742 citations · 807 across the 9 of their papers we have counts for
11 papers
Processing-in-memory for genomics workloads
William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi +12
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized,…
Parallel decompression of gzip-compressed files and random access to DNA sequences
Maël Kerbiriou, Rayan Chikhi
Decompressing a file made by the gzip program at an arbitrary location is in principle impossible, due to the nature of the DEFLATE compression algorithm. Consequently, no existing…
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…
Dualities in Tree Representations
Rayan Chikhi, Alexander Schönhuth
A characterization of the tree such that , the reversal of is given. An immediate consequence is…
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-Linear Chaining Extended
Anna Kuosmanen, Topi Paavilainen, Travis Gagie +3
Aligning sequencing reads on graph representations of genomes is an important ingredient of pan-genomics. Such approaches typically find a set of local anchors that indicate plausi…
Fast and scalable minimal perfect hashing for massive key sets
Antoine Limasset, Guillaume Rizk, Rayan Chikhi +1
Minimal perfect hash functions provide space-efficient and collision-free hashing on static sets. Existing algorithms and implementations that build such functions have practical l…
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…
On the representation of de Bruijn graphs
Rayan Chikhi, Antoine Limasset, Shaun Jackman +2
The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a comp…
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…
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov +88
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished g…