Bartek Wilczyński

This study performs a systematic review and transcriptomic meta-analysis of environmental enrichment in rodents, identifying core molecular programs associated with brain plasticity.

The paper shows that environmental enrichment and impoverishment affect cognitive abilities and AP-1 signaling in hippocampal neurons differently depending on cell type.

The paper introduces a new analytical pipeline for metatranscriptomic analysis and applies it to study gut microbiome changes in a Down syndrome mouse model under high-fat diet.

This paper shows that black chromatin is essential for accurate Drosophila melanogaster chromatin structure simulations, while other methods like loop extrusion or Hi-C data are not required for basic structure reconstruction.

The paper characterizes the microbiome of Down syndrome mouse models under standard and high-fat diets, finding increased microbial diversity and specific bacterial enrichment in trisomic mice.

This paper identifies that normalization techniques for Hi-C data can worsen contact decay bias and proposes using generalized linear models on non-normalized data to better detect differential contacts.

The paper introduces BPscore, a metric for comparing structural chromosome segmentations, showing it satisfies mathematical properties and correlates with gene expression and methylation changes.

The paper introduces a parallelized algorithm for reconstructing Bayesian networks on a large scale, improving efficiency while maintaining accuracy in gene regulatory network inference.

The paper introduces a Python library for enrichment analysis and visualization of gene sets and rankings using biological ontologies.

DiffTAD provides two statistical methods to detect differential contact frequency in Hi-C Topologically Associating Domains between conditions.