30 citations · 30 across the 2 of their papers we have counts for
6 papers
Data structures to represent a set of k-long DNA sequences
Rayan Chikhi, Jan Holub, Paul Medvedev
The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of…
Bipartite Graphs of Small Readability
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch +4
We study a parameter of bipartite graphs called readability, introduced by Chikhi et al. (Discrete Applied Mathematics, 2016) and motivated by applications of overlap graphs in bio…
Modeling Biological Problems in Computer Science: A Case Study in Genome Assembly
Paul Medvedev
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in m…
TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes
Ilia Minkin, Son Pham, Paul Medvedev
Motivation: De Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic setti…
On the readability of overlap digraphs
Rayan Chikhi, Paul Medvedev, Martin Milanic +1
We introduce the graph parameter readability and study it as a function of the number of vertices in a graph. Given a digraph D, an injective overlap labeling assigns a unique stri…
Informed and Automated k-Mer Size Selection for Genome Assembly
Rayan Chikhi, Paul Medvedev
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. T…