Publications
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*, BG Bruneau* (*equal contribution)
Bioinformatics Advances (2022)
Paper
PubMed
Software
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, BG 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