Fanny Perraudeau
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View article: CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS
CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS Open
Motivation Genome-wide association studies (GWAS), aiming to find genetic variants associated with a trait, have widely been used on bacteria to identify genetic determinants of drug resistance or hypervirulence. Recent bacterial GWAS meth…
View article: CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS
CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS Open
Genome wide association studies (GWAS), aiming to find genetic variants associated with a trait, have widely been used on bacteria to identify genetic determinants of drug resistance or hypervirulence. Recent bacterial GWAS methods usually…
View article: FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes
FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes Open
Dietary fibers impact gut colonic health, through the production of short-chain fatty acids. A low-fiber diet has been linked to lower bacterial diversity, obesity, type 2 diabetes, and promotion of mucosal pathogens. Glycoside hydrolases …
View article: Comparative Analysis of Patient-Matched PDOs Revealed a Reduction in OLFM4-Associated Clusters in Metastatic Lesions in Colorectal Cancer
Comparative Analysis of Patient-Matched PDOs Revealed a Reduction in OLFM4-Associated Clusters in Metastatic Lesions in Colorectal Cancer Open
View article: Medical Food Assessment Using a Smartphone App With Continuous Glucose Monitoring Sensors: Proof-of-Concept Study
Medical Food Assessment Using a Smartphone App With Continuous Glucose Monitoring Sensors: Proof-of-Concept Study Open
Background Novel wearable biosensors, ubiquitous smartphone ownership, and telemedicine are converging to enable new paradigms of clinical research. A new generation of continuous glucose monitoring (CGM) devices provides access to clinica…
View article: Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation
Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation Open
Introduction A growing body of evidence suggests that specific, naturally occurring gut bacteria are under-represented in the intestinal tracts of subjects with type 2 diabetes (T2D) and that their functions, like gut barrier stability and…
View article: Publisher Correction: A general and flexible method for signal extraction from single-cell RNA-seq data
Publisher Correction: A general and flexible method for signal extraction from single-cell RNA-seq data Open
The original PDF version of this Article contained errors in two equations. In Eq. (1), all Γ symbols were inadvertently omitted. In the second equation in the subsection entitled ‘1. Dispersion optimization’ within the Methods section ‘ZI…
View article: Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications Open
View article: Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications
Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications Open
Dropout events in single-cell transcriptome sequencing (scRNA-seq) cause many transcripts to go undetected and induce an excess of zero read counts, leading to power issues in differential expression (DE) analysis. This has triggered the d…
View article: Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications
Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications Open
Dropout events in single-cell transcriptome sequencing (scRNA-seq) cause many transcripts to go undetected and induce an excess of zero read counts, leading to power issues in differential expression (DE) analysis. This has triggered the d…
View article: A general and flexible method for signal extraction from single-cell RNA-seq data
A general and flexible method for signal extraction from single-cell RNA-seq data Open
View article: Additional file 2 of Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
Additional file 2 of Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications Open
countsimQC evaluation of simulated Islam dataset. (HTML 11,492 kb)
View article: Additional file 3 of Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
Additional file 3 of Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications Open
countsimQC evaluation of simulated Trapnell dataset. (HTML 11,639 kb)
View article: Additional file 4 of Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
Additional file 4 of Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications Open
countsimQC evaluation of simulated 10x dataset. (HTML 9933 kb)
View article: Accurate Determination of Bacterial Abundances in Human Metagenomes Using Full-length 16S Sequencing Reads
Accurate Determination of Bacterial Abundances in Human Metagenomes Using Full-length 16S Sequencing Reads Open
DNA sequencing of PCR-amplified marker genes, especially but not limited to the 16S rRNA gene, is perhaps the most common approach for profiling microbial communities. Due to technological constraints of commonly available DNA sequencing, …
View article: Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference
Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference Open
Novel single-cell transcriptome sequencing assays allow researchers to measure gene expression levels at the resolution of single cells and offer the unprecendented opportunity to investigate at the molecular level fundamental biological q…
View article: Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference: fperraudeau/singlecellworkflow First release.
Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference: fperraudeau/singlecellworkflow First release. Open
This is the first release.
View article: ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq data
ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq data Open
Single-cell RNA sequencing (scRNA-seq) is a powerful high-throughput technique that enables researchers to measure genome-wide transcription levels at the resolution of single cells. Because of the low amount of RNA present in a single cel…
View article: Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire‐associated fungus<i>Neurospora discreta</i>
Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire‐associated fungus<i>Neurospora discreta</i> Open
Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces …
View article: Identification of Allorecognition Loci in<i>Neurospora crassa</i>by Genomics and Evolutionary Approaches
Identification of Allorecognition Loci in<i>Neurospora crassa</i>by Genomics and Evolutionary Approaches Open
Understanding the genetic and molecular bases of the ability to distinguish self from nonself (allorecognition) and mechanisms underlying evolution of allorecognition systems is an important endeavor for understanding cases where it become…