Sharma V. Thankachan

CoRR, 2023

Non-overlapping Indexing in BWT-Runs Bounded Space.

[BibT_eX]

[DOI]

Paul Macnichol

Proceedings of the String Processing and Information Retrieval, 2023

Contextual Pattern Matching in Less Space.

[BibT_eX]

[DOI]

Proceedings of the Data Compression Conference, 2023

Suffix-Prefix Queries on a Dictionary.

[BibT_eX]

[DOI]

Proceedings of the 34th Annual Symposium on Combinatorial Pattern Matching, 2023

2022

Algorithms for Colinear Chaining with Overlaps and Gap Costs.

[BibT_eX]

[DOI]

Chirag Jain

J. Comput. Biol., 2022

On the Hardness of Sequence Alignment on De Bruijn Graphs.

[BibT_eX]

[DOI]

J. Comput. Biol., 2022

On the Complexity of Recognizing Wheeler Graphs.

[BibT_eX]

[DOI]

Algorithmica, 2022

The Heaviest Induced Ancestors Problem: Better Data Structures and Applications.

[BibT_eX]

[DOI]

Algorithmica, 2022

Feasibility of Flow Decomposition with Subpath Constraints in Linear Time.

[BibT_eX]

[DOI]

Proceedings of the 22nd International Workshop on Algorithms in Bioinformatics, 2022

Quantum Time Complexity and Algorithms for Pattern Matching on Labeled Graphs.

[BibT_eX]

[DOI]

Parisa Darbari

Proceedings of the String Processing and Information Retrieval, 2022

Co-linear Chaining with Overlaps and Gap Costs.

[BibT_eX]

[DOI]

Chirag Jain

Proceedings of the Research in Computational Molecular Biology, 2022

The Complexity of Approximate Pattern Matching on de Bruijn Graphs.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2022

Fully Functional Parameterized Suffix Trees in Compact Space.

[BibT_eX]

[DOI]

Proceedings of the 49th International Colloquium on Automata, Languages, and Programming, 2022

Compact Text Indexing for Advanced Pattern Matching Problems: Parameterized, Order-Isomorphic, 2D, etc. (Invited Talk).

[BibT_eX]

[DOI]

Proceedings of the 33rd Annual Symposium on Combinatorial Pattern Matching, 2022

Memory-Efficient FM-Index Construction for Reference Genomes.

[BibT_eX]

[DOI]

Arghya Kusum Das

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021

I/O-efficient data structures for non-overlapping indexing.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2021

A framework for designing space-efficient dictionaries for parameterized and order-preserving matching.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2021

I/O-optimal categorical 3-sided skyline queries.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2021

Guest Editorial for Selected Papers From BIOKDD 2019.

[BibT_eX]

[DOI]

Da Yan

Jake Y. Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

An Ultra-Fast and Parallelizable Algorithm for Finding $k$k-Mismatch Shortest Unique Substrings.

[BibT_eX]

[DOI]

Daniel R. Allen

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Text Indexing for Regular Expression Matching.

[BibT_eX]

[DOI]

Algorithms, 2021

Finding an Optimal Alphabet Ordering for Lyndon Factorization Is Hard.

[BibT_eX]

[DOI]

Proceedings of the 38th International Symposium on Theoretical Aspects of Computer Science, 2021

Simple Reductions from Formula-SAT to Pattern Matching on Labeled Graphs and Subtree Isomorphism.

[BibT_eX]

[DOI]

Gary Hoppenworth

Proceedings of the 4th Symposium on Simplicity in Algorithms, 2021

LF Successor: Compact Space Indexing for Order-Isomorphic Pattern Matching.

[BibT_eX]

[DOI]

Proceedings of the 48th International Colloquium on Automata, Languages, and Programming, 2021

2020

Ranked document selection.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2020

A linear-space data structure for range-LCP queries in poly-logarithmic time.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2020

Sequential and parallel algorithms for all-pair k-mismatch maximal common substrings.

[BibT_eX]

[DOI]

J. Parallel Distributed Comput., 2020

A brief history of parameterized matching problems.

[BibT_eX]

[DOI]

Juan Mendivelso

Yoan J. Pinzón

Discret. Appl. Math., 2020

An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction.

