List of works - Mark D. Robinson

A comparison of Affymetrix gene expression arrays

scientific article published on 15 November 2007

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

scientific article published on 31 July 2019

A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments

scientific article

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

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

scientific article published on 17 January 2019

A panoramic view of yeast noncoding RNA processing

scientific article

A scaling normalization method for differential expression analysis of RNA-seq data

scientific article

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

scholarly article by Angelo Duò et al published 2018 in F1000Research

A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription

scientific article published on 17 July 2017

ALT-803, an IL-15 superagonist, in combination with nivolumab in patients with metastatic non-small cell lung cancer: a non-randomised, open-label, phase 1b trial

scientific article published on 5 April 2018

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

scientific article published on 09 July 2019

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

scientific article published on 17 July 2021

Abscisic acid is a substrate of the ABC transporter encoded by the durable wheat disease resistance gene Lr34

scientific article published on 22 April 2019

Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer

scientific article published on 25 July 2011

Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish

scientific article published on 16 July 2019

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.

scientific article published on 15 November 2017

Author Correction: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

scientific article published on 01 November 2018

BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence

scientific article

BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

scientific article (publication date: 11 February 2014)

Benchmarking comes of age

scientific article published on 09 October 2019

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

article

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

scientific article

CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo

scientific article published on 30 May 2019

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

scientific article published in 2021

Channel crosstalk correction in suspension and imaging mass cytometry

Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens

scientific article published on 29 January 2014

Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis

scientific article published on 19 January 2020

Common Features of Regulatory T Cell Specialization During Th1 Responses.

scientific article

Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data

Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data.

scientific article

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias

scientific article published on January 2011

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.

scientific article published on 23 March 2018

Computational epigenomics: challenges and opportunities

scientific article published on 5 March 2015

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity

scientific article

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis.

scientific article published on May 2015

Copy-number-aware differential analysis of quantitative DNA sequencing data

scientific article

Correction: TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP

scientific article published on 23 January 2020

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

2013 scientific article

Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair.

scientific article published on 29 May 2018

CrispRVariants charts the mutation spectrum of genome engineering experiments

scientific article

CrispRVariants: precisely charting the mutation spectrum in genome engineering experiments

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.

scientific article

DAMEfinder: a method to detect differential allele-specific methylation

scientific article published on 01 June 2020

DNA methylation profiles of elderly individuals subjected to indentured childhood labor and trauma

scientific article

DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics.

scientific article

De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

scientific article published on 23 October 2015

Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis of complex protein mixtures.

scientific article

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

scientific article

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows

scientific article

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

scientific article published on 22 July 2013

Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription

scientific article

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

scientific article

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

article

Eleven grand challenges in single-cell data science

scientific article published on 07 February 2020

Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions ⬇️

scientific article published on July 15, 2013

Essential guidelines for computational method benchmarking.

scientific article

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation

scientific article

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

From RNA-seq reads to differential expression results

scientific article

FunSpec: a web-based cluster interpreter for yeast

scientific article

Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors

scientific article

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs

scientific article published on 28 August 2005

Genomics by the beach.

scientific article published on 14 April 2014

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

scientific article

High-definition macromolecular composition of yeast RNA-processing complexes

scientific article

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

scientific article published on 8 January 2018

High-dimensional single-cell analysis reveals the immune signature of narcolepsy.

scientific article

High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants.

scientific article

Highly efficient DNA-free gene disruption in the agricultural pest Ceratitis capitata by CRISPR-Cas9 ribonucleoprotein complexes

scientific article published on 30 August 2017

Identifying transcription factor functions and targets by phenotypic activation

scientific article

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

scientific article published on 26 January 2016

Large-scale mapping of human protein-protein interactions by mass spectrometry

scientific article

Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters

scientific article

MINI REVIEW: Statistical methods for detecting differentially methylated loci and regions

scholarly article published 15 July 2014

Male sex in houseflies is determined by Mdmd, a paralog of the generic splice factor gene CWC22.

scientific article

Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests

scientific article published on 29 August 2019

Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms

scientific article published on 01 January 2019

Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines

publication published on 09 February 2022

Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes.

scientific article

Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem

scientific article published in December 2013

Moderated statistical tests for assessing differences in tag abundance

scientific article

Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen.

scientific article published on 30 January 2018

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

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

scientific article published on 15 April 2019

Pro-inflammatory Aorta-Associated Macrophages Are Involved in Embryonic Development of Hematopoietic Stem Cells

scientific article published on 06 June 2019

Protocol matters: which methylome are you actually studying?

