Dudoit, Sandrine

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

Street, K., Risso, D., Fletcher, R. B., Das, D., Ngai, J., Yosef, N., Purdom, E., & Dudoit, S. (2018) · BMC Genomics

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 3,159

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

Risso, D., Ngai, J., Speed, T. P., & Dudoit, S. (2014) · Nature Biotechnology

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 2,052

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

Bullard, J. H., Purdom, E., Hansen, K. D., & Dudoit, S. (2010) · BMC Bioinformatics

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 1,680

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

Brann, D. H., Tsukahara, T., Weinreb, C., Lipovsek, M., Van den Berge, K., Gong, B., Chance, R., Macaulay, I. C., Chou, H.-J., Fletcher, R. B., et al. (2020) · Science Advances

Olfactory and Sensory Function StudiesSARS-CoV-2 and COVID-19 Research

Cited by 1,198

GC-Content Normalization for RNA-Seq Data

Risso, D., Schwartz, K., Sherlock, G., & Dudoit, S. (2011) · BMC Bioinformatics

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 867

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

Risso, D., Perraudeau, F., Gribkova, S., Dudoit, S., & Vert, J.-P. (2018) · Nature Communications

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 718

Biases in Illumina transcriptome sequencing caused by random hexamer priming

Hansen, K. D., Brenner, S. E., & Dudoit, S. (2010) · Nucleic Acids Research

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 713

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

BRAIN Initiative Cell Census Network (BICCN), BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, Callaway, E. M., Dong, H.-W., Ecker, J. R., Hawrylycz, M. J., Huang, Z. J., Lein, E. S., Ngai, J., Osten, P., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 522

Normalizing single-cell RNA sequencing data: challenges and opportunities

Vallejos, C. A., Risso, D., Scialdone, A., Dudoit, S., & Marioni, J. C. (2017) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 436

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

Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 398

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

Yao, Z., Liu, H., Xie, F., Fischer, S., Booeshaghi, A. S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Pinto-Duarte, A., Bartlett, A., et al. (2020) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 397

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

Van den Berge, K., Perraudeau, F., Soneson, C., Love, M. I., Risso, D., Vert, J.-P., Robinson, M. D., Dudoit, S., & Clement, L. (2018) · Genome Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 228

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

Cole, M. B., Risso, D., Wagner, A., DeTomaso, D., Ngai, J., Purdom, E., Dudoit, S., & Yosef, N. (2019) · Cell Systems

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 173

Oracle inequalities for multi-fold cross validation

Vaart, A. W. V. D., Dudoit, S., & Laan, M. J. V. D. (2006) · Statistics & Decisions

Statistical Methods and InferenceStatistical Methods and Applications

Cited by 156