Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? by Erik van Nimwegen

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Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters. by Ionas Erb, Erik van Nimwegen

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Disentangling direct from indirect co-evolution of residues in protein alignments. by Lukas Burger, Erik van Nimwegen

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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

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Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species by Thomas Sakoparnig, Chris Field, Erik van Nimwegen

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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

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Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs by Maria Katsantoni, Erik van Nimwegen, Mihaela Zavolan

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Expression noise facilitates the evolution of gene regulation by Luise Wolf, Olin K Silander, Erik van Nimwegen

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PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. by Rahul Siddharthan, Eric D Siggia, Erik van Nimwegen

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SPA: a probabilistic algorithm for spliced alignment. by Erik van Nimwegen, Nicodeme Paul, Robert Sheridan, Mihaela Zavolan

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Subpopulations of sensorless bacteria drive fitness in fluctuating environments. by Thomas Julou, Ludovit Zweifel, Diana Blank, Athos Fiori, Erik van Nimwegen

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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

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Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network. by Arantxa Urchueguía, Luca Galbusera, Dany Chauvin, Gwendoline Bellement, Thomas Julou, Erik van Nimwegen

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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

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Timescales and bottlenecks in miRNA‐dependent gene regulation by Jean Hausser, Afzal Pasha Syed, Nathalie Selevsek, Erik van Nimwegen, Lukasz Jaskiewicz, Ruedi Aebersold, Mihaela Zavolan

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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

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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

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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

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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

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