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02/25/2021
A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs
The hierarchical overlap graph (HOG) is a graph that encodes overlaps fr...
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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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12/16/2020
Greedy-reduction from Shortest Linear Superstring to Shortest Circular Superstring
A superstring of a set of strings correspond to a string which contains ...
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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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05/25/2018
Strong link between BWT and XBW via Aho-Corasick automaton and applications to Run-Length Encoding
The boom of genomic sequencing makes compression of set of sequences ine...
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05/09/2018
Minimum Segmentation for Pan-genomic Founder Reconstruction in Optimal Time
Given a threshold L and a set R = {R_1, ..., R_m} of m haplotype sequenc...
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02/13/2018