Anthony Gitter

I've moved to Microsoft Research

ang...@microsoft.com

About me

I'm a postdoc at Microsoft Research New England and a visiting scientist at MIT working in close collaboration with Ernest Fraenkel of MIT and Riccardo Zecchina of Politecnico di Torino. In May 2012 I defended my Ph.D. thesis 'Identifying the Signaling Cascades and Regulatory Mechanisms that Control Stress Responses' and obtained my Ph.D. in Computer Science from Carnegie Mellon University. My advisor was Ziv Bar-Joseph, which made me a proud member of the Systems Biology Group.

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.

My research involves developing algorithms that leverage biological networks to connect different types of experimental data and detect surprising relationships among them. I am working to use such techniques to study human disease, in particular cancer and viral infection.

Research

Publications

Identifying proteins controlling key disease signaling pathways.
Anthony Gitter, Ziv Bar-Joseph.
Bioinformatics. To appear.
21st Annual International Conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology (ISMB/ECCB 2013) Proceedings.
Linking the signaling cascades and dynamic regulatory networks controlling stress responses.
Anthony Gitter, Miri Carmi, Naama Barkai, Ziv Bar-Joseph.
Genome Research. 23:2, 2013.
Supporting website
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.
Marcel H Schulz, William E Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph.
BMC Systems Biology. 6:1, 2012.
A network-based approach for predicting missing pathway interactions.
Saket Navlakha, Anthony Gitter, Ziv Bar-Joseph.
PLoS Computational Biology. 8:8, 2012.
Studying and modelling dynamic biological processes using time-series gene expression data.
Ziv Bar-Joseph, Anthony Gitter, Itamar Simon.
Nature Reviews Genetics. 13:8, 2012.
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

Linking signaling pathways and dynamic regulatory networks.
Brown University pattern theory seminar. November 14, 2012.
Identifying the signaling cascades and regulatory mechanisms that control stress responses.
6th Annual RECOMB Satellite on Systems Biology. November 17, 2010.
Redundancy in the Eukaryotic regulatory code explains differences between binding and knockout experiments.
5th Annual RECOMB Satellite on Regulatory Genomics. November 1, 2008.
Video, Proceedings

Posters

Identifying signaling pathways associated with medulloblastoma subtypes from "omic" data.
Tenley C. Archer, Aviad Tsherniak, Nurcan Tuncbag, Anthony Gitter, Shyamal Dilhan Weeraratne, Jessica Pierre Francois, Pablo Tamayo, Jill Mesirov, Ernest Fraenkel, Scott L. Pomeroy.
American Association for Cancer Research Annual Meeting 2013.
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 evaluation platform for biomedical information extraction systems.
Graciela Gonzalez, Anthony Gitter, Craig Teegarden, Chitta Baral.
ISCB Rocky Mountain Bioinformatics Conference, 2006.

Theses

Identifying the Signaling Cascades and Regulatory Mechanisms that Control Stress Responses.
Ph.D. thesis.
Carnegie Mellon University, 2012.
Constituent Tree-Based Extraction and Evaluation of Protein-Protein Interactions from Biomedical Literature.
Undergraduate honors thesis.
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.