Anthony Gitter

GHC 9221

School of Computer Science

Carnegie Mellon University

a...@cs.cmu.edu

About me

I successfully defended my Ph.D. thesis 'Identifying the Signaling Cascades and Regulatory Mechanisms that Control Stress Responses'. Soon I'll be starting a postdoc at Microsoft Research New England working in close collaboration with Ernest Fraenkel of MIT and Riccardo Zecchina of Politecnico di Torino.

I'm finishing my fifth (and final) year in the Computer Science Department at Carnegie Mellon University. My advisor is Ziv Bar-Joseph, which makes me a proud member of the Systems Biology Group. My research interests are computational biology and machine learning, and I am especially interested in dynamic models of signaling and transcriptional regulatory networks.

During the summer of 2010 I interned with David Heckerman's group at Microsoft Research, where I developed techniques for learning causal networks from SNP, gene expression, and disease phenotype data. I received my M.S. in Computer Science from Carnegie Mellon in May 2010 and my B.S. in Computer Science from Arizona State University, where I worked with Chitta Baral and Graciela Gonzalez in the BioAI lab.

Research

Publications

Computationally efficient measure of topological redundancy of biological and social networks.
Réka Albert, Bhaskar DasGupta, Rashmi Hegde, Gowri Sangeetha Sivanathan, Anthony Gitter, Gamze Gürsoy, Pradyut Paul, Eduardo Sontag.
Physical Review E. 84:3, 2011.
Supporting website
Discovering pathways by orienting edges in protein interaction networks.
Anthony Gitter, Judith Klein-Seetharaman, Anupam Gupta, Ziv Bar-Joseph.
Nucleic Acids Research. 39:4, 2011.
Featured article representing the top 5% of papers in terms of originality, significance, and scientific excellence.
Supporting website
Backup in gene regulatory networks explains differences between binding and knockout results.
Anthony Gitter, Zehava Siegfried, Michael Klutstein, Oriol Fornes, Baldo Oliva, Itamar Simon, Ziv Bar-Joseph.
Molecular Systems Biology. 5:276, 2009.
CBioC: Beyond a Prototype for Collaborative Annotation of Molecular Interactions from the Literature.
Chitta Baral, Graciela Gonzalez, Anthony Gitter, Craig Teegarden, Amanda Zeigler, Geeta Joshi-Topé.
Proceedings of the Life Sciences Society Computational Systems Bioinformatics Conference (CSB 2007). Vol 6, pp 381-384, 2007.
Supporting website
Integrating Knowledge from Biomedical Literature: Normalization and Evidence Statements for Interactions.
Graciela Gonzalez, Luis Tari, Anthony Gitter, Robert Leaman, Shawn Nikkila, Ryan Wendt, Amanda Zeigler, Chitta Baral.
Proceedings of the Second BioCreative Challenge Evaluation Workshop. 2007.

Book chapters

Computational Methods for Analyzing Dynamic Regulatory Networks.
Anthony Gitter, Yong Lu, Ziv Bar-Joseph.
In Computational Biology of Transcription Factor Binding, Methods in Molecular Biology series. Vol 674, pp 419-441, 2010.

Talks

Identifying the Signaling Cascades and Regulatory Mechanisms that Control Stress Responses.
Anthony Gitter, Miri Carmi, Naama Barkai, Ziv Bar-Joseph.
6th Annual RECOMB Satellite on Systems Biology. November 17, 2010.
Redundancy in the Eukaryotic regulatory code explains differences between binding and knockout experiments.
Anthony Gitter, Oriol Fornes Crespo, Baldo Oliva, Itamar Simon, Ziv Bar-Joseph.
5th Annual RECOMB Satellite on Regulatory Genomics. November 1, 2008.
Video, Proceedings

Posters

Backup in gene regulatory networks explains differences between binding and knockout results.
Anthony Gitter, Zehava Siegfried, Michael Klutstein, Oriol Fornes, Baldo Oliva, Itamar Simon, Ziv Bar-Joseph.
6th Annual RECOMB Satellite on Regulatory Genomics, 2009.
Proceedings
A Customizable Evalutation Platform for Biomedical Information Extraction Systems.
Graciela Gonzalez, Anthony Gitter, Craig Teegarden, Chitta Baral.
ISCB Rocky Mountain Bioinformatics Conference, 2006.

Undergraduate honors thesis

Constituent Tree-Based Extraction and Evaluation of Protein-Protein Interactions from Biomedical Literature.
Anthony Gitter.
Arizona State University, The Barrett Honors College, 2007.

Press

Cells Are Like Robust Computational Systems, Carnegie Mellon-Led Team Reports : CMU Press Release
Annotate While You Read: Science

Teaching

In the Fall 2010 semester I was a TA for 10-601, Machine Learning.

During the Fall 2008 semester I was a TA for 15-211, Fundamental Data Structures and Algorithms.