List of works - Erik van Nimwegen

A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets

article

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

scientific article

A probabilistic method to detect regulatory modules

scientific article published in January 2003

A promoter-level mammalian expression atlas

scientific article

A simple physical model predicts small exon length variations

scientific article published on 28 April 2006

ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data

scientific article

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

scientific article published on 12 February 2008

Adipose tissue microRNAs as regulators of CCL2 production in human obesity

scientific article

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants

scientific article published in February 2014

Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture

scientific article

Authors' Reply

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

scientific article

Automated reconstruction of whole-genome phylogenies from short-sequence reads

scientific article published on 05 March 2014

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels

scientific article

Co-expression of FBN1 with mesenchyme-specific genes in mouse cell lines: implications for phenotypic variability in Marfan syndrome

scientific article

Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs

scientific article published on 14 February 2008

Computational analysis of small RNA cloning data

scientific article

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion

scientific article published on 23 January 2014

Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8).

scientific article published on 25 October 2013

Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae

scientific article published on 9 September 2010

Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].

scientific article

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

scientific article published in Nature

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

scientific article published on 14 December 2011

Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes

scientific article

Detecting Regulatory Sites Using PhyloGibbs

Detecting regulatory sites using PhyloGibbs

scientific article published in January 2007

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

scientific article

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways

scientific article published on 16 July 2014

Ewing sarcoma breakpoint region 1 prevents transcription-associated genome instability

Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets

article

Expression noise facilitates the evolution of gene regulation

scientific article published on 17 June 2015

Expression noise facilitates the evolution of gene regulation

article

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

scientific article published on 19 April 2009

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

scientific article

Finding regulatory elements and regulatory motifs: a general probabilistic framework

scientific article

Finite populations induce metastability in evolutionary search

Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast

scientific article published on 27 February 2008

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network

scientific article published in 2021

Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells

scientific article

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

scientific article

Identification of clustered microRNAs using an ab initio prediction method

scientific article

Inference of miRNA targets using evolutionary conservation and pathway analysis

scientific article

Inference of miRNA targets using evolutionary conservation and pathway analysis

article

Influenza Escapes Immunity Along Neutral Networks

scientific article published in Science

Investigate the origins of COVID-19

scientific article

Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8).

scientific article

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

scientific article

MicroRNA-221-222 regulate the cell cycle in mast cells

scientific article

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

scientific article

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

scientific article published in February 2012

Neutral evolution of mutational robustness

scientific article

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

scientific article

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

article

Optimizing epochal evolutionary search: population-size independent theory

Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium

scientific article published on 29 April 2013

Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation

scientific article published on 24 February 2014

PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information

scholarly article by Rahul Siddharthan et al published 2005 in Lecture Notes in Computer Science

PhyloGibbs: A Gibbs Sampling Motif Finder that Incorporates Phylogeny

scholarly article by Rahul Siddharthan et al published 2005 in PLOS Computational Biology

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny

scientific article

Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics

scientific article

Quantifying the strength of miRNA-target interactions

scientific article published on 16 April 2015

Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli

scientific article

SPA: a probabilistic algorithm for spliced alignment

scientific article published on 28 April 2006

Scaling Laws in the Functional Content of Genomes

article published in 2006

Scaling laws in functional genome content across prokaryotic clades and lifestyles

Scaling laws in the functional content of genomes

scientific article

Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming

scientific article published on June 2013

Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome

scientific article published on September 2002

Statistical Dynamics of the Royal Road Genetic Algorithm

article

Subpopulations of sensorless bacteria drive fitness in fluctuating environments

scientific article published on 03 December 2020

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

scientific article (publication date: 2013)

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

scientific article published on 27 November 2006

Tead transcription factors differentially regulate cortical development

scientific article published on 13 March 2020

Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition

scientific article published on 19 February 2014

The Evolutionary Unfolding of Complexity

The corepressor NCoR1 antagonizes PGC-1α and estrogen-related receptor α in the regulation of skeletal muscle function and oxidative metabolism

scientific article

The evolution of domain-content in bacterial genomes

scientific article (publication date: 11 December 2008)

The frequency distribution of gene family sizes in complete genomes

scientific article published in May 1998

The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion

scientific article published on 29 January 2009

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

scientific article

The types and prevalence of alternative splice forms

scientific article

The types and prevalence of alternative splice forms [Current Opinion in Structural Biology 2006, 16:362–367]

Timescales and bottlenecks in miRNA-dependent gene regulation

scientific article published on 03 December 2013

Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters ⬇️

scientific article published on September 9, 2011

Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program

scientific article

Transformation fingerprint: induced STAT3-C, v-Src and Ha-Ras cause small initial changes but similar established profiles in mRNA

scholarly article by Keren Paz published in September 2004

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

scientific article

Universal patterns of purifying selection at noncoding positions in bacteria

scientific article published on 21 November 2007

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

scientific article published on 12 November 2010

Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria

scientific article published on 12 October 2020

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species

scientific article published on 08 January 2021

List of works by Erik van Nimwegen

A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

A probabilistic method to detect regulatory modules

A promoter-level mammalian expression atlas

A simple physical model predicts small exon length variations

ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data

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

Adipose tissue microRNAs as regulators of CCL2 production in human obesity

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of combinatorial transcriptional regulation in mouse and man

An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants

Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture

Authors' Reply

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

Automated reconstruction of whole-genome phylogenies from short-sequence reads

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels

Co-expression of FBN1 with mesenchyme-specific genes in mouse cell lines: implications for phenotypic variability in Marfan syndrome

Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs

Computational analysis of small RNA cloning data

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion

Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8).

Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae

Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].

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

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

Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes

Detecting Regulatory Sites Using PhyloGibbs

Detecting regulatory sites using PhyloGibbs

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

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways

Ewing sarcoma breakpoint region 1 prevents transcription-associated genome instability

Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets

Expression noise facilitates the evolution of gene regulation

Expression noise facilitates the evolution of gene regulation

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

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

Finding regulatory elements and regulatory motifs: a general probabilistic framework

Finite populations induce metastability in evolