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Archisman Rudra
NYU Bioinformatics Group,
715 Broadway, Rm 1014
New York, NY 10003
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Phone: 212 998 33xx
Fax: 212 998 33xx
e-mail:archi [at] cs.nyu.edu
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Research Interest
I have a strong background in computer vision, learning, geometry and
other areas of mathematics. Bioinformatics is a fertile ground for applying
these skills. Specifically, I am interested in probabilistic modeling of
genomic evolution, their effect on protein network structures, as well as
understanding the properties of these networks with tools from the theory
of dynamical systems.
Current Projects
I am currently involved with several projects at the NYU bioinformatics group.
- VALIS Project: VALIS is a software architecture for biology
that includes many algorithms of biological interest, a visualization tool,
an efficient backend for handling operations on multiple long sequences,
as well as a plugin architecture for rapid prototyping.
- Genome Evolution Models: Our genomic sequence is not a static
object, but, like pretty much everything in biology, undergoes changes through
mutation and selective survival, i.e. evolution. Understanding the factors
which affect this is interesting in its own right. Moreover, because of the
differential evolution in the different parts of the DNA, it leads to an
understanding of the statistical properties of these different regions. We
study genomic evolution at several different levels. We use coarse
grained models designed for easy analysis, but which nevertheless capture
enough interesting dynamics, to give us an idea of the overall structure
of sequence evolution. At a finer scale, we use a gene grammar, which
is a part of VALIS, to efficiently simulate the evolutionary process
and thus obtain a more refined model.
Publications
Papers:
- A Random Walk down the Genomes: DNA Evolution in Valis.
Salvatore Paxia, Archisman Rudra, Yi Zhou, Bud Mishra.Computer,
35 (7):73--79, IEEE Press, July, 2002.
- Informative Features for Vision and Learning
Phd Thesis, Department of Computer Science, Courant Institute of Mathematical
Sciences, New York University. 2002.
- Fragment Completion in Humans and Machines
D. Jacobs, B. Rokers, A. Rudra and Z. Liu. in Advances in Neural
Information Processing Systems,14, MIT Press, Cambridge, MA,
to appear (2003).
- An Iterative Projection Model of Memory
David W. Jacobs and Archisman Rudra, NEC Technical Report, NEC Research
Institute, Princeton, New Jersey, 2000.
- Features as Sufficient Statistics
D. Geiger, A. Rudra and L. Maloney. in Advances in Neural Information
Processing Systems 10, Eds. M. Jordan, M. Kearns and S. Solla,
Denver,Colorado, 1997.
Abstracts:
- Detecting and Modeling Long Range Correlation in Genomic Sequences,
Yi Zhou, Archisman Rudra, Salvatore Paxia, Bud Mishra. International
Conference on Complex Systems (ICCS2002), Nashua, NH, June 9-14, 2002. Organized
by New England Complex System Institute.
- Genome Evolution Models, Gene Grammar and VALIS Genome Analysis
Tool,
Yi Zhou, Archisman Rudra, Salvatore Paxia and Bud Mishra. 15th annual
meeting on Genome Sequencing & Biology, Cold Spring Harbor Lab, Long
Island, May 2002.
- A Random Walk Down the Genomes: a Case Study of DNA Evolution
in VALIS
Yi Zhou, Archisman Rudra, Salvatore Paxia and Bud Mishra. Ninth DOE
Genome Contractor and Grantee Workshop, Oakland, CA, January 2002.
- Goals, Design, and Implementation of a Versatile MicroArray Data
Base
Marc Rejali, Marco Antoniotti, Vera Cherpinsky, Caroline Leventhal,
Salvatore Paxia, Archisman Rudra, Joe West and Bud Mishra. Ninth DOE Genome
Contractor and Grantee Workshop, Oakland, CA, January 2002.
- Program Transformation using the APTS System,
Deepak Goyal, Archisman Rudra and Bob Paige. Mid-Atlantic Student
Workshop on Programming Languages and Systems, East Stroudsburg, PA. 1995.
Other Links
My Courant home page.
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