[BibT_eX]

[DOI]

BMC Bioinform., 2020

A Survey on Shortest Unique Substring Queries.

[BibT_eX]

[DOI]

Paniz Abedin

Algorithms, 2020

Efficient Data Structures for Range Shortest Unique Substring Queries.

[BibT_eX]

[DOI]

Algorithms, 2020

Succinct Non-overlapping Indexing.

[BibT_eX]

[DOI]

Algorithmica, 2020

The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance.

[BibT_eX]

[DOI]

Proceedings of the 28th Annual European Symposium on Algorithms, 2020

On the Complexity of BWT-Runs Minimization via Alphabet Reordering.

[BibT_eX]

[DOI]

Jason W. Bentley

Srivathsan Srinivasagopalan

Proceedings of the 28th Annual European Symposium on Algorithms, 2020

FM-Index Reveals the Reverse Suffix Array.

[BibT_eX]

[DOI]

Proceedings of the 31st Annual Symposium on Combinatorial Pattern Matching, 2020

2019

A deep learning approach for diagnosing schizophrenic patients.

[BibT_eX]

[DOI]

Justin Barry

Varadraj Prabhu Gurupur

J. Exp. Theor. Artif. Intell., 2019

Range Shortest Unique Substring Queries.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2019

Categorical Range Reporting with Frequencies.

[BibT_eX]

[DOI]

Proceedings of the 22nd International Conference on Database Theory, 2019

On the Hardness and Inapproximability of Recognizing Wheeler Graphs.

[BibT_eX]

[DOI]

Proceedings of the 27th Annual European Symposium on Algorithms, 2019

Parameterized Text Indexing with One Wildcard.

[BibT_eX]

[DOI]

Proceedings of the Data Compression Conference, 2019

I/O Optimal Data Structures for Categorical Range Skyline Queries.

[BibT_eX]

Proceedings of the 31st Canadian Conference on Computational Geometry, 2019

2018

Ranked document retrieval for multiple patterns.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2018

Space-efficient indexes for forbidden extension queries.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2018

On Computing Average Common Substring Over Run Length Encoded Sequences.

[BibT_eX]

[DOI]

Fundam. Informaticae, 2018

A Linear Space Data Structure for Range LCP Queries.

[BibT_eX]

[DOI]

Fundam. Informaticae, 2018

Dictionary Matching with a Bounded Gap in Pattern or in Text.

[BibT_eX]

[DOI]

Algorithmica, 2018

Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis.

[BibT_eX]

[DOI]

Chaitanya Aluru

Proceedings of the Research in Computational Molecular Biology, 2018

Faster Computation of Genome Mappability with one Mismatch.

[BibT_eX]

[DOI]

Proceedings of the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2018

Compact Encoding for Galled-Trees and Its Applications.

[BibT_eX]

[DOI]

Kuang-Yu Chang

Proceedings of the 2018 Data Compression Conference, 2018

Non-Overlapping Indexing - Cache Obliviously.

[BibT_eX]

[DOI]

Proceedings of the Annual Symposium on Combinatorial Pattern Matching, 2018

The Heaviest Induced Ancestors Problem Revisited.

[BibT_eX]

[DOI]

Proceedings of the Annual Symposium on Combinatorial Pattern Matching, 2018

A Linear-Space Data Structure for Range-LCP Queries in Poly-Logarithmic Time.

[BibT_eX]

[DOI]

Proceedings of the Computing and Combinatorics - 24th International Conference, 2018

An Alignment-free Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction.

[BibT_eX]

[DOI]

Jodh Pannu

Srivathsan Srinivasagopalan

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

Faster Computation of Genome Mappability.

[BibT_eX]

[DOI]

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

Diagnosing Schizophrenia: A Deep Learning Approach.

[BibT_eX]

[DOI]

Justin Barry

Varadraj Prabhu Gurupur

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

A Practical and Efficient Algorithm for the k-mismatch Shortest Unique Substring Finding Problem.

[BibT_eX]

[DOI]

Daniel R. Allen

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017

In-place algorithms for exact and approximate shortest unique substring problems.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2017

Space-time trade-offs for finding shortest unique substrings and maximal unique matches.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2017

Range selection and predecessor queries in data aware space and time.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2017

Position-restricted substring searching over small alphabets.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2017

A greedy alignment-free distance estimator for phylogenetic inference.

[BibT_eX]

[DOI]

Yongchao Liu

Ambujam Krishnan

BMC Bioinform., 2017

Top-k Term-Proximity in Succinct Space.

[BibT_eX]

[DOI]

J. Ian Munro

Jesper Sindahl Nielsen

Algorithmica, 2017

pBWT: Achieving Succinct Data Structures for Parameterized Pattern Matching and Related Problems.

[BibT_eX]

[DOI]

Proceedings of the Twenty-Eighth Annual ACM-SIAM Symposium on Discrete Algorithms, 2017

Structural Pattern Matching - Succinctly.

[BibT_eX]

[DOI]

Proceedings of the 28th International Symposium on Algorithms and Computation, 2017

2016

Compressed Document Retrieval on String Collections.

[BibT_eX]

[DOI]

Encyclopedia of Algorithms, 2016

Reporting consecutive substring occurrences under bounded gap constraints.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2016

Document retrieval with one wildcard.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2016

ALFRED: A Practical Method for Alignment-Free Distance Computation.

[BibT_eX]

[DOI]

Yongchao Liu

Alberto Apostolico

J. Comput. Biol., 2016

A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem.

[BibT_eX]

[DOI]

Alberto Apostolico

J. Comput. Biol., 2016

Parameterized Pattern Matching - Succinctly.

[BibT_eX]

[DOI]

CoRR, 2016

Optimal Encodings for Range Majority Queries.

[BibT_eX]

[DOI]

Algorithmica, 2016

Linear-Space Data Structures for Range Frequency Queries on Arrays and Trees.

[BibT_eX]

[DOI]

Algorithmica, 2016

A parallel algorithm for finding all pairs k-mismatch maximal common substrings.

[BibT_eX]

[DOI]

Proceedings of the International Conference for High Performance Computing, 2016

An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

Space-Time Trade-Offs for the Shortest Unique Substring Problem.

[BibT_eX]

[DOI]

Proceedings of the 27th International Symposium on Algorithms and Computation, 2016

Probabilistic Threshold Indexing for Uncertain Strings.

[BibT_eX]

[DOI]

Proceedings of the 19th International Conference on Extending Database Technology, 2016

Space-Efficient Dictionaries for Parameterized and Order-Preserving Pattern Matching.

[BibT_eX]

[DOI]

Proceedings of the 27th Annual Symposium on Combinatorial Pattern Matching, 2016

2015

On hardness of several string indexing problems.

[BibT_eX]

[DOI]

Kasper Green Larsen

J. Ian Munro

Jesper Sindahl Nielsen

Theor. Comput. Sci., 2015

Low space data structures for geometric range mode query.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2015

Succinct indexes for reporting discriminating and generic words.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2015

Bottom-k document retrieval.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2015

Compressing Dictionary Matching Index via Sparsification Technique.

[BibT_eX]

[DOI]

Algorithmica, 2015

Geometric BWT: Compressed Text Indexing via Sparse Suffixes and Range Searching.

[BibT_eX]

[DOI]

Algorithmica, 2015

Range LCP Queries Revisited.

[BibT_eX]

[DOI]

Amihood Amir

Moshe Lewenstein

Proceedings of the String Processing and Information Retrieval, 2015

Efficient Alignment Free Sequence Comparison with Bounded Mismatches.

[BibT_eX]

[DOI]

Alberto Apostolico

Proceedings of the Research in Computational Molecular Biology, 2015

An In-place Framework for Exact and Approximate Shortest Unique Substring Queries.

[BibT_eX]

[DOI]

Proceedings of the Algorithms and Computation - 26th International Symposium, 2015

Shared-Constraint Range Reporting.

[BibT_eX]

[DOI]

Proceedings of the 18th International Conference on Database Theory, 2015

A greedy alignment-free distance estimator for phylogenetic inference (extended abstract).

[BibT_eX]

[DOI]

Yongchao Liu

Ambujam Krishnan

Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2015

Efficient detection of viral transmission with threshold-based methods.

