4th Workshop Single-Cell 2022 - Single-Cell : Transcriptomics, Spatial and Multi-Omics (sincellTE)
Date: From 01/09/2022 to 01/14/2022 Place: Station Biologique, Roscoff, France This workshop focuses on the large-scale study of...
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- Jul 14, 2021
Quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
Published in Bioinformatics Mallet V, Nilges M, Bouvier G Summary: We implemented the Self-Organizing Maps algorithm running efficiently...
- Mar 31, 2021
Data Structures to Represent a Set of k-long DNA Sequences
ACM Computing Surveys Chikhi R, Holub J, Medvedev P The analysis of biological sequencing data has been one of the biggest applications...
- Dec 1, 2020
Data structures based on kmers for querying large collections of sequencing data sets
Genome Res Marchet C, Boucher C, Puglisi SJ, Medvedev P, Salson M, Chikhi R High-throughput sequencing data sets are usually deposited...
- Nov 23, 2020
Identifying neural substrates of competitive interactions and sequence transitions
Plos Genetics Jean-Baptiste Masson, Francois Laurent, Albert Cardona, Chloe Barre, Nicolas Skatchkovsky, Marta Zlatic, Tihana Jovanic...
- Sep 6, 2020
Disk Compression of k-mer Sets
WABI Rahman A, Chikhi R, Medvedev P K-mer based methods have become prevalent in many areas of bioinformatics. In applications such as...
- Aug 24, 2020
Graph-Theoretic Barcode Ordering Model for Linked-Reads
WABI 2020 Dufresne Y, Sun C, Marijon P, Lavenier D, Chauve C, Chikhi R Considering a set of intervals on the real line, an interval...
- Jul 1, 2020
ARIAweb: a server for automated NMR structure calculation
Nucleic Acids Res Fabrice Allain, Fabien Mareuil, Hervé Ménager, Michael Nilges, Benjamin Bardiaux. Nuclear magnetic resonance (NMR)...
- Jun 30, 2020
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing
Brief Bioinform Lima L, Marchet C, Caboche S, da Silva C, Istace B, Aury JM, Touzet H, Chikhi R Motivation Nanopore long-read sequencing...
- Jun 30, 2020
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Bioinformatics Marchet C, Iqbal Z, Gautheret D, Salson M, Chikhi R. Motivation: In this work we present REINDEER, a novel computational...
- May 31, 2020
Yacrd and fpa: upstream tools for long-read genome assembly
Bioinformatics Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré Motivation: Genome assembly is increasingly performed on long,...
- Apr 30, 2020
A Darwinian Uncertainty Principle
Systematic Biology Olivier Gascuel, Mike Steel Reconstructing ancestral characters and traits along a phylogenetic tree is central to...
- Apr 20, 2020
Identification and molecular characterization of the first complete genome sequence
Scientific Reports Fernandez-Garcia MD, Simon-Loriere E, Kebe O, Sakuntabhai A, Ndiaye K Using a metagenomics approach, we have...
- Apr 14, 2020
Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics
Phylogenetics in the Genomic Era Zhukova A, Gascuel O, Duchene S, Ayres D, Lemey P, Baele G Viral evolutionary analyses are confronted...
- Mar 1, 2020
JASS: command line and web interface for the joint analysis of GWAS results
Nar Genomics and Bioinformatics Julienne H, Lechat P, Guillemot V, Lasry C, Yao C, Araud R, Laville V, Vilhjalmsson B, Ménager H,...
- Feb 6, 2020
Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria
Nature Communications Marc Garcia-Garcera & Eduardo P. C. Rocha We test the hypothesis that the frequency and cost of extracellular...
- Feb 1, 2020
Genome Assembly and Analysis of the North American Mountain Goat Species-Level Responses
G3 Genes Genomes Genetics Daria Martchenko, Rayan Chikhi, and Aaron B. A. Shafer The North American mountain goat (Oreamnos americanus)...
- Jan 24, 2020
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes
Nucleic Acids Research Aude Bernheim, David Bikard, Marie Touchon, Eduardo P C Rocha Prokaryotes use CRISPR–Cas systems for adaptive...
- Sep 11, 2019
Highly pathogenic avian influenza H5N8 in south-west France 2016–2017
Epidemics Alessio Andronic, Aurélie Courcoul, Anne Bronner, Axelle Scoizec, Sophie Lebouquin-Leneveu, Claire Guinat, Mathilde C.Paul,...
- Aug 1, 2019
PastView: a user-friendly interface to explore ancestral scenarios
BMC Evolutionary Biology François Chevenet, Guillaume Castel, Emmanuelle Jousselin, and Olivier Gascuel. BACKGROUND: Ancestral character...
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