Daniel E. Cook

The paper analyzes the genomic diversity of C. tropicalis, finding geographic correlation and hyper-divergent regions linked to environmental adaptation.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

The paper analyzes over 2,000 Caenorhabditis briggsae wild strains to uncover genetic diversity, population structure, and evolutionary mechanisms shaping phenotypic variation.

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

This study compares Element Avidity sequencing to Illumina sequencing, finding higher accuracy in mapping and variant calling, especially at lower coverages and in challenging genomic regions.

DeepPolisher improves genome assembly accuracy by reducing errors using a transformer model and phasing method, achieving over 70% indel error reduction.

This paper introduces pangenome-aware DeepVariant, a variant caller that improves accuracy by using a pangenome reference, outperforming linear-reference-based DeepVariant by up to 25.5%.

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

The paper develops a benchmark for detecting low-frequency mosaic variants in the HG002 reference material using high-coverage sequencing data and validates its utility across multiple technologies.

This paper introduces a local haplotype approximation method to improve variant calling accuracy across long-read sequencing platforms without increasing computational overhead.

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

This paper develops a deep-learning based RNA-seq germline variant caller that outperforms existing tools like Platypus and GATK.

The paper introduces a tool called best for efficiently quantifying sequencing errors in aligned reads and shows it is 16 times faster than existing methods.

The paper introduces reciprocal introgression line populations in C. elegans to study genetic interactions and complex trait architectures through QTL mapping and expression analysis.

This paper introduces an automated method for quantifying chemotaxis index in C. elegans using liquid-handling robots and a custom image analysis tool.

DeepConsensus improves PacBio HiFi read accuracy and assembly quality using a gap-aware transformer model.

This study identifies a nematode-specific gene, scb-1, as a genetic determinant of bleomycin-response variation in C. elegans using linkage mapping and CRISPR-Cas9 experiments.

The paper identifies QTL underlying toxin response variation in C. elegans and validates their contributions through experimental assays.

The paper identifies QTL associated with benzimidazole resistance in nematodes using genetic mapping and phenotyping.

The paper identifies a single amino acid substitution in topoisomerase II that explains variation in drug sensitivity across C. elegans isolates and human cell lines.