Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?

by Erik van Nimwegen
Published 2016-05-01

Disentangling direct from indirect co-evolution of residues in protein alignments.

by Lukas Burger, Erik van Nimwegen
Published 2010-01-01

Authors' Reply

by Erik van Nimwegen, Mihaela Zavolan
Published 2006-11-01

Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

by Ionas Erb, Erik van Nimwegen
Published 2011-01-01

Authors' Reply.

by Erik van Nimwegen, Mihaela Zavolan
Published 2006-11-01

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

by Evgeniy A Ozonov, Erik van Nimwegen
Published 2013-01-01

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species

by Thomas Sakoparnig, Chris Field, Erik van Nimwegen
Published 2021-01-01

Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism

by Guillaume Witz, Erik van Nimwegen, Thomas Julou
Published 2019-11-01

Expression noise facilitates the evolution of gene regulation

by Luise Wolf, Olin K Silander, Erik van Nimwegen
Published 2015-06-01

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

by Rahul Siddharthan, Eric D Siggia, Erik van Nimwegen
Published 2005-12-01

SPA: a probabilistic algorithm for spliced alignment.

by Erik van Nimwegen, Nicodeme Paul, Robert Sheridan, Mihaela Zavolan
Published 2006-04-01

Subpopulations of sensorless bacteria drive fitness in fluctuating environments.

by Thomas Julou, Ludovit Zweifel, Diana Blank, Athos Fiori, Erik van Nimwegen
Published 2020-12-01

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

by Luca Galbusera, Gwendoline Bellement-Theroue, Arantxa Urchueguia, Thomas Julou, Erik van Nimwegen
Published 2020-01-01

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

by Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen
Published 2017-07-01

The ISMARA client [version 1; referees: 2 approved]

by Panu Artimo, Séverine Duvaud, Mikhail Pachkov, Vassilios Ioannidis, Erik van Nimwegen, Heinz Stockinger
Published 2016-12-01

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

by Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Published 2013-01-01

Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8).

by Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Published 2013-01-01

A simple physical model predicts small exon length variations.

by Tzu-Ming Chern, Erik van Nimwegen, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Mihaela Zavolan
Published 2006-04-01

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

by Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Published 2013-01-01

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

by Andreas J. Gruber, Ralf Schmidt, Souvik Ghosh, Georges Martin, Andreas R. Gruber, Erik van Nimwegen, Mihaela Zavolan
Published 2018-03-01