Speaker: Anthony Gitter

 Title:

Linking the Signaling Cascades and Dynamic Regulatory Networks Controlling Infection Response

 Abstract:

Cells undergo rapid and drastic changes to mount a response to pathogen infection.  The response is triggered when upstream proteins detect the pathogen and propagate signals via cascades of protein-protein interactions to transcription factors, which selectively activate or inhibit genes.  Although these upstream initiators and the resulting transcriptional effects can be characterized experimentally, the intermediate proteins driving signaling and transcription cannot be directly observed.  We present a technique for integrating large-scale data sources to predict temporal transcription factor activity as well as the directed signaling pathways that activate these regulators.  Studies of stress response in yeast validate our algorithm’s ability to recover known pathways and identify missing participants.  Our approach also provides new insights into the human response to influenza infection.  The pathways we recover can be used to accurately predict RNA interference effects by estimating the impact a gene knockdown has on downstream transcription factors.

 Bio:

Anthony Gitter is a joint postdoctoral researcher at Microsoft Research New England and the Department of Biological Engineering at the Massachusetts Institute of Technology.  His PhD in Computer Science is from Carnegie Mellon University.  His computational systems biology research involves using probabilistic graphical models and graph theory to model how biological networks are perturbed in human diseases.  Specific interests include viral infection, cancer, and the dynamics of biological processes.  He was awarded a National Science Foundation Graduate Research Fellowship, and his study of temporal stress responses was recognized as a top ten paper of 2012-2013 in regulatory and systems genomics.

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