Pawel F. Przytycki

A Compact Regulatory Logic Governs Fibroblast Cell State Plasticity in Fibrosis

The paper identifies a compact regulatory logic governing fibroblast plasticity in fibrosis by analyzing enhancer repression and gene perturbations across multiple tissues.

HyperCom: a hypergraph-based method to infer cell-resolved cell-cell communication

HyperCom infers cell-resolved cell-cell communication using hypergraphs from single-cell transcriptomics data, providing a continuous sender-receiver score for ligand-receptor pairs.

Cis-TERN: a graph-based method to integrate single-cell chromatin accessibility with gene expression data to infer the pseudotime ordering of cells

Cis-TERN integrates scRNA-seq and scATAC-seq data to infer pseudotime ordering without prior biological knowledge, aligning with known lineages and tracing cancer cells to progenitors.

A multimodal approach for visualization and identification of electrophysiological cell types in vivo

This paper introduces PhysMAP, a framework that uses multimodal electrophysiological data to identify and study cell types in vivo, showing improved alignment with transcriptomic cell types and circuit dynamics.

Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations

CellWalker2 improves cell type annotation and mapping by integrating multi-omic data and hierarchical relationships, outperforming existing methods in simulations and demonstrating applications in brain and immune system data.

PhysMAP - interpretable in vivo neuronal cell type identification using multi-modal analysis of electrophysiological data

PhysMAP identifies neuronal cell types from electrophysiological data by integrating multiple modalities, outperforming single-modal approaches in mouse brain recordings.

Hierarchical annotation of eQTLs enables identification of genes with cell-type divergent regulation

The paper develops a hierarchical model to annotate bulk eQTLs with cell-type specificity using single-cell chromatin data, identifying genes with divergent regulation across cell types.

Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain

The paper constructs a cross-ancestry, cell-type-informed gene regulatory atlas of the developing human brain, identifying genetic regulation and linking it to neuropsychiatric disorders.

Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis

The paper identifies BRD4-dependent immune-fibroblast crosstalk via IL1B in heart failure, showing IL1B inhibition reduces fibroblast activation and improves cardiac function.

Single Cell Epigenetics Reveal Cell-Cell Communication Networks in Normal and Abnormal Cardiac Morphogenesis

The paper uses single-cell epigenomics and machine learning to model cell-cell communication networks in cardiac development and identify dysregulation in TBX1 deletion.

CellWalkR: An R Package for integrating single-cell and bulk data to resolve regulatory elements

CellWalkR integrates scATAC-seq with bulk epigenetic data to improve identification of cell type-specific regulatory regions by using a network-based random walk model.

Cell Layers: Uncovering clustering structure and knowledge in unsupervised single-cell transcriptomic analysis

Cell Layers provides an interactive tool to explore single-cell clustering across resolutions, linking molecular data with cluster evaluation metrics.

A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease

The paper identifies a reversible transcriptional switch in cardiac fibroblasts that governs fibroblast plasticity and contributes to chronic heart disease, with MEOX1 as a key regulator.

CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues

CellWalker integrates single-cell and bulk data to improve cell labeling and annotate cell-type specific regulatory elements in complex tissues.

A Chromatin Accessibility Atlas of the Developing Human Telencephalon

The paper creates a chromatin accessibility atlas of the developing human telencephalon to identify regulatory elements and their role in gene expression and neurodevelopmental disorders.

Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated By Cis Noncoding Mutations

Single cell epigenomic atlas of the developing human brain and organoids

The paper maps chromatin accessibility in developing human brain and organoids using scATAC-seq, revealing cell type-specific regulatory elements and their role in neurodevelopment.