List of works - Simon J van Heeringen

A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development

scientific article

A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.

scientific article

ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination

scientific article published on 28 June 2021

APR-246/PRIMA-1(MET) rescues epidermal differentiation in skin keratinocytes derived from EEC syndrome patients with p63 mutations

scientific article

Antisense transcription of the myotonic dystrophy locus yields low-abundant RNAs with and without (CAG)n repeat.

scientific article published on 19 January 2017

ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands

scientific article published on 04 April 2009

ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation

scientific article

ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications.

scientific article

Characterization of genome-wide p53-binding sites upon stress response.

scientific article

Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates

scientific article published on 08 February 2021

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.

scientific article published on 16 May 2012

Embryonic transcription is controlled by maternally defined chromatin state.

scientific article

Genome evolution in the allotetraploid frog Xenopus laevis

scientific article

Genome-wide profiling of liver X receptor, retinoid X receptor, and peroxisome proliferator-activated receptor α in mouse liver reveals extensive sharing of binding sites

scientific article published on 12 December 2011

Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.

scientific article

Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis

scientific article

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments ⬇️

scientific article published on November 15, 2010

Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.

scientific article

Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos

scientific article

Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis

scientific article published on 01 May 2020

MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding

scientific article published on 28 May 2018

Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2.

scientific article

Nucleotide composition-linked divergence of vertebrate core promoter architecture.

scientific article

Principles of nucleation of H3K27 methylation during embryonic development.

scientific article published on 11 December 2013

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

scientific article published on 24 October 2017

Role of p53 serine 46 in p53 target gene regulation

scientific article

The epigenome in early vertebrate development.

scientific article published on 27 December 2011

The novel p53 target gene IRF2BP2 participates in cell survival during the p53 stress response

scientific article

Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation.

scientific article

fluff: exploratory analysis and visualization of high-throughput sequencing data

scientific article

genomepy: download genomes the easy way

scientific article published on 15 August 2017

p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate

scientific article

β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance

scientific article

List of works by Simon J van Heeringen

A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development

A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.

ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination

APR-246/PRIMA-1(MET) rescues epidermal differentiation in skin keratinocytes derived from EEC syndrome patients with p63 mutations

Antisense transcription of the myotonic dystrophy locus yields low-abundant RNAs with and without (CAG)n repeat.

ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands

ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation

ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications.

Characterization of genome-wide p53-binding sites upon stress response.

Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.

Embryonic transcription is controlled by maternally defined chromatin state.

Genome evolution in the allotetraploid frog Xenopus laevis

Genome-wide profiling of liver X receptor, retinoid X receptor, and peroxisome proliferator-activated receptor α in mouse liver reveals extensive sharing of binding sites

Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.

Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments ⬇️

Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.

Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos

Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis

MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding

Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2.

Nucleotide composition-linked divergence of vertebrate core promoter architecture.

Principles of nucleation of H3K27 methylation during embryonic development.

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

Role of p53 serine 46 in p53 target gene regulation

The epigenome in early vertebrate development.

The novel p53 target gene IRF2BP2 participates in cell survival during the p53 stress response

Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation.

fluff: exploratory analysis and visualization of high-throughput sequencing data

genomepy: download genomes the easy way

p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate

β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance