List of works - Sandrine Dudoit

A fine-scale linkage-disequilibrium measure based on length of haplotype sharing

scientific article

A general and flexible method for signal extraction from single-cell RNA-seq data.

scientific article published on 18 January 2018

A method to increase the power of multiple testing procedures through sample splitting.

scientific article published in August 2006

A multimodal cell census and atlas of the mammalian primary motor cortex

scientific article

A prediction-based resampling method for estimating the number of clusters in a dataset

scientific article

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

scientific article

An untargeted metabolomics method for archived newborn dried blood spots in epidemiologic studies.

scientific article

Asymptotic optimality of likelihood-based cross-validation

scientific article published on 22 March 2004

Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives.

scientific article published on 15 June 2004

Bagging to improve the accuracy of a clustering procedure

scientific article published in June 2003

Biases in Illumina transcriptome sequencing caused by random hexamer priming

scientific article

Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference.

scientific article published on 21 July 2017

Bioconductor: open software development for computational biology and bioinformatics

scientific article

Colon cancer prognosis prediction by gene expression profiling

scientific article published on 01 September 2005

Conservation of an RNA regulatory map between Drosophila and mammals

scientific article

Cross-Validated Loss-Based Covariance Matrix Estimator Selection in High Dimensions

scientific article published in 2022

Cys34 Adductomics Links Colorectal Cancer with the Gut Microbiota and Redox Biology

scientific article published on 22 October 2019

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution

scientific article

Diverse transcriptional programs associated with environmental stress and hormones in the Arabidopsis receptor-like kinase gene family

scientific article published on January 2009

Diversity, topographic differentiation, and positional memory in human fibroblasts

scientific article

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

scientific article (publication date: 18 February 2010)

Exploration of global gene expression in human liver steatosis by high-density oligonucleotide microarray

scientific article

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

scientific article published on 16 March 2020

Filtering procedures for untargeted LC-MS metabolomics data

scientific article published on 14 June 2019

GC-content normalization for RNA-Seq data

scientific article

Gene expression patterns in human liver cancers

scientific article

Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patients

scientific article published on 01 December 2005

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila

scientific article

GenomeGraphs: integrated genomic data visualization with R

scientific article

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities

scientific article published on 17 November 2017

Ischemic preconditioning modulates the expression of several genes, leading to the overproduction of IL-1Ra, iNOS, and Bcl-2 in a human model of liver ischemia-reperfusion

scientific article published on 01 October 2005

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

scientific article published on 01 November 2021

Metabolomics of neonatal blood spots reveal distinct phenotypes of pediatric acute lymphoblastic leukemia and potential effects of early-life nutrition

scientific article published on 20 March 2019

Multiple testing methods for ChIP-Chip high density oligonucleotide array data

scientific article

Multiple testing. Part I. Single-step procedures for control of general type I error rates

scientific article published on 9 June 2004

Multiple testing. Part II. Step-down procedures for control of the family-wise error rate

scientific article published on 14 June 2004

Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients

scientific article (preprint)

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

scientific article published on 24 July 2020

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

scientific article

Normalization of RNA-seq data using factor analysis of control genes or samples

scientific article

Normalizing single-cell RNA sequencing data: challenges and opportunities

scientific article

Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species

scientific article

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

scholarly article published 18 January 2018

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

scientific article published on 26 February 2018

Open Source Software for the Analysis of Microarray Data

scientific article published in 2003

Open source software for the analysis of microarray data.

scientific article

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

scientific article published on 01 April 2019

Polygenic and directional regulatory evolution across pathways in Saccharomyces

scientific article

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

scientific article published in Nature Communications

Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: focus on the false discovery rate and simulation study

scientific article published on October 2008

Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.

scientific article

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

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

scientific article published on 19 June 2018

Special issue on computational statistical methods for genomics and systems biology

scientific article published on 06 January 2012

Stage II colon cancer prognosis prediction by tumor gene expression profiling

scientific article published on 11 September 2006

Stage III Colon Cancer Prognosis Prediction by Tumor Gene Expression Profiling ⬇️

scholarly article

Stereotyped and specific gene expression programs in human innate immune responses to bacteria

scientific article

Supervised detection of regulatory motifs in DNA sequences

scientific article published on 25 August 2003

Survival ensembles.

