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05/16/2023
Finding Maximal Exact Matches in Graphs
We study the problem of finding maximal exact matches (MEMs) between a q...
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03/09/2023
Elastic Founder Graphs Improved and Enhanced
Indexing labeled graphs for pattern matching is a central challenge of p...
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02/03/2023
Chaining of Maximal Exact Matches in Graphs
We study the problem of finding maximal exact matches (MEMs) between a q...
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01/17/2022
Linear Time Construction of Indexable Elastic Founder Graphs
Pattern matching on graphs has been widely studied lately due to its imp...
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12/24/2021
Quantum Linear Algorithm for Edit Distance Using the Word QRAM Model
Many problems that can be solved in quadratic time have bit-parallel spe...
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02/25/2021
Algorithms and Complexity on Indexing Founder Graphs
We study the problem of matching a string in a labeled graph. Previous r...
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06/10/2020
Tailoring r-index for metagenomics
A basic problem in metagenomics is to assign a sequenced read to the cor...
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05/19/2020
Linear Time Construction of Indexable Founder Block Graphs
We introduce a compact pangenome representation based on an optimal segm...
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02/03/2020
Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails
We consider the following string matching problem on a node-labeled grap...
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02/03/2020
Conditional Indexing Lower Bounds Through Self-Reducibility
We provide a general technique to turn a conditional lower bound result ...
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01/19/2020
Chaining with overlaps revisited
Chaining algorithms aim to form a semi-global alignment of two sequences...
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02/10/2019
On the Complexity of Exact Pattern Matching in Graphs: Determinism and Zig-Zag Matching
Exact pattern matching in labeled graphs is the problem of searching pat...
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01/16/2019
On the Complexity of Exact Pattern Matching in Graphs: Binary Strings and Bounded Degree
Exact pattern matching in labeled graphs is the problem of searching pat...
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05/14/2018
Assembling Omnitigs using Hidden-Order de Bruijn Graphs
De novo DNA assembly is a fundamental task in Bioinformatics, and findin...
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05/09/2018