Sharma V. Thankachan

ORCID

Publication Activity (10 Years)

Years Active: 2009-2024
Publications (10 Years): 106

Top Venues

Publications

Daniel Gibney, Ce Jin, Tomasz Kociumaka, Sharma V. Thankachan
Near-Optimal Quantum Algorithms for Bounded Edit Distance and Lempel-Ziv Factorization. SODA (2024)
Wiktor Zuba, Grigorios Loukides, Solon P. Pissis, Sharma V. Thankachan
Approximate Suffix-Prefix Dictionary Queries. MFCS (2024)
Rahul Shah, Cheng Sheng, Sharma V. Thankachan, Jeffrey Vitter
Ranked Document Retrieval in External Memory. ACM Trans. Algorithms 19 (1) (2023)
Daniel Gibney, Paul Macnichol, Sharma V. Thankachan
Non-overlapping Indexing in BWT-Runs Bounded Space. SPIRE (2023)
Grigorios Loukides, Solon P. Pissis, Sharma V. Thankachan, Wiktor Zuba
Suffix-Prefix Queries on a Dictionary. CPM (2023)
Paniz Abedin, Oliver A. Chubet, Daniel Gibney, Sharma V. Thankachan
Contextual Pattern Matching in Less Space. DCC (2023)
Daniel Gibney, Sharma V. Thankachan
Compressibility-Aware Quantum Algorithms on Strings. CoRR (2023)
Daniel Gibney, Ce Jin, Tomasz Kociumaka, Sharma V. Thankachan
Near-Optimal Quantum Algorithms for Bounded Edit Distance and Lempel-Ziv Factorization. CoRR (2023)
Daniel Gibney, Sharma V. Thankachan
On the Complexity of Recognizing Wheeler Graphs. Algorithmica 84 (3) (2022)
Arghya Kusum Das, M. Oguzhan Külekci, Sharma V. Thankachan
Memory-Efficient FM-Index Construction for Reference Genomes. BIBM (2022)
Paniz Abedin, Sahar Hooshmand, Arnab Ganguly, Sharma V. Thankachan
The Heaviest Induced Ancestors Problem: Better Data Structures and Applications. Algorithmica 84 (7) (2022)
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
The Complexity of Approximate Pattern Matching on de Bruijn Graphs. RECOMB (2022)
Parisa Darbari, Daniel Gibney, Sharma V. Thankachan
Quantum Time Complexity and Algorithms for Pattern Matching on Labeled Graphs. SPIRE (2022)
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
On the Hardness of Sequence Alignment on De Bruijn Graphs. J. Comput. Biol. 29 (12) (2022)
Chirag Jain, Daniel Gibney, Sharma V. Thankachan
Co-linear Chaining with Overlaps and Gap Costs. RECOMB (2022)
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
The Complexity of Approximate Pattern Matching on De Bruijn Graphs. CoRR (2022)
Chirag Jain, Daniel Gibney, Sharma V. Thankachan
Algorithms for Colinear Chaining with Overlaps and Gap Costs. J. Comput. Biol. 29 (11) (2022)
Sharma V. Thankachan
Compact Text Indexing for Advanced Pattern Matching Problems: Parameterized, Order-Isomorphic, 2D, etc. (Invited Talk). CPM (2022)
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
Feasibility of Flow Decomposition with Subpath Constraints in Linear Time. WABI (2022)
Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
Fully Functional Parameterized Suffix Trees in Compact Space. ICALP (2022)
Arnab Ganguly, Wing-Kai Hon, Kunihiko Sadakane, Rahul Shah, Sharma V. Thankachan, Yilin Yang
A framework for designing space-efficient dictionaries for parameterized and order-preserving matching. Theor. Comput. Sci. 854 (2021)
Daniel Gibney, Sharma V. Thankachan
Text Indexing for Regular Expression Matching. Algorithms 14 (5) (2021)
Daniel R. Allen, Sharma V. Thankachan, Bojian Xu
An Ultra-Fast and Parallelizable Algorithm for Finding $k$k-Mismatch Shortest Unique Substrings. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (1) (2021)
Sahar Hooshmand, Paniz Abedin, M. Oguzhan Külekci, Sharma V. Thankachan
I/O-efficient data structures for non-overlapping indexing. Theor. Comput. Sci. 857 (2021)
Arnab Ganguly, Daniel Gibney, Sharma V. Thankachan, Rahul Shah
I/O-optimal categorical 3-sided skyline queries. Theor. Comput. Sci. 896 (2021)
