Erik van Nimwegen

发表

Crunch: Completely Automated Analysis of ChIP-seq Data

Severin Berger, Saeed Omidi, Mikhail Pachkov, 2016 .

Inference of miRNA targets using evolutionary conservation and pathway analysis

Mihaela Zavolan, Erik van Nimwegen, Jean Hausser, 2007, BMC Bioinformatics.

Identification of Clustered Micrornas Using an Ab Initio Prediction Method

Mihaela Zavolan, Erik van Nimwegen, Thomas Tuschl, 2022 .

Reproductive toxicology. Trichloroethylene.

Mihaela Zavolan, Erik van Nimwegen, Jean Hausser, 1997, BMC Bioinformatics.

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences

Mikhail Pachkov, Phil Arnold, Erik van Nimwegen, 2012, Bioinform..

Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?

Erik van Nimwegen, E. Nimwegen, 2016, PLoS Comput. Biol..

PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny

Erik van Nimwegen, Eric D. Siggia, Rahul Siddharthan, 2005, PLoS Comput. Biol..

A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks

Erik van Nimwegen, Lukas Burger, 2006, WABI.

A probabilistic method to detect regulatory modules

Saurabh Sinha, Erik van Nimwegen, Eric D. Siggia, 2003, ISMB.

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors

Mihaela Zavolan, Severin Berger, Saeed Omidi, 2016, bioRxiv.

A promoter-level mammalian expression atlas

Cesare Furlanello, Finn Drabløs, Carsten O. Daub, 2015 .

PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information

Erik van Nimwegen, Eric D. Siggia, Rahul Siddharthan, 2004, Regulatory Genomics.

Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory

James P. Crutchfield, Erik van Nimwegen, 2001, Mach. Learn..

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Oliver Horlacher, Damian Szklarczyk, Christian von Mering, 2015, Nucleic Acids Res..

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

Erik van Nimwegen, Lukas Burger, Lukas Burger, 2010, PLoS Comput. Biol..

Statistical Dynamics of the Royal Road Genetic Algorithm

James P. Crutchfield, Melanie Mitchell, Erik van Nimwegen, 1999, Theor. Comput. Sci..

Inferring intrinsic and extrinsic noise from a dual fluorescent reporter

Erik van Nimwegen, E. Nimwegen, 2016 .

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

Mikhail Pachkov, Phil Arnold, Erik van Nimwegen, 2012, Nucleic Acids Res..

Corrigendum: DNA-binding factors shape the mouse methylome at distal regulatory regions

Erik van Nimwegen, Vijay K. Tiwari, Michael B. Stadler, 2012, Nature.

Automated Incorporation of Pairwise Dependency in Transcription Factor Binding Site Prediction Using Dinucleotide Weight Tensors

Mihaela Zavolan, Severin Berger, Saeed Omidi, 2016 .

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Christian von Mering, Ron D. Appel, Evgeny M. Zdobnov, 2014, Nucleic Acids Res..

Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine

Eugene W. Myers, Carsten Rother, Florian Jug, 2014, BAMBI.

Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers

Erik van Nimwegen, Evgeniy A. Ozonov, E. Nimwegen, 2013, PLoS Comput. Biol..

SwissRegulon: a database of genome-wide annotations of regulatory sites

Erik van Nimwegen, Ionas Erb, Nacho Molina, 2006, Nucleic Acids Res..

Finding regulatory elements and regulatory motifs: a general probabilistic framework

Erik van Nimwegen, E. Nimwegen, 2007, BMC Bioinformatics.

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki, 2010, Nucleic Acids Res..

Power Laws in the Size Distribution of Gene Families in Complete Genomes: Biological Interpretations

Martijn A. Huynen, Erik van Nimwegen, 1997 .

Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop

Stephen J. Elledge, Mikhail Pachkov, Erik van Nimwegen, 2012, Nature Medicine.

The types and prevalence of alternative splice forms.

Mihaela Zavolan, Erik van Nimwegen, E. van Nimwegen, 2006, Current opinion in structural biology.

Influenza Escapes Immunity Along Neutral Networks

Erik van Nimwegen, E. Nimwegen, 2006 .

Statistical Features of Yeast ’ s Transcriptional Regulatory Code

Erik van Nimwegen, Ionas Erb, E. Nimwegen, 2006 .