Rachel J. Waugh O'Neill

This study generates transgene-free iPSCs from the fat-tailed dunnart, demonstrating their pluripotency and potential for use in conservation biotechnology.

The paper presents chromosome-scale genomes for two walnut species and identifies gene presence/absence differences linked to fungal defense mechanisms between tolerant and susceptible populations.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

This study uses paleogenomes of dire wolves to resolve their evolutionary relationships and identify genes under diversifying selection.

This paper develops a DNA extraction protocol for museum-grade insects, enabling long-read sequencing, phylogenetics, and methylation profiling from degraded samples.

This study examines microbial, dietary, and pathogen communities in fresh and decomposing bat guano from anthropic maternity colonies, showing how decomposition and roost environment affect these communities.

This study establishes a long-term culture system for rock dove primordial germ cells, enabling germline manipulation and conservation applications.

The paper generates genome assemblies for two arid-zone marsupials and finds contrasting demographic responses to historical climate changes.

The paper constructs a pangenome of threatened mink subspecies to identify adaptive signatures and evolutionary history using genome assemblies and functional analysis.

This study investigates genetic factors contributing to high cancer susceptibility in marsupials by comparing genome expansions of oncogenes between dasyurid and non-dasyurid species.

The paper investigates how neocentromeres reshape chromatin and identifies conserved features of native centromeres using haplotype-resolved assemblies and multi-omics data.

The paper studies NUMTs in great ape T2T genomes, showing they recapitulate species tree topology and are enriched in non-functional regions.

The paper uses Fiber-seq to show that regional centromeres have dichromatin organization, with accessible and compacted chromatin, which is conserved across species despite DNA sequence differences.

The paper identifies centromeric transposable elements and epigenetic features in the eastern hoolock gibbon that contribute to karyotypic variation and chromosomal instability.

This study investigates Jockey-3 retroelement transcription and RNA localization at centromeres in Drosophila, showing its correlation with CENP-A and potential role in centromere maintenance.

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.

This paper presents the first chromosome-level genome assembly and annotation for the desert hairy scorpion Hadrurus arizonensis, providing a critical resource for arachnid phylogeny and functional genomics.

The paper investigates Alu-driven DNA transductions in primate genomes and finds no evidence of Alu-mediated transductions in humans, chimpanzees, or rhesus monkeys.

The paper presents methylation profiles for two maple species using long-read sequencing to quantify methylation across all 5mC contexts, revealing patterns in transposable elements and gene regulation.

The paper generates a chromosome-scale reference genome for the eastern quoll and identifies genomic signatures of historical decline and pelage color evolution.

The paper presents a chromosome-scale reference genome for butternut (Juglans cinerea), an endangered species, using Oxford Nanopore sequencing and scaffolding with a related species genome.

The paper presents long-read assemblies of 43 diverse human Y chromosomes, revealing extensive structural complexity and variation across 180,000 years of evolution.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

The paper uses a complete human genome assembly to analyze epigenetic patterns in previously uncharacterized genomic regions, revealing methylation and chromatin accessibility features in satellite DNA and centromeres.

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 the first de novo repeat discovery and annotation of a complete human reference genome, identifying novel satellite arrays and characterizing new classes of complex repeats.

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

This study examines how chromosomal rearrangements in the gibbon genome affect TAD boundaries and epigenetic features, finding overlap between rearrangement breakpoints and TAD boundaries.

This paper introduces a probabilistic model to compare multi-species functional genomic data, showing it can identify genomic regions with distinct evolutionary patterns of DNA replication timing across primates.

This study presents a tissue-specific transcriptome of Poeciliopsis prolifica to identify genetic adaptations related to placental evolution in fish.