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Erik van Nimwegen

Erik van Nimwegen

D-Index & Metrics

Genetics

D-Index
60
Citations
21315
World Ranking
3112
National Ranking
46

Overview

Erik van Nimwegen is affiliated with the University of Basel in Switzerland. Their research primarily focuses on the domain of Biochemistry, Genetics, and Molecular Biology, with significant contributions to Molecular Biology, Genetics, Endocrinology, Biophysics, and Developmental Neuroscience.

Their work encompasses several specialized topics, including:

  • Gene Regulatory Network Analysis
  • Bacterial Genetics and Biotechnology
  • Single-cell and spatial transcriptomics
  • Evolution and Genetic Dynamics
  • RNA Research and Splicing
  • RNA and protein synthesis mechanisms
  • Escherichia coli research studies

Erik van Nimwegen's recent papers highlight their involvement in diverse biological and computational research areas. Notable publications include:

  • Investigate the origins of COVID-19, 2021, Science
  • Bayesian inference of gene expression states from single-cell RNA-seq data, 2021, Nature Biotechnology
  • Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species, 2021, eLife
  • Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements, 2022, Nature Genetics
  • Tead transcription factors differentially regulate cortical development, 2020, Scientific Reports

Frequent coauthors collaborating with van Nimwegen include Thomas Julou, Jérémie Breda, Mihaela Zavolan, Pascal Grobecker, and Théo Gervais. The collaborations indicate a network of research intersecting molecular and computational biology.

The scholar has a consistent publication record in a range of venues. Most contributions appear in bioRxiv (Cold Spring Harbor Laboratory), followed by works published in Zenodo (CERN European Organization for Nuclear Research), PLoS Biology, Science, and Nature Biotechnology.

Best Publications

  • The Transcriptional Landscape of the Mammalian Genome

    P. Carninci;T. Kasukawa;S. Katayama;J. Gough

  • A promoter-level mammalian expression atlas

    Alistair R.R. Forrest;Hideya Kawaji;Michael Rehli;J. Kenneth Baillie

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

    Michael B. Stadler;Rabih Murr;Lukas Burger;Lukas Burger;Robert Ivanek

  • An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

    Timothy Ravasi;Harukazu Suzuki;Carlo Vittorio Cannistraci;Shintaro Katayama

  • Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence Attributes

    Edward Yang;Erik van Nimwegen;Mihaela Zavolan;Nikolaus Rajewsky

  • Neutral evolution of mutational robustness.

    Erik van Nimwegen;James P. Crutchfield;Martijn Huynen

  • Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming

    Neha Tiwari;Vijay K. Tiwari;Lorenz Waldmeier;Piotr J. Balwierz

  • The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

    Harukazu Suzuki;Alistair R.R. Forrest;Erik Van Nimwegen;Carsten O. Daub

  • Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

    Frederic Bertels;Olin K. Silander;Mikhail Pachkov;Paul B. Rainey

  • Scaling Laws in the Functional Content of Genomes

    Erik van Nimwegen

  • Inference of miRNA targets using evolutionary conservation and pathway analysis

    Dimos Gaidatzis;Dimos Gaidatzis;Erik van Nimwegen;Erik van Nimwegen;Jean Hausser;Jean Hausser;Mihaela Zavolan;Mihaela Zavolan

  • PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

    Rahul Siddharthan;Eric D Siggia;Erik Jan van Nimwegen;Erik Jan van Nimwegen

  • ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

    Piotr J Balwierz;Mikhail Pachkov;Phild Arnold;Andreas J Gruber

  • Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity

    Erik Arner;Niklas Mejhert;Agné Kulyté;Piotr J. Balwierz

  • Identification of clustered microRNAs using an ab initio prediction method

    Alain Sewer;Nicodème Paul;Pablo Landgraf;Alexei Aravin

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

    Nicola Aceto;Nina Sausgruber;Heike Brinkhaus;Dimos Gaidatzis

  • A probabilistic method to detect regulatory modules.

    Saurabh Sinha;Erik van Nimwegen;Eric D. Siggia

  • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method.

    Lukas Burger;Erik van Nimwegen

  • Disentangling direct from indirect co-evolution of residues in protein alignments.

    Lukas Burger;Erik van Nimwegen

  • Statistical dynamics of the Royal Road genetic algorithm

    Erik van Nimwegen;James P. Crutchfield;Melanie Mitchell

Frequent Co-Authors

Mihaela Zavolan
Mihaela Zavolan University of Basel
James P. Crutchfield
James P. Crutchfield University of California, Davis
Winston Hide
Winston Hide Harvard Medical School
David A. Hume
David A. Hume University of Queensland
Carsten O. Daub
Carsten O. Daub Karolinska Institute
Jesper Tegnér
Jesper Tegnér King Abdullah University of Science and Technology
Oliver Hofmann
Oliver Hofmann University of Melbourne
Dirk Schübeler
Dirk Schübeler Friedrich Miescher Institute

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