scientific article published on 12 December 2005

The establishment of gene silencing at single-cell resolution

scientific article published on 21 June 2009

Trajectory inference across multiple conditions with condiments

scholarly article

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

scientific article published on 05 March 2020

Untargeted Metabolomics of Archived Dried Blood Spots Reveals Lipid Modulation at Birth Associated with Pediatric Acute Lymphoblastic Leukemia ⬇️

scholarly article

Untargeted adductomics of Cys34 modifications to human serum albumin in newborn dried blood spots

scientific article published on 19 February 2019

Untargeted adductomics of newborn dried blood spots identifies modifications to human serum albumin associated with childhood leukemia

scientific article published on 06 November 2019

Untargeted lipidomic features associated with colorectal cancer in a prospective cohort

journal article published in 2018

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

scholarly article published 6 April 2017

[Gene expression profiling in colon cancer]

scientific article published on 01 June 2007

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

article

cvCovEst: Cross-validated covariance matrix estimator selection and evaluation in R

scientific article published on 26 July 2021

scPCA: A toolbox for sparse contrastive principal component analysis in R

scientific article published on 25 February 2020

List of works by Sandrine Dudoit

A fine-scale linkage-disequilibrium measure based on length of haplotype sharing

A general and flexible method for signal extraction from single-cell RNA-seq data.

A method to increase the power of multiple testing procedures through sample splitting.

A multimodal cell census and atlas of the mammalian primary motor cortex

A prediction-based resampling method for estimating the number of clusters in a dataset

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

An untargeted metabolomics method for archived newborn dried blood spots in epidemiologic studies.

Asymptotic optimality of likelihood-based cross-validation

Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives.

Bagging to improve the accuracy of a clustering procedure

Biases in Illumina transcriptome sequencing caused by random hexamer priming

Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference.

Bioconductor: open software development for computational biology and bioinformatics

Colon cancer prognosis prediction by gene expression profiling

Conservation of an RNA regulatory map between Drosophila and mammals

Cross-Validated Loss-Based Covariance Matrix Estimator Selection in High Dimensions

Cys34 Adductomics Links Colorectal Cancer with the Gut Microbiota and Redox Biology

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution

Diverse transcriptional programs associated with environmental stress and hormones in the Arabidopsis receptor-like kinase gene family

Diversity, topographic differentiation, and positional memory in human fibroblasts

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

Exploration of global gene expression in human liver steatosis by high-density oligonucleotide microarray

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

Filtering procedures for untargeted LC-MS metabolomics data

GC-content normalization for RNA-Seq data

Gene expression patterns in human liver cancers

Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patients

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila

GenomeGraphs: integrated genomic data visualization with R

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities

Ischemic preconditioning modulates the expression of several genes, leading to the overproduction of IL-1Ra, iNOS, and Bcl-2 in a human model of liver ischemia-reperfusion

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

Metabolomics of neonatal blood spots reveal distinct phenotypes of pediatric acute lymphoblastic leukemia and potential effects of early-life nutrition

Multiple testing methods for ChIP-Chip high density oligonucleotide array data

Multiple testing. Part I. Single-step procedures for control of general type I error rates

Multiple testing. Part II. Step-down procedures for control of the family-wise error rate

Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients

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

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

Normalization of RNA-seq data using factor analysis of control genes or samples

Normalizing single-cell RNA sequencing data: challenges and opportunities

Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species

Observation weights to 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 Source Software for the Analysis of Microarray Data

Open source software for the analysis of microarray data.

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

Polygenic and directional regulatory evolution across pathways in Saccharomyces

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

Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: focus on the false discovery rate and simulation study

Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.

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

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

Special issue on computational statistical methods for genomics and systems biology

Stage II colon cancer prognosis prediction by tumor gene expression profiling

Stage III Colon Cancer Prognosis Prediction by Tumor Gene Expression Profiling ⬇️

Stereotyped and specific gene expression programs in human innate immune responses to bacteria

Supervised detection of regulatory motifs in DNA sequences

Survival ensembles.

The establishment of gene silencing at single-cell resolution

Trajectory inference across multiple conditions with condiments

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

Untargeted Metabolomics of Archived Dried Blood Spots Reveals Lipid Modulation at Birth Associated with Pediatric Acute Lymphoblastic Leukemia ⬇️

Untargeted adductomics of Cys34 modifications to human serum albumin in newborn dried blood spots

Untargeted adductomics of newborn dried blood spots identifies modifications to human serum albumin associated with childhood leukemia

Untargeted lipidomic features associated with colorectal cancer in a prospective cohort

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

[Gene expression profiling in colon cancer]

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

cvCovEst: Cross-validated covariance matrix estimator selection and evaluation in R

scPCA: A toolbox for sparse contrastive principal component analysis in R