Eugene Wimberly Myers

Efficient and precise discovery of LTR-retrotransposon families using HiRepEat

The paper introduces HiRepEat, a method for efficiently discovering and clustering LTR-retrotransposon families across genomes, showing results on vertebrate and Drosophila genomes.

Scientific computing in the age of agentic AI: an exploratory field report

This paper explores the use of LLM-based coding agents in scientific computing, presenting case studies in the life sciences and discussing their potential and challenges.

The genome sequence of Seabra's wing-gland bat, Cistugo seabrae Thomas, 1912

The paper presents a high-quality genome assembly for the Seabra's wing-gland bat, Cistugo seabrae.

Side-necked turtle genomes reveal chromosomal dynamics, skeletal innovation and cancer resistance

This study presents seven reference genomes of side-necked turtles, revealing chromosomal dynamics, sex chromosome evolution, and molecular mechanisms underlying skeletal innovation and cancer resistance.

Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans

This study presents chromosome-level genomes for sloths and anteaters, revealing retrocopy formation and domestication as key drivers of xenarthran genome evolution and physiological specializations.

Evaluation of sequencing reads at scale using rdeval

The paper introduces rdeval, a tool for efficiently evaluating and visualizing sequencing read metrics, showing improvements in read quality and genome assembly with PacBio data.

FastGA: Fast Genome Alignment

FastGA aligns genomes significantly faster than existing methods while maintaining sensitivity and efficiently storing alignments.

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity

This paper presents a chromosome-level, haplotype-resolved genome assembly for the Eurasian minnow, revealing haplotype diversity and structural variations.

Repeated extrinsic and anisotropic mechanical inputs promote polarized adherens junction elongation

This study shows how muscle contractions and anisotropic tension drive polarized elongation of epidermal adherens junctions in C. elegans embryos.

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads

MitoHiFi assembles mitochondrial genomes from PacBio HiFi reads, identifying heteroplasmy variants and excluding nuclear contaminants, and has been used to assemble 374 mitochondrial genomes.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

The paper analyzes genomes of leatherback and green turtles to identify gene family expansions and demographic differences that may influence their ecological adaptations and conservation status.

Estimating chromosome sizes from karyotype images enables validation of de novo assemblies.

KICS estimates chromosome sizes from karyotype images to validate de novo genome assemblies, showing strong linear correlation between pixel counts and DNA content.

The complete sequence of a human genome

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

Merfin: improved variant filtering and polishing via k-mer validation

Merfin improves variant filtering and polishing by using k-mer validation, enhancing precision and reducing errors in long-read assemblies.

A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva

The paper identifies a new nematode species from Siberian permafrost and shows it shares cryptobiosis mechanisms with C. elegans dauer larvae.

DENTIST - using long reads for closing assembly gaps at high accuracy

DENTIST closes assembly gaps in short-read assemblies using long reads with high accuracy and sensitivity, outperforming existing methods on multiple species.

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

The paper develops a pipeline for mitochondrial genome assembly and identifies errors and novel duplications in reference mitogenomes.

Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization

The paper introduces EASI-FISH, a method for spatial gene expression profiling in thick brain sections, and applies it to discover novel subregions in the lateral hypothalamus.

Bidirectional neuronal migration coordinates retinal morphogenesis bypreventing spatial competition

The paper shows bidirectional neuronal migration prevents spatial competition during retinal morphogenesis in zebrafish, human tissue, and organoids.

Interactive design of GPU-accelerated Image Data Flow Graphs and cross-platform deployment using multi-lingual code generation

The paper introduces CLIJ-assistant, a tool that enables interactive GPU-accelerated image processing and cross-platform code generation for bio-image analysis.

Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations

The paper generates six reference-quality bat genomes, identifies genomic adaptations related to echolocation, immunity, and viral tolerance, and reveals regulatory elements contributing to bat traits.

CLIJ: GPU-accelerated image processing for everyone

CLIJ provides GPU-accelerated image processing through a Fiji plugin, enabling faster workflows on consumer hardware.

Long-read Data Revealed Structural Diversity in Human Centromere Sequences

The paper uses long-read sequencing to analyze human centromere sequences, revealing substantial structural diversity and novel higher-order repeats across individuals.

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

This paper develops a long-read sequencing protocol to improve variant detection and genome assembly in a human genome, achieving high accuracy and contiguity.

Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy

This paper demonstrates how deep learning-based image restoration extends fluorescence microscopy's capabilities by improving resolution, reducing photon exposure, and increasing frame rates.

Multi-scale coordination of planar cell polarity in planarians

This study investigates multi-scale coordination of planar cell polarity in planarians, identifying core pathways that mediate global polarization fields.

Non Hybrid Long Read Consensus Using Local De Bruijn Graph Assembly

The paper introduces a non-hybrid long read error correction method using De Bruijn graph assembly, showing improved correction over existing non-hybrid approaches.

Cell Dynamics Underlying Oriented Growth Of The Drosophila Imaginal Wing Disc

The paper quantifies how cell divisions and rearrangements drive anisotropic growth in Drosophila wing discs under 20E treatment.