Brian M. Schilder

Cell type-specific contextualisation of the human phenome: towards the systematic treatment of all rare diseases

The paper systematically identifies cell type-specific mechanisms for 86.7% of rare disease phenotypes using transcriptomic data and the Human Phenotype Ontology, with results accessible via an interactive web portal.

Genetic background shapes AI-predicted variant effects

This study introduces pVEP, a framework showing how genetic background affects AI predictions of variant effects, revealing variant effects vary across haplotypes.

orthogene: a Bioconductor package to easily map genes within and across hundreds of species

orthogene simplifies gene mapping across species and identifier systems, providing a unified framework for reproducible and scalable workflows.

CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

This study benchmarks CUT&Tag against ENCODE ChIP-seq for histone modifications, finding 54% average recall of known peaks and comparable peak caller performance.

Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk

This paper presents a single-nucleus RNA sequencing atlas of human craniofacial development, revealing cell type contributions to facial variation and disease risk.

Harnessing generative AI to annotate the severity of all phenotypic abnormalities within the Human Phenotype Ontology

This paper uses GPT-4 to automatically annotate the severity of phenotypic abnormalities in the Human Phenotype Ontology, achieving high accuracy in clinical characteristic identification.

EpiCompare: R package for the comparison and quality control of epigenomic peak files

EpiCompare is an R package that compares and quality controls epigenomic peak files, providing an interactive HTML report with minimal user input.

Atlas of genetic effects in human microglia transcriptome across brain regions, aging and disease pathologies

The paper analyzes the transcriptome of human microglia across brain regions, aging, and disease to identify genetic effects on gene expression and splicing, linking them to neurological disorders.

Fine-mapping of Parkinson's disease susceptibility loci identifies putative causal variants

This study fine-maps Parkinson's disease susceptibility loci to identify putative causal variants and their mechanisms of action.

MungeSumstats: A Bioconductor package for the standardisation and quality control of many GWAS summary statistics

MungeSumstats standardises and quality controls GWAS summary statistics, enabling secondary analysis and meta-analysis by converting them into a common format.

Discordant transcriptional signatures of mitochondrial genes in Parkinson's disease human myeloid cells

The paper identifies discordant mitochondrial gene expression patterns in PD monocytes and microglia, revealing distinct transcriptomic alterations in these myeloid cell types.

echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline

echolocatoR provides an automated pipeline for fine-mapping causal variants using summary statistics and integrates multiple functional genomic datasets.

Genome-wide association study of over 40,000 bipolar disorder cases provides new insights into the underlying biology

Meta-analysis of 41,917 European-ancestry bipolar disorder cases versus 371,549 controls yields 64 risk loci (33 novel), neuronal and synaptic gene enrichment, and 15 eQTL-prioritized genes.

Tensor Decomposition of Stimulated Monocyte and Macrophage Gene Expression Profiles Identifies Neurodegenerative Disease-specific Trans-eQTLs

The paper identifies neurodegenerative disease-specific trans-eQTLs by analyzing gene expression in stimulated monocytes and macrophages using tensor decomposition.

FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

FAIRshake evaluates the FAIRness of research digital resources through community-driven metrics, automated assessments, and visualization tools, revealing opportunities for improvement.