Daniel Gibney

According to our database, Daniel Gibney authored at least 38 papers between 2018 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

Contextual Pattern Mining and Counting.

Ling Li, Daniel Gibney, Sharma V. Thankachan, Solon P. Pissis, Grigorios Loukides

CoRR, June, 2025

Non-overlapping indexing in BWT-runs bounded space.

Daniel Gibney, Paul Macnichol, Sharma V. Thankachan

Theor. Comput. Sci., 2025

Haplotype-Aware Long-Read Error Correction.

Parvesh Barak, Daniel Gibney, Chirag Jain

Proceedings of the 25th International Conference on Algorithms for Bioinformatics, 2025

Two-Dimensional Longest Common Extension Queries in Compact Space.

Arnab Ganguly, Daniel Gibney, Rahul Shah, Sharma V. Thankachan

Proceedings of the 42nd International Symposium on Theoretical Aspects of Computer Science, 2025

Integer Programming Framework for Pangenome-Based Genome Inference.

Ghanshyam Chandra, Md. Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, Chirag Jain

Proceedings of the Research in Computational Molecular Biology, 2025

A Work-Optimal Parallel Algorithm for Aligning Sequences to Genome Graphs.

Aranya Banerjee, Daniel Gibney, Helen Xu, Srinivas Aluru

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2025

Repetition Aware Text Indexing for Matching Patterns with Wildcards.

Daniel Gibney, Jackson Huffstutler, Mano Prakash Parthasarathi, Sharma V. Thankachan

Proceedings of the 52nd International Colloquium on Automata, Languages, and Programming, 2025

Wheeler Graphs and Wheeler Languages.

Nicola Cotumaccio, Giovanna D'Agostino, Daniel Gibney, Alberto Policriti, Nicola Prezza, Sharma V. Thankachan

Proceedings of the Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday, 2025

2024

GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants.

Neda Tavakoli, Daniel Gibney, Srinivas Aluru

J. Comput. Biol., 2024

Quantum Algorithms for Longest Common Substring with a Gap.

Daniel Gibney, Md. Helal Hossen

Proceedings of the String Processing and Information Retrieval, 2024

Bounded-Ratio Gapped String Indexing.

Arnab Ganguly, Daniel Gibney, Paul Macnichol, Sharma V. Thankachan

Proceedings of the String Processing and Information Retrieval, 2024

Near-Optimal Quantum Algorithms for Bounded Edit Distance and Lempel-Ziv Factorization.

Daniel Gibney, Ce Jin, Tomasz Kociumaka, Sharma V. Thankachan

Proceedings of the 2024 ACM-SIAM Symposium on Discrete Algorithms, 2024

Haplotype-Aware Sequence Alignment to Pangenome Graphs.

Ghanshyam Chandra, Daniel Gibney, Chirag Jain

Proceedings of the Research in Computational Molecular Biology, 2024

Longest Common Substring with Gaps and Related Problems.

Aranya Banerjee, Daniel Gibney, Sharma V. Thankachan

Proceedings of the 32nd Annual European Symposium on Algorithms, 2024

2023

Compressibility-Aware Quantum Algorithms on Strings.

Daniel Gibney, Sharma V. Thankachan

CoRR, 2023

On the Hardness of Wildcard Pattern Matching on de Bruijn Graphs.

Arnab Ganguly, Daniel Gibney, Arghya Kusum Das, Sharma V. Thankachan

Proceedings of the Computational Advances in Bio and Medical Sciences, 2023

Contextual Pattern Matching in Less Space.

Paniz Abedin, Oliver A. Chubet, Daniel Gibney, Sharma V. Thankachan

Proceedings of the Data Compression Conference, 2023

2022

Algorithms for Colinear Chaining with Overlaps and Gap Costs.

Chirag Jain, Daniel Gibney, Sharma V. Thankachan

J. Comput. Biol., 2022

On the Hardness of Sequence Alignment on De Bruijn Graphs.

Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru

J. Comput. Biol., 2022

On the Complexity of Recognizing Wheeler Graphs.

Daniel Gibney, Sharma V. Thankachan

Algorithmica, 2022

Feasibility of Flow Decomposition with Subpath Constraints in Linear Time.

Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru

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

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

Parisa Darbari, Daniel Gibney, Sharma V. Thankachan

Proceedings of the String Processing and Information Retrieval, 2022

Co-linear Chaining with Overlaps and Gap Costs.

Chirag Jain, Daniel Gibney, Sharma V. Thankachan

Proceedings of the Research in Computational Molecular Biology, 2022

The Complexity of Approximate Pattern Matching on de Bruijn Graphs.

Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru

Proceedings of the Research in Computational Molecular Biology, 2022

Haplotype-aware variant selection for genome graphs.

Neda Tavakoli, Daniel Gibney, Srinivas Aluru

Proceedings of the BCB '22: 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Northbrook, Illinois, USA, August 7, 2022

2021

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

Arnab Ganguly, Daniel Gibney, Sharma V. Thankachan, Rahul Shah

Theor. Comput. Sci., 2021

Text Indexing for Regular Expression Matching.

Daniel Gibney, Sharma V. Thankachan

Algorithms, 2021

Finding an Optimal Alphabet Ordering for Lyndon Factorization Is Hard.

Daniel Gibney, Sharma V. Thankachan

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.

Daniel Gibney, Gary Hoppenworth, Sharma V. Thankachan

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

2020

Quantifying Membership Inference Vulnerability via Generalization Gap and Other Model Metrics.

Jason W. Bentley, Daniel Gibney, Gary Hoppenworth, Sumit Kumar Jha

CoRR, 2020

An Efficient Elastic-Degenerate Text Index? Not Likely.

Daniel Gibney

Proceedings of the String Processing and Information Retrieval, 2020

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

Gary Hoppenworth, Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan

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

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

Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan

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

FM-Index Reveals the Reverse Suffix Array.

Arnab Ganguly, Daniel Gibney, Sahar Hooshmand, M. Oguzhan Külekci, Sharma V. Thankachan

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

2019

On the Hardness and Inapproximability of Recognizing Wheeler Graphs.

Daniel Gibney, Sharma V. Thankachan

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

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

Daniel Gibney, Sharma V. Thankachan, Arnab Ganguly, Rahul Shah

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

2018

Faster Computation of Genome Mappability with one Mismatch.

Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan

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

Faster Computation of Genome Mappability.

Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018