Search filters

List of works by Andrew G. Clark

A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set.

scientific article

A CRISPR homing gene drive targeting a haplolethal gene removes resistance alleles and successfully spreads through a cage population

scientific article published on 14 September 2020

A General Population Genetic Framework for Antagonistic Selection That Accounts for Demography and Recurrent Mutation ⬇️

scientific article published on January 31, 2012

A chip off the old block: a model for the evolution of genomic imprinting via selection for parental similarity

scientific article

A hierarchical Bayesian model for a novel sparse partial diallel crossing design

scientific article

A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles

scientific article published in 2022

A numerical simulation of the one-locus, multiple-allele fertility model

scientific article

A scan for positively selected genes in the genomes of humans and chimpanzees

scientific article

A slippery boundary ⬇️

scientific article published on April 18, 2003

A survey for novel imprinted genes in the mouse placenta by mRNA-seq

scientific article

A toxin-antidote CRISPR gene drive system for regional population modification

scientific article published on 27 February 2020

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

scientific article

APOA5polymorphisms influence plasma triglycerides in young, healthy African Americans and whites of the CARDIA Study

scientific article published on 16 December 2004

Allele frequency dynamics in a pedigreed natural population

scientific article published on 31 December 2018

Allele-specific expression elucidates cis-regulatory logic

scientific article published on 01 November 2018

An integrated map of genetic variation from 1,092 human genomes

scientific article

Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing

scientific article

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping

scientific article

Antagonistic versus nonantagonistic models of balancing selection: characterizing the relative timescales and hitchhiking effects of partial selective sweeps ⬇️

scientific article published on September 27, 2012

Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism

scientific article

Ascertainment bias in studies of human genome-wide polymorphism.

scientific article

Assessing the evolutionary impact of amino acid mutations in the human genome

scientific article

Association between sex-biased gene expression and mutations with sex-specific phenotypic consequences in Drosophila

scientific article

Associations between Variation in X Chromosome Male Reproductive Genes and Sperm Competitive Ability in Drosophila melanogaster ⬇️

scientific article published on May 5, 2011

Author Correction: Genus-wide sequencing support a two-locus model for sex-determination in Phoenix

scientific article published in Nature Communications

Balancing selection in species with separate sexes: insights from Fisher's geometric model

scientific article

Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation

scientific article

Biologic phenotyping of the human small airway epithelial response to cigarette smoking

scientific article

Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits

scientific article published on January 2015

Birth of a new gene on the Y chromosome of Drosophila melanogaster ⬇️

scientific article

Brain-derived neurotrophic factor as a model system for examining gene by environment interactions across development

scientific article

Causes and consequences of variation in energy storage in Drosophila melanogaster

scientific article

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

scientific article published on 18 July 2016

Characterizing the infection-induced transcriptome of Nasonia vitripennis reveals a preponderance of taxonomically-restricted immune genes

scientific article

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution

scientific article

Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing

scientific article

Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila

scientific article

Constraints on intron evolution in the gene encoding the myosin alkali light chain in Drosophila

scientific article

Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster

scientific article published on 26 October 2007

Contrasting methods of quantifying fine structure of human recombination.

scientific article

Contrasting multi-site genotypic distributions among discordant quantitative phenotypes: theAPOA1/C3/A4/A5 gene cluster and cardiovascular disease risk factors

article

Contrasting the efficacy of selection on the X and autosomes in Drosophila

scientific article published on 13 December 2007

Contributions of 18 additional DNA sequence variations in the gene encoding apolipoprotein E to explaining variation in quantitative measures of lipid metabolism

scientific article published on 5 August 2002

Correlated variation and population differentiation in satellite DNA abundance among lines of Drosophila melanogaster

scientific article

Cross-species comparison of Drosophila male accessory gland protein genes

scientific article

Cross-species comparisons of host genetic associations with the microbiome

scientific article

Darwinian and demographic forces affecting human protein coding genes

scientific article published on 11 March 2009

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

scientific article published on 3 August 2017

Deep resequencing reveals excess rare recent variants consistent with explosive population growth

scientific article published on 30 November 2010

Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues

scientific article published on 05 May 2020

Demographic history and rare allele sharing among human populations

scientific article

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response

scientific article published on 26 April 2021

Density-Dependent Fertility Selection in Experimental Populations of DROSOPHILA MELANOGASTER

scientific article

Detecting directional selection in the presence of recent admixture in African-Americans

scientific article

Determinants of the success of whole-genome association testing

scientific article

Differences in post-mating transcriptional responses between conspecific and heterospecific matings in Drosophila

scientific article published on 09 October 2020

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

Disentangling the relationship between sex-biased gene expression and X-linkage.

