My research interests are broadly in the area of computational
biology. This would include problems related to sequence analysis,
modeling protein structure and algorithms for finding patterns in
protein structures, and functional genomics. Of late, I have gotten quite
interested in systems biology, in particular the analysis of protein-protein
interaction networks. In general, I am
interested in problems which pose interesting computational
challenges and also have significant biological relevance.
Academic/Research/Work Background
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Indian Institute of Technology Kanpur, 1996-2000: Bachelor of Technology, majoring in
Computer Science. Took courses in algorithms, discrete math, toc,
programming languages, compilers, databases, A.I., architecture etc.
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Stanford University, 2000-2002: Master of Science in C.S. Took
courses in A.I (grad level), Machine Learning, Vision, OOP,
Multi-Agent Systems, Structural Biology, Statistics in Comp Bio,
Algos in Comp Bio, Graphical Models in A.I. etc. Did my M.S.
research on finding structural motifs in proteins. We published a
related paper in the Pacific Symp. on Biocomputing '03, Hawaii. The
research report was also awarded the CS Dept's Best Masters
Research Award.
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Accelrys Inc, 2002-2003: Part of the BioInformatics group in the
Life Sciences R&D Divn. Was working on sequence analysis programs
and software. Check out some of their cool software!
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UCSD Extension, 2002-2003: Took courses in Molecular Biology and
Drug Discovery: Tools and Techniques.
Publications
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Influence Flow: Integrating Pathway-specific RNAi
Data with Protein Interaction Networks.
Rohit Singh and Bonnie Berger.
Presented at the PLoS Track of the 15th Int'l Conference on
Intelligent Systems for Molecular Biology (ISMB 2007).
This was an abstract and, as per guidelines of the PLoS
track at ISMB, should be cited as "Personal Communication".
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Predicting and Annotating Catalytic Residues: An Information Theoretic Approach.
Beckett Sterner, Rohit Singh and Bonnie Berger.
Journal of Computational Biology, To Appear.
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Pairwise Global Alignment of Protein Interaction
Networks by Matching Neighborhood Topology.
Rohit Singh, Jinbo Xu and Bonnie Berger.
Proceedings of the 11th Int'l Conference on Research in Comp. Mol. Biol (RECOMB), 2007
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Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments.
David Sontag*, Rohit Singh* and Bonnie Berger. (*: contributed equally)
Proceedings of the 12th Pacific Symposium On BioComputing, Hawaii 2007
Project Webpage
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Struct2Net: Integrating Structure Into Protein-Protein
Interaction Prediction.
Rohit Singh*, Jinbo Xu* and Bonnie Berger.(*: contributed equally)
Proceedings of the 11th Pacific Symposium On BioComputing, Hawaii 2006
Project Webpage
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An Active Learning Approach to Sampling in
Time-Series Experiments: With Applications to Gene Expression
Analysis.
Rohit Singh, Nathan Palmer, David Gifford, Bonnie
Berger, and Ziv Bar-Joseph.
Proceedings of the 22nd Int'l Conf. on
Machine Learning, 2005.
Project Webpage
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ChainTweak: Sampling From the Neighbourhood of a
Protein Conformation.
Identifying Structural Motifs in
Proteins, Rohit Singh and Bonnie Berger.
Proceedings of the 10th Pacific Symposium On BioComputing, Hawaii 2005.
Project Webpage
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Identifying Structural Motifs in Proteins.
Rohit Singh and Mitul Saha.
Proceedings of the 8th Pacific Symposium On BioComputing, Hawaii 2003
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Classification of Music Signals In The Visual Domain
Hrishikesh Deshpande, U. Nam, Rohit Singh.
Presented in Digital Audio Effects Conf `01, Ireland
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A Multidimensional Interval Algebra Approach for Identifying Block-Structured Media
Ankur Lahoti, Rohit Singh and Amitabha Mukerjee.
Presented in The Third IAPR Int'l Workshop on Graphics
Recognition (GREC) '99, India. Reprinted in
Lecture Notes in Computer Science (vol. 1941), Springer Verlag.
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Document Block Layout Analysis and Document Template Generation
Rohit Singh, Ankur Lahoti and Amitabha Mukerjee.
Presented in Document Layout Interpretation and Analysis Workshop ( DLIA)'99, Bangalore, India