Brad Balderson

Systematic Regional Bias is Widespread in ChIP-seq

The paper identifies systematic regional bias in ChIP-seq data across multiple experiments and proposes metrics to improve data integration.

Vgll2 and Tead1 Govern Generation of Mouse and Human Hypothalamic Hypocretin (Orexin) Neurons

This paper identifies Vgll2 and Tead1 as key regulators of Hcrt neuron generation in mouse and human, showing their role in differentiation and potential for cell therapy.

Comprehensive molecular impact mapping of common and rare variants at GWAS loci

DNACipher predicts variant effects across cell types and assays, identifying imVars at most GWAS loci with support from experimental data.

Joint single-cell capture of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression

Superb-seq captures single-cell Cas9 edits and transcriptomes, revealing on- and off-target effects on gene expression in over 34,000 cells.

stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues

Cytocipher determines significantly different populations of cells in single cell RNA-seq data

Cytocipher identifies significant cell populations in scRNA-seq data by statistically determining transcriptionally distinct clusters, revealing new cell types and subpopulations across various biological contexts.

Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition

The paper uses spatial transcriptomics to analyze how CDK4/6 inhibition affects tumor response in SHH medulloblastoma by mapping cellular states and spatial organization.

i-stLearn: An interactive platform for spatial transcriptomics analysis

i-stLearn provides an interactive web platform for analyzing spatial transcriptomics data, enabling cell clustering, interaction analysis, and trajectory inference.

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)

The paper introduces GRASP, a method for ancestral sequence reconstruction that handles large datasets and indels, demonstrating its ability to generate biologically active enzyme ancestors.

Selective Requirement for Polycomb Repressor Complex 2 in the Generation of Specific Hypothalamic Neuronal Sub-types

This study shows that while most hypothalamic neurons develop normally without the H3K27me3 epigenetic mark, specific neuronal subtypes are sensitive to its loss.

ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates

ChIP-R improves the reproducibility of ChIP-seq and ATAC-seq peak calls by statistically combining replicates, outperforming existing methods in recovering transcription factor binding sites.