scientific article

RNA sequencing data: hitchhiker's guide to expression analysis

Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex

scientific article published in March 2006

Regional activation of the cancer genome by long-range epigenetic remodeling

scientific article published on 13 December 2012

Relationship between genome and epigenome--challenges and requirements for future research

scientific article published on 18 June 2014

Repitools: an R package for the analysis of enrichment-based epigenomic data

scientific article

Robustly detecting differential expression in RNA sequencing data using observation weights

scientific article

Savant Genome Browser 2: visualization and analysis for population-scale genomics

scientific article published on 25 May 2012

Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

scientific article published on 06 August 2018

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

scientific article

Statistical methods for detecting differentially methylated loci and regions

scientific article published on 16 September 2014

T-cell acute leukaemia exhibits dynamic interactions with bone marrow microenvironments

scientific article

TCF/LEF dependent and independent transcriptional regulation of Wnt/β-catenin target genes

scientific article published on 13 November 2018

TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP

scientific article published on 20 September 2019

The Spinal Transcriptome after Cortical Stroke: In Search of Molecular Factors Regulating Spontaneous Recovery in the Spinal Cord

scientific article published on 08 April 2019

The functional landscape of mouse gene expression

scientific article

The promise of functional genomics: completing the encyclopedia of a cell

scientific article published in October 2004

The proto CpG island methylator phenotype of sessile serrated adenomas/polyps

scientific article published on 22 November 2018

The synthetic genetic interaction spectrum of essential genes

article

Towards unified quality verification of synthetic count data with countsimQC.

scientific article published on 4 October 2017

Transcriptional networks: reverse-engineering gene regulation on a global scale

scientific article

Treatment of a metabolic liver disease by in vivo genome base editing in adult mice

TreeSummarizedExperiment: a S4 class for data with hierarchical structure

scientific article published on 15 October 2020

Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma

scientific article published on 5 January 2015

benchmarkR: an R package for benchmarking genome-scale methods

scholarly article published 17 April 2015

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

scientific article published on 14 May 2019

edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology

scientific article published on January 2014

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

scientific article (publication date: 2010)

iCOBRA: open, reproducible, standardized and live method benchmarking

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

miRNA-Seq normalization comparisons need improvement

scientific article

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

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses

scientific article published on 17 May 2021

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

scholarly article published 30 June 2017

List of works by Mark D. Robinson

A comparison of Affymetrix gene expression arrays

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

A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments

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

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 panoramic view of yeast noncoding RNA processing

A scaling normalization method for differential expression analysis of RNA-seq data

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

A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription

ALT-803, an IL-15 superagonist, in combination with nivolumab in patients with metastatic non-small cell lung cancer: a non-randomised, open-label, phase 1b trial

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

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

Abscisic acid is a substrate of the ABC transporter encoded by the durable wheat disease resistance gene Lr34

Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer

Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.

Author Correction: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence

BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

Benchmarking comes of age

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

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo

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

Channel crosstalk correction in suspension and imaging mass cytometry

Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens

Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis

Common Features of Regulatory T Cell Specialization During Th1 Responses.

Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data

Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data.

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.

Computational epigenomics: challenges and opportunities

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis.

Copy-number-aware differential analysis of quantitative DNA sequencing data

Correction: TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair.

CrispRVariants charts the mutation spectrum of genome engineering experiments

CrispRVariants: precisely charting the mutation spectrum in genome engineering experiments

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.

DAMEfinder: a method to detect differential allele-specific methylation

DNA methylation profiles of elderly individuals subjected to indentured childhood labor and trauma

DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics.

De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis of complex protein mixtures.

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

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

Eleven grand challenges in single-cell data science

Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions ⬇️

Essential guidelines for computational method benchmarking.

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation

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

From RNA-seq reads to differential expression results

FunSpec: a web-based cluster interpreter for yeast

Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs

Genomics by the beach.

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

High-definition macromolecular composition of yeast RNA-processing complexes

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

High-dimensional single-cell analysis reveals the immune signature of narcolepsy.

High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants.

Highly efficient DNA-free gene disruption in the agricultural pest Ceratitis capitata by CRISPR-Cas9 ribonucleoprotein complexes

Identifying transcription factor functions and targets by phenotypic activation

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

Large-scale mapping of human protein-protein interactions by mass spectrometry

Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters

MINI REVIEW: Statistical methods for detecting differentially methylated loci and regions

Male sex in houseflies is determined by Mdmd, a paralog of the generic splice factor gene CWC22.

Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests

Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms