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

por Georgiou, Georgios, van Heeringen, Simon J.
Publicado 2016

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

por van Heeringen, Simon J., Veenstra, Gert Jan C.
Publicado 2011

Computational approaches to understand transcription regulation in development

por van der Sande, Maarten, Frölich, Siebren, van Heeringen, Simon J.
Publicado 2023

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

por Lederer, Simone, Heskes, Tom, van Heeringen, Simon J., Albers, Cornelis A.
Publicado 2020

genomepy: genes and genomes at your fingertips

por Frölich, Siebren, van der Sande, Maarten, Schäfers, Tilman, van Heeringen, Simon J
Publicado 2023

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

por Paranjpe, Sarita S, Jacobi, Ulrike G, van Heeringen, Simon J, C Veenstra, Gert Jan
Publicado 2013

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

por Koeppel, Max, van Heeringen, Simon J., Smeenk, Leonie, Navis, Anna C., Janssen-Megens, Eva M., Lohrum, Marion
Publicado 2009

Role of p53 Serine 46 in p53 Target Gene Regulation

por Smeenk, Leonie, van Heeringen, Simon J., Koeppel, Max, Gilbert, Bianca, Janssen-Megens, Eva, Stunnenberg, Hendrik G., Lohrum, Marion
Publicado 2011

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

por Smits, Arne H., Lindeboom, Rik G.H., Perino, Matteo, van Heeringen, Simon J., Veenstra, Gert Jan C., Vermeulen, Michiel
Publicado 2014

Embryonic transcription is controlled by maternally defined chromatin state

por Hontelez, Saartje, van Kruijsbergen, Ila, Georgiou, Georgios, van Heeringen, Simon J., Bogdanovic, Ozren, Lister, Ryan, Veenstra, Gert Jan C.
Publicado 2015

Erratum: Embryonic transcription is controlled by maternally defined chromatin state

por Hontelez, Saartje, van Kruijsbergen, Ila, Georgiou, Georgios, van Heeringen, Simon J., Bogdanovic, Ozren, Lister, Ryan, Veenstra, Gert Jan C.
Publicado 2016

ChIP-Chip Designs to Interrogate the Genome of Xenopus Embryos for Transcription Factor Binding and Epigenetic Regulation

por Akkers, Robert C., van Heeringen, Simon J., Manak, J. Robert, Green, Roland D., Stunnenberg, Hendrik G., Veenstra, Gert Jan C.
Publicado 2010

Crosstalk between c-Jun and TAp73α/β contributes to the apoptosis–survival balance

por Koeppel, Max, van Heeringen, Simon J., Kramer, Daniela, Smeenk, Leonie, Janssen-Megens, Eva, Hartmann, Marianne, Stunnenberg, Hendrik G., Lohrum, Marion
Publicado 2011

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

por Xu, Quan, Georgiou, Georgios, Frölich, Siebren, van der Sande, Maarten, Veenstra, Gert Jan C, Zhou, Huiqing, van Heeringen, Simon J
Publicado 2021

Seq2science: an end-to-end workflow for functional genomics analysis

por van der Sande, Maarten, Frölich, Siebren, Schäfers, Tilman, Smits, Jos G.A., Snabel, Rebecca R., Rinzema, Sybren, van Heeringen, Simon J.
Publicado 2023

Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation

por Kouwenhoven, Evelyn N, Oti, Martin, Niehues, Hanna, van Heeringen, Simon J, Schalkwijk, Joost, Stunnenberg, Hendrik G, van Bokhoven, Hans, Zhou, Huiqing
Publicado 2015

Principles of nucleation of H3K27 methylation during embryonic development

por van Heeringen, Simon J., Akkers, Robert C., van Kruijsbergen, Ila, Arif, M. Asif, Hanssen, Lars L.P., Sharifi, Nilofar, Veenstra, Gert Jan C.
Publicado 2014

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

por San, Bilge, Chrispijn, Naomi D., Wittkopp, Nadine, van Heeringen, Simon J., Lagendijk, Anne K., Aben, Marco, Bakkers, Jeroen, Ketting, René F., Kamminga, Leonie M.
Publicado 2016

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

por Bright, Ann Rose, van Genesen, Siebe, Li, Qingqing, Grasso, Alexia, Frölich, Siebren, van der Sande, Maarten, van Heeringen, Simon J, Veenstra, Gert Jan C
Publicado 2021

Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework

por Heuts, B. M. H., Arza-Apalategi, S., Frölich, S., Bergevoet, S. M., van den Oever, S. N., van Heeringen, S. J., van der Reijden, B. A., Martens, J. H. A.
Publicado 2022