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Efficient detection of viral transmissions with Next-Generation Sequencing data.
BMC Genomics. 2017 May 24;18(Suppl 4):372. doi: 10.1186/s12864-017-3732-4.
BMC Genomics. 2017.
PMID: 28589864
Free PMC article.
A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem.
Thankachan SV, Apostolico A, Aluru S.
Thankachan SV, et al.
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
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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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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 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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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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