List of works - Charlotte Soneson

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part two: National Harbor, MD, USA. 9-13 November 2016

scientific article published oln 16 November 2016

A Composite Gene Expression Signature Optimizes Prediction of Colorectal Cancer Metastasis and Outcome.

scientific article published on 7 October 2015

A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data

scientific article published in 2022

A Well-Controlled Experimental System to Study Interactions of Cytotoxic T Lymphocytes with Tumor Cells

scientific article published on 30 August 2016

A comparison of methods for differential expression analysis of RNA-seq data

scientific article

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

scientific article published on 31 July 2019

A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities

scientific article published on 10 September 2011

A general and powerful stage-wise testing procedure for differential expression and differential transcript usage

A glioma classification scheme based on coexpression modules of EGFR and PDGFRA.

scientific article published on 18 February 2014

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

scientific article published on 17 January 2019

A systematic performance evaluation of clustering methods for single-cell RNA-seq data

scholarly article by Angelo Duò et al published 2018 in F1000Research

ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data

scientific article published on 09 July 2019

Alignment and mapping methodology influence transcript abundance estimation

scientific article published on 07 September 2020

Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation

scientific article

Bias, robustness and scalability in single-cell differential expression analysis

article

Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells

scientific article published on 19 January 2017

Caloric dose-responsive genes in blood cells differentiate the metabolic status of obese men.

scientific article

CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data

scientific article published in 2021

Community-driven ELIXIR activities in single-cell omics

scientific article published on 29 July 2022

Convergence of multiple RNA-silencing pathways on GW182/TNRC6

scientific article published in July 2023

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

scientific article

Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features.

scientific article

Early changes in the hypothalamic region in prodromal Huntington disease revealed by MRI analysis

scientific article

Essential guidelines for computational method benchmarking.

scientific article

ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R

scientific article published on 04 June 2020

Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila

scientific article published on 13 January 2017

Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity

article

Fission yeast Cactin restricts telomere transcription and elongation by controlling Rap1 levels

scientific article

Genome-wide RNA profiling of long-lasting stem cell-like memory CD8 T cells induced by Yellow Fever vaccination in humans.

scientific article

HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats

scientific article published on 19 August 2019

Human Mpn1 promotes post-transcriptional processing and stability of U6atac

scientific article published on 23 July 2015

Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion

scientific article published on 6 January 2017

Increased ex vivo antigen presentation profile of B cells in multiple sclerosis

scientific article published on 8 August 2016

Integrative analysis of gene expression and copy number alterations using canonical correlation analysis

scientific article

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage.

scientific article published on 26 January 2016

Long-lasting stem cell-like memory CD8+ T cells with a naïve-like profile upon yellow fever vaccination

scientific article

Low Bias Local Intrinsic Dimension Estimation from Expected Simplex Skewness.

scientific article published on January 2015

Massively parallel quantification of substrate turnover defines protease subsite cooperativity

scientific article published on 17 November 2023

MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome

scientific article published on 09 December 2020

Modulation of mTOR Signalling Triggers the Formation of Stem Cell-like Memory T Cells

scientific article published on 16 January 2016

Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3'-to-5' RNA exonuclease processing U6 small nuclear RNA.

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

Optimization of continuous in vivo DOPA production and studies on ectopic DA synthesis using rAAV5 vectors in Parkinsonian rats

scientific article published on 17 August 2009

Orchestrating Single-Cell Analysis with Bioconductor

Orchestrating single-cell analysis with Bioconductor

scientific article published on 02 December 2019

Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp

scientific article published on 15 April 2019

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

scientific article published on 11 January 2021

Publisher Correction: Orchestrating single-cell analysis with Bioconductor

scientific article published on 01 February 2020

RNA sequencing data: hitchhiker's guide to expression analysis

Serum neurofilament light chain in early relapsing remitting MS is increased and correlates with CSF levels and with MRI measures of disease severity.

scientific article published on 11 January 2016

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

article by Michael I Love et al published 1 October 2018 in F1000Research

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

article by Michael I Love et al published 27 June 2018 in F1000Research

The ABCs of viral hepatitis that define biomarker signatures of acute viral hepatitis

scientific article

The consensus molecular subtypes of colorectal cancer

scientific article

The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias

scientific article

The projection score--an evaluation criterion for variable subset selection in PCA visualization

scientific article

Towards unified quality verification of synthetic count data with countsimQC.

