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C. Soneson · SciRah

Researcher profile · Semantic Scholar

C. Soneson

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C. Soneson — researcher profile on SciRah

h-index: 42
Works: 118
Citations: 18K

Most-cited papers

The Consensus Molecular Subtypes of Colorectal Cancer
J. Guinney, R. Dienstmann, Xin Wang, A. de Reyniès +36 more
2015Nature Medicine4,812 citations Open access
Semantic Scholar
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
C. Soneson, M. Love, Mark D. Robinson
2015F1000Research3,810 citations Open access
Semantic Scholar
Orchestrating Single-Cell Analysis with Bioconductor
R. Amezquita, A. Lun, Etienne Becht, V. Carey +13 more
2019Nature Methods892 citations Open access
Semantic Scholar
Differential analyses for RNA-seq : transcript-level estimates improve gene-level inferences Supplementary Material
C. Soneson, Michael I. Love, Mark D. Robinson
2015790 citations
Semantic Scholar
Bias, robustness and scalability in single-cell differential expression analysis
C. Soneson, Mark D. Robinson
2018Nature Methods693 citations Open access
Semantic Scholar
Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features.
E. Missiaglia, B. Jacobs, G. d'Ario, A. Di Narzo +11 more
2014Annals of Oncology613 citations Open access
Semantic Scholar
muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data
Helena L. Crowell, C. Soneson, Pierre-Luc Germain, Daniela Calini +4 more
2020Nature Communications425 citations Open access
Semantic Scholar
A systematic performance evaluation of clustering methods for single-cell RNA-seq data
A. Duò, Mark D. Robinson, C. Soneson
2018F1000Research347 citations Open access
Semantic Scholar
Serum neurofilament light chain in early relapsing remitting MS is increased and correlates with CSF levels and with MRI measures of disease severity
J. Kuhle, C. Barro, G. Disanto, A. Mathias +10 more
2016Multiple Sclerosis269 citations
Semantic Scholar
A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes
C. Soneson, Yao Yao, Anna Bratus-Neuenschwander, A. Patrignani +2 more
2019Nature Communications235 citations Open access
Semantic Scholar
diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
Lukas M. Weber, M. Nowicka, C. Soneson, Mark D. Robinson
2018Communications Biology225 citations Open access
Semantic Scholar
Long-lasting stem cell–like memory CD8+ T cells with a naïve-like profile upon yellow fever vaccination
Silvia A. Fuertes Marraco, C. Soneson, Laurene Cagnon, P. Gannon +7 more
2015Science Translational Medicine214 citations Open access
Semantic Scholar
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
K. Van den Berge, Fanny Perraudeau, C. Soneson, M. Love +5 more
2018Genome Biology193 citations Open access
Semantic Scholar
Essential guidelines for computational method benchmarking
Lukas M. Weber, Wouter Saelens, Robrecht Cannoodt, C. Soneson +5 more
2018Genome Biology179 citations Open access
Semantic Scholar
Alignment and mapping methodology influence transcript abundance estimation
A. Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri +5 more
2019Genome Biology167 citations Open access
Semantic Scholar
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
M. Love, C. Soneson, Rob Patro
2018F1000Research152 citations Open access
Semantic Scholar
Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
C. Soneson, K. Matthes, M. Nowicka, C. Law +1 more
2016Genome Biology134 citations Open access
Semantic Scholar
stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
K. Van den Berge, C. Soneson, Mark D. Robinson, Lieven Clement
2017Genome Biology133 citations Open access
Semantic Scholar
RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis
K. Van den Berge, Katharina M. Hembach, C. Soneson, S. Tiberi +4 more
2018Annual Review of Biomedical Data Science118 citations Open access
Semantic Scholar
Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp
Hung-Wei Cheng, L. Onder, M. Novkovic, C. Soneson +11 more
2019Nature Communications110 citations Open access
Semantic Scholar
Modulation of mTOR Signalling Triggers the Formation of Stem Cell-like Memory T Cells
Godehard A. Scholz, C. Jandus, Lianjun Zhang, C. Grandclément +7 more
2016EBioMedicine109 citations Open access
Semantic Scholar
Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data
Dong-Ze He, Mohsen Zakeri, Hirak Sarkar, C. Soneson +2 more
2021Nature Methods104 citations Open access
Semantic Scholar
A glioma classification scheme based on coexpression modules of EGFR and PDGFRA
Yingyu Sun, Wei Zhang, Dong-Feng Chen, Yuhong Lv +12 more
2014Proceedings of the National Academy of Sciences of the United States of America97 citations Open access
Semantic Scholar
monaLisa: an R/Bioconductor package for identifying regulatory motifs
Dania Machlab, Lukas Burger, C. Soneson, F. Rijli +2 more
2021bioRxiv94 citations Open access
Semantic Scholar
iSEE: Interactive SummarizedExperiment Explorer
K. Rue-Albrecht, F. Marini, C. Soneson, A. Lun
