Stephen J. Bush

The paper shows that somatic variants' transcriptomic impact depends on cellular context, not just sequence, using single-cell transcriptomics and new tools.

This study uses Hi-C data from 1,025 species to trace the evolution of 3D genome architecture, revealing distinct patterns in global folding and checkerboard structures across different lineages.

The paper presents a telomere-to-telomere diploid reference genome for the Chinese Quartet, improving centromere structure annotation and enabling population-specific structural variant analysis.

The paper investigates the molecular overlap between spermatogonia and neural programs, showing enrichment of brain-expansion genes in spermatogonia across mammals.

The paper develops LTR_Stream to cluster LTR-RTs in Papaver species, revealing complex interactions between retrotransposons and the host genome, including effects of allopolyploidization.

This study shows that wild-type bone marrow cells can restore macrophage populations and reverse developmental defects in Csf1rko rats, but not in the brain.

The paper analyzes centromere diversity across hundreds of human genomes using HiFi sequencing and a novel HOR annotation pipeline, identifying 23 HORs with significant copy number variation and three centromere genotypes on chromosomes 5, 8, and 17.

This study identifies a foetal-like state 0B in human spermatogonial stem cells that maintains a suppressive transcriptomic program, contrasting with rodent models where this state is not maintained into adulthood.

This study generates haplotype-resolved assemblies and a variant benchmark for a Chinese monozygotic twin quartet using advanced sequencing and computational methods.

The paper presents a method to assess recurrence risk of de novo mutations in families using deep-sequencing and haplotyping, finding that 59% of DNMs had reduced risk below 0.1%.

The paper generates a rat RNA-seq transcriptomic atlas and uses gene correlation networks to identify tissue-specific transcript clusters and biological processes.

This study shows that Csf1r mutation in mice, rats, and humans causes developmental defects, and bone marrow transfer can reverse some phenotypes by restoring macrophages.

This study evaluates the impact of read trimming on bacterial SNP calling accuracy and finds minimal, statistically insignificant improvements, suggesting trimming adds little value in most cases.

This study investigates gene expression in sheep cardiovascular tissues to understand vascular calcification, highlighting gene balance and extracellular matrix roles.

This study identifies genetic loci and gene expression patterns associated with Campylobacter resistance in broiler chickens, providing insights for breeding programs.

This study evaluates SNP calling pipelines' performance on bacterial data, finding that reference genome selection strongly impacts accuracy, with Snippy performing consistently well across diverse genomes.

The paper evaluates methods for detecting human contamination in microbial sequencing data and finds that classification-based methods are most effective, though combining methods improves accuracy for short reads.

The paper assesses the feasibility of improving milk yield and mastitis resistance in dairy sheep through genomic analysis, finding no significant genetic correlation between the traits.

This study develops an unbiased pipeline for allele-specific expression analysis in sheep, revealing pervasive and tissue-specific allelic imbalance across genes and SNVs.

The paper creates a gene expression atlas for goats, identifying transcriptional differences in immune signatures compared to sheep.

The paper identifies a missense variant in OLFML3 as a candidate for severe goniodysgenesis and glaucoma in Border Collies.

This study characterizes gene expression changes in the gastrointestinal tract of sheep from birth to adulthood, identifying developmental stage-specific differences, particularly in the rumen complex and immune-related genes.

The paper integrates public and new RNA-seq data to create a chicken mRNA expression atlas, revealing tissue-specific gene clusters and developmental patterns.

The paper characterizes the metagenome of UK honey bee colonies, identifying microbial diversity and potential pathogens in their microbiota.

This study shows that environmental enrichment in pigs increases neuronal activity and synaptic plasticity genes while reducing microglial activity, similar to findings in rodents.

The paper identifies a consensus set of ruminant lncRNAs by combining cross-species RNA-seq data and positional conservation, showing that stochastic sampling can be mitigated through this approach.

This study identifies TIM4-expressing mononuclear phagocytes in chickens, distinguishing phagocytic Kupffer cells from non-phagocytic DC-like cells using CSF1R reporters.

This paper presents a high-resolution gene expression atlas for sheep, identifying transcriptional signatures and functional annotations across tissues and developmental stages.