Dariusz Plewczyński

BFWalk: backtrack-free network propagation with in-degree normalization

BFWalk is a network propagation algorithm that avoids bias toward highly connected proteins, outperforming existing methods in identifying phenotype-associated genes across four human diseases.

β-catenin-independent regulation by TCF7L2 underlies isoform redundancy during embryonic thalamic development

The paper investigates TCF7L2 isoform redundancy in thalamic development, finding β-catenin-independent regulation and a developmental switch in activity.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The challenge of chromatin model comparison and validation a project from the first international 4D Nucleome Hackathon

The paper describes a project from the 4D Nucleome Hackathon aimed at developing a workflow for comparing and validating chromatin models, identifying challenges in model comparison and software development.

Unveiling epigenetic regulatory elements associated with breast cancer development

This study identifies epigenetic regulatory elements linked to breast cancer by analyzing multi-omics data and reveals potential biomarkers and therapeutic targets.

ConsensuSV-ONT - a modern method for accurate structural variant calling

ConsensuSV-ONT combines six structural variant callers with a neural network to improve accuracy in Oxford Nanopore long-read structural variant calling.

ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps

ChromMovie models 3D chromatin structure changes across cellular trajectories using single-cell Hi-C data and cell cycle information.

Tri-omic mapping revealed concerted dynamics of 3D epigenome and transcriptome in brain cells

The paper introduces a tri-omic method to study 3D epigenome and transcriptome dynamics in brain cells across mouse lifespan, revealing distinct genomic mechanisms in neurons and non-neuronal cells.

Chromatin as a Coevolutionary Graph: Modeling the Interplay of Replication with Chromatin Dynamics

The paper introduces RepliSage, a framework that dynamically integrates replication timing, loop extrusion, and compartmentalization to simulate chromatin architecture during the cell cycle.

HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences

The paper introduces HiCDiffusion, a diffusion model that improves Hi-C matrix prediction by integrating an encoder-decoder architecture, achieving higher resolution and better resemblance to experimental data.

Multiscale Molecular Modelling of Chromatin with MultiMM: From Nucleosomes to the Whole Genome

The paper introduces MultiMM, a 3D chromatin simulation model that generates genome-wide structures from nucleosome data using energy minimization.

Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes

The paper introduces an improved cohesin HiChIP protocol and analysis pipeline to enhance detection of chromatin loops and stripes.

LoopSage: An Energy-Based Monte Carlo approach for the Loop Extrusion Modelling of Chromatin

LoopSage simulates chromatin loop extrusion using a Monte Carlo method, showing significant correlation with ChIA-PET data and phase transitions in chromatin structure.

cudaMMC - GPU-enhanced Multiscale Monte Carlo Chromatin 3D Modelling

The paper introduces cudaMMC, a GPU-accelerated Monte Carlo method for chromatin 3D modeling, showing faster performance and better model scores than previous methods.

Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions

The paper improves gene expression prediction models by incorporating protein-mediated spatial chromatin interactions, resulting in significant performance gains across multiple cell lines.

Inferring CTCF binding patterns and anchored loops across human tissues and cell types

The paper develops DeepAnchor, a deep learning model to characterize CTCF binding patterns and predict CTCF-anchored loops across human tissues, revealing sequence and chromatin features that influence loop formation and disease mechanisms.

The 3D enhancer network of the developing T cell genome is controlled by SATB1

The paper identifies SATB1 as a tissue-specific genome organizer that regulates 3D enhancer networks in developing T cells, affecting immune system homeostasis and lineage specification.

MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification

MCIBox is a toolkit for analyzing single-molecule chromatin interactions and identifying micro-domains through visualization and clustering algorithms.

Intrinsic linking of chromatin fiber in human cells

The paper introduces a graph-theoretic algorithm to identify CTCF-mediated chromatin loops that are linked in 3D space using ChIA-PET data, finding non-random linked regions with distinct centrality metrics.

Multi-scale phase separation by explosive percolation with single chromatin loop resolution

The paper models chromatin folding using explosive percolation theory and shows that 80% of loops are needed for 3D condensation across cell lines.

3dSpAn: an interactive software for 3D segmentation and analysis of dendritic spines

3dSpAn is a software tool for 3D segmentation and morphological analysis of dendritic spines, addressing segmentation and quantification challenges using multiscale algorithms and feature extraction.

PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for Dummies

PartSeg is a tool for automated segmentation and reconstruction of 3D microscopy images, designed for cell nucleus analysis with a user-friendly interface and bulk processing capabilities.

FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data

FIREcaller detects frequently interacting regions from Hi-C data and shows their association with gene regulation and GWAS variants in human tissues.

SeqPIP-2020: Sequence based Protein InteractionPrediction Contest

The paper summarizes results from a competition to develop PPI predictive models using sequence data with high-quality datasets.

Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia

This study investigates how PML/RARα alters chromatin topology and transcription in APL cells, revealing its role in repressing myeloid differentiation genes.

Ultrastructural Visualization of 3D Chromatin Folding Using Serial Block-Face Scanning Electron Microscopy and In Situ Hybridization (3D-EMISH)

This paper develops a new electron microscopy method to visualize 3D chromatin folding at ultra-resolution in human cells and finds high heterogeneity in chromatin structures.

Spring Model - chromatin modeling tool based on OpenMM

The paper introduces a tool for modeling chromatin structures using molecular mechanics and OpenMM, allowing users to generate 3D structures from contact data.

Spatial Chromatin Architecture Alteration by Structural Variations in Human Genomes at Population Scale

This study examines how structural variants in 26 human populations affect 3D chromatin structure and gene transcription, showing a link between chromatin loops and transcriptional variation.

Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells

The paper uses super-resolution microscopy to visualize a chromatin loop in human cells and validates the results with Hi-C data.

Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genome

The paper develops a thermodynamic model to predict chromatin loop stability and activity based on CTCF-mediated interactions in human B-lymphoblastoid cells.