2018F1000Research91 citations Open access
Semantic Scholar
TreeSummarizedExperiment: a S4 class for data with hierarchical structure
Rui-Zhu Huang, C. Soneson, Felix G. M. Ernst, K. Rue-Albrecht +3 more
2020F1000Research62 citations Open access
Semantic Scholar
Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity
C. Perez-Shibayama, C. Gil-Cruz, Hung-Wei Cheng, L. Onder +13 more
2018Science immunology60 citations Open access
Semantic Scholar
Low Bias Local Intrinsic Dimension Estimation from Expected Simplex Skewness
K. Johnsson, C. Soneson, Magnus Fontes
2015IEEE Transactions on Pattern Analysis and Machine Intelligence56 citations
Semantic Scholar
compcodeR - an R package for benchmarking differential expression methods for RNA-seq data
C. Soneson
2014Bioinform.55 citations Open access
Semantic Scholar
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
C. Soneson, A. Srivastava, Rob Patro, Michael B. Stadler
2020bioRxiv51 citations Open access
Semantic Scholar
ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data
Stephany Orjuela, Rui-Zhu Huang, Katharina M. Hembach, Mark D. Robinson +1 more
2019G3: Genes, Genomes, Genetics50 citations Open access
Semantic Scholar
Conserved stromal–immune cell circuits secure B cell homeostasis and function
M. Lütge, Angelina De Martin, C. Gil-Cruz, C. Perez-Shibayama +10 more
2023Nature Immunology45 citations Open access
Semantic Scholar
CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data
Almut Lutge, J. Zyprych-Walczak, Urszula Brykczynska Kunzmann, Helena L. Crowell +4 more
2020Life Science Alliance45 citations Open access
Semantic Scholar
The shaky foundations of simulating single-cell RNA sequencing data
Helena L. Crowell, Sarah X. Morillo Leonardo, C. Soneson, Mark D. Robinson
2023Genome Biology43 citations Open access
Semantic Scholar
iCOBRA: open, reproducible, standardized and live method benchmarking
C. Soneson, Mark D. Robinson
2015Nature Methods43 citations Open access
Semantic Scholar
On the discovery of subpopulation-specific state transitions from multi-sample multi-condition single-cell RNA sequencing data
Helena L. Crowell, C. Soneson, Pierre-Luc Germain, Daniela Calini +4 more
2019bioRxiv40 citations Open access
Semantic Scholar
Increased ex vivo antigen presentation profile of B cells in multiple sclerosis
A. Mathias, G. Perriard, Mathieu Canales, C. Soneson +3 more
2017Multiple Sclerosis39 citations
Semantic Scholar
A composite gene expression signature optimizes prediction of colorectal cancer metastasis and outcome
M. Schell, Mingli Yang, E. Missiaglia, M. Delorenzi +6 more
2015Clinical Cancer Research39 citations Open access
Semantic Scholar
treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses
Rui-Zhu Huang, C. Soneson, Pierre-Luc Germain, Thomas S. B. Schmidt +2 more
2020Genome Biology38 citations Open access
Semantic Scholar
Towards unified quality verification of synthetic count data with countsimQC
C. Soneson, Mark D. Robinson
2017Bioinform.38 citations Open access
Semantic Scholar
Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma
K. D. Prummel, Helena L. Crowell, Susan Nieuwenhuize, E. Brombacher +19 more
2020Nature Communications32 citations Open access
Semantic Scholar
HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats
Lukas M. Weber, C. Soneson
2019F1000Research28 citations Open access
Semantic Scholar
Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion
Isabella M. Y. Zanini, C. Soneson, Luca Lorenzi, Claus M. Azzalin
2017Journal of Cell Science25 citations
Semantic Scholar
A Unique Bipartite Polycomb Signature Regulates Stimulus-Response Transcription during Development
Taro Kitazawa, Dania Machlab, O. Joshi, N. Maiorano +9 more
2021Nature Genetics24 citations Open access
Semantic Scholar
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
C. Soneson, M. Love, Rob Patro, S. Hussain +2 more
2018Life Science Alliance23 citations Open access
Semantic Scholar
Bias, robustness and scalability in differential expression analysis of single-cell RNA-seq data
C. Soneson, Mark D. Robinson
2017bioRxiv23 citations Open access
Semantic Scholar
A Well-Controlled Experimental System to Study Interactions of Cytotoxic T Lymphocytes with Tumor Cells
N. Neubert, C. Soneson, D. Barras, P. Baumgaertner +4 more
2016Frontiers in Immunology23 citations Open access
Semantic Scholar
Publisher Correction: Directed evolution improves the catalytic efficiency of TEV protease
R. Amezquita, A. Lun, E. Becht, V. Carey +13 more
2019Nature Methods22 citations Open access
Semantic Scholar
A systematic performance evaluation of clustering methods for single-cell RNA-seq data [version 1; peer review: 2 approved with reservations]
A. Duò, Mark D. Robinson, C. Soneson
202120 citations
Semantic Scholar
Alignment and mapping methodology influence transcript abundance estimation
A. Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri +5 more
2020Genome Biology20 citations Open access
Semantic Scholar

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