Publications

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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

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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

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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

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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

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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

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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

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

PF Przytycki and M Singh
Cell Systems (2020)

Paper PubMed Code

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

PF Przytycki and M Singh
Genome Medicine (2017)

Paper PubMed Software

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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

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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