Subpopulations of sensorless bacteria drive fitness in fluctuating environments

di Julou, Thomas, Zweifel, Ludovit, Blank, Diana, Fiori, Athos, van Nimwegen, Erik
Pubblicazione 2020

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

di Pachkov, Mikhail, Balwierz, Piotr J., Arnold, Phil, Ozonov, Evgeniy, van Nimwegen, Erik
Pubblicazione 2013

Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria

di Galbusera, Luca, Bellement-Theroue, Gwendoline, Urchueguia, Arantxa, Julou, Thomas, van Nimwegen, Erik
Pubblicazione 2020

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

di Bertels, Frederic, Silander, Olin K., Pachkov, Mikhail, Rainey, Paul B., van Nimwegen, Erik
Pubblicazione 2014

The ISMARA client

di Artimo, Panu, Duvaud, Séverine, Pachkov, Mikhail, Ioannidis, Vassilios, van Nimwegen, Erik, Stockinger, Heinz
Pubblicazione 2016

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors

di Omidi, Saeed, Zavolan, Mihaela, Pachkov, Mikhail, Breda, Jeremie, Berger, Severin, van Nimwegen, Erik
Pubblicazione 2017

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network

di Urchueguía, Arantxa, Galbusera, Luca, Chauvin, Dany, Bellement, Gwendoline, Julou, Thomas, van Nimwegen, Erik
Pubblicazione 2021

Effective bet-hedging through growth rate dependent stability

di de Groot, Daan H., Tjalma, Age J., Bruggeman, Frank J., van Nimwegen, Erik
Pubblicazione 2023

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

di Balwierz, Piotr J., Pachkov, Mikhail, Arnold, Phil, Gruber, Andreas J., Zavolan, Mihaela, van Nimwegen, Erik
Pubblicazione 2014

Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs

di Berger, Severin, Pachkov, Mikhail, Arnold, Phil, Omidi, Saeed, Kelley, Nicholas, Salatino, Silvia, van Nimwegen, Erik
Pubblicazione 2019

A Simple Physical Model Predicts Small Exon Length Variations

di Chern, Tzu-Ming, van Nimwegen, Erik, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Zavolan, Mihaela
Pubblicazione 2006

Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)

di Tiwari, Neha, Meyer-Schaller, Nathalie, Arnold, Phil, Antoniadis, Helena, Pachkov, Mikhail, van Nimwegen, Erik, Christofori, Gerhard
Pubblicazione 2013

Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)

di Tiwari, Neha, Meyer-Schaller, Nathalie, Arnold, Phil, Antoniadis, Helena, Pachkov, Mikhail, van Nimwegen, Erik, Christofori, Gerhard
Pubblicazione 2013

Timescales and bottlenecks in miRNA-dependent gene regulation

di Hausser, Jean, Syed, Afzal Pasha, Selevsek, Nathalie, van Nimwegen, Erik, Jaskiewicz, Lukasz, Aebersold, Ruedi, Zavolan, Mihaela
Pubblicazione 2013

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion

di Luisier, Raphaëlle, Unterberger, Elif B., Goodman, Jay I., Schwarz, Michael, Moggs, Jonathan, Terranova, Rémi, van Nimwegen, Erik
Pubblicazione 2014

Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC

di Gruber, Andreas J., Schmidt, Ralf, Ghosh, Souvik, Martin, Georges, Gruber, Andreas R., van Nimwegen, Erik, Zavolan, Mihaela
Pubblicazione 2018

Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software

di Kaiser, Matthias, Jug, Florian, Julou, Thomas, Deshpande, Siddharth, Pfohl, Thomas, Silander, Olin K., Myers, Gene, van Nimwegen, Erik
Pubblicazione 2018

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

di Arnold, Phil, Schöler, Anne, Pachkov, Mikhail, Balwierz, Piotr J., Jørgensen, Helle, Stadler, Michael B., van Nimwegen, Erik, Schübeler, Dirk
Pubblicazione 2013

Tead transcription factors differentially regulate cortical development

di Mukhtar, Tanzila, Breda, Jeremie, Grison, Alice, Karimaddini, Zahra, Grobecker, Pascal, Iber, Dagmar, Beisel, Christian, van Nimwegen, Erik, Taylor, Verdon
Pubblicazione 2020

Identification of clustered microRNAs using an ab initio prediction method

di Sewer, Alain, Paul, Nicodème, Landgraf, Pablo, Aravin, Alexei, Pfeffer, Sébastien, Brownstein, Michael J, Tuschl, Thomas, van Nimwegen, Erik, Zavolan, Mihaela
Pubblicazione 2005