Balaji Venkatachalam

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The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n3) time using Nussinov’s dynamic programming algorithm. The Four-Russians method is a technique that reduces the running time for certain dynamic programming algorithms by a multiplicative factor after(More)
CONTEXT Limited Indian data are available on the rate of colistin nephrotoxicity and other risk factors contributing to the development of this important side effect. AIM This study aims to generate data on colistin nephrotoxicity from a large cohort of Indian patients. DESIGN Retrospective cohort study. MATERIALS AND METHODS Case record analysis of(More)
A tanglegram is a pair of trees on the same set of leaves with matching leaves in the two trees joined by an edge. Tanglegrams are widely used in biology—to compare evolutionary histories of host and parasite species and to analyze genes of species in the same geographical area. We consider optimization problems in tanglegram drawings. We show a(More)
Current P2P systems employ tit-for-tat strategies, where peers only upload when they are simultaneously downloading, to avoid free riding. We derive optimal tit-for-tat strategies and obtain theoretical bounds on the performance of any P2P network employing such strategies. These are fundamental limitations that stem from peers unwillingness to cooperate(More)
Efficient sensitivity analysis algorithms are presented for two problems arising in the study of Markov models of sequence evolution: ancestral reconstruction in evolutionary trees and local ungapped alignment under log-odds scoring. The algorithms generate complete descriptions of the optimum solutions for all possible values of the evolutionary distance.(More)
BACKGROUND Colistin-based combination therapy (CCT) is extensively used to treat infections due to carbapenem-resistant Gram-negative bacteria (CRGNB). There are no data available from India on the usefulness of combination therapy, especially in the oncology setup. The aim of this study was to analyze the clinical effectiveness of CCT over monotherapy in(More)
Software watermarking has been proposed as a way to prove ownership of software intellectual property in order to contain software piracy. In this paper, we propose a novel watermarking technique based on Zero Knowledge Proofs. The advantages are multi-fold. The watermark recognizer can now be distributed publicly. This helps in watermark being used as a(More)