Faster Computation of Genome Mappability. - Sahar Hooshmand; Paniz Abedin; Daniel Gibney; Srinivas Aluru; Sharma V. Thankachan (BCB, 2018)

Faster Computation of Genome Mappability with one Mismatch. - Sahar Hooshmand; Paniz Abedin; Daniel Gibney; Srinivas Aluru; Sharma V. Thankachan (ICCABS, 2018)

I/O Optimal Data Structures for Categorical Range Skyline Queries. - Daniel Gibney; Sharma V. Thankachan; Arnab Ganguly 002; Rahul Shah 001 (CCCG, 2019)

On the Hardness and Inapproximability of Recognizing Wheeler Graphs. - Daniel Gibney; Sharma V. Thankachan (ESA, 2019)

FM-Index Reveals the Reverse Suffix Array. - Arnab Ganguly 002; Daniel Gibney; Sahar Hooshmand; M. Oguzhan Külekci; Sharma V. Thankachan (CPM, 2020)

On the Complexity of BWT-Runs Minimization via Alphabet Reordering. - Jason W. Bentley; Daniel Gibney; Sharma V. Thankachan (ESA, 2020)

The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance. - Gary Hoppenworth; Jason W. Bentley; Daniel Gibney; Sharma V. Thankachan (ESA, 2020)

An Efficient Elastic-Degenerate Text Index? Not Likely. - Daniel Gibney (SPIRE, 2020)

Quantifying Membership Inference Vulnerability via Generalization Gap and Other Model Metrics. - Jason W. Bentley; Daniel Gibney; Gary Hoppenworth; Sumit Kumar Jha 001 (CoRR, 2020)

Simple Reductions from Formula-SAT to Pattern Matching on Labeled Graphs and Subtree Isomorphism. - Daniel Gibney; Gary Hoppenworth; Sharma V. Thankachan (SOSA, 2021)

Finding an Optimal Alphabet Ordering for Lyndon Factorization Is Hard. - Daniel Gibney; Sharma V. Thankachan (STACS, 2021)

Text Indexing for Regular Expression Matching. - Daniel Gibney; Sharma V. Thankachan (Algorithms, 2021)

I/O-optimal categorical 3-sided skyline queries. - Arnab Ganguly 002; Daniel Gibney; Sharma V. Thankachan; Rahul Shah 001 (Theor. Comput. Sci., 2021)

Haplotype-aware variant selection for genome graphs. - Neda Tavakoli; Daniel Gibney; Srinivas Aluru (BCB, 2022)

The Complexity of Approximate Pattern Matching on de Bruijn Graphs. - Daniel Gibney; Sharma V. Thankachan; Srinivas Aluru (RECOMB, 2022)

Co-linear Chaining with Overlaps and Gap Costs. - Chirag Jain; Daniel Gibney; Sharma V. Thankachan (RECOMB, 2022)

Quantum Time Complexity and Algorithms for Pattern Matching on Labeled Graphs. - Parisa Darbari; Daniel Gibney; Sharma V. Thankachan (SPIRE, 2022)

Feasibility of Flow Decomposition with Subpath Constraints in Linear Time. - Daniel Gibney; Sharma V. Thankachan; Srinivas Aluru (WABI, 2022)

On the Complexity of Recognizing Wheeler Graphs. - Daniel Gibney; Sharma V. Thankachan (Algorithmica, 2022)

On the Hardness of Sequence Alignment on De Bruijn Graphs. - Daniel Gibney; Sharma V. Thankachan; Srinivas Aluru (J. Comput. Biol., 2022)

Algorithms for Colinear Chaining with Overlaps and Gap Costs. - Chirag Jain; Daniel Gibney; Sharma V. Thankachan (J. Comput. Biol., 2022)

Contextual Pattern Matching in Less Space. - Paniz Abedin; Oliver A. Chubet; Daniel Gibney; Sharma V. Thankachan (DCC, 2023)

On the Hardness of Wildcard Pattern Matching on de Bruijn Graphs. - Arnab Ganguly 002; Daniel Gibney; Arghya Kusum Das; Sharma V. Thankachan (ICCABS, 2023)

Compressibility-Aware Quantum Algorithms on Strings. - Daniel Gibney; Sharma V. Thankachan (CoRR, 2023)

Longest Common Substring with Gaps and Related Problems. - Aranya Banerjee; Daniel Gibney; Sharma V. Thankachan (ESA, 2024)

Haplotype-Aware Sequence Alignment to Pangenome Graphs. - Ghanshyam Chandra; Daniel Gibney; Chirag Jain (RECOMB, 2024)

Near-Optimal Quantum Algorithms for Bounded Edit Distance and Lempel-Ziv Factorization. - Daniel Gibney; Ce Jin 001; Tomasz Kociumaka; Sharma V. Thankachan (SODA, 2024)

Bounded-Ratio Gapped String Indexing. - Arnab Ganguly 002; Daniel Gibney; Paul Macnichol; Sharma V. Thankachan (SPIRE, 2024)

Quantum Algorithms for Longest Common Substring with a Gap. - Daniel Gibney; Md. Helal Hossen (SPIRE, 2024)

GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants. - Neda Tavakoli; Daniel Gibney; Srinivas Aluru (J. Comput. Biol., 2024)

Wheeler Graphs and Wheeler Languages. - Nicola Cotumaccio; Giovanna D'Agostino; Daniel Gibney; Alberto Policriti; Nicola Prezza; Sharma V. Thankachan (The Expanding World of Compressed Data, 2025)

Repetition Aware Text Indexing for Matching Patterns with Wildcards. - Daniel Gibney; Jackson Huffstutler; Mano Prakash Parthasarathi; Sharma V. Thankachan (ICALP, 2025)

A Work-Optimal Parallel Algorithm for Aligning Sequences to Genome Graphs. - Aranya Banerjee; Daniel Gibney; Helen Xu; Srinivas Aluru (IPDPS, 2025)

Integer Programming Framework for Pangenome-Based Genome Inference. - Ghanshyam Chandra; Md. Helal Hossen; Stephan Scholz; Alexander T. Dilthey; Daniel Gibney; Chirag Jain (RECOMB, 2025)

Two-Dimensional Longest Common Extension Queries in Compact Space. - Arnab Ganguly 002; Daniel Gibney; Rahul Shah 001; Sharma V. Thankachan (STACS, 2025)

Haplotype-Aware Long-Read Error Correction. - Parvesh Barak; Daniel Gibney; Chirag Jain (WABI, 2025)

Non-overlapping indexing in BWT-runs bounded space. - Daniel Gibney; Paul Macnichol; Sharma V. Thankachan (Theor. Comput. Sci., 2025)

Contextual Pattern Mining and Counting. - Ling Li 012; Daniel Gibney; Sharma V. Thankachan; Solon P. Pissis; Grigorios Loukides (CoRR, 2025)