Erik van Nimwegen

发表

Vassilios Ioannidis, Mikhail Pachkov, Heinz Stockinger, 2016, F1000Research.

Bayesian inference of the gene expression states of single cells from scRNA-seq data

Erik van Nimwegen, Jérémie Breda, Mihaela Zavolan, 2019, bioRxiv.

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

Severin Berger, Saeed Omidi, Phil Arnold, 2018 .

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

Thomas Julou, Matthias Kaiser, Thomas Pfohl, 2018, Nature Communications.

Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].

Mihaela Zavolan, Rafal Gumienny, Erik van Nimwegen, 2016, Methods.

Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast.

Ulrich Schlecht, Michael Primig, Alain Nicolas, 2008, Molecular biology of the cell.

Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome.

Terry Gaasterland, Mihaela Zavolan, Erik van Nimwegen, 2002, Genome research.

Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters

Ionas Erb, Erik van Nimwegen, E. van Nimwegen, 2011, PloS one.

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

Mikhail Pachkov, Phil Arnold, Michael B. Stadler, 2013, Genome research.

Detecting regulatory sites using PhyloGibbs.

Rahul Siddharthan, Erik van Nimwegen, E. van Nimwegen, 2007, Methods in molecular biology.

Quantifying the strength of miRNA-target interactions.

Mihaela Zavolan, Rafal Gumienny, Erik van Nimwegen, 2015, Methods.

The evolution of domain-content in bacterial genomes

Erik van Nimwegen, E. van Nimwegen, Nacho Molina, 2008, Biology Direct.

Universal patterns of purifying selection at noncoding positions in bacteria.

Erik van Nimwegen, E. van Nimwegen, Nacho Molina, 2007, Genome research.

Additional data file 5

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2003 .

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels

Peter F Stadler, Robert Ivanek, Michael B. Stadler, 2012 .

A Simple Physical Model Predicts Small Exon Length Variations

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, PLoS genetics.

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

Mikhail Pachkov, Paul B. Rainey, Olin K. Silander, 2014, Molecular biology and evolution.

Epidemiology. Influenza escapes immunity along neutral networks.

Erik van Nimwegen, E. van Nimwegen, 2006, Science.

Analysis of Human Immunodeficiency Virus Cytopathicity by Using a New Method for Quantitating Viral Dynamics in Cell Culture

Alan S. Perelson, Mihaela Zavolan, Richard Siegel, 2005, Journal of Virology.

The types and prevalence of alternative splice forms.

Mihaela Zavolan, Erik van Nimwegen, 2006, Current opinion in structural biology.

MicroRNA-221–222 Regulate the Cell Cycle in Mast Cells1

Mikhail Pachkov, Erik van Nimwegen, Anjana Rao, 2009, The Journal of Immunology.

Timescales and bottlenecks in miRNA-dependent gene regulation

Ruedi Aebersold, Mihaela Zavolan, Nathalie Selevsek, 2013, Molecular systems biology.

Correlating Gene Expression Variation with cis-Regulatory Polymorphism in Saccharomyces cerevisiae

Nikolaus Rajewsky, Mark L. Siegal, Erik van Nimwegen, 2010, Genome biology and evolution.

Scaling laws in functional genome content across prokaryotic clades and lifestyles.

Erik van Nimwegen, E. van Nimwegen, Nacho Molina, 2009, Trends in genetics : TIG.

ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data.

Mikhail Pachkov, Peter J Pemberton-Ross, Erik van Nimwegen, 2015, Methods.

Computational analysis of small RNA cloning data.

Mihaela Zavolan, Dimos Gaidatzis, Erik van Nimwegen, 2008, Methods.

Single‐cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction

Mihaela Zavolan, Christian Beisel, Souvik Ghosh, 2018, Molecular systems biology.