Data Structures to Represent a Set of k-long DNA Sequences
R Chikhi, J Holub, P Medvedev - ACM Computing Surveys (CSUR), 2021 - dl.acm.org
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 …
string algorithms. The approaches used in many such applications are based on the …
[HTML][HTML] Mash Screen: high-throughput sequence containment estimation for genome discovery
The MinHash algorithm has proven effective for rapidly estimating the resemblance of two
genomes or metagenomes. However, this method cannot reliably estimate the containment …
genomes or metagenomes. However, this method cannot reliably estimate the containment …
To petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics
As computational biologists continue to be inundated by ever increasing amounts of
metagenomic data, the need for data analysis approaches that keep up with the pace of …
metagenomic data, the need for data analysis approaches that keep up with the pace of …
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Motivation In this work we present REINDEER, a novel computational method that performs
indexing of sequences and records their abundances across a collection of datasets. To the …
indexing of sequences and records their abundances across a collection of datasets. To the …
BLight: efficient exact associative structure for k-mers
C Marchet, M Kerbiriou, A Limasset - Bioinformatics, 2021 - academic.oup.com
Motivation A plethora of methods and applications share the fundamental need to associate
information to words for high-throughput sequence analysis. Doing so for billions of k-mers …
information to words for high-throughput sequence analysis. Doing so for billions of k-mers …
[HTML][HTML] Gut-microbial adaptation and transformation of silver nanoparticles mediated the detoxification of Daphnia magna and their offspring
Despite extensive studies on the toxicity of antibacterial silver (either ionic Ag+ or
nanoparticles–AgNPs) at the cellular or organism level, little is known about the differences …
nanoparticles–AgNPs) at the cellular or organism level, little is known about the differences …
Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters
Alignment-free classification tools have enabled high-throughput processing of sequencing
data in many bioinformatics analysis pipelines primarily due to their computational …
data in many bioinformatics analysis pipelines primarily due to their computational …
[HTML][HTML] Nutrient-imbalanced conditions shift the interplay between zooplankton and gut microbiota
Background Nutrient stoichiometry of phytoplankton frequently changes with aquatic
ambient nutrient concentrations, which is mainly influenced by anthropogenic water …
ambient nutrient concentrations, which is mainly influenced by anthropogenic water …
Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome
W Li, J Freudenberg, J Freudenberg - Gene, 2019 - Elsevier
The nuclear human genome harbors sequences of mitochondrial origin, indicating an
ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments …
ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments …
[PDF][PDF] Indexing De Bruijn graphs with minimizers
C Marchet, M Kerbiriou, A Limasset - BioRxiv, 2019 - pdfs.semanticscholar.org
Background: The need to associate information to words is shared among a plethora of
applications and methods in high throughput sequence analysis, and could be marked as …
applications and methods in high throughput sequence analysis, and could be marked as …