Kasper D. Hansen

The paper creates a single-cell atlas of sex-differentially expressed genes in human hypothalamus regions, revealing molecular sex differences and their links to neurodevelopmental disorders.

The paper provides an open-source online book for analyzing spatial transcriptomics data using Bioconductor in R, with reproducible code and datasets.

This study investigates the molecular consequences of epigenetic machinery disruption in neuronal progenitors by knocking out EM factors and analyzing gene expression and DNA methylation changes.

CosMx spatial transcriptomics of bone marrow from 6 refractory/relapsed AML patients shows CD14+ monocytes rising in leukemia-cell neighborhoods after pembrolizumab in responders, dendritic cells in nonresponders.

This paper introduces mNSF, a framework for analyzing multi-sample spatial transcriptomics data that identifies factors, shared regions, and biological functions without requiring spatial alignment.

The paper introduces a likelihood-based method to identify sample-specific CpG loci in long-read sequencing data, improving accuracy in methylation analysis by reducing reference bias.

The paper examines chromatin disruption in different cell types of Kabuki syndrome mice and finds that neuronal chromatin abnormalities differ from those in B and T cells, with unique disruptions at CpG islands and aging-related regions.

The paper introduces BNBC, a normalization and batch correction method for Hi-C data, improving cross-sample comparisons and analyses.

The paper aggregates RNA-seq data to infer consensus and tissue-specific gene co-expression networks, finding that larger sample sizes improve network quality and trait heritability annotations.

The paper creates a mouse model of Weaver syndrome and shows that inhibiting KDM6A/6B can reverse excessive osteogenesis caused by an EZH2 mutation.

This paper analyzes the limitations of RNA velocity estimates by examining how different workflow steps affect the vector field and concludes that RNA velocity should not be interpreted as predicting future cellular states.

The paper predicts genotypes for 336,463 samples using RNA-seq data from Recount3, achieving high accuracy and enabling population structure analysis.

This study compares growth retardation in mouse models of Kabuki syndrome 1 and 2, finding similar transcriptional profiles in their chondrocyte models.

The paper introduces nnSVG, a scalable method for identifying spatially variable genes using nearest-neighbor Gaussian processes, and demonstrates its performance on experimental data and simulations.

The paper uses mouse models to study diet-induced metabolic syndrome, identifies strain-specific transcriptional and epigenomic changes, and tests genotype-targeted pharmacological interventions.

The paper identifies high-value CpGs in the human methylome associated with allergic sensitization using a custom array and WGBS data from airway epithelial cells.

recountmethylation provides processed blood DNA methylation data and analysis tools, showing genetic ancestry and cell fractions explain most DNAm variation and validating DMPs between sexes.

The paper introduces modbamtools, a tool for analyzing single-molecule epigenetic data, enabling visualization, manipulation, and downstream analysis of base modifications in long-read sequencing data.

This study quantifies and models Chromium-based snRNA-seq data, finding they follow a negative binomial distribution and highlighting the impact of quantification strategies on downstream analysis.

The paper develops a mammalian methylation array to profile methylation levels at conserved sequences across species, enabling cross-species comparisons and epigenetic biomarker development.

The paper introduces tricycle, a method to predict cell cycle position from single-cell RNA-seq data using transfer learning, showing it generalizes across datasets and species.

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.

recount3 provides uniformly processed RNA-seq data and tools for querying and analyzing large-scale human and mouse expression and splicing data.

The paper identifies shared epigenetic and transcriptomic disruptions across three MDEMs to map functional epigenetic variation.

Compartmap infers higher-order chromatin structure from scRNA-seq and scATAC-seq data, matching specialized chromatin capture methods and identifying clinically relevant structural alterations in single cells.

The paper identifies brain region-specific variably methylated regions (VMRs) enriched for schizophrenia heritability using DNA methylation data from neuronal nuclei across multiple brain regions.

The paper analyzes 35,360 DNAm array samples from GEO, identifies tissue sources, evaluates quality assessments, and provides a database with annotated data through an R/Bioconductor package.

The paper identifies DNA methylation at ZNF300 associated with fetal sex and placental morphology using whole genome bisulfite sequencing and multiple datasets.

This study introduces nanoNOMe, a method combining NOMe-seq and nanopore sequencing to profile chromatin accessibility and methylation in human cell lines, revealing phased methylation, large-scale patterns, and structural variations.

The paper shows that promoter CpG density predicts gene loss-of-function intolerance and improves prediction models for LoF-intolerant genes.