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List of works by Peter A.C. 't Hoen

204th ENMC International Workshop on Biomarkers in Duchenne Muscular Dystrophy 24-26 January 2014, Naarden, The Netherlands

scientific article

A 3 months mild functional test regime does not affect disease parameters in young mdx mice.

scientific article published on 21 March 2010

A SNP panel for identification of DNA and RNA specimens

scientific article

A characterization of cis- and trans-heritability of RNA-Seq-based gene expression

scientific article published on 26 September 2019

A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients

scientific article published on 08 March 2022

A decline in PABPN1 induces progressive muscle weakness in oculopharyngeal muscle dystrophy and in muscle aging

scientific article published on June 2013

A promoter-level mammalian expression atlas

scientific article

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data

scientific article

Accurate quantification of dystrophin mRNA and exon skipping levels in duchenne muscular dystrophy.

scientific article published on 10 May 2010

Addendum: The FAIR Guiding Principles for scientific data management and stewardship

article by Mark D Wilkinson et al published 19 March 2019 in Scientific Data

Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies

scientific article

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

scientific article published on 22 September 2016

Aging as accelerated accumulation of somatic variants: whole-genome sequencing of centenarian and middle-aged monozygotic twin pairs

scientific article

Alternative mRNA transcription, processing, and translation: insights from RNA sequencing

scientific article

An alanine expanded PABPN1 causes increased utilization of intronic polyadenylation sites

scientific article published on 7 April 2017

Antisense oligonucleotide mediated exon skipping as a potential strategy for the treatment of a variety of inflammatory diseases such as rheumatoid arthritis

scientific article published on 01 April 2012

Antisense-oligonucleotide mediated exon skipping in activin-receptor-like kinase 2: inhibiting the receptor that is overactive in fibrodysplasia ossificans progressiva

scientific article

Author Correction: Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy

scientific article published in March 2018

Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles

scientific article (publication date: 9 December 2013)

Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation

scientific article published in Nature Communications

B15 CTCF in Huntington's disease

BMP antagonists enhance myogenic differentiation and ameliorate the dystrophic phenotype in a DMD mouse model

scientific article published on 16 October 2010

Benchmarking deep learning splice prediction tools using functional splice assays

scientific article published on 20 May 2021

Blood lipids influence DNA methylation in circulating cells

scientific article published on 27 June 2016

Brain Transcriptomic Analysis of Hereditary Cerebral Hemorrhage With Amyloidosis-Dutch Type.

scientific article

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

scientific article

Calpain 3 is a rapid-action, unidirectional proteolytic switch central to muscle remodeling

scientific article

Can subtle changes in gene expression be consistently detected with different microarray platforms?

scientific article

Cell-type specific regulation of myostatin signaling

scientific article

Coexpression network analysis identifies transcriptional modules related to proastrocytic differentiation and sprouty signaling in glioma.

scientific article published in December 2010

Combined effect of AAV-U7-induced dystrophin exon skipping and soluble activin Type IIB receptor in mdx mice

scientific article published on 24 September 2012

Common pathological mechanisms in mouse models for muscular dystrophies

article

Comparison of skeletal muscle pathology and motor function of dystrophin and utrophin deficient mouse strains

scholarly article by Maaike van Putten et al published May 2012 in Neuromuscular Disorders

Comprehensive gene-expression survey identifies wif1 as a modulator of cardiomyocyte differentiation

scientific article

Computational approaches for the analysis of RNA-protein interactions: A primer for biologists

scientific article published on 19 November 2018

Consistency of biological networks inferred from microarray and sequencing data

scientific article

Cortical Spreading Depression Causes Unique Dysregulation of Inflammatory Pathways in a Transgenic Mouse Model of Migraine

scientific article published on 31 March 2016

Csde1 binds transcripts involved in protein homeostasis and controls their expression in an erythroid cell line.

scientific article published on 8 February 2018

DMD transcript imbalance determines dystrophin levels

scientific article published on 23 August 2013

Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions

scientific article

DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts

scientific article

Deregulation of the ubiquitin-proteasome system is the predominant molecular pathology in OPMD animal models and patients

scientific article published on 4 April 2011

Despite differential gene expression profiles pediatric MDS derived mesenchymal stromal cells display functionality in vitro

scientific article published on 28 January 2015

Determining the quality and complexity of next-generation sequencing data without a reference genome

scientific article

Disease variants alter transcription factor levels and methylation of their binding sites

scientific article published on 5 December 2016

Downregulation of the acetyl-CoA metabolic network in adipose tissue of obese diabetic individuals and recovery after weight loss.

scientific article published on 7 August 2014

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer

scientific article

Dual exon skipping in myostatin and dystrophin for Duchenne muscular dystrophy

scientific article

Dysfunctional transcripts are formed by alternative polyadenylation in OPMD.

