Hi!
I am Manikandan Narayanan (Mani for short), a graduate student in the Computer Science division at the University of California, Berkeley. I am doing my PhD in Computational Biology with Professor Richard Karp.
UPDATE: Since June 2007, I am a postdoctoral researcher at Rosetta Inpharmatics' Research Genetics department headed by Eric Schadt. I graduated from Berkeley beginning of Summer 2007 and moved to Seattle (technically, the dissertation was submitted Fall 2007 - see below for the dissertation text!).
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PhD Research:I am interested in designing computational methods to study how the molecular mechanisms underlying cellular processes evolve. I am also interested in contemporary research topics in sequence analysis.
Manikandan Narayanan. Comparative and Evolutionary Analysis of Cellular Pathways. PhD thesis, Computer Sciences Division, University of California at Berkeley, 2007. [thesis as technical report]
Manikandan Narayanan and Richard M. Karp. Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm. Journal of Computational Biology, 14(7): 892-907, 2007. [journal link, supplemental website (software, results, etc.), arxiv preprint]
Manikandan Narayanan, Amoolya H. Singh and Richard M. Karp. Estimating the Phylogeny of a Pathway : A Probabilistic Approach. [Manuscript in Preparation]
Manikandan Narayanan and Richard M. Karp. Gapped Local Similarity Search with Provable Guarantees. Workshop on Algorithms in Bioinformatics (WABI), 2004. [ps, qhash software, talk]
Note: The copyright of published papers listed here is held by the publishers © Springer-Verlag and others.
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Teaching: I was a teaching assistant for the undergraduate randomized algorithms course CS 174 (Fall 2004).-----------------------------------------
Master's Research:Manikandan Narayanan and Katherine A. Yelick. Generating Permutation Instructions from a High-Level Description. Workshop on Media and Streaming Processors (MSP), 2004. [ps]
Manikandan Narayanan. Compiling Communication Access Patterns for a Vector Processor. Master's thesis, Computer Sciences Division, University of California at Berkeley, 2003. [ps]
Sourav Chatterji, Manikandan Narayanan, Jason Duell and Leonid Oliker. Performance Evaluation of Two Emerging Media Processors: VIRAM and Imagine. Workshop on Parallel and Distributed Image Processing, Video Processing, and Multimedia (PDIVM), 2003. [pdf]
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Random picks:
Neither attach to nor detach from your mind! A man of old said:
The mind changes, following along with ten thousand environments;
The way it changes is truly most mysterious.
If you follow its flow and can perceive its nature,
You will have neither joy nor sorrow.
Some pics! (at last got around to putting some)
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CONTACT (Updated Jan, 2007):
Email:
nmani "AT" cs.berkeley.edu
Home:
1321 Addison St #C,
Berkeley, CA - 94702-1731.
Ph: 510-849-4722
Work:
Room 593 Soda Hall,
UC Berkeley, CA - 94720.
Ph: 510-642-2128