Daniel Gibney, Sharma V. Thankachan
Finding an Optimal Alphabet Ordering for Lyndon Factorization Is Hard. STACS (2021)
Arnab Ganguly, Dhrumil Patel, Rahul Shah, Sharma V. Thankachan
LF Successor: Compact Space Indexing for Order-Isomorphic Pattern Matching. ICALP (2021)
Da Yan, Sharma V. Thankachan, Jake Y. Chen
Guest Editorial for Selected Papers From BIOKDD 2019. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (3) (2021)
Daniel Gibney, Gary Hoppenworth, Sharma V. Thankachan
Simple Reductions from Formula-SAT to Pattern Matching on Labeled Graphs and Subtree Isomorphism. SOSA (2021)
Sriram P. Chockalingam, Jodh Pannu, Sahar Hooshmand, Sharma V. Thankachan, Srinivas Aluru
An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction. BMC Bioinform. (6) (2020)
Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
Succinct Non-overlapping Indexing. Algorithmica 82 (1) (2020)
Paniz Abedin, Arnab Ganguly, Wing-Kai Hon, Kotaro Matsuda, Yakov Nekrich, Kunihiko Sadakane, Rahul Shah, Sharma V. Thankachan
A linear-space data structure for range-LCP queries in poly-logarithmic time. Theor. Comput. Sci. 822 (2020)
Arnab Ganguly, Daniel Gibney, Sahar Hooshmand, M. Oguzhan Külekci, Sharma V. Thankachan
FM-Index Reveals the Reverse Suffix Array. CPM (2020)
Gary Hoppenworth, Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan
The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance. ESA (2020)
Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan
On the Complexity of BWT-Runs Minimization via Alphabet Reordering. ESA (2020)
Paniz Abedin, Arnab Ganguly, Solon P. Pissis, Sharma V. Thankachan
Efficient Data Structures for Range Shortest Unique Substring Queries. Algorithms 13 (11) (2020)
J. Ian Munro, Gonzalo Navarro, Rahul Shah, Sharma V. Thankachan
Ranked document selection. Theor. Comput. Sci. 812 (2020)
Juan Mendivelso, Sharma V. Thankachan, Yoan J. Pinzón
A brief history of parameterized matching problems. Discret. Appl. Math. 274 (2020)
Daniel Gibney, Gary Hoppenworth, Sharma V. Thankachan
Simple Reductions from Formula-SAT to Pattern Matching on Labeled Graphs and Subtree Isomorphism. CoRR (2020)
Paniz Abedin, M. Oguzhan Külekci, Sharma V. Thankachan
A Survey on Shortest Unique Substring Queries. Algorithms 13 (9) (2020)
Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru
Sequential and parallel algorithms for all-pair k-mismatch maximal common substrings. J. Parallel Distributed Comput. 144 (2020)
Arnab Ganguly, J. Ian Munro, Yakov Nekrich, Rahul Shah, Sharma V. Thankachan
Categorical Range Reporting with Frequencies. ICDT (2019)
Arnab Ganguly, Wing-Kai Hon, Yu-An Huang, Solon P. Pissis, Rahul Shah, Sharma V. Thankachan
Parameterized Text Indexing with One Wildcard. DCC (2019)
Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan
On the Complexity of BWT-runs Minimization via Alphabet Reordering. CoRR (2019)
Daniel Gibney, Sharma V. Thankachan, Arnab Ganguly, Rahul Shah
I/O Optimal Data Structures for Categorical Range Skyline Queries. CCCG (2019)
Daniel Gibney, Sharma V. Thankachan
On the Hardness and Inapproximability of Recognizing Wheeler Graphs. CoRR (2019)
Srivathsan Srinivasagopalan, Justin Barry, Varadraj Prabhu Gurupur, Sharma V. Thankachan
A deep learning approach for diagnosing schizophrenic patients. J. Exp. Theor. Artif. Intell. 31 (6) (2019)
Paniz Abedin, Arnab Ganguly, Solon P. Pissis, Sharma V. Thankachan
Range Shortest Unique Substring Queries. SPIRE (2019)
Daniel Gibney, Sharma V. Thankachan
On the Hardness and Inapproximability of Recognizing Wheeler Graphs. ESA (2019)
Paniz Abedin, Sahar Hooshmand, Arnab Ganguly, Sharma V. Thankachan
The Heaviest Induced Ancestors Problem Revisited. CPM (2018)
