About Me

I'm an Assistant Professor in The Department of Computer Science at The University of Texas at Dallas.

I received my Ph.D. in Computer Science at The University of Central Florida under the supervision of Sharma V. Thankachan, where I focused on string algorithms and related problems in computational complexity. Following my Ph.D., I received two years of postdoctoral experience at The Georgia Institute of Technology under the supervision of Srinivas Aluru.

My research interests include:

• Algorithm and data structure design/analysis
• Computational biology
• Quantum algorithms

Contact

• Office location: ECSS 4.706
• Email: daniel.gibney@utdallas.edu

Research Group

• Ph.D. student: Md Helal Hossen
• Ph.D. student: Jackson Huffstutler
• Ph.D. student: William Doan

Teaching

• Spring 2026: CS 4301 Fundamentals of Quantum Computing
• Fall 2024 - Fall 2025: CS 2305 Discrete Mathematics
• Spring 2024: CS 6301 Special topics - Quantum Computing
• Fall 2023: CS 4349.006 Advance Algorithm Design & Analysis

Select Publications

Please refer to my dblp and Google Scholar for a complete list.

• Repetition Aware Text Indexing for Matching Patterns with Wildcards
  Daniel Gibney, Jackson Huffstutler, Mano Prakash, 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
• Near-Optimal Quantum Algorithms for Bounded Edit Distance and Lempel-Ziv Factorization
  Daniel Gibney, Ce Jin, Tomasz Kociumaka, Sharma V. Thankachan. SODA 2024
• Co-linear Chaining with Overlaps and Gap Costs
  Chirag Jain, Daniel Gibney, Sharma V. Thankachan. RECOMB 2022
• The Complexity of Approximate Pattern Matching on De Bruijn Graphs
  Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru. RECOMB 2022
• 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
• 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