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ORCIDErik van Nimwegen
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2020 – today
- 2024
[j18]Pascal Grobecker
, Thomas Sakoparnig, Erik van Nimwegen:
Identifying cell states in single-cell RNA-seq data at statistically maximal resolution. PLoS Comput. Biol. 20(7): 1012224 (2024)
2010 – 2019
- 2017
- [j17]Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen:
Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Comput. Biol. 13(7) (2017) - 2016
- [j16]Erik van Nimwegen:
Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? PLoS Comput. Biol. 12(5) (2016) - 2014
- [j15]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:
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Res. 42(Webserver-Issue): 436-441 (2014) - [c4]Florian Jug, Tobias Pietzsch, Dagmar Kainmüller, Jan Funke, Matthias Kaiser, Erik van Nimwegen, Carsten Rother, Gene Myers:
Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine. BAMBI 2014: 25-36 - 2013
- [j14]Mikhail Pachkov, Piotr J. Balwierz, Phil Arnold, Evgeniy A. Ozonov, Erik van Nimwegen:
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res. 41(Database-Issue): 214-220 (2013) - [j13]Evgeniy A. Ozonov, Erik van Nimwegen:
Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers. PLoS Comput. Biol. 9(8) (2013) - 2012
- [j12]Phil Arnold, Ionas Erb, Mikhail Pachkov, Nacho Molina, Erik van Nimwegen:
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinform. 28(4): 487-494 (2012) - [j11]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:
Corrigendum: DNA-binding factors shape the mouse methylome at distal regulatory regions. Nat. 484(7395): 550 (2012) - 2011
- [j10]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:
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Res. 39(Database-Issue): 856-860 (2011) - 2010
- [j9]Lukas Burger, Erik van Nimwegen:
Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments. PLoS Comput. Biol. 6(1) (2010)
2000 – 2009
- 2007
- [j8]Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan:
Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinform. 8 (2007) - [j7]Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan:
Correction: Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinform. 8 (2007) - [j6]Erik van Nimwegen:
Finding regulatory elements and regulatory motifs: a general probabilistic framework. BMC Bioinform. 8(S-6) (2007) - [j5]Mikhail Pachkov, Ionas Erb, Nacho Molina, Erik van Nimwegen:
SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res. 35(Database-Issue): 127-131 (2007) - 2006
- [c3]Lukas Burger, Erik van Nimwegen:
A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks. WABI 2006: 44-55 - 2005
- [j4]Alain Sewer, Nicodème Paul, Pablo Landgraf, Alexei Aravin, Sébastien Pfeffer, Michael J. Brownstein, Thomas Tuschl, Erik van Nimwegen, Mihaela Zavolan:
Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinform. 6: 267 (2005) - [j3]Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen:
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny. PLoS Comput. Biol. 1(7) (2005) - 2004
- [c2]Rahul Siddharthan, Erik van Nimwegen, Eric D. Siggia:
PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information. Regulatory Genomics 2004: 30-41 - 2003
- [c1]Saurabh Sinha, Erik van Nimwegen, Eric D. Siggia:
A probabilistic method to detect regulatory modules. ISMB (Supplement of Bioinformatics) 2003: 292-301 - 2001
- [j2]Erik van Nimwegen, James P. Crutchfield:
Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory. Mach. Learn. 45(1): 77-114 (2001)
1990 – 1999
- 1999
- [j1]Erik van Nimwegen, James P. Crutchfield, Melanie Mitchell:
Statistical Dynamics of the Royal Road Genetic Algorithm. Theor. Comput. Sci. 229(1): 41-102 (1999)
Coauthor Index
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