferences from dense genotype data
    Andrew Clark; Fiscal Year: 2005
    ..These tests will help identify the attributes of local LD that best predict the power of association tests, and will serve as additional guidance to identify regions requiring more dense SNP coverage. ..
  39. Modeling DNA Diversity in Reverse Cholesterol Transport
    Andrew Clark; Fiscal Year: 2005
    ..Novel approaches to genotype-phenotype associations will be pursued, in close collaboration with Component 3, by testing the fit of the neutral site frequency spectrum to data stratified by phenotypic measures. ..
  40. Inferring Multiple-SNP Disease Association with DNA Resequence Data
    Rasmus Nielsen; Fiscal Year: 2010
    ..These methods will also be extended to include prior information about molecular mechanisms of gene function, where available, as well as environmental contributions to disease risk. ..