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Plos Computational Biology|February 16, 2006
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogenyRahul Siddharthan, Eric D Siggia, Erik van NimwegenBMC Microbiology|February 6, 2013
Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coliNiels Hofsteenge, Erik van Nimwegen, Olin K SilanderPlos Genetics|May 10, 2006
SPA: a probabilistic algorithm for spliced alignmentErik van Nimwegen, Nicodeme Paul, Robert Sheridan, et al.Methods (San Diego, Calif.)|December 26, 2007
Computational analysis of small RNA cloning dataPhilipp Berninger, Dimos Gaidatzis, Erik van Nimwegen, et al.Nucleic Acids Research|November 30, 2006
SwissRegulon: a database of genome-wide annotations of regulatory sitesMikhail Pachkov, Ionas Erb, Nacho Molina, et al.Nature Methods|January 22, 2013
A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targetsMohsen Khorshid, Jean Hausser, Mihaela Zavolan, et al.Methods (San Diego, Calif.)|July 13, 2015
ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression dataPeter J Pemberton-Ross, Mikhail Pachkov, Erik van NimwegenBMC Bioinformatics|March 3, 2007
Inference of miRNA targets using evolutionary conservation and pathway analysisDimos Gaidatzis, Erik van Nimwegen, Jean Hausser, et al.DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes|February 16, 2008
Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programsTzu-Ming Chern, Nicodeme Paul, Erik van Nimwegen, et al.Genome Biology and Evolution|September 11, 2010
Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiaeKevin Chen, Erik van Nimwegen, Nikolaus Rajewsky, et al.Pageof 10