J. J. Emerson

Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping

This study introduces TEforest, a machine learning method that improves short-read TE detection and genotyping by leveraging long-read assemblies, achieving better accuracy than traditional methods.

Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome

This study assembles and analyzes repetitive genomic regions in Drosophila melanogaster, revealing structural variation and mechanisms of concerted evolution in histone and Stellate clusters.

Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline

The paper benchmarks and evaluates SVGAP, a pipeline for structural variant discovery, genotyping, and annotation in whole-genome assemblies, showing its effectiveness in maize genomes.

The 3D architecture of the pepper (Capsicum annum) genome and its relationship to function and evolution

This study investigates the 3D genome organization of pepper, showing how chromatin structure relates to gene expression and evolution.

Evolution of genome structure in the Drosophila simulans species complex

The paper generates high-quality genomes for Drosophila simulans species complex to study repetitive DNA evolution and structural divergence between species.

Hidden genomic features of an invasivemalaria vector, Anopheles stephensi

The paper generates a high-quality genome assembly for Anopheles stephensi, identifies novel genomic features, and reveals hidden genetic elements contributing to insecticide resistance and male development.

Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi

This paper develops a gene-drive rescue system in Anopheles stephensi to efficiently modify mosquito populations for malaria control.

Physiological genomics of dietary adaptation in a marine herbivorous fish

The paper studies the physiological and genomic adaptations of a marine herbivorous fish to its diet, identifying gene family expansions and expression changes related to carbohydrate and lipid digestion.

Structural variants exhibit allelic heterogeneity and shape variation in complex traits

The paper identifies numerous structural variants in Drosophila genomes and shows they contribute to complex trait variation through allelic heterogeneity.

Inferring the genetic architecture of expression variation from replicated high throughput allele-specific expression experiments

The paper introduces a beta-binomial model to better estimate cis-effect variance in allele-specific expression experiments, reducing false positives and showing cis effects affect ~70% of genes in yeast.

Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing

The paper presents a low-cost method to assemble the Drosophila melanogaster reference genome using long-read sequencing and optical mapping, revealing structural variants and demonstrating cost-effective genome assembly.

Extensive hidden genetic variation shapes the structure of functional elements in Drosophila

The paper identifies extensive hidden genetic variation in Drosophila melanogaster by assembling a new reference genome and comparing it to the existing one, revealing structural variants linked to phenotypic traits.