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Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|November 30, 2022
On the Hardness of Sequence Alignment on De Bruijn GraphsDaniel Gibney, Sharma V Thankachan, Srinivas AluruJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|April 9, 2016
A Provably Efficient Algorithm for the k-Mismatch Average Common Substring ProblemSharma V Thankachan, Alberto Apostolico, Srinivas AluruJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|November 9, 2022
Algorithms for Colinear Chaining with Overlaps and Gap CostsChirag Jain, Daniel Gibney, Sharma V ThankachanJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|July 11, 2024
GraphSlimmer: Preserving Read Mappability with the Minimum Number of VariantsNeda Tavakoli, Daniel Gibney, Srinivas AluruBMC Bioinformatics|November 18, 2020
An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstructionSriram P Chockalingam, Jodh Pannu, Sahar Hooshmand, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|May 4, 2016
ALFRED: A Practical Method for Alignment-Free Distance ComputationSharma V Thankachan, Sriram P Chockalingam, Yongchao Liu, et al.BMC Bioinformatics|June 16, 2017
A greedy alignment-free distance estimator for phylogenetic inferenceSharma V Thankachan, Sriram P Chockalingam, Yongchao Liu, et al.BMC Genomics|June 8, 2017
Efficient detection of viral transmissions with Next-Generation Sequencing dataInna Rytsareva, David S Campo, Yueli Zheng, et al.Journal of Bioinformatics and Computational Biology|July 5, 2006
Efficient algorithms and software for detection of full-length LTR retrotransposonsAnantharaman Kalyanaraman, Srinivas AluruIEEE/ACM Transactions on Computational Biology and Bioinformatics|February 18, 2016
Discovering Motifs in Biological Sequences Using the Micron Automata ProcessorIndranil Roy, Srinivas AluruPageof 7