| 2026 | DCC | On the Size of Higher-Order Prefix-Free Parse Representations. | Md. Helal Hossen, Daniel Gibney |
| 2026 | ESA | Indexing Integer Strings Using Local Difference Bounds. | Daniel Gibney, Kaamil Kaka, Sharma V. Thankachan |
| 2026 | ICDE | Contextual Pattern Mining and Counting. | Ling Li, Daniel Gibney, Sharma V. Thankachan, Solon P. Pissis, Grigorios Loukides |
| 2025 | ICALP | Repetition Aware Text Indexing for Matching Patterns with Wildcards. | Daniel Gibney, Jackson Huffstutler, Mano Prakash Parthasarathi, Sharma V. Thankachan |
| 2025 | RECOMB | Integer Programming Framework for Pangenome-Based Genome Inference. | Ghanshyam Chandra, Md. Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, Chirag Jain |
| 2025 | STACS | Two-Dimensional Longest Common Extension Queries in Compact Space. | Arnab Ganguly, Daniel Gibney, Rahul Shah, Sharma V. Thankachan |
| 2025 | WABI | Haplotype-Aware Long-Read Error Correction. | Parvesh Barak, Daniel Gibney, Chirag Jain |
| 2024 | ESA | Longest Common Substring with Gaps and Related Problems. | Aranya Banerjee, Daniel Gibney, Sharma V. Thankachan |
| 2024 | RECOMB | Haplotype-Aware Sequence Alignment to Pangenome Graphs. | Ghanshyam Chandra, Daniel Gibney, Chirag Jain |
| 2024 | SODA | Near-Optimal Quantum Algorithms for Bounded Edit Distance and Lempel-Ziv Factorization. | Daniel Gibney, Ce Jin, Tomasz Kociumaka, Sharma V. Thankachan |
| 2024 | SPIRE | Bounded-Ratio Gapped String Indexing. | Arnab Ganguly, Daniel Gibney, Paul Macnichol, Sharma V. Thankachan |
| 2024 | SPIRE | Quantum Algorithms for Longest Common Substring with a Gap. | Daniel Gibney, Md. Helal Hossen |
| 2023 | DCC | Contextual Pattern Matching in Less Space. | Paniz Abedin, Oliver A. Chubet, Daniel Gibney, Sharma V. Thankachan |
| 2023 | SPIRE | Non-overlapping Indexing in BWT-Runs Bounded Space. | Daniel Gibney, Paul Macnichol, Sharma V. Thankachan |
| 2022 | RECOMB | The Complexity of Approximate Pattern Matching on de Bruijn Graphs. | Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru |
| 2022 | RECOMB | Co-linear Chaining with Overlaps and Gap Costs. | Chirag Jain, Daniel Gibney, Sharma V. Thankachan |
| 2022 | SPIRE | Quantum Time Complexity and Algorithms for Pattern Matching on Labeled Graphs. | Parisa Darbari, Daniel Gibney, Sharma V. Thankachan |
| 2022 | WABI | Feasibility of Flow Decomposition with Subpath Constraints in Linear Time. | Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru |
| 2021 | STACS | Finding an Optimal Alphabet Ordering for Lyndon Factorization Is Hard. | Daniel Gibney, Sharma V. Thankachan |
| 2020 | CPM | FM-Index Reveals the Reverse Suffix Array. | Arnab Ganguly, Daniel Gibney, Sahar Hooshmand, M. Oguzhan Klekci, Sharma V. Thankachan |
| 2020 | ESA | On the Complexity of BWT-Runs Minimization via Alphabet Reordering. | Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan |
| 2020 | ESA | The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance. | Gary Hoppenworth, Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan |
| 2020 | SPIRE | An Efficient Elastic-Degenerate Text Index? Not Likely. | Daniel Gibney |
| 2019 | ESA | On the Hardness and Inapproximability of Recognizing Wheeler Graphs. | Daniel Gibney, Sharma V. Thankachan |