143 citations · 241 across the 6 of their papers we have counts for
9 papers
Computing Phylo-k-mers
Nikolai Romashchenko, Benjamin Linard, Fabio Pardi +1
Phylogenetically informed k-mers, or phylo-k-mers for short, are k-mers that are predicted to appear within a given genomic region at predefined locations of a fixed phylogeny. Giv…
Convergence of the number of period sets in strings
Eric Rivals, Michelle Sweering, Pengfei Wang
Consider words of length . The set of all periods of a word of length is a subset of . However, any subset of is not necessarily…
A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs
Sangsoo Park, Sung Gwan Park, Bastien Cazaux +2
The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| l…
Greedy-reduction from Shortest Linear Superstring to Shortest Circular Superstring
Bastien Cazaux, Eric Rivals
A superstring of a set of strings correspond to a string which contains all the other strings as substrings. The problem of finding the Shortest Linear Superstring is a well-know a…
Strong link between BWT and XBW via Aho-Corasick automaton and applications to Run-Length Encoding
Bastien Cazaux, Eric Rivals
The boom of genomic sequencing makes compression of set of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data.…
Hierarchical Overlap Graph
Bastien Cazaux, Eric Rivals
Given a set of finite words, the Overlap Graph (OG) is a complete weighted digraph where each word is a node and where the weight of an arc equals the length of the longest overlap…