Publications

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

PF Przytycki and KS Pollard
Genome Biology (2024)

Paper PubMed Code

Chromatin remodelling drives immune cell–fibroblast communication in heart failure

M Alexanian, A Padmanabhan, T Nishino, JG Travers, L Ye, A Pelonero, CY Lee, N Sadagopan, Y Huang, K Auclair, A Zhu, Y An, CA Ekstrand, C Martinez, B Gonzalez Teran, WR Flanigan, CK-S Kim, K Lumbao-Conradson, Z Gardner, L Li, MW Costa, R Jain, I Charo, AJ Combes, SM Haldar, KS Pollard, RJ Vagnozzi, TA McKinsey, PF Przytycki+, and D Srivastava (+computational lead)
Nature (2024)

Paper PubMed

Massively parallel characterization of regulatory elements in the developing human cortex

C Deng, S Whalen, M Steyert, R Ziffra, PF Przytycki, F Inoue, DA Pereira, D Capauto, S Norton, FM Vaccarino, PsychENCODE Consortium, AA Pollen, TJ Nowakowski, N Ahituv, and KS Pollard
Science (2024)

Paper PubMed

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

C Wen, M Margolis, R Dai, P Zhang, PF Przytycki, DD Vo, A Bhattacharya, N Matoba, C Jiao, M Kim, E Tsai, C Hoh, N Aygün, RL Walker, C Chatzinakos, D Clarke, H Pratt, PsychENCODE Consortium, MA Peters, M Gerstein, NP Daskalakis, Z Weng, AE Jaffe, JE Kleinman, TM Hyde, DR Weinberger, NJ Bray, N Sestan, DH Geschwind, K Roeder, A Gusev, B Pasaniuc, JL Stein, MI Love, KS Pollard, C Liu, and MJ Gandal
Science (2024)

Paper PubMed

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

Z Hu, PF Przytycki, and KS Pollard
bioRxiv (2024)

Preprint Software

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

EK Lee, AE Gul, G Heller, A Lakunina, S Jaramillo, PF Przytycki, and C Chandrasekaran
bioRxiv (2024)

Preprint

Three-dimensional genome re-wiring in loci with Human Accelerated Regions

KC Keough, S Whalen, F Inoue, PF Przytycki, T Fair, C Deng, M Steyert, H Ryu, K Lindblad-Toh, E Karlsson, TJ Nowakowski, NJ Ahituv, AA Pollen, KS Pollard, and the Zoonomia Consortium
Science (2023)

Paper PubMed

Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis

AP Blair, RK Hu, EN Farah, NC Chi, KS Pollard, PF Przytycki*, IS Kathiriya*, and BG Bruneau* (*equal contribution)
Bioinformatics Advances (2022)

Paper PubMed Software

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

S Ranade, S Whalen, I Zlatanova, T Nishino, B van Soldt, L Ye, A Pelonero, LG Wallace, Y Huang, M Alexanian, A Padmanabhan, B Gonzalez Teran, P Przytycki, MW Costa, CA Gifford, B Black, KS Pollard, and D Srivastava
bioRxiv (2022)

Preprint

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

PF Przytycki and KS Pollard
Bioinformatics (2022)

Paper PubMed Software

Single-cell epigenomics reveals mechanisms of human cortical development

RS Ziffra, CN Kim, JM Ross, A Wilfert, TN Turner, M Haeussler, AM Casella, PF Przytycki, KC Keough, D Shin, D Bogdanoff, A Kreimer, KS Pollard, SA Ament, EE Eichler, N Ahituv, and TJ Nowakowski
Nature (2021)

Paper PubMed

A transcriptional switch governs fibroblast activation in heart disease

M Alexanian, PF Przytycki+, R Micheletti, A Padmanabhan, L Ye, JG Travers, B Gonzalez-Teran, AC Silva, Q Duan, SS Ranade, F Felix, R Linares-Saldana, L Li, CY Lee, N Sadagopan, Y Huang, G Andreoletti, R Jain, TA McKinsey, MG Rosenfeld, C Gifford, KS Pollard, SM Haldar, and D Srivastava (+computational lead)
Nature (2021)

Paper PubMed Code

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

PF Przytycki and KS Pollard
Genome Biology (2021)

Paper PubMed Code

A Chromatin Accessibility Atlas of the Developing Human Telencephalon

E Markenscoff-Papadimitriou, S Whalen, P Przytycki, R Thomas, F Binyameen, TJ Nowakowski, SJ Sanders, MW State, KS Pollard, and JL Rubenstein
Cell (2020)

Paper PubMed

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

PF Przytycki and M Singh
Cell Systems (2020)

Paper PubMed Code

Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes

PF Przytycki and M Singh
Genome Medicine (2017)

Paper PubMed Software

SimBoolNet - a Cytoscape plugin for dynamic simulation of signaling networks

J Zheng, D Zhang, PF Przytycki, R Zielinski, J Capala, and TM Przytycka
Bioinformatics (2010)

Paper PubMed Software

The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis

R Zielinski*, PF Przytycki*, J Zheng, D Zhang, TM Przytycka, and J Capala (*equal contribution)
BMC Systems Biology (2009)

Paper PubMed