scientific article published on 5 September 2017

Evaluation of serum MMP-9 as predictive biomarker for antisense therapy in Duchenne.

scientific article published on 20 December 2017

Exploiting the full power of temporal gene expression profiling through a new statistical test: application to the analysis of muscular dystrophy data

scientific article

Exploring the transcriptome of ciliated cells using in silico dissection of human tissues

scientific article

F03 Whole blood SAGE digital gene expression profiling from Huntington's disease patients

article

FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research

scientific article published on 13 April 2022

Fcγ receptor IIb strongly regulates Fcγ receptor-facilitated T cell activation by dendritic cells

scientific article

Fibronectin is a serum biomarker for Duchenne muscular dystrophy

Fluorescent labelling of cRNA for microarray applications

scientific article

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

scientific article published on 29 March 2018

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

Gene expression profiling highlights defective myogenesis in DMD patients and a possible role for bone morphogenetic protein 4.

scientific article

Gene expression profiling to monitor therapeutic and adverse effects of antisense therapies for Duchenne muscular dystrophy.

scientific article

Gene expression variation between mouse inbred strains

scientific article

Gene-expression and in vitro function of mesenchymal stromal cells are affected in juvenile myelomonocytic leukemia

scientific article published on 20 August 2015

Generation and Characterization of Transgenic Mice with the Full-length HumanDMDGene

scientific article published in Journal of Biological Chemistry

Generic information can retrieve known biological associations: implications for biomedical knowledge discovery.

scientific article

Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer

scientific article

Genetics of the human metabolome, what is next?

scientific article published in October 2014

Genome-wide assessment of differential roles for p300 and CBP in transcription regulation

scientific article

Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels

scientific article

Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure

scientific article

Genome-wide identification of directed gene networks using large-scale population genomics data

scientific article published in Nature Communications

Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference

scientific article published on 28 August 2020

Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood

scientific article

Huntington’s disease blood and brain show a common gene expression pattern and share an immune signature with Alzheimer’s disease

scientific article (publication date: 21 March 2017)

Identification of context-dependent expression quantitative trait loci in whole blood

scientific article published on 5 December 2016

Identifying a gene expression signature of cluster headache in blood

scientific article published on 11 January 2017

Immune stimuli shape the small non-coding transcriptome of extracellular vesicles released by dendritic cells

scientific article published on 28 May 2018

In silico discovery and experimental validation of new protein-protein interactions

scientific article (publication date: 31 January 2011)

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA.

scientific article

Increasing phenotypic annotation improves the diagnostic rate of exome sequencing in a rare neuromuscular disorder

scientific article published on 23 June 2019

Inhibition of IL-1 Signaling by Antisense Oligonucleotide-mediated Exon Skipping of IL-1 Receptor Accessory Protein (IL-1RAcP).

scientific article published on 22 January 2013

Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses

scientific article

Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions

scientific article published on 14 June 2013

Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington's disease peripheral blood samples

scientific article published on 27 July 2016

Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs.

scientific article published on 24 February 2004

Interspecies translation of disease networks increases robustness and predictive accuracy.

scientific article

Joint modeling of ChIP-seq data via a Markov random field model

scientific article

LPAR1 and ITGA4 regulate peripheral blood monocyte counts

Large-scale gene expression analysis of human skeletal myoblast differentiation.

scientific article

Large-scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine

scientific article published on 03 April 2019

Literature-aided interpretation of gene expression data with the weighted global test

scientific article

Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease

scientific article

Literature-based priors for gene regulatory networks.

scientific article published on 23 April 2009

Low dystrophin levels increase survival and improve muscle pathology and function in dystrophin/utrophin double-knockout mice

scientific article

Meeting on data sharing for Duchenne 21-22 March 2019 Amsterdam, the Netherlands

scientific article published on 28 August 2019

Meta-analysis of polycystic kidney disease expression profiles defines strong involvement of injury repair processes.

scientific article

Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data

scientific article

Molecular and phenotypic characterization of a mouse model of oculopharyngeal muscular dystrophy reveals severe muscular atrophy restricted to fast glycolytic fibres

scientific article

Molecular signatures of age-associated chronic degeneration of shoulder muscles

scientific article published on 14 February 2016

Muscle regeneration in dystrophin-deficient mdx mice studied by gene expression profiling

scientific article

New methods for next generation sequencing based microRNA expression profiling

scientific article

Non-sequential and multi-step splicing of the dystrophin transcript.

