Statistical Dynamics of the Royal Road Genetic Algorithm. - Erik van Nimwegen; James P. Crutchfield; Melanie Mitchell (Theor. Comput. Sci., 1999)

Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory. - Erik van Nimwegen; James P. Crutchfield (Mach. Learn., 2001)

A probabilistic method to detect regulatory modules. - Saurabh Sinha; Erik van Nimwegen; Eric D. Siggia (ISMB (Supplement of Bioinformatics), 2003)

PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information. - Rahul Siddharthan; Erik van Nimwegen; Eric D. Siggia (Regulatory Genomics, 2004)

Identification of clustered microRNAs using an ab initio prediction method. - Alain Sewer; Nicodème Paul; Pablo Landgraf; Alexei Aravin; Sébastien Pfeffer; Michael J. Brownstein; Thomas Tuschl; Erik van Nimwegen; Mihaela Zavolan (BMC Bioinform., 2005)

PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny. - Rahul Siddharthan; Eric D. Siggia; Erik van Nimwegen (PLoS Comput. Biol., 2005)

A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks. - Lukas Burger; Erik van Nimwegen (WABI, 2006)

Inference of miRNA targets using evolutionary conservation and pathway analysis. - Dimos Gaidatzis; Erik van Nimwegen; Jean Hausser; Mihaela Zavolan (BMC Bioinform., 2007)

Correction: Inference of miRNA targets using evolutionary conservation and pathway analysis. - Dimos Gaidatzis; Erik van Nimwegen; Jean Hausser; Mihaela Zavolan (BMC Bioinform., 2007)

Finding regulatory elements and regulatory motifs: a general probabilistic framework. - Erik van Nimwegen (BMC Bioinform., 2007)

SwissRegulon: a database of genome-wide annotations of regulatory sites. - Mikhail Pachkov; Ionas Erb; Nacho Molina; Erik van Nimwegen (Nucleic Acids Res., 2007)

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments. - Lukas Burger; Erik van Nimwegen (PLoS Comput. Biol., 2010)

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. - Hideya Kawaji; Jessica Severin; Marina Lizio; Alistair R. R. Forrest; Erik van Nimwegen; Michael Rehli; Kate Schroder; Katharine M. Irvine; Harukazu Suzuki; Piero Carninci; Yoshihide Hayashizaki; Carsten O. Daub (Nucleic Acids Res., 2011)

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. - Phil Arnold; Ionas Erb; Mikhail Pachkov; Nacho Molina; Erik van Nimwegen (Bioinform., 2012)

Corrigendum: DNA-binding factors shape the mouse methylome at distal regulatory regions. - Michael B. Stadler; Rabih Murr; Lukas Burger; Robert Ivanek; Florian Lienert; Anne Schöler; Erik van Nimwegen; Christiane Wirbelauer; Edward J. Oakeley; Dimos Gaidatzis; Vijay K. Tiwari; Dirk Schübeler (Nat., 2012)

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. - Mikhail Pachkov; Piotr J. Balwierz; Phil Arnold; Evgeniy A. Ozonov; Erik van Nimwegen (Nucleic Acids Res., 2013)

Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers. - Evgeniy A. Ozonov; Erik van Nimwegen (PLoS Comput. Biol., 2013)

Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine. - Florian Jug; Tobias Pietzsch; Dagmar Kainmüller; Jan Funke; Matthias Kaiser; Erik van Nimwegen; Carsten Rother; Gene Myers (BAMBI, 2014)

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. - Heinz Stockinger; Adrian M. Altenhoff; Konstantin Arnold; Amos Bairoch; Frederic B. Bastian; Sven Bergmann; Lydie Bougueleret; Philipp Bucher; Mauro Delorenzi; Lydie Lane; Philippe Le Mercier; Frédérique Lisacek; et al. (Nucleic Acids Res., 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? - Erik van Nimwegen (PLoS Comput. Biol., 2016)

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. - Saeed Omidi; Mihaela Zavolan; Mikhail Pachkov; Jeremie Breda; Severin Berger; Erik van Nimwegen (PLoS Comput. Biol., 2017)

Identifying cell states in single-cell RNA-seq data at statistically maximal resolution. - Pascal Grobecker; Thomas Sakoparnig; Erik van Nimwegen (PLoS Comput. Biol., 2024)