Lista de obras - Mark D. Robinson - Dominio Público Uruguay

A comparison of Affymetrix gene expression arrays

artículo científico publicado en 2007

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

artículo científico publicado en 2019

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

artículo científico publicado en 2007

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

artículo científico publicado en 2003

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

artículo científico publicado en 2010

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

artículo científico

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.

artículo científico publicado en 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

artículo científico publicado en 2021

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

artículo científico publicado en 2019

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

artículo científico publicado en 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.

artículo científico publicado en 2017

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

artículo científico publicado en 2018

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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

Benchmarking comes of age

artículo científico publicado en 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

artículo científico publicado en 2012

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

artículo científico publicado en 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

artículo científico publicado en 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.

artículo científico publicado en 2018

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.

artículo científico publicado en 2016

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

artículo científico publicado en 2011

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.

artículo científico publicado en 2018

Computational epigenomics: challenges and opportunities

artículo científico publicado en 2015

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

artículo científico publicado en 2010

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

artículo científico publicado en 2015

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

artículo científico publicado en 2012

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

artículo científico publicado en 2013

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

artículo científico publicado en 2018

CrispRVariants charts the mutation spectrum of genome engineering experiments

artículo científico publicado en 2016

CrispRVariants: precisely charting the mutation spectrum in genome engineering experiments

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

artículo científico publicado en 2017

DAMEfinder: a method to detect differential allele-specific methylation

artículo científico publicado en 2020

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

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

artículo científico publicado en 2004

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

artículo científico publicado en 2015

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

artículo científico publicado en 2011

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

artículo científico publicado en 2013

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

artículo científico publicado en 2011

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

artículo científico publicado en 2015

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

artículo científico publicado en 2020

Essential guidelines for computational method benchmarking.

artículo científico publicado en 2019

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

artículo científico publicado en 2010

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

artículo científico publicado en 2017

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

article

From RNA-seq reads to differential expression results

artículo científico publicado en 2010

FunSpec: a web-based cluster interpreter for yeast

artículo científico publicado en 2002

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

artículo científico publicado en 2004

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

artículo científico publicado en 2005

Genomics by the beach.

artículo científico publicado en 2014

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

artículo científico publicado en 2006

High-definition macromolecular composition of yeast RNA-processing complexes

artículo científico publicado en 2004

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

artículo científico publicado en 2018

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

artículo científico publicado en 2016

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

artículo científico publicado en 2002

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

artículo científico

Identifying transcription factor functions and targets by phenotypic activation

artículo científico publicado en 2006

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

artículo científico publicado en 2016

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

artículo científico publicado en 2007

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

artículo científico publicado en 2002

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.

artículo científico publicado en 2017

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

artículo científico publicado en 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.

artículo científico publicado en 2016

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

artículo científico publicado en 2013

Moderated statistical tests for assessing differences in tag abundance

artículo científico publicado en 2007

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.

artículo científico publicado en 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.

artículo científico publicado en 2018

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

artículo científico publicado en 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?

artículo científico publicado en 2010

RNA sequencing data: hitchhiker's guide to expression analysis

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

artículo científico publicado en 2006

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

artículo científico publicado en 2012

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

artículo científico publicado en 2014

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

artículo científico publicado en 2010

Robustly detecting differential expression in RNA sequencing data using observation weights

artículo científico publicado en 2014

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

artículo científico publicado en 2012

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

artículo científico publicado en 2018

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

artículo científico publicado en 2007

Statistical methods for detecting differentially methylated loci and regions

artículo científico

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

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

artículo científico publicado en 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

artículo científico publicado en 2004

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

artículo científico publicado en 2004

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

artículo científico publicado en 2018

The synthetic genetic interaction spectrum of essential genes

article

Towards unified quality verification of synthetic count data with countsimQC.

artículo científico publicado en 2017

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

artículo científico publicado en 2004

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

TreeSummarizedExperiment: a S4 class for data with hierarchical structure

artículo científico publicado en 2020

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

artículo científico publicado en 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

artículo científico publicado en 2019

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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2013

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

artículo científico publicado en 2020

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

artículo científico publicado en 2017

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses

artículo científico publicado en 2021

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

scholarly article published 30 June 2017

Lista de obras de 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

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

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