6 citations · 11 across the 6 of their papers we have counts for
6 papers
Practical colinear chaining on sequences revisited
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Colinear chaining is a classical heuristic for sequence alignment and is widely used in modern practical aligners. Jain et al. (J. Comput. Biol. 2022) proposed an t…
Finding Maximal Exact Matches in Graphs
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
We study the problem of finding maximal exact matches (MEMs) between a query string and a labeled graph . MEMs are an important class of seeds, often used in seed-chain-exte…
Elastic Founder Graphs Improved and Enhanced
Nicola Rizzo, Massimo Equi, Tuukka Norri +1
Indexing labeled graphs for pattern matching is a central challenge of pangenomics. Equi et al. (Algorithmica, 2022) developed the Elastic Founder Graph () representi…
Chaining of Maximal Exact Matches in Graphs
Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
We show how to chain maximal exact matches (MEMs) between a query string and a labeled directed acyclic graph (DAG) to solve the longest common subsequence (LCS) prob…
Linear Time Construction of Indexable Elastic Founder Graphs
Nicola Rizzo, Veli Mäkinen
Pattern matching on graphs has been widely studied lately due to its importance in genomics applications. Unfortunately, even the simplest problem of deciding if a string appears a…
The Labeled Direct Product Optimally Solves String Problems on Graphs
Nicola Rizzo, Alexandru I. Tomescu, Alberto Policriti
Suffix trees are an important data structure at the core of optimal solutions to many fundamental string problems, such as exact pattern matching, longest common substring, matchin…