scientific article published on 15 December 2015

Novel Ex Vivo Culture Method for the Study of Dupuytren's Disease: Effects of TGFβ Type 1 Receptor Modulation by Antisense Oligonucleotides

scientific article published on 21 January 2014

Novel protein-protein interactions inferred from literature context

scientific article (publication date: 18 November 2009)

Overactive bone morphogenetic protein signaling in heterotopic ossification and Duchenne muscular dystrophy

scientific article

P1.44 Development of heart failure in mice with low dystrophin levels

P1.52 BIO-NMD: Discovery and validation of biomarkers for neuromuscular diseases (NMDs) – An EU funded FP7 project

P2.44 Accelerated skeletal muscle ageing is a molecular signature in OPMD

P4.29 Differential tissue expression and decay of dystrophin mRNA and protein

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data

scientific article

PhD7Faster: predicting clones propagating faster from the Ph.D.-7 phage display peptide library

scientific article published on 21 January 2014

Phage display screening without repetitious selection rounds

scientific article

Phenopackets for the Semantic Web ⬇️

Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation

scientific article

Prorenin Induces Intracellular Signaling in Cardiomyocytes Independently of Angiotensin II

scientific article published on 28 August 2006

Proteomic analysis of the dysferlin protein complex unveils its importance for sarcolemmal maintenance and integrity

scientific article

RNA sequencing: from tag-based profiling to resolving complete transcript structure

scientific article

Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes

scientific article published in 2024

Regulation of skeletal muscle energy/nutrient-sensing pathways during metabolic adaptation to fasting in healthy humans.

scientific article published on 23 September 2014

Relative power and sample size analysis on gene expression profiling data.

scientific article

Repeated FcεRI triggering reveals modified mast cell function related to chronic allergic responses in tissue

article

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

scientific article published on 15 September 2013

Response to: Evaluation of the serum matrix metalloproteinase-9 as a biomarker for monitoring disease progression in Duchenne muscular dystrophy

article

Ribosome profiling uncovers selective mRNA translation associated with eIF2 phosphorylation in erythroid progenitors

scientific article published on 10 April 2018

Roux-en-Y gastric bypass surgery, but not calorie restriction, reduces plasma branched-chain amino acids in obese women independent of weight loss or the presence of type 2 diabetes

scientific article published on 14 October 2014

Selection of effective antisense oligodeoxynucleotides with a green fluorescent protein-based assay. Discovery of selective and potent inhibitors of glutathione S-transferase Mu expression

scientific journal article

Serum protein profiling in mice: identification of Factor XIIIa as a potential biomarker for muscular dystrophy

scientific article

Skewed X-inactivation is common in the general female population

scientific article published on 14 December 2018

Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases

scientific article published on 01 June 2021

SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing

scientific article published on 23 March 2015

SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing

scientific article published on 07 October 2015

Structuring research methods and data with the research object model: genomics workflows as a case study

scientific article

Systematic genomic and translational efficiency studies of uveal melanoma

scientific article

Systematic identification of trans eQTLs as putative drivers of known disease associations

scientific article (publication date: October 2013)

T-box transcription factor TBX3 reprogrammes mature cardiac myocytes into pacemaker-like cells.

scientific article published on 14 March 2012

T.P.26 Low dystrophin levels increase survival and improve pathology and motor function in dystrophin/utrophin double knockout mice

scholarly article by M. van Putten et al published October 2012 in Neuromuscular Disorders

TCTEX1D1 is a genetic modifier of disease progression in Duchenne muscular dystrophy

scientific article published on 02 January 2020

Targeting TGF-β Signaling by Antisense Oligonucleotide-mediated Knockdown of TGF-β Type I Receptor

scientific article

Tbx2 and Tbx3 induce atrioventricular myocardial development and endocardial cushion formation

scientific article

Ten quick tips for building FAIR workflows

scientific article published in 2023

The FAIR Guiding Principles for scientific data management and stewardship

scientific article (publication date: 15 March 2016)

The Implicitome: A Resource for Rationalizing Gene-Disease Associations

scientific article

The de novo FAIRification process of a registry for vascular anomalies

scientific article published on 04 September 2021

The distinct transcriptomes of slow and fast adult muscles are delineated by noncoding RNAs.

scientific article published on 15 November 2017

The effects of low levels of dystrophin on mouse muscle function and pathology

scientific article

The identification of informative genes from multiple datasets with increasing complexity

scientific article

Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy

scientific article

Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.

scientific article

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model.

scientific article published on 22 June 2018

Transcriptome and genome sequencing uncovers functional variation in humans

scientific article

Tumor cell migration screen identifies SRPK1 as breast cancer metastasis determinant

scientific article

Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis

scholarly article published 19 October 2018

Validation of genetic modifiers for Duchenne muscular dystrophy: a multicentre study assessing SPP1 and LTBP4 variants

scientific article

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