A5005162570- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Neurobiology and Insect Physiology Research
- Sex and Gender in Healthcare
- Evolution and Genetic Dynamics
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Animal Behavior and Reproduction
- Insect and Arachnid Ecology and Behavior
- Hormonal Regulation and Hypertension
- Plant and animal studies
- Chromosomal and Genetic Variations
- Genetics, Aging, and Longevity in Model Organisms
- Insect behavior and control techniques
- Insect Resistance and Genetics
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Nutrition, Genetics, and Disease
- Open Source Software Innovations
- Insect symbiosis and bacterial influences
- Invertebrate Immune Response Mechanisms
- Microbial Natural Products and Biosynthesis
- Genetic Associations and Epidemiology
- Cell Image Analysis Techniques
Temple University
2013-2023
Fox Chase Cancer Center
2023
Temple College
2012-2022
Université Paris Cité
2021
Centre National de la Recherche Scientifique
2021
Institut Jacques Monod
2021
Block Center
2015
University of Arizona
2014
Harvard University
2003-2010
University of Florida
2010
Abstract A large portion of the annotated genes in Drosophila melanogaster show sex-biased expression, indicating that sex and reproduction-related (SRR genes) represent an appreciable component genome. Previous studies, which subsets were compared among few species, have found SRR exhibit unusual evolutionary patterns. Here, we used newly released genome sequences from 12 coupled to a larger set genes, comprehensively test generality these Among 2505 examined, including ESTs with biased...
In nature, closely related species may hybridize while still retaining their distinctive identities. Chromosomal regions that experience reduced recombination in hybrids, such as within inversions, have been hypothesized to contribute the maintenance of integrity. Here, we examine genomic sequences from fruit fly taxa Drosophila pseudoobscura subgroup reconstruct evolutionary histories and past patterns genic exchange. Partial assemblies were generated two subspecies (D. ps.) an outgroup...
A growing number of genes involved in sex and reproduction have been demonstrated to be rapidly evolving. Here, we show that expressed solely spermatozoa represent a highly diverged subset among mouse human tissue-specific orthologs. The average rate nonsynonymous substitutions per site (Ka) is significantly higher sperm proteins (mean Ka = 0.18; N 35) than specifically all other tissues 0.074; 473). No differences, however, are found the synonymous substitution (Ks) between tissues,...
Regional rates of recombination often correlate with levels nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. also differences between human chimpanzee, consistent models where is mutagenic; however, a lack correlation observed in the Drosophila melanogaster group, invoking natural selection. Here, we revisit relationship among recombination, interspecies difference by generating empirical estimates these parameters pseudoobscura. To measure...
The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of process. Here, we compare full genome sequences 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns introgression and infer how divergence evolves Our analyses reveal that initial restricted small fraction genome, largely clustered around known wing-patterning genes. Over time, rapidly, due primarily origin new divergent...
The availability of sequenced genomes from 12 Drosophila species has enabled the use comparative genomics for systematic discovery functional elements conserved within this genus. We have developed quantitative metrics evolutionary signatures specific to protein-coding regions and applied them genome-wide, resulting in 1193 candidate new exons D. melanogaster genome. reviewed these predictions by manual curation validated a subset directed cDNA screening sequencing, revealing both genes...
Large clusters of coexpressed tissue-specific genes are abundant on chromosomes diverse species. The coordinately misexpressed in diseases also found similar clusters, suggesting that evolutionarily conserved mechanisms regulate expression large multigenic regions both normal development and its pathological disruptions. Studies individual loci suggest silent coregulated embedded repressed chromatin domains, often localized to the nuclear periphery. To test this model at genome-wide scale,...
Relatively little is known about the importance of amino acid interactions in protein and phenotypic evolution. Here we examine whether mutations that are pathogenic Drosophila melanogaster become fixed via epistasis other Dipteran genomes. Overall divergence at sites reduced. However, approximately 10% substitutions these carry exact same found D. mutants. Hence compensatory mutation(s) must have evolved. Surprisingly, fraction not affected by phylogenetic distance. These results support a...
Short-read sequencing techniques provide the opportunity to capture genome-wide sequence data in a single experiment. A current challenge is identify questions that shallow-depth genomic can address successfully and develop corresponding analytical methods are statistically sound. Here, we apply Roche/454 platform survey natural variation strains of Drosophila melanogaster from an African (n = 3) North American 6) population. Reads were aligned reference D. assembly, nucleotide polymorphisms...
Squamates include all lizards and snakes, display some of the most diverse extreme morphological adaptations among vertebrates. However, compared with birds mammals, relatively few resources exist for comparative genomic analyses squamates, hampering efforts to understand molecular bases phenotypic diversification in such a speciose clade. In particular, ∼400 species anole lizard represent an extensive squamate radiation. Here, we sequence assemble draft genomes three species-Anolis...
We compare the functional spectrum of protein evolution in two separate animal lineages with respect to hypotheses: (1) rates divergence are distributed similarly among classes within both lineages, indicating that selective pressure on proteome is largely independent organismic-level biological requirements; and (2) differently each lineage, species-specific regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence data from tissue-specific...
Expression patterns between males and females vary in every adult tissue, even organs with no conspicuous dimorphisms such as the heart. While studies of male female differences have traditionally focused on influence sex hormones, these do not account for all at molecular epigenetic levels. We previously reported that a substantial number genes were differentially expressed mouse embryonic stem (ES) cells revealed dose-dependent enhancer activity response to Prdm14, key pluripotency factor...
Abstract Data-driven phenotype analyses on Electronic Health Record (EHR) data have recently drawn benefits across many areas of clinical practice, uncovering new links in the medical sciences that can potentially affect well-being millions patients. In this paper, EHR is used to discover novel relationships between diseases by studying their comorbidities (co-occurrences patients). A embedding model designed extract knowledge from disease learning a large-scale database comprising more than...
Abstract With arguably the best finished and expertly annotated genome assembly, Drosophila melanogaster is a formidable genetics model to study all aspects of biology. Nearly decade ago, 12 genomes project expanded D. melanogaster’s breadth as comparative through community-development an unprecedented genus- genome-wide resource. However, since its inception, these datasets for evolutionary inference biological discovery have become increasingly outdated, outmoded, inaccessible. Here, we...
While developmentally regulated genes are generally conserved, transformer (tra), a key locus involved in the regulation of sexual differentiation, is highly diverged between species Drosophila. With an aim to understand its divergence sibling species, we investigated tra sequence variation among members Drosophila melanogaster complex, D. melanogaster, simulans, mauritiana, and sechellia. In this group, rapid yet clocklike exhibits large differences protein size. contains 13–amino acid...
Domesticated animals quickly evolve docile and submissive behaviors after isolation from their wild conspecifics. Model organisms reared for prolonged periods in the laboratory also exhibit similar shifts towards these domesticated behaviors. Yet whether this divergence is due to inadvertent selection lab or fixation of deleterious mutations remains unknown.Here, we compare genomes lab-reared wild-caught Drosophila melanogaster understand genetic basis recently endowed common models. From...
Abstract Deep‐sea coral communities are key components of the Gulf Mexico ecosystem and were adversely affected by Deepwater Horizon ( DWH ) oil spill. Coral colonies exposed to dispersant exhibited mortality, damage physiological signatures stress. Understanding how corals respond exposure at molecular level is important elucidate sublethal effects disaster reveal broader patterns stress responses. Gene expression profiles from RNA seq data compared between an impacted site a reference...
Charles Darwin remarked that "males, with their superior strength, pugnacity, armaments, unwieldly passion and love songs, are almost always the more active most often, initiators of sexual interactions". Here, we propose such male sex drive directly impacts genome by leading to its progressive masculinization--genes possess sex-specific effects on fitness accumulate a much greater extent generally diverged. The larger proportion versus female modifiers in combination stronger selection may...