Sahar Hooshmand, Paniz Abedin, M. Oguzhan Külekci, Sharma V. Thankachan
Non-Overlapping Indexing - Cache Obliviously. CPM (2018)
Wing-Kai Hon, Tak Wah Lam, Rahul Shah, Sharma V. Thankachan, Hing-Fung Ting, Yilin Yang
Dictionary Matching with a Bounded Gap in Pattern or in Text. Algorithmica 80 (2) (2018)
Daniel R. Allen, Sharma V. Thankachan, Bojian Xu
A Practical and Efficient Algorithm for the k-mismatch Shortest Unique Substring Finding Problem. BCB (2018)
Jodh Pannu, Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru
An Alignment-free Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction. BCB (2018)
Kuang-Yu Chang, Wing-Kai Hon, Sharma V. Thankachan
Compact Encoding for Galled-Trees and Its Applications. DCC (2018)
Sudip Biswas, Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
Ranked document retrieval for multiple patterns. Theor. Comput. Sci. 746 (2018)
Sahar Hooshmand, Neda Tavakoli, Paniz Abedin, Sharma V. Thankachan
On Computing Average Common Substring Over Run Length Encoded Sequences. Fundam. Informaticae 163 (3) (2018)
Arnab Ganguly, Manish Patil, Rahul Shah, Sharma V. Thankachan
A Linear Space Data Structure for Range LCP Queries. Fundam. Informaticae 163 (3) (2018)
Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan
Faster Computation of Genome Mappability. BCB (2018)
Justin Barry, Srivathsan Srinivasagopalan, Sharma V. Thankachan, Varadraj Prabhu Gurupur
Diagnosing Schizophrenia: A Deep Learning Approach. BCB (2018)
Paniz Abedin, Arnab Ganguly, Wing-Kai Hon, Yakov Nekrich, Kunihiko Sadakane, Rahul Shah, Sharma V. Thankachan
A Linear-Space Data Structure for Range-LCP Queries in Poly-Logarithmic Time. COCOON (2018)
Sahar Hooshmand, Neda Tavakoli, Paniz Abedin, Sharma V. Thankachan
On Computing Average Common Substring Over Run Length Encoded Sequences. CoRR (2018)
Sudip Biswas, Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
Space-efficient indexes for forbidden extension queries. J. Discrete Algorithms 50 (2018)
Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan
Faster Computation of Genome Mappability with one Mismatch. ICCABS (2018)
Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam, Srinivas Aluru
Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis. RECOMB (2018)
Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
pBWT: Achieving Succinct Data Structures for Parameterized Pattern Matching and Related Problems. SODA (2017)
J. Ian Munro, Gonzalo Navarro, Jesper Sindahl Nielsen, Rahul Shah, Sharma V. Thankachan
Top-k Term-Proximity in Succinct Space. Algorithmica 78 (2) (2017)
Sudip Biswas, Tsung-Han Ku, Rahul Shah, Sharma V. Thankachan
Position-restricted substring searching over small alphabets. J. Discrete Algorithms (2017)
Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru
A greedy alignment-free distance estimator for phylogenetic inference. BMC Bioinform. 18 (8) (2017)
Arnab Ganguly, Wing-Kai Hon, Rahul Shah, Sharma V. Thankachan
Space-time trade-offs for finding shortest unique substrings and maximal unique matches. Theor. Comput. Sci. 700 (2017)
M. Oguzhan Külekci, Sharma V. Thankachan
Range selection and predecessor queries in data aware space and time. J. Discrete Algorithms 43 (2017)
Wing-Kai Hon, Sharma V. Thankachan, Bojian Xu
In-place algorithms for exact and approximate shortest unique substring problems. Theor. Comput. Sci. 690 (2017)
Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
Structural Pattern Matching - Succinctly. ISAAC (2017)
Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Alberto Apostolico, Srinivas Aluru
ALFRED: A Practical Method for Alignment-Free Distance Computation. J. Comput. Biol. 23 (6) (2016)
