Andrew G. Clark

piRNA loss unleashes episodic transposition bursts

This study shows that loss of the piRNA pathway in Drosophila leads to episodic and stochastic transposition bursts, not just increased transposition rates.

No detectable effect of P2 neurons on female post-mating changes in sleep and feeding in Drosophila melanogaster

This study investigates the role of P2 neurons in post-mating behavioral changes in Drosophila melanogaster and finds they are not responsible for altered sleep and food consumption after mating.

Directionality of Transcriptional Regulatory Elements

This study compares divergent and unidirectional transcriptional regulatory elements, finding that unidirectional elements are younger and less constrained, with some transcription factors modulating their directionality.

Cross-Kingdom Control: Yeast Prion Protein Modulates Host Physiology in Drosophila

This study shows that a yeast prion modulates host physiology in Drosophila by affecting cold tolerance and locomotion through gut-brain signaling pathways.

Application of the Bradley-Terry model to quantify components of sperm competition

The paper applies the Bradley-Terry model to quantify sperm competition outcomes in Drosophila melanogaster by analyzing pairwise mating trials and estimating genotype-specific competitive success.

Comparative population genomics reveals adaptive convergence in two Drosophila species across global environments

This study identifies convergent adaptive genes in two Drosophila species across global environments, showing shared evolutionary responses to environmental pressures.

Female genetic variation controlling timing of mating plug ejection in Drosophila melanogaster

The paper identifies genetic variation in Drosophila melanogaster that influences mating plug ejection timing, linking it to reproductive physiology and paternity outcomes.

Correlated Gene Copy Number Changes in a Seminal Fluid Protein Network in Drosophila

The paper examines gene copy number variation in the Drosophila Sex Peptide seminal fluid protein network, finding correlated duplication and loss events among network members.

The Stellate meiotic drive system of Drosophila melanogaster is active in contemporary populations

The paper demonstrates that the Stellate meiotic drive system is active in contemporary Drosophila melanogaster populations by showing non-Mendelian sex chromosome transmission.

e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology

The paper introduces e3SIM, a simulator that models epidemiological, ecological, and evolutionary processes in pathogens, demonstrating its use with SARS-CoV-2 and Mycobacterium tuberculosis.

The nascent transcriptome delineates the regulatory landscape in human health and disease

The paper presents a high-resolution atlas of transcriptional regulatory elements in human tissues and disease states using PRO-cap and deep learning models to prioritize noncoding variants.

Genome-wide associations of fitness components reveal antagonistic pleiotropy and sexual conflict in the Florida Scrub-Jay

The paper identifies genetic trade-offs and antagonistic pleiotropy in Florida Scrub-Jays by analyzing fitness components and their genomic associations.

Longitudinal sequencing reveals polygenic andepistatic nature of genomic response to selection

This study uses longitudinal sequencing in Drosophila to show that genomic response to selection involves both polygenic shifts and epistatic interactions, with DEGs enriched for selected SNPs.

Bayesian phylodynamic inference of population dynamics with dormancy

This paper develops a Bayesian framework to infer population dynamics with dormancy using molecular sequence data under the strong seedbank coalescent model.

Whole-genome sequencing across space and time reveals impact of population decline and reduced gene flow in Florida Scrub-Jays

This study uses whole-genome sequencing to analyze genetic diversity and inbreeding in Florida Scrub-Jays, showing reduced diversity and increased inbreeding in isolated subpopulations due to habitat fragmentation.

The structure of simple satellite variation in the human genome and its correlation with centromere ancestry

The paper quantifies simple satellite variation in 2,504 human genomes, identifies new tandem repeats, and links centromeric ancestry to satellite abundance.

The Drosophila melanogaster Y-linked gene, WDY, is required for sperm to swim in the female reproductive tract.

This study identifies WDY as a Y-linked gene essential for Drosophila sperm motility and storage, revealing its role in tail beating and propulsion.

High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the Drosophila virilis sub-group

The paper presents high-quality genome assemblies of three Drosophila virilis sub-group species, revealing repetitive DNA dynamics and structural rearrangements driving genome divergence.

The seminal odorant binding protein Obp56g is required for mating plug formation and male fertility in Drosophila melanogaster

This study identifies Obp56g as essential for mating plug formation and male fertility in Drosophila melanogaster through functional and evolutionary analyses.

An Empirical Bayes Approach to Estimating Dynamic Models of Co-regulated Gene Expression

The paper introduces an empirical Bayes method to estimate ODE models of gene expression and derives a biologically-informed similarity metric to identify co-regulated gene clusters.

Finding the strongest gene drive: Simulations reveal unexpected performance differences between Anopheles homing suppression drive candidates

The paper simulates two Anopheles homing gene drives and finds the combined drive with X-shredder is less effective than drives using the nos promoter.

Time series transcriptome analysis uncovers regulatory networks and a role for the circadian clock in the Drosophila melanogaster female's response to Sex Peptide

The paper uses time series RNA-sequencing to analyze the female Drosophila melanogaster's transcriptional response to Sex Peptide, revealing metabolic and neuronal gene regulatory networks and interactions with the circadian clock.

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

This paper develops a homing suppression gene drive in Drosophila using multiplexed gRNAs to prevent resistance alleles, achieving high conversion efficiency and moderate population suppression.

The Genetic Architecture of DNA Replication Timing in Human Pluripotent Stem Cells

This study identifies genetic regulators of DNA replication timing in human pluripotent stem cells, revealing a histone code and combinatorial regulatory mechanisms.

Patterns of piRNA regulation in Drosophila revealed through transposable element clade inference

The paper investigates piRNA regulation in Drosophila by analyzing transposable element clade evolution and finds that younger clades are associated with higher antisense piRNA abundance.

The genetic basis of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping

This study investigates the genetic basis of Drosophila melanogaster's defense against Beauveria bassiana using QTL mapping and evolve and resequence approaches, revealing genetic variation and trade-offs in immune defense.

A polygenic score-based approach to identify gene-drug interactions stratifying breast cancer risk

This study identifies gene-drug interactions that stratify breast cancer risk using polygenic scores and UK Biobank data, finding significant associations with corticosteroid use.

Experimental demonstration of tethered gene drive systems for confined population modification or suppression

This paper demonstrates a tethered gene drive system in Drosophila that confines homing drives to target populations, enabling controlled modification or suppression.

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

The paper performs high-resolution RNA-seq time course analysis of Drosophila immune response to Imd stimulation, identifying gene expression dynamics and trade-offs with metabolic processes.

High-resolution QTL mapping with Diversity Outbred mice identifies genetic variants that impact gut microbiome composition

This study uses 16S rRNA gene sequencing in Diversity Outbred mice to identify genetic variants affecting gut microbiome composition, finding significant heritability and novel QTLs related to immune and metabolic pathways.