Risso, Davide

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

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

Orchestrating single-cell analysis with Bioconductor

Amezquita, R. A., Lun, A. T. L., Becht, E., Carey, V. J., Carpp, L. N., Geistlinger, L., Marini, F., Rue-Albrecht, K., Risso, D., Soneson, C., et al. (2020) · Nature Methods

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 945

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

Rapid non-uniform adaptation to conformation-specific KRAS(G12C) inhibition

Xue, J. Y., Zhao, Y., Aronowitz, J., Mai, T. T., Vides, A., Qeriqi, B., Kim, D., Li, C., de Stanchina, E., Mazutis, L., et al. (2020) · Nature

Protein Kinase Regulation and GTPase SignalingLung Cancer Treatments and Mutations

Cited by 543

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

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

Gaiti, F., Chaligne, R., Gu, H., Brand, R. M., Kothen-Hill, S., Schulman, R. C., Grigorev, K., Risso, D., Kim, K.-T., Pastore, A., et al. (2019) · Nature

Chronic Lymphocytic Leukemia ResearchEpigenetics and DNA Methylation

Cited by 262

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

Joglekar, A., Prjibelski, A., Mahfouz, A., Collier, P., Lin, S., Schlusche, A. K., Marrocco, J., Williams, S. R., Haase, B., Hayes, A., et al. (2021) · Nature Communications

RNA Research and SplicingSingle-cell and spatial transcriptomics

Cited by 229

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

Complementary networks of cortical somatostatin interneurons enforce layer specific control

Naka, A., Veit, J., Shababo, B., Chance, R. K., Risso, D., Stafford, D., Snyder, B., Egladyous, A., Chu, D., Sridharan, S., et al. (2019) · eLife

Neuroscience and Neuropharmacology ResearchNeural dynamics and brain function

Cited by 117

How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets

Peixoto, L., Risso, D., Poplawski, S. G., Wimmer, M. E., Speed, T. P., Wood, M. A., & Abel, T. (2015) · Nucleic Acids Research

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 105

Combinatorial Expression of Grp and Neurod6 Defines Dopamine Neuron Populations with Distinct Projection Patterns and Disease Vulnerability

Kramer, D. J., Risso, D., Kosillo, P., Ngai, J., & Bateup, H. S. (2018) · eNeuro

Neurotransmitter Receptor Influence on BehaviorParkinson's Disease Mechanisms and Treatments

Cited by 70