The Shoemaker Immunosystems Laboratory

Immunopathology and Systems Biology

We develop computational tools to capture and predict immune response dynamics. Our current major research topics are Simulation and Control of the DNA and RNA Sensing Pathways, Immune Cell Inference (Data Convolution) and Network Approaches to Antiviral Drug Discovery.

The Team


Jason Shoemaker, PhD
Assistant Professor


Emily Ackerman, PhD Student
Network Virology


Robert Gregg, PhD Student
DNA Sensing


Muying Wang, PhD Student
Innate Immunity


Kyler Madara
REU Student


Serena Chang
Former REU Student


Travis La Fleur
Former REU Student


Emily Youwakim
Former REU Student


Samantha Hong
Former REU Student


James Clarke
Former REU Student

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Journal Publications

C646, a novel p300/CREB-binding protein-specific inhibitor of histone acetyltransferase, attenuates influenza A virus infection Antimicrob Agents Chemother (2016)

Identifying problematic drugs based on the characteristics of their targets Front. Pharmacol. (2015)

Multi-spectral fluorescent reporter influenza viruses (Color-flu) as powerful tools for in vivo studies Nat Commun (2015)

An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation PLoS Path (2015)

Influenza virus-host interactome screen as a platform for antiviral drug development Cell Host Microb (2014)

Disease severity is associated with differential gene expression at the early and late phases of infection in non-human primates infected with different H5N1 highly pathogenic avian influenza viruses Journal of Virology (2014)

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions PLoS Comp Bio (2013)

A comprehensive map of the influenza A virus replication cycle BMC Syst Biol (2013)

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data BMC Genomics (2012)

Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs BMC Syst Biol (2012)

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases Bioinfo (2011)

Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk BMC Syst Biol (2010)

Confidence from uncertainty--a multi-target drug screening method from robust control theory BMC Syst Biol (2010)

Design Principles in Apoptotic Signaling identified by Robust Performance Analysis Foundations of Systems Biology in Engineering Proceedings (2007)

Identifying Fragilities in Biochemical Networks: Robust Performance Analysis of the Fas Signaling-Induced Apoptosis Bio Phys J (2007)

A Hybrid Stochastic/Boolean Approach to Understanding the PAP Epigenetic Switch Foundations of Systems Biology in Engineering Proceedings (2005)

The dynamics of single-substrate continuous cultures: the role of transport enzymes J Theor Biol (2003)


3700 O'Hara Street
Office 932
Pittsburgh, PA 15261

Phone: 412 624 3318