Kerstin Howe

This study presents the first comprehensive phylogenomic analysis of Cypriniformes, establishing a robust backbone topology and identifying unresolved conflicts in evolutionary relationships.

The paper assembles chromosome-scale diploid genomes of prairie and meadow voles using a single-library approach, identifying a prairie-vole-specific duplication of Avpr1a associated with pair bonding.

The Vertebrate Genomes Project Phase I provides high-quality reference genomes for 816 species, enabling evolutionary and conservation insights across vertebrates.

The paper presents a mouse pangenome with 17 strains, resolving structural complexity and improving RNA-Seq analysis by identifying non-reference genes and VNTR polymorphisms.

This study investigates the genomic and genetic factors underlying speciation and pigment pattern diversification in Danio fishes, revealing introgression, functional divergence of specific genes, and evolutionary changes in protein and regulatory sequences.

Across 4883 species, standardised high-molecular-weight DNA extraction passed 96% of chordate and 91% of plant species, while fungi failed at 34.2%; ultra-low-input PacBio libraries rescue many low-yield samples.

The paper examines sex chromosomes in 14 elasmobranch species, identifying conserved X chromosomes and a shared candidate gene for sex determination.

The paper presents the reference genome of Cheirolophus tagananensis, providing tools for studying genetic adaptation and supporting conservation strategies.

This study integrates genomic, transcriptomic, and morphological data from the small-spotted catshark to uncover molecular mechanisms underlying sensory organ evolution in jawed vertebrates.

The paper describes the European Reference Genome Atlas (ERGA) pilot project, which tests a decentralized model for producing high-quality reference genomes across 98 European species.

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

The paper generates and analyzes genome assemblies for 24 Antarctic notothenioid fish species to study cold adaptations, identifying genomic changes related to antifreeze proteins and haemoglobin loss.

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.

The paper uses genome assembly and population genomics to show Altai falcons are a distinct species with unique genetic traits.

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.

The paper presents a pangenome for the barn swallow and identifies genes under selection linked to synanthropy and domestication traits.

This paper presents a haplotype-resolved genome assembly of the Nile rat, revealing unique genomic features relevant to type 2 diabetes and metabolic dysfunctions.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper quantifies false duplications in genome assemblies of platypus, zebra finch, and Anna's hummingbird, showing they lead to overestimated gene family expansions.

The paper evaluates new vertebrate genome assemblies from the VGP against previous references, finding significant improvements in completeness and accuracy.

This paper introduces Asset, a tool to evaluate genome assemblies using long-range data, demonstrating its ability to detect structural misassemblies in human, goat, and fish genomes.

The paper generates the first chromosome-length annotated genomes and transcriptomes of black and mute swans, revealing immune system limitations and plumage-related genetic differences.

The paper improves a telomere-to-telomere human genome assembly by developing a repeat-aware polishing strategy, fixing 51% of errors and increasing assembly quality.

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.

The paper presents a high-quality genome and transcriptome of the tufted duck, comparing short and long-read sequencing technologies for transcriptome assembly.

The paper presents a high-quality chromosome-level genome assembly of the reed warbler and identifies two macrochromosomal fusions.

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