[BibT_eX]

[DOI]

Inna Rytsareva

Seth Sims

Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2015

Forbidden Extension Queries.

[BibT_eX]

[DOI]

Proceedings of the 35th IARCS Annual Conference on Foundation of Software Technology and Theoretical Computer Science, 2015

Range Selection Queries in Data Aware Space and Time.

[BibT_eX]

[DOI]

Proceedings of the 2015 Data Compression Conference, 2015

Dictionary Matching with Uneven Gaps.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 26th Annual Symposium, 2015

Ranked Document Retrieval with Forbidden Pattern.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 26th Annual Symposium, 2015

Range Counting with Distinct Constraints.

[BibT_eX]

[DOI]

J. Ian Munro

Yakov Nekrich

Proceedings of the 27th Canadian Conference on Computational Geometry, 2015

2014

New space/time tradeoffs for top-k document retrieval on sequences.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2014

Less space: Indexing for queries with wildcards.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2014

Space-Efficient Frameworks for Top-k String Retrieval.

[BibT_eX]

[DOI]

J. ACM, 2014

Categorical range maxima queries.

[BibT_eX]

[DOI]

Proceedings of the 33rd ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems, 2014

Encodings for Range Majority Queries.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 25th Annual Symposium, 2014

Indexed Geometric Jumbled Pattern Matching.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 25th Annual Symposium, 2014

2013

Faster compressed dictionary matching.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2013

Compressed text indexing with wildcards.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2013

Compressed property suffix trees.

[BibT_eX]

[DOI]

Inf. Comput., 2013

Faster Range LCP Queries.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2013

Faster Top-k Document Retrieval in Optimal Space.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2013

Top-k Color Queries on Tree Paths.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2013

Top-k Document Retrieval in Compact Space and Near-Optimal Time.

[BibT_eX]

[DOI]

Proceedings of the Algorithms and Computation - 24th International Symposium, 2013

Top-k join queries: overcoming the curse of anti-correlation.

[BibT_eX]

[DOI]

Proceedings of the 17th International Database Engineering & Applications Symposium, 2013

Top-k Document Retrieval in External Memory.

[BibT_eX]

[DOI]

Proceedings of the Algorithms - ESA 2013, 2013

Approximate string matching by position restricted alignment.

[BibT_eX]

[DOI]

Proceedings of the Joint 2013 EDBT/ICDT Conferences, 2013

Faster Compressed Top-k Document Retrieval.

[BibT_eX]

[DOI]

Proceedings of the 2013 Data Compression Conference, 2013

Space-Efficient Construction Algorithm for the Circular Suffix Tree.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 24th Annual Symposium, 2013

Indexes for Document Retrieval with Relevance.

[BibT_eX]

[DOI]

Proceedings of the Space-Efficient Data Structures, 2013

2012

Succinct representations of weighted trees supporting path queries.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2012

On position restricted substring searching in succinct space.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2012

On Optimal Top-K String Retrieval

[BibT_eX]

[DOI]

CoRR, 2012

Document Listing for Queries with Excluded Pattern.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

Towards an Optimal Space-and-Query-Time Index for Top-k Document Retrieval.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

Efficient Algorithm for Circular Burrows-Wheeler Transform.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

2011

A Truly Dynamic Data Structure for Top-k Queries on Uncertain Data.

[BibT_eX]

[DOI]

Proceedings of the Scientific and Statistical Database Management, 2011

Compressed Indexes for Aligned Pattern Matching.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2011

Inverted indexes for phrases and strings.

[BibT_eX]

[DOI]

Sabrina Chandrasekaran

Proceedings of the Proceeding of the 34th International ACM SIGIR Conference on Research and Development in Information Retrieval, 2011

Succinct Indexes for Circular Patterns.

[BibT_eX]

[DOI]

Proceedings of the Algorithms and Computation - 22nd International Symposium, 2011

Compressed Dictionary Matching with One Error.

[BibT_eX]

[DOI]

Proceedings of the 2011 Data Compression Conference (DCC 2011), 2011

2010

Fully Dynamic Data Structure for Top-k Queries on Uncertain Data

[BibT_eX]

[DOI]