112 citations · 369 across the 25 of their papers we have counts for
6 papers · 1 filter
Evolution of biosequence search algorithms: a brief survey
Gregory Kucherov
The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interco…
Ococo: an online variant and consensus caller
Karel Břinda, Valentina Boeva, Gregory Kucherov
Motivation: Identifying genomic variants is an essential step for connecting genotype and phenotype. The usual approach consists of statistical inference of variants from alignment…
Dynamic read mapping and online consensus calling for better variant detection
Karel Břinda, Valentina Boeva, Gregory Kucherov
Variant detection from high-throughput sequencing data is an essential step in identification of alleles involved in complex diseases and cancer. To deal with these massive data, e…
RNF: a general framework to evaluate NGS read mappers
Karel Břinda, Valentina Boeva, Gregory Kucherov
Aligning reads to a reference sequence is a fundamental step in numerous bioinformatics pipelines. As a consequence, the sensitivity and precision of the mapping tool, applied with…
Spaced seeds improve k-mer-based metagenomic classification
Karel Brinda, Maciej Sykulski, Gregory Kucherov
Metagenomics is a powerful approach to study genetic content of environmental samples that has been strongly promoted by NGS technologies. To cope with massive data involved in mod…
Reconsidering the significance of genomic word frequency
Miklós Csűrös, Laurent Noé, Gregory Kucherov
We propose that the distribution of DNA words in genomic sequences can be primarily characterized by a double Pareto-lognormal distribution, which explains lognormal and power-law…