Erik van Nimwegen

22 papers C 1Journal 18Unranked 3
YearRankTypeTitle / Venue / Authors
2024 J jnl
Identifying cell states in single-cell RNA-seq data at statistically maximal resolution.
PLoS Comput. Biol.
Pascal Grobecker, Thomas Sakoparnig, Erik van Nimwegen
2017 J jnl
Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.
PLoS Comput. Biol.
Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen
2016 J jnl
Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?
PLoS Comput. Biol.
Erik van Nimwegen
2014 J jnl
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.
Nucleic Acids Res.
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, Olivier Michielin, Patricia M. Palagi, Jacques Rougemont, Torsten Schwede, Christian von Mering, Erik van Nimwegen, Daniel Walther, Ioannis Xenarios, Mihaela Zavolan, Evgeny M. Zdobnov, Vincent Zoete, Ron D. Appel
2014 — conf
Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine.
BAMBI
Florian Jug, Tobias Pietzsch, Dagmar Kainmüller, Jan Funke, Matthias Kaiser, Erik van Nimwegen, Carsten Rother, Gene Myers
2013 J jnl
Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers.
PLoS Comput. Biol.
Evgeniy A. Ozonov, Erik van Nimwegen
2013 J jnl
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.
Nucleic Acids Res.
Mikhail Pachkov, Piotr J. Balwierz, Phil Arnold, Evgeniy A. Ozonov, Erik van Nimwegen
2012 J jnl
Corrigendum: DNA-binding factors shape the mouse methylome at distal regulatory regions.
Nat.
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
2012 J jnl
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences.
Bioinform.
Phil Arnold, Ionas Erb, Mikhail Pachkov, Nacho Molina, Erik van Nimwegen
2011 J jnl
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Nucleic Acids Res.
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
2010 J jnl
Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments.
PLoS Comput. Biol.
Lukas Burger, Erik van Nimwegen
2007 J jnl
Correction: Inference of miRNA targets using evolutionary conservation and pathway analysis.
BMC Bioinform.
Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan
2007 J jnl
Finding regulatory elements and regulatory motifs: a general probabilistic framework.
BMC Bioinform.
Erik van Nimwegen
2007 J jnl
Inference of miRNA targets using evolutionary conservation and pathway analysis.
BMC Bioinform.
Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan
2007 J jnl
SwissRegulon: a database of genome-wide annotations of regulatory sites.
Nucleic Acids Res.
Mikhail Pachkov, Ionas Erb, Nacho Molina, Erik van Nimwegen
2006 C conf
A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks.
WABI
Lukas Burger, Erik van Nimwegen
2005 J jnl
Identification of clustered microRNAs using an
BMC Bioinform.
Alain Sewer, Nicodème Paul, Pablo Landgraf, Alexei Aravin, Sébastien Pfeffer, Michael J. Brownstein, Thomas Tuschl, Erik van Nimwegen, Mihaela Zavolan
2005 J jnl
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.
PLoS Comput. Biol.
Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen
2004 — conf
PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information.
Regulatory Genomics
Rahul Siddharthan, Erik van Nimwegen, Eric D. Siggia
2003 — conf
A probabilistic method to detect regulatory modules.
ISMB (Supplement of Bioinformatics)
Saurabh Sinha, Erik van Nimwegen, Eric D. Siggia
2001 J jnl
Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory.
Mach. Learn.
Erik van Nimwegen, James P. Crutchfield
1999 J jnl
Statistical Dynamics of the Royal Road Genetic Algorithm.
Theor. Comput. Sci.
Erik van Nimwegen, James P. Crutchfield, Melanie Mitchell