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A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem.
J Comput Biol. 2016 Jun;23(6):472-82. doi: 10.1089/cmb.2015.0235. Epub 2016 Apr 8.
J Comput Biol. 2016.
PMID: 27058840
ALFRED: A Practical Method for Alignment-Free Distance Computation.
Thankachan SV, Chockalingam SP, Liu Y, Apostolico A, Aluru S.
Thankachan SV, et al.
J Comput Biol. 2016 Jun;23(6):452-60. doi: 10.1089/cmb.2015.0217. Epub 2016 May 3.
J Comput Biol. 2016.
PMID: 27138275
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Efficient detection of viral transmissions with Next-Generation Sequencing data.
Rytsareva I, Campo DS, Zheng Y, Sims S, Thankachan SV, Tetik C, Chirag J, Chockalingam SP, Sue A, Aluru S, Khudyakov Y.
Rytsareva I, et al. Among authors: thankachan sv.
BMC Genomics. 2017 May 24;18(Suppl 4):372. doi: 10.1186/s12864-017-3732-4.
BMC Genomics. 2017.
PMID: 28589864
Free PMC article.
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A greedy alignment-free distance estimator for phylogenetic inference.
Thankachan SV, Chockalingam SP, Liu Y, Krishnan A, Aluru S.
Thankachan SV, et al.
BMC Bioinformatics. 2017 Jun 7;18(Suppl 8):238. doi: 10.1186/s12859-017-1658-0.
BMC Bioinformatics. 2017.
PMID: 28617225
Free PMC article.
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An Ultra-Fast and Parallelizable Algorithm for Finding k-Mismatch Shortest Unique Substrings.
Allen DR, Thankachan SV, Xu B.
Allen DR, et al. Among authors: thankachan sv.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Jan-Feb;18(1):138-148. doi: 10.1109/TCBB.2020.2968531. Epub 2021 Feb 3.
IEEE/ACM Trans Comput Biol Bioinform. 2021.
PMID: 31985439
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An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction.
Chockalingam SP, Pannu J, Hooshmand S, Thankachan SV, Aluru S.
Chockalingam SP, et al. Among authors: thankachan sv.
BMC Bioinformatics. 2020 Nov 18;21(Suppl 6):404. doi: 10.1186/s12859-020-03738-5.
BMC Bioinformatics. 2020.
PMID: 33203364
Free PMC article.
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On the Hardness of Sequence Alignment on De Bruijn Graphs.
Gibney D, Thankachan SV, Aluru S.
Gibney D, et al. Among authors: thankachan sv.
J Comput Biol. 2022 Dec;29(12):1377-1396. doi: 10.1089/cmb.2022.0411. Epub 2022 Nov 25.
J Comput Biol. 2022.
PMID: 36450127
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Algorithms for Colinear Chaining with Overlaps and Gap Costs.
Jain C, Gibney D, Thankachan SV.
Jain C, et al. Among authors: thankachan sv.
J Comput Biol. 2022 Nov;29(11):1237-1251. doi: 10.1089/cmb.2022.0266.
J Comput Biol. 2022.
PMID: 36351202
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