Marioni, John C.

Computational principles and challenges in single-cell data integration

Argelaguet, R., Cuomo, A. S. E., Stegle, O., & Marioni, J. C. (2021) · Nature Biotechnology

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 472

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

Single-cell transcriptomics uncovers zonation of function in the mesenchyme during liver fibrosis

Dobie, R., Wilson-Kanamori, J. R., Henderson, B. E. P., Smith, J. R., Matchett, K. P., Portman, J. R., Wallenborg, K., Picelli, S., Zagorska, A., Pendem, S. V., et al. (2019) · Cell Reports

Liver physiology and pathologyLiver Disease Diagnosis and Treatment

Cited by 420

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

Achim, K., Pettit, J.-B., Saraiva, L. R., Gavriouchkina, D., Larsson, T., Arendt, D., & Marioni, J. C. (2015) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 395

Aging increases cell-to-cell transcriptional variability upon immune stimulation

Martinez-Jimenez, C. P., Eling, N., Chen, H.-C., Vallejos, C. A., Kolodziejczyk, A. A., Connor, F., Stojic, L., Rayner, T. F., Stubbington, M. J. T., Teichmann, S. A., et al. (2017) · Science

Single-cell and spatial transcriptomicsGenetics, Aging, and Longevity in Model Organisms

Cited by 339

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Cuomo, A. S. E., Seaton, D. D., McCarthy, D. J., Martinez, I., Bonder, M. J., Garcia-Bernardo, J., Amatya, S., Madrigal, P., Isaacson, A., Buettner, F., et al. (2020) · Nature Communications

Pluripotent Stem Cells ResearchSingle-cell and spatial transcriptomics

Cited by 331

A reference human induced pluripotent stem cell line for large-scale collaborative studies

Pantazis, C. B., Yang, A., Lara, E., McDonough, J. A., Blauwendraat, C., Peng, L., Oguro, H., Kanaujiya, J., Zou, J., Sebesta, D., et al. (2022) · Cell Stem Cell

Pluripotent Stem Cells ResearchCRISPR and Genetic Engineering

Cited by 310

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

Vallejos, C. A., Marioni, J. C., & Richardson, S. (2015) · PLOS Computational Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 302

Resolving early mesoderm diversification through single-cell expression profiling

Scialdone, A., Tanaka, Y., Jawaid, W., Moignard, V., Wilson, N. K., Macaulay, I. C., Marioni, J. C., & Göttgens, B. (2016) · Nature

Developmental Biology and Gene RegulationPluripotent Stem Cells Research

Cited by 293

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

Kim, J. K., Kolodziejczyk, A. A., Ilicic, T., Teichmann, S. A., & Marioni, J. C. (2015) · Nature Communications

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 251

Using single-cell genomics to understand developmental processes and cell fate decisions

Griffiths, J. A., Scialdone, A., & Marioni, J. C. (2018) · Molecular Systems Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 250

Challenges in measuring and understanding biological noise

Eling, N., Morgan, M. D., & Marioni, J. C. (2019) · Nature Reviews Genetics

Gene Regulatory Network AnalysisSingle-cell and spatial transcriptomics

Cited by 247

Mitochondrial complex I activity in microglia sustains neuroinflammation

Peruzzotti-Jametti, L., Willis, C. M., Krzak, G., Hamel, R., Pirvan, L., Ionescu, R.-B., Reisz, J. A., Prag, H. A., Garcia-Segura, M. E., Wu, V., et al. (2024) · Nature

Neuroinflammation and Neurodegeneration MechanismsMitochondrial Function and Pathology

Cited by 239

Impact of Alternative Splicing on the Human Proteome

Liu, Y., Gonzàlez-Porta, M., Santos, S., Brazma, A., Marioni, J. C., Aebersold, R., Venkitaraman, A. R., & Wickramasinghe, V. O. (2017) · Cell Reports

RNA Research and SplicingAdvanced Proteomics Techniques and Applications

Cited by 190

Testing for differential abundance in mass cytometry data

Lun, A. T. L., Richard, A. C., & Marioni, J. C. (2017) · Nature Methods

Single-cell and spatial transcriptomicsMetabolomics and Mass Spectrometry Studies

Cited by 181

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using <tt>CellBender</tt>

Fleming, S. J., Chaffin, M. D., Arduini, A., Akkad, A.-D., Banks, E., Marioni, J. C., Philippakis, A. A., Ellinor, P. T., & Babadi, M. (2019) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 164

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data

Lun, A. T. L., & Marioni, J. C. (2017) · Biostatistics

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 159

Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution

Messmer, T., von Meyenn, F., Savino, A., Santos, F., Mohammed, H., Lun, A. T. L., Marioni, J. C., & Reik, W. (2019) · Cell Reports

Pluripotent Stem Cells ResearchSingle-cell and spatial transcriptomics

Cited by 156

A human embryonic limb cell atlas resolved in space and time

Zhang, B., He, P., Lawrence, J. E. G., Wang, S., Tuck, E., Williams, B. A., Roberts, K., Kleshchevnikov, V., Mamanova, L., Bolt, L., et al. (2024) · Nature

Single-cell and spatial transcriptomicsDevelopmental Biology and Gene Regulation

Cited by 143

Identification of a regeneration-organizing cell in the Xenopus tail

Aztekin, C., Hiscock, T. W., Marioni, J. C., Gurdon, J. B., Simons, B. D., & Jullien, J. (2019) · Science

Planarian Biology and ElectrostimulationDevelopmental Biology and Gene Regulation

Cited by 142

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

Laumer, C. E., Gruber-Vodicka, H., Hadfield, M. G., Pearse, V. B., Riesgo, A., Marioni, J. C., & Giribet, G. (2018) · eLife

Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic Studies

Cited by 112

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

Eling, N., Richard, A. C., Richardson, S., Marioni, J. C., & Vallejos, C. A. (2018) · Cell Systems

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 99

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

Ballester, B., Medina-Rivera, A., Schmidt, D., Gonzàlez-Porta, M., Carlucci, M., Chen, X., Chessman, K., Faure, A. J., Funnell, A. P., Goncalves, A., et al. (2014) · eLife

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 96

A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans

Saraiva, L. R., Riveros-McKay, F., Mezzavilla, M., Abou-Moussa, E. H., Arayata, C. J., Makhlouf, M., Trimmer, C., Ibarra-Soria, X., Khan, M., Van Gerven, L., et al. (2019) · Science Advances

Olfactory and Sensory Function StudiesBiochemical Analysis and Sensing Techniques

Cited by 92