Sandrine Dudoit

Evolving stem cell fate capacities and transcriptional priming in the developing olfactory epithelium

This study uses single-cell RNA sequencing to trace the developmental trajectory of olfactory epithelium in mice, identifying Ascl1+ cells as multipotent progenitors that become transcriptionally primed over time.

Unlocking Multi-Sample Differential Expression for Spatial Transcriptomics Data with TESSERA

TESSERA is a method for analyzing multi-sample spatial transcriptomics data, enabling differential expression analysis while accounting for spatial correlation and sample-specific factors.

A Latent Activated Olfactory Stem Cell State Revealed by Single Cell Transcriptomic and Epigenomic Profiling

This study identifies a latent activated stem cell state in olfactory epithelium using single-cell transcriptomic and epigenomic profiling during injury-induced regeneration.

transfactor: Transcription factor activity estimation via probabilistic gene expression deconvolution

This paper introduces a statistical model to estimate transcription factor activity from gene expression data by leveraging gene regulatory networks, improving interpretation of biological differences.

Improving replicability in single-cell RNA-Seq cell type discovery with Dune

Dune improves replicability of cell type discovery in scRNA-Seq by optimizing the trade-off between cluster resolution and cross-dataset consistency.

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

The paper benchmarks ATAC-seq normalization methods and shows that GC-content effects must be accounted for to improve downstream analysis accuracy.

CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

CALDERA improves bacterial GWAS by testing subgraphs of De Bruijn graphs, enhancing power and interpretability while managing computational complexity.

Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes

This study identifies Klf5 as a key regulator of bi-potential cell fate in mouse preimplantation embryos by controlling both ICM and TE specification genes.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression.

The paper introduces a method to infer and compare cell trajectories across multiple conditions, detecting differences in progression, population structure, and gene expression.

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

The paper identifies non-neuronal cell types in the olfactory system expressing SARS-CoV-2 entry genes, suggesting indirect mechanisms for COVID-19-associated anosmia.

Exploring High-Dimensional Biological Data with Sparse Contrastive Principal Component Analysis

This paper introduces sparse contrastive principal component analysis to extract stable and relevant biological signals from high-dimensional data and evaluates it on multiple datasets.

Trajectory-based differential expression analysis for single-cell sequencing data

The paper introduces a generalized additive model framework for trajectory-based differential expression analysis in single-cell RNA-seq data, enabling flexible inference of within and between lineage gene expression differences.

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-seq

This paper evaluates normalization methods for scRNA-seq using a framework called scone, showing that top methods improve agreement with validation data.

adductomicsR: A package for detection and quantification of protein adducts from mass spectra of tryptic digests

The paper introduces adductomicsR, an R package for detecting and quantifying protein adducts from LC-HRMS data of tryptic digests.

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

The paper introduces clusterExperiment, a Bioconductor package for clustering large gene expression datasets using Resampling-based Sequential Ensemble Clustering (RSEC) to identify biologically meaningful subtypes.

Data-adaptive pipeline for filtering and normalizing metabolomics data.

The paper introduces a data-adaptive pipeline for filtering and normalizing metabolomics data, showing it outperforms traditional methods in reducing technical noise and preserving biological signals.

Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics

Slingshot builds a cluster-level minimum spanning tree to find branching lineages without fixing their number, then fits simultaneous principal curves for stable per-lineage pseudotimes.

Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications

The paper introduces a weighting strategy using a zero-inflated negative binomial model to improve bulk RNA-seq tools for single-cell RNA-seq data with zero inflation.

ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq data

The paper introduces ZINB-WaVE, a method for improving low-dimensional representations of scRNA-seq data by accounting for dropouts and over-dispersion, outperforming PCA and ZIFA.

Accurate Determination of Bacterial Abundances in Human Metagenomes Using Full-length 16S Sequencing Reads

The paper presents a method to accurately estimate bacterial abundances in human metagenomes using full-length 16S sequencing reads and a generalized pair hidden Markov chain model.