Moshe Lewenstein, J. Ian Munro, Yakov Nekrich, Sharma V. Thankachan
Document retrieval with one wildcard. Theor. Comput. Sci. 635 (2016)
Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
Parameterized Pattern Matching - Succinctly. CoRR (2016)
Sudip Biswas, Manish Patil, Sharma V. Thankachan, Rahul Shah
Probabilistic Threshold Indexing for Uncertain Strings. EDBT (2016)
Stephane Durocher, Rahul Shah, Matthew Skala, Sharma V. Thankachan
Linear-Space Data Structures for Range Frequency Queries on Arrays and Trees. Algorithmica 74 (1) (2016)
Gonzalo Navarro, Sharma V. Thankachan
Reporting consecutive substring occurrences under bounded gap constraints. Theor. Comput. Sci. 638 (2016)
Arnab Ganguly, Wing-Kai Hon, Rahul Shah, Sharma V. Thankachan
Space-Time Trade-Offs for the Shortest Unique Substring Problem. ISAAC (2016)
Sharma V. Thankachan, Alberto Apostolico, Srinivas Aluru
-Mismatch Average Common Substring Problem. J. Comput. Biol. 23 (6) (2016)
Gonzalo Navarro, Sharma V. Thankachan
Optimal Encodings for Range Majority Queries. Algorithmica 74 (3) (2016)
Arnab Ganguly, Wing-Kai Hon, Kunihiko Sadakane, Rahul Shah, Sharma V. Thankachan, Yilin Yang
Space-Efficient Dictionaries for Parameterized and Order-Preserving Pattern Matching. CPM (2016)
Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru
-mismatch maximal common substrings. SC (2016)
Sharma V. Thankachan, Sriram P. Chockalingam, Srinivas Aluru
An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings. ISBRA (2016)
Sudip Biswas, Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
Ranked Document Retrieval with Forbidden Pattern. CPM (2015)
Gonzalo Navarro, Sharma V. Thankachan
Bottom-k document retrieval. J. Discrete Algorithms 32 (2015)
Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
Succinct Non-overlapping Indexing. CPM (2015)
Sudip Biswas, Arnab Ganguly, Rahul Shah, Sharma V. Thankachan
Forbidden Extension Queries. FSTTCS (2015)
Gonzalo Navarro, Sharma V. Thankachan
Reporting Consecutive Substring Occurrences Under Bounded Gap Constraints. CPM (2015)
Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru
A greedy alignment-free distance estimator for phylogenetic inference (extended abstract). ICCABS (2015)
Kasper Green Larsen, J. Ian Munro, Jesper Sindahl Nielsen, Sharma V. Thankachan
On hardness of several string indexing problems. Theor. Comput. Sci. 582 (2015)
Yu-Feng Chien, Wing-Kai Hon, Rahul Shah, Sharma V. Thankachan, Jeffrey Scott Vitter
Geometric BWT: Compressed Text Indexing via Sparse Suffixes and Range Searching. Algorithmica 71 (2) (2015)
Inna Rytsareva, Seth Sims, Sriram P. Chockalingam, Srinivas Aluru, David S. Campo, Cansu Tetik, Sharma V. Thankachan, Yury Khudyakov, Yueli Zheng, Chirag Jain, Amanda Sue
Efficient detection of viral transmission with threshold-based methods. ICCABS (2015)
Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan
Efficient Alignment Free Sequence Comparison with Bounded Mismatches. RECOMB (2015)
Sudip Biswas, Manish Patil, Rahul Shah, Sharma V. Thankachan
Shared-Constraint Range Reporting. ICDT (2015)
Amihood Amir, Moshe Lewenstein, Sharma V. Thankachan
Range LCP Queries Revisited. SPIRE (2015)
Wing-Kai Hon, Sharma V. Thankachan, Bojian Xu
An In-place Framework for Exact and Approximate Shortest Unique Substring Queries. CoRR (2015)
M. Oguzhan Külekci, Sharma V. Thankachan
Range Selection Queries in Data Aware Space and Time. DCC (2015)
Wing-Kai Hon, Sharma V. Thankachan, Bojian Xu
An In-place Framework for Exact and Approximate Shortest Unique Substring Queries. ISAAC (2015)

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Publication Activity (10 Years)

Top Topics

Top Venues

Sharma V. Thankachan