Erik van Nimwegen
Erik van Nimwegen
Professor of computational systems biology, Biozentrum, University of Basel
Verified email at unibas.ch - Homepage
Title
Cited by
Cited by
Year
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
34432005
DNA-binding factors shape the mouse methylome at distal regulatory regions
MB Stadler, R Murr, L Burger, R Ivanek, F Lienert, A Schöler, ...
Nature 480 (7378), 490-495, 2011
11252011
A promoter-level mammalian expression atlas
ARR Forrest, H Kawaji, M Rehli, JK Baillie, MJL De Hoon, V Haberle, ...
Nature 507 (7493), 462-470, 2014
9172014
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
6712010
Neutral evolution of mutational robustness
E Van Nimwegen, JP Crutchfield, M Huynen
Proceedings of the National Academy of Sciences 96 (17), 9716-9720, 1999
6171999
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
5262003
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
H Suzuki, ARR Forrest, E Van Nimwegen, CO Daub, PJ Balwierz, ...
Nature genetics 41 (5), 553, 2009
4302009
Inference of miRNA targets using evolutionary conservation and pathway analysis
D Gaidatzis, E van Nimwegen, J Hausser, M Zavolan
BMC bioinformatics 8 (1), 69, 2007
3882007
Scaling laws in the functional content of genomes
E van Nimwegen
Power Laws, Scale-Free Networks and Genome Biology, 236-253, 2006
3542006
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny
R Siddharthan, ED Siggia, E Van Nimwegen
PLoS Comput Biol 1 (7), e67, 2005
3452005
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
3332013
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), 267, 2005
2842005
A probabilistic method to detect regulatory modules
S Sinha, E Van Nimwegen, ED Siggia
Bioinformatics 19 (suppl_1), i292-i301, 2003
2752003
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
2532014
The frequency distribution of gene family sizes in complete genomes.
MA Huynen, E Van Nimwegen
Molecular biology and evolution 15 (5), 583-589, 1998
2491998
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
2302012
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, 2012
2152012
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
2022008
Statistical dynamics of the royal road genetic algorithm
E Van Nimwegen, JP Crutchfield, M Mitchell
Theoretical Computer Science 229 (1-2), 41-102, 1999
1961999
Disentangling direct from indirect co-evolution of residues in protein alignments
L Burger, E Van Nimwegen
PLoS computational biology 6 (1), e1000633, 2010
1942010
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Articles 1–20