scientific article published on 4 October 2017

TreeSummarizedExperiment: a S4 class for data with hierarchical structure

scientific article published on 15 October 2020

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

scientific article published on 25 February 2020

compcodeR--an R package for benchmarking differential expression methods for RNA-seq data.

scientific article

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

scientific article published on 14 May 2019

iCOBRA: open, reproducible, standardized and live method benchmarking

article by Charlotte Soneson & Mark D. Robinson published April 2016 in Nature Methods

iSEE: Interactive SummarizedExperiment Explorer.

scientific article published on 14 June 2018

monaLisa: an R/Bioconductor package for identifying regulatory motifs

scientific article published in 2022

muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data

scientific article published on 30 November 2020

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

scientific article

zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications

scholarly article published 30 June 2017

List of works by Charlotte Soneson

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part two: National Harbor, MD, USA. 9-13 November 2016

A Composite Gene Expression Signature Optimizes Prediction of Colorectal Cancer Metastasis and Outcome.

A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data

A Well-Controlled Experimental System to Study Interactions of Cytotoxic T Lymphocytes with Tumor Cells

A comparison of methods for differential expression analysis of RNA-seq data

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities

A general and powerful stage-wise testing procedure for differential expression and differential transcript usage

A glioma classification scheme based on coexpression modules of EGFR and PDGFRA.

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

A systematic performance evaluation of clustering methods for single-cell RNA-seq data

ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data

Alignment and mapping methodology influence transcript abundance estimation

Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation

Bias, robustness and scalability in single-cell differential expression analysis

Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells

Caloric dose-responsive genes in blood cells differentiate the metabolic status of obese men.

CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data

Community-driven ELIXIR activities in single-cell omics

Convergence of multiple RNA-silencing pathways on GW182/TNRC6

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features.

Early changes in the hypothalamic region in prodromal Huntington disease revealed by MRI analysis

Essential guidelines for computational method benchmarking.

ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R

Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila

Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity

Fission yeast Cactin restricts telomere transcription and elongation by controlling Rap1 levels

Genome-wide RNA profiling of long-lasting stem cell-like memory CD8 T cells induced by Yellow Fever vaccination in humans.

HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats

Human Mpn1 promotes post-transcriptional processing and stability of U6atac

Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion

Increased ex vivo antigen presentation profile of B cells in multiple sclerosis

Integrative analysis of gene expression and copy number alterations using canonical correlation analysis

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage.

Long-lasting stem cell-like memory CD8+ T cells with a naïve-like profile upon yellow fever vaccination

Low Bias Local Intrinsic Dimension Estimation from Expected Simplex Skewness.

Massively parallel quantification of substrate turnover defines protease subsite cooperativity

MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome

Modulation of mTOR Signalling Triggers the Formation of Stem Cell-like Memory T Cells

Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3'-to-5' RNA exonuclease processing U6 small nuclear RNA.

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.

Optimization of continuous in vivo DOPA production and studies on ectopic DA synthesis using rAAV5 vectors in Parkinsonian rats

Orchestrating Single-Cell Analysis with Bioconductor

Orchestrating single-cell analysis with Bioconductor

Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

Publisher Correction: Orchestrating single-cell analysis with Bioconductor

RNA sequencing data: hitchhiker's guide to expression analysis

RNA sequencing data: hitchhiker's guide to expression analysis

Serum neurofilament light chain in early relapsing remitting MS is increased and correlates with CSF levels and with MRI measures of disease severity.

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

The ABCs of viral hepatitis that define biomarker signatures of acute viral hepatitis

The consensus molecular subtypes of colorectal cancer

The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias

The projection score--an evaluation criterion for variable subset selection in PCA visualization

Towards unified quality verification of synthetic count data with countsimQC.

TreeSummarizedExperiment: a S4 class for data with hierarchical structure

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

compcodeR--an R package for benchmarking differential expression methods for RNA-seq data.

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

iCOBRA: open, reproducible, standardized and live method benchmarking

iSEE: Interactive SummarizedExperiment Explorer.

monaLisa: an R/Bioconductor package for identifying regulatory motifs

muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications