Concept
Assemblage (bio-informatique)
Publications associées (60)
Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics
Tamar Kohn, Xavier Fernandez Cassi
Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...
2024Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics
Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...
PUBLIC LIBRARY SCIENCE2023Evaluation of genetic demultiplexing of single-cell sequencing data from model species
Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address thes ...
LIFE SCIENCE ALLIANCE LLC2023Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter
Christof Holliger, Julien Maillard, Aline Sondra Adler, Marco Pagni, Simon Marius Jean Poirier
Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...
WILEY2022Towards mouse genetic-specific RNA-sequencing read mapping
Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using ...
2022Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics
We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples and to prepare these cells for bulk whole-genome sequencing without cultivation. We characterize this approach by recovering bacteria spike ...
2022Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells
We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimul ...
NATURE RESEARCH2021The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya
Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). As plants transitioned to land the EDF sub-phylum, arbuscular mycorrhizal fungi (AMF; Glom ...
NATURE PORTFOLIO2021A Crowdsourced Gameplay for Whole-Genome Assembly via Short Reads
Next-generation sequencing has revolutionized the field of genomics by producing accurate, rapid and cost-effective genome analysis with the use of high throughput sequencing technologies. This has intensified the need for accurate and performance efficien ...
INT ASSOC ONLINE ENGINEERING2020Comparison of chitin‐induced natural transformation in pandemic Vibrio cholerae O1 El Tor strains
Melanie Blokesch, Sandrine Stutzmann
The human pathogen Vibrio cholerae serves as a model organism for many important processes ranging from pathogenesis to natural transformation, which has been extensively studied in this bacterium. Previous work has deciphered important regulatory circuits ...
2020