Erik van Nimwegen

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Mihaela ZavolanProfessor of Computational Biology, Biozentrum, University of BaselVerified email at unibas.ch
Piotr J BalwierzPostdoctoral Researcher, Imperial College LondonVerified email at imperial.ac.uk
James CrutchfieldProfessor of Physics, University of California at DavisVerified email at ucdavis.edu
Dirk SchübelerDirector, Friedrich Miescher Institute for Biomedical Research, Basel, SwitzerlandVerified email at fmi.ch
Lukas BurgerResearch Associate, Friedrich Miescher Institute for Biomedical ResearchVerified email at fmi.ch
Robert IvanekHead of Bioinformatics at the Department of Biomedicine, University of BaselVerified email at unibas.ch
Eric SiggiaRockefeller UniversityVerified email at cornell.edu
Andreas J. GruberUniversity of KonstanzVerified email at uni-konstanz.de
Olin SilanderAssociate Professor, Massey University, New ZealandVerified email at massey.ac.nz
Ionas ErbCentre for Genomic Regulation (CRG), BarcelonaVerified email at crg.eu
Martijn HuynenMBS, Radboud University Medical CentreVerified email at radboudumc.nl
Nacho MolinaIGBMC - CNRS - INSERM - University of StrasbourgVerified email at igbmc.fr
Carsten O. DaubAssociate Professor, Karolinska InstitutetVerified email at ki.se
Nikolaus RajewskyProfessor, Systems Biology, Max Delbruck Center for Molecular Medicine, BerlinVerified email at mdc-berlin.de
Carninci PieroRIKEN IMS (Yokohama, JP) and Human Technopole (Milan, IT)Verified email at postman.riken.jp
Thomas JulouBiozentrum BaselVerified email at normalesup.org
Christian BeiselHead Genomics Facility Basel, ETH ZurichVerified email at bsse.ethz.ch
Jean HausserKarolinska Institutet & SciLifeLabVerified email at ki.se
Christoph HandschinUniversity of Basel, BiozentrumVerified email at unibas.ch
Jeremie BredaNetherlands Cancer InstituteVerified email at nki.nl

Erik van Nimwegen

Professor of computational systems biology, Biozentrum, University of Basel

Verified email at unibas.ch - Homepage

computational biology genomics systems biology transcription regulation genome evolution


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The transcriptional landscape of the mammalian genome P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, ... science 309 (5740), 1559-1563, 2005	3929	2005
A promoter-level mammalian expression atlas Nature 507 (7493), 462-470, 2014	1605	2014
DNA-binding factors shape the mouse methylome at distal regulatory regions MB Stadler, R Murr, L Burger, R Ivanek, F Lienert, A Schöler, E Nimwegen, ... Nature 480 (7378), 490-495, 2011	1419	2011
An atlas of combinatorial transcriptional regulation in mouse and man T Ravasi, H Suzuki, CV Cannistraci, S Katayama, VB Bajic, K Tan, ... Cell 140 (5), 744-752, 2010	801	2010
Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes E Yang, E van Nimwegen, M Zavolan, N Rajewsky, M Schroeder, ... Genome research 13 (8), 1863-1872, 2003	703	2003
Neutral evolution of mutational robustness E Van Nimwegen, JP Crutchfield, M Huynen Proceedings of the National Academy of Sciences 96 (17), 9716-9720, 1999	691	1999
Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming N Tiwari, VK Tiwari, L Waldmeier, PJ Balwierz, P Arnold, M Pachkov, ... Cancer cell 23 (6), 768-783, 2013	462	2013
Inference of miRNA targets using evolutionary conservation and pathway analysis D Gaidatzis, E van Nimwegen, J Hausser, M Zavolan BMC bioinformatics 8, 1-22, 2007	431	2007
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line Nature genetics 41 (5), 553-562, 2009	413	2009
Automated reconstruction of whole-genome phylogenies from short-sequence reads F Bertels, OK Silander, M Pachkov, PB Rainey, E Van Nimwegen Molecular biology and evolution 31 (5), 1077-1088, 2014	397	2014
Scaling laws in the functional content of genomes E van Nimwegen Trends in Genetics 19 (9), 479-484, 2003	388	2003
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny R Siddharthan, ED Siggia, E Van Nimwegen PLoS computational biology 1 (7), e67, 2005	353	2005
Adipose tissue microRNAs as regulators of CCL2 production in human obesity E Arner, N Mejhert, A Kulyté, PJ Balwierz, M Pachkov, M Cormont, ... Diabetes 61 (8), 1986-1993, 2012	317	2012
Identification of clustered microRNAs using an ab initio prediction method A Sewer, N Paul, P Landgraf, A Aravin, S Pfeffer, MJ Brownstein, T Tuschl, ... BMC bioinformatics 6, 1-15, 2005	312	2005
Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop N Aceto, N Sausgruber, H Brinkhaus, D Gaidatzis, G Martiny-Baron, ... Nature medicine 18 (4), 529-537, 2012	292	2012
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs PJ Balwierz, M Pachkov, P Arnold, AJ Gruber, M Zavolan, ... Genome research 24 (5), 869-884, 2014	284	2014
A probabilistic method to detect regulatory modules S Sinha, E Van Nimwegen, ED Siggia Bioinformatics-Oxford 19 (1), 292-301, 2003	275	2003
The frequency distribution of gene family sizes in complete genomes. MA Huynen, E Van Nimwegen Molecular biology and evolution 15 (5), 583-589, 1998	266	1998
Disentangling direct from indirect co-evolution of residues in protein alignments L Burger, E Van Nimwegen PLoS computational biology 6 (1), e1000633, 2010	233	2010
Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method L Burger, E Van Nimwegen Molecular systems biology 4 (1), 165, 2008	226	2008

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