scientific article

Dissecting disease inheritance modes in a three-dimensional protein network challenges the "guilt-by-association" principle

scientific article published on 20 June 2013

Distilling pathophysiology from complex disease genetics

scientific article

Diversity of human copy number variation and multicopy genes

scientific article

Drosophila duplication hotspots are associated with late-replicating regions of the genome

scientific article

Dynamic evolution of the innate immune system in Drosophila

scientific article published on 7 November 2007

Efficient identification of Y chromosome sequences in the human and Drosophila genomes

scientific article published on 06 August 2013

Environmental and genetic perturbations reveal different networks of metabolic regulation ⬇️

scientific article published on December 20, 2011

Epistasis in measured genotypes: Drosophila P-element insertions

scientific article

Erratum to: signatures of early frailty in the gut microbiota

scientific article published on 17 February 2016

Estimating the mutation load in human genomes

scientific article published on 12 May 2015

Estimation of fine-scale recombination intensity variation in the white-echinus interval of D. melanogaster

scientific article published on 06 June 2009

Evidence for consistent intragenic and intergenic interactions between SNP effects in the APOA1/C3/A4/A5 gene cluster

scientific article

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolution of protein-coding genes in Drosophila

scientific article published on 4 February 2008

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Evolutionary constraint and adaptation in the metabolic network of Drosophila

scientific article published on 17 September 2008

Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence

scientific article

Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection

scientific article

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

scientific article published on 12 September 2019

Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group

scientific article

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

scientific article

Faster-X evolution of gene expression in Drosophila

scientific article

Female Genetic Contributions to Sperm Competition in Drosophila melanogaster

scientific article published on 17 May 2019

Female genotypes affect sperm displacement in Drosophila.

scientific article

Female influence on pre- and post-copulatory sexual selection and its genetic basis in Drosophila melanogaster

scientific article published on 9 September 2011

Finding genes underlying risk of complex disease by linkage disequilibrium mapping

scientific article

Finding the missing heritability of complex diseases

scientific article

Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome

scientific article published on 14 February 2013

Full-exon resequencing reveals toll-like receptor variants contribute to human susceptibility to tuberculosis disease

scientific article

Function and evolution of DNA methylation in Nasonia vitripennis

scientific article

Functional regulatory divergence of the innate immune system in interspecific Drosophila hybrids

scientific article

Gene duplication, gene conversion and the evolution of the Y chromosome

scientific article

Gene-based testing of interactions in association studies of quantitative traits

scientific article

Genes involved in convergent evolution of eusociality in bees

scientific article

Genetic Determinants of the Gut Microbiome in UK Twins

scientific article published on May 2016

Genetic conflicts, multiple paternity and the evolution of genomic imprinting.

scientific article

Genetic variation in Drosophila melanogaster resistance to infection: a comparison across bacteria

scientific article

Genetics. Harvesting medical information from the human family tree

scientific article published on 01 February 2005

Genome Diversity and the Origin of the Arabian Horse

scientific article published on 16 June 2020

Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment

scientific article

Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33.

scholarly article

Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations

scientific article

Genomic scans for selective sweeps using SNP data

scientific article

Genomics of ecological adaptation in cactophilic Drosophila.

scientific article

Genotype and gene expression associations with immune function in Drosophila

scientific article

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

scientific article published in Nature Communications

Genus-wide sequencing supports a two-locus model for sex-determination inPhoenix

Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains

scientific article

Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance

scientific article (publication date: 20 July 2001)

Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase

scientific article

Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers

scientific article

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

scientific article published on 26 September 2016

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

scientific article

Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster.

scientific article

Host genetic variation impacts microbiome composition across human body sites

scientific article

Human genetics shape the gut microbiome.

scientific article

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

scientific article

INTERACTIONS BETWEEN THE AMYLASE AND ADIPOSE CHROMOSOMAL REGIONS OF DROSOPHILA MELANOGASTER

scientific article published on 01 September 1984

Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla.

scientific article

Identification of avian W-linked contigs by short-read sequencing ⬇️

scientific article published on May 14, 2012

Identification of five new genes on the Y chromosome of Drosophila melanogaster

scientific article

Impact of genetic architecture on the relative rates of X versus autosomal adaptive substitution

scientific article

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

scientific article published on 4 January 2016

Induction of excessive endoplasmic reticulum stress in the Drosophila male accessory gland results in infertility.

scientific article

Inferences of demography and selection in an African population of Drosophila melanogaster

scientific article

Inferring genetic ancestry: opportunities, challenges, and implications

scientific article

Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios

scientific article (publication date: 12 December 2003)

Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis

scientific article published on 18 February 2019

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

scientific article published on 7 September 2016

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

scientific article

Integrative annotation of variants from 1092 humans: application to cancer genomics

scientific article

Intragenic duplication and divergence in the spectrin superfamily of proteins ⬇️

scientific article published on 01 December 1997

Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations

scientific article

Limited gene misregulation is exacerbated by allele-specific upregulation in lethal hybrids between Drosophila melanogaster and Drosophila simulans

scientific article

Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome

scientific article

Linkage disequilibrium and the mapping of complex human traits ⬇️

scientific article published on January 1, 2002

Localizing recent adaptive evolution in the human genome

scientific article

Low conservation of gene content in the Drosophila Y chromosome

scientific article

Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins

scientific article published on June 2009

Mapping copy number variation by population-scale genome sequencing

scientific article

Mapping determinants of variation in energy metabolism, respiration and flight in Drosophila.

scientific article

Mapping multiple Quantitative Trait Loci by Bayesian classification

scientific article

Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data

scientific article

Mining genetic epidemiology data with Bayesian networks application to APOE gene variation and plasma lipid levels

scientific article

Molecular population genetics of Drosophila immune system genes

scientific article

Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster

scientific article published on 25 April 2003

Molecular population genetics of male accessory gland proteins in Drosophila

scientific article

Mutation Rate Variability across Human Y-Chromosome Haplogroups

scientific article published on 13 October 2020

Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing.

scientific article

Mutation-selection balance with multiple alleles

scientific article published on 01 January 1998

Natural genetic variation in male reproductive genes contributes to nontransitivity of sperm competitive ability in Drosophila melanogaster ⬇️

scientific article published on November 21, 2012

Natural selection and Y-linked polymorphism

scientific article

Natural selection on protein-coding genes in the human genome

scientific article (publication date: 20 October 2005)

Natural selection shaped regional mtDNA variation in humans

scientific article

Natural selection with nuclear and cytoplasmic transmission. I. A deterministic model

scientific article

Natural variation in human membrane transporter genes reveals evolutionary and functional constraints

scholarly article

Natural variation in male-induced 'cost-of-mating' and allele-specific association with male reproductive genes in Drosophila melanogaster

scientific article

Neutral behavior of shared polymorphism ⬇️

scientific article published on July 22, 1997

Neutral genomic regions refine models of recent rapid human population growth

scientific article published on 30 December 2013

Non-Mendelian segregation of sex chromosomes in heterospecific Drosophila males

scientific article

Non-conflict theories for the evolution of genomic imprinting.

scientific article

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

scientific article published on 20 July 2017

Origin and evolution of Y chromosomes: Drosophila tales

scientific article

P-element-induced variation in metabolic regulation in Drosophila

scientific article

Paternally biased X inactivation in mouse neonatal brain

scientific article

Patterns of piRNA Regulation in Drosophila Revealed through Transposable Element Clade Inference

scientific article published on 01 January 2022

Polymorphism at the self-incompatibility locus in Solanaceae predates speciation

scientific article

Polymorphism in genes that influence sperm displacement

scientific article

Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function

scientific article (publication date: July 2002)

Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila

scientific article

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

scientific article published on 14 April 2008

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation

scientific article

Population genetic structure of the people of Qatar

scientific article

Population genetic tools for dissecting innate immunity in humans

scientific article

Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions.

scientific article

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster

scientific article

Population growth inflates the per-individual number of deleterious mutations and reduces their mean effect

scientific article published on 26 August 2013

Positive and purifying selection on the Drosophila Y chromosome

scientific article

Proportionally more deleterious genetic variation in European than in African populations.

scientific article

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

scientific article

Recent and ongoing selection in the human genome

scientific article

Recent explosive human population growth has resulted in an excess of rare genetic variants

scientific article published on May 2012

Recent selection on the Y-to-dot translocation in Drosophila pseudoobscura

scientific article published on 03 January 2014

Recombinational and mutational hotspots within the human lipoprotein lipase gene

scientific article

Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data

scientific article

Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection.

scientific article published on 31 May 2011

RepeatModeler2 for automated genomic discovery of transposable element families

scientific article published on 16 April 2020

Reproduction and immunity-driven natural selection in the human WFDC locus

scientific article published on 4 January 2013

Ribosomal DNA and Stellate gene copy number variation on the Y chromosome of Drosophila melanogaster

scientific article

Selfish genetic elements

scientific article published on 15 November 2018

Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene

scientific article

Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity

scientific article published on January 2013

Sequence polymorphism at the human apolipoprotein AII gene ( APOA2): unexpected deficit of variation in an African-American sample

scientific article published on 14 June 2002

Sequence variation and linkage disequilibrium in the human T-cell receptor beta (TCRB) locus

scientific article

Sequencing errors and molecular evolutionary analysis ⬇️

scientific article published on July 1, 1992

Sex linkage, sex-specific selection, and the role of recombination in the evolution of sexually dimorphic gene expression

scientific article

Sex-differential selection and the evolution of X inactivation strategies

scientific article

Sex-ratio meiotic drive and Y-linked resistance in Drosophila affinis.

scientific article

Sex-ratio meiotic drive and interspecific competition

scientific article

Sexually antagonistic cytonuclear fitness interactions in Drosophila melanogaster

scientific article

Short tandem-repeat polymorphism/alu haplotype variation at the PLAT locus: implications for modern human origins.

scientific article

Signatures of early frailty in the gut microbiota

scientific article published on 29 January 2016

Spontaneous mutation rate of modifiers of metabolism in Drosophila

scientific article

Stress and metabolic regulation in Drosophila ⬇️

scientific article published on January 1, 1997

Strong Constraint on Human Genes Escaping X-Inactivation Is Modulated by their Expression Level and Breadth in Both Sexes

scientific article published on 22 October 2015

Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila

scientific article published on 07 April 2009

Surprising Differences in the Variability of Y Chromosomes in African and Cosmopolitan Populations ofDrosophila melanogaster ⬇️

scientific article published on October 19, 2012

Targets of balancing selection in the human genome

scientific article published on 27 August 2009

The 1000 Genomes Project: data management and community access

scientific article (publication date: 27 April 2012)

The Effects of Interspecific Competition on the Dynamics of a Polymorphism in an Experimental Population of DROSOPHILA MELANOGASTER.

scientific article

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

scientific article

The Relationship Between the Human Genome and Microbiome Comes into View

scientific article published on 20 September 2017

The Sequence of the Human Genome

scientific article

The brain-derived neurotrophic factor Val66Met polymorphism moderates early deprivation effects on attention problems ⬇️

scientific article published on November 1, 2012

The contribution of individual and pairwise combinations of SNPs in the APOA1 and APOC3 genes to interindividual HDL-C variability

scientific article

The effect of genetic conflict on genomic imprinting and modification of expression at a sex-linked locus

scientific article

The effect of recent admixture on inference of ancient human population history

scientific article

The effects of scale: variation in the APOA1/C3/A4/A5 gene cluster

scientific article

The evolution of the Y chromosome with X-Y recombination.

scientific article

The evolutionary costs of immunological maintenance and deployment

scientific article

The functional spectrum of low-frequency coding variation ⬇️

scientific article published on September 14, 2011

The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse

scientific article

The genetic basis for male x female interactions underlying variation in reproductive phenotypes of Drosophila

scientific article

The human microbiome in evolution.

scientific article published on 27 December 2017

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

scientific article

The resolution of sexual antagonism by gene duplication

scientific article

Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes

scientific article published on 12 October 2021

Thrice out of Africa: ancient and recent expansions of the honey bee, Apis mellifera

scientific article

Trachea epithelium as a "canary" for cigarette smoking-induced biologic phenotype of the small airway epithelium

scientific article published on August 2009

Transcriptome Differences between Alternative Sex Determining Genotypes in the House Fly, Musca domestica.

scientific article published on 2 July 2015

Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain

scientific article

Translocation of Y-linked genes to the dot chromosome in Drosophila pseudoobscura.

scientific article

Two tests of Y chromosomal variation in male fertility of Drosophila melanogaster

scientific article

Understanding the accuracy of statistical haplotype inference with sequence data of known phase

scientific article

Using Mendelian inheritance to improve high-throughput SNP discovery

scientific article

Using natural variation in Drosophila to discover previously unknown endoplasmic reticulum stress genes ⬇️

scientific article published on May 10, 2013

Using next-generation RNA sequencing to identify imprinted genes.

scientific article

Validated context-dependent associations of coronary heart disease risk with genotype variation in the chromosome 9p21 region: the Atherosclerosis Risk in Communities study

scientific article

Variation among extracted lines of Drosophila melanogaster in triacylglycerol and carbohydrate storage

scientific article

Variation in Y chromosome segregation in natural populations of Drosophila melanogaster

scientific article

Variation in genome-wide mutation rates within and between human families

scientific article

Variation in sperm displacement and its association with accessory gland protein loci in Drosophila melanogaster.

scientific article

Whole-genome shotgun assembly and comparison of human genome assemblies

scientific article

Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go?

scientific article

Y chromosome of D. pseudoobscura is not homologous to the ancestral Drosophila Y.

scientific article

Paulina is supported by:

About Paulina

Help