Daniel Gibney

45 papers A* 2A 7B 6C 7Journal 16Unranked 7
YearRankTypeTitle / Venue / Authors
2025 A conf
A Work-Optimal Parallel Algorithm for Aligning Sequences to Genome Graphs.
IPDPS
Aranya Banerjee, Daniel Gibney, Helen Xu, Srinivas Aluru
2025 J jnl
Contextual Pattern Mining and Counting.
CoRR
Ling Li, Daniel Gibney, Sharma V. Thankachan, Solon P. Pissis, Grigorios Loukides
2025 C conf
Haplotype-Aware Long-Read Error Correction.
WABI
Parvesh Barak, Daniel Gibney, Chirag Jain
2025 B conf
Integer Programming Framework for Pangenome-Based Genome Inference.
RECOMB
Ghanshyam Chandra, Md. Helal Hossen, Stephan Scholz, Alexander T. Dilthey, Daniel Gibney, Chirag Jain
2025 J jnl
Non-overlapping indexing in BWT-runs bounded space.
Theor. Comput. Sci.
Daniel Gibney, Paul Macnichol, Sharma V. Thankachan
2025 A* conf
Repetition Aware Text Indexing for Matching Patterns with Wildcards.
ICALP
Daniel Gibney, Jackson Huffstutler, Mano Prakash Parthasarathi, Sharma V. Thankachan
2025 A conf
Two-Dimensional Longest Common Extension Queries in Compact Space.
STACS
Arnab Ganguly, Daniel Gibney, Rahul Shah, Sharma V. Thankachan
2025 — conf
Wheeler Graphs and Wheeler Languages.
The Expanding World of Compressed Data
Nicola Cotumaccio, Giovanna D'Agostino, Daniel Gibney, Alberto Policriti, Nicola Prezza, Sharma V. Thankachan
2024 C conf
Bounded-Ratio Gapped String Indexing.
SPIRE
Arnab Ganguly, Daniel Gibney, Paul Macnichol, Sharma V. Thankachan
2024 J jnl
GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants.
J. Comput. Biol.
Neda Tavakoli, Daniel Gibney, Srinivas Aluru
2024 B conf
Haplotype-Aware Sequence Alignment to Pangenome Graphs.
RECOMB
Ghanshyam Chandra, Daniel Gibney, Chirag Jain
2024 A conf
Longest Common Substring with Gaps and Related Problems.
ESA
Aranya Banerjee, Daniel Gibney, Sharma V. Thankachan
2024 A* conf
Near-Optimal Quantum Algorithms for Bounded Edit Distance and Lempel-Ziv Factorization.
SODA
Daniel Gibney, Ce Jin, Tomasz Kociumaka, Sharma V. Thankachan
2024 C conf
Quantum Algorithms for Longest Common Substring with a Gap.
SPIRE
Daniel Gibney, Md. Helal Hossen
2024 J jnl
Text Indexing for Faster Gapped Pattern Matching.
Algorithms
Md. Helal Hossen, Daniel Gibney, Sharma V. Thankachan
2023 J jnl
Compressibility-Aware Quantum Algorithms on Strings.
CoRR
Daniel Gibney, Sharma V. Thankachan
2023 B conf
Contextual Pattern Matching in Less Space.
DCC
Paniz Abedin, Oliver A. Chubet, Daniel Gibney, Sharma V. Thankachan
2023 J jnl
Near-Optimal Quantum Algorithms for Bounded Edit Distance and Lempel-Ziv Factorization.
CoRR
Daniel Gibney, Ce Jin, Tomasz Kociumaka, Sharma V. Thankachan
2023 C conf
Non-overlapping Indexing in BWT-Runs Bounded Space.
SPIRE
Daniel Gibney, Paul Macnichol, Sharma V. Thankachan
2023 — conf
On the Hardness of Wildcard Pattern Matching on de Bruijn Graphs.
ICCABS
Arnab Ganguly, Daniel Gibney, Arghya Kusum Das, Sharma V. Thankachan
2022 J jnl
Algorithms for Colinear Chaining with Overlaps and Gap Costs.
J. Comput. Biol.
Chirag Jain, Daniel Gibney, Sharma V. Thankachan
2022 B conf
Co-linear Chaining with Overlaps and Gap Costs.
RECOMB
Chirag Jain, Daniel Gibney, Sharma V. Thankachan
2022 C conf
Feasibility of Flow Decomposition with Subpath Constraints in Linear Time.
WABI
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
2022 — conf
Haplotype-aware variant selection for genome graphs.
BCB
Neda Tavakoli, Daniel Gibney, Srinivas Aluru
2022 J jnl
On the Complexity of Recognizing Wheeler Graphs.
Algorithmica
Daniel Gibney, Sharma V. Thankachan
2022 J jnl
On the Hardness of Sequence Alignment on De Bruijn Graphs.
J. Comput. Biol.
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
2022 C conf
Quantum Time Complexity and Algorithms for Pattern Matching on Labeled Graphs.
SPIRE
Parisa Darbari, Daniel Gibney, Sharma V. Thankachan
2022 J jnl
The Complexity of Approximate Pattern Matching on De Bruijn Graphs.
CoRR
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
2022 B conf
The Complexity of Approximate Pattern Matching on de Bruijn Graphs.
RECOMB
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
2021 A conf
Finding an Optimal Alphabet Ordering for Lyndon Factorization Is Hard.
STACS
Daniel Gibney, Sharma V. Thankachan
2021 J jnl
I/O-optimal categorical 3-sided skyline queries.
Theor. Comput. Sci.
Arnab Ganguly, Daniel Gibney, Sharma V. Thankachan, Rahul Shah
2021 — conf
Simple Reductions from Formula-SAT to Pattern Matching on Labeled Graphs and Subtree Isomorphism.
SOSA
Daniel Gibney, Gary Hoppenworth, Sharma V. Thankachan
2021 J jnl
Text Indexing for Regular Expression Matching.
Algorithms
Daniel Gibney, Sharma V. Thankachan
2020 C conf
An Efficient Elastic-Degenerate Text Index? Not Likely.
SPIRE
Daniel Gibney
2020 B conf
FM-Index Reveals the Reverse Suffix Array.
CPM
Arnab Ganguly, Daniel Gibney, Sahar Hooshmand, M. Oguzhan Külekci, Sharma V. Thankachan
2020 A conf
On the Complexity of BWT-Runs Minimization via Alphabet Reordering.
ESA
Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan
2020 J jnl
Quantifying Membership Inference Vulnerability via Generalization Gap and Other Model Metrics.
CoRR
Jason W. Bentley, Daniel Gibney, Gary Hoppenworth, Sumit Kumar Jha
2020 J jnl
Simple Reductions from Formula-SAT to Pattern Matching on Labeled Graphs and Subtree Isomorphism.
CoRR
Daniel Gibney, Gary Hoppenworth, Sharma V. Thankachan
2020 A conf
The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance.
ESA
Gary Hoppenworth, Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan
2019 — conf
I/O Optimal Data Structures for Categorical Range Skyline Queries.
CCCG
Daniel Gibney, Sharma V. Thankachan, Arnab Ganguly, Rahul Shah
2019 J jnl
On the Complexity of BWT-runs Minimization via Alphabet Reordering.
CoRR
Jason W. Bentley, Daniel Gibney, Sharma V. Thankachan
2019 A conf
On the Hardness and Inapproximability of Recognizing Wheeler Graphs.
ESA
Daniel Gibney, Sharma V. Thankachan
2019 J jnl
On the Hardness and Inapproximability of Recognizing Wheeler Graphs.
CoRR
Daniel Gibney, Sharma V. Thankachan
2018 — conf
Faster Computation of Genome Mappability with one Mismatch.
ICCABS
Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan
2018 — conf
Faster Computation of Genome Mappability.
BCB
Sahar Hooshmand, Paniz Abedin, Daniel Gibney, Srinivas Aluru, Sharma V. Thankachan
2023 — conf
Not What You've Signed Up For: Compromising Real-World LLM-Integrated Applications with Indirect Prompt Injection.
AISec
Kai Greshake, Sahar Abdelnabi, Shailesh Mishra, Christoph Endres, Thorsten Holz, Mario Fritz
2026 — preprint
CCX: Enabling Unmodified Intel SGX Applications on Arm CCA.
arXiv
Matti Schulze, Thorsten Holz, Felix C. Freiling