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Author Details

Erik van Nimwegen
University of Basel
1998
88
44
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36780518Effective bet-hedging through growth rate dependent stability.Proc Natl Acad Sci U S A2023
36780518Effective bet-hedging through growth rate dependent stability.Proc Natl Acad Sci U S A2023
37069586Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs.Genome Biol2023
37069586Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs.Genome Biol2023
35789323Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.Nat Genet2022
35789323Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.Nat Genet2022
33416498Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species.Elife2021
33986172Investigate the origins of COVID-19.Science2021
33927416Bayesian inference of gene expression states from single-cell RNA-seq data.Nat Biotechnol2021
33416498Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species.Elife2021
33927416Bayesian inference of gene expression states from single-cell RNA-seq data.Nat Biotechnol2021
33986172Investigate the origins of COVID-19.Science2021
32170161Tead transcription factors differentially regulate cortical development.Sci Rep2020
32170161Tead transcription factors differentially regulate cortical development.Sci Rep2020
33045012Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria.PLoS One2020
33270631Subpopulations of sensorless bacteria drive fitness in fluctuating environments.PLoS Biol2020
33270631Subpopulations of sensorless bacteria drive fitness in fluctuating environments.PLoS Biol2020
33045012Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria.PLoS One2020
31138617Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs.Genome Res2019
31710292Initiation of chromosome replication controls both division and replication cycles in <i>E. coli</i> through a double-adder mechanism.Elife2019
31138617Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs.Genome Res2019
31710292Initiation of chromosome replication controls both division and replication cycles in <i>E. coli</i> through a double-adder mechanism.Elife2019
29335514Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software.Nat Commun2018
30150282Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction.Mol Syst Biol2018
29335514Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software.Nat Commun2018
29592812Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC.Genome Biol2018
30150282Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction.Mol Syst Biol2018
29592812Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC.Genome Biol2018
28753602Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.PLoS Comput Biol2017
28753602Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.PLoS Comput Biol2017
27372217Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].Methods2016
27372217Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].Methods2016
27171220Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?PLoS Comput Biol2016
28232860The ISMARA client.F1000Res2016
28232860The ISMARA client.F1000Res2016
27171220Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?PLoS Comput Biol2016
25568052A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development.Genome Res2015
25568052A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development.Genome Res2015
25892562Quantifying the strength of miRNA-target interactions.Methods2015
26080931Expression noise facilitates the evolution of gene regulation.Elife2015
26164700ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data.Methods2015
26080931Expression noise facilitates the evolution of gene regulation.Elife2015
26164700ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data.Methods2015
25892562Quantifying the strength of miRNA-target interactions.Methods2015
24464994Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion.Nucleic Acids Res2014
25413384Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells.Nat Commun2014
24374622An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants.Eur J Immunol2014
24464994Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion.Nucleic Acids Res2014
24912679Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program.Mol Cell Biol2014
25030899Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways.Nucleic Acids Res2014
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Collaborators

Mihaela Zavolan
Co-authored papers 27
Piotr J Balwierz
MRC London Institute of Medical Sciences
Co-authored papers 15
Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 9
Yoshihide Hayashizaki
Center for Integrative Medical Sciences
Co-authored papers 9
Carsten O Daub
International Institute of Molecular and Cell Biology in Warsaw
Co-authored papers 7
Hideya Kawaji
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
Jun Kawai
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
Harukazu Suzuki
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
David A Hume
Mater Research Institute-UQ, Translational Research Institute
Co-authored papers 6
Alistair R R Forrest
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
Boris Lenhard
MRC London Institute of Medical Sciences
Co-authored papers 5
Noriko Ninomiya
Japan Tobacco Inc.
Co-authored papers 4
Shiro Fukuda
Graduate School of Medicine, Osaka University
Co-authored papers 4
Takahiro Arakawa
Tokyo University of Technology
Co-authored papers 4
Julian Gough
Medical Research Council Laboratory of Molecular Biology
Co-authored papers 4
Shintaro Katayama
Folkhalsan Research Center
Co-authored papers 4
Timothy Ravasi
Okinawa Institute of Science and Technology Graduate University
Co-authored papers 4
Jessica Severin
Center for Integrative Medical Sciences
Co-authored papers 4
Mutsumi Kanamori-Katayama
Karolinska Institutet
Co-authored papers 4
Chikatoshi Kai
Co-authored papers 4
Timo Lassmann
Telethon Kids Institute, University of Western Australia
Co-authored papers 4
Vladimir B Bajic
King Abdullah University of Science and Technology (KAUST)
Co-authored papers 4
Michihira Tagami
RIKEN Center for Integrative Medical Sciences
Co-authored papers 4
Winston Hide
Harvard Medical School
Co-authored papers 4
Colin A Semple
Institute of Genetics and Cancer, University of Edinburgh
Co-authored papers 3
Sean M Grimmond
The University of Melbourne
Co-authored papers 3
Oliver Hofmann
University of Melbourne
Co-authored papers 3
Rohan D Teasdale
The University of Queensland
Co-authored papers 3
Jesper Tegn??r
King Abdullah University of Science and Technology (KAUST)
Co-authored papers 3
Martin S Taylor
Institute of Genetics and Cancer, University of Edinburgh
Co-authored papers 3
Release 1.2