Anthony Gitter I've moved to Microsoft Research ang...@microsoft.com

About me

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. 29:13, 2013.
  21st Annual International Conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology (ISMB/ECCB 2013) Proceedings.
  Supporting website
• 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.
  Supporting website
• 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 common and patient-specific pathways in heterogeneous diseases.
  Anthony Gitter, Nurcan Tuncbag, Andrea Pagnani, Carlo Baldassi, Alfredo Braunstein, Riccardo Zecchina, Ernest Fraenkel.
  MIT Center for Environmental Health Sciences 2013 Annual Poster Session.
• 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

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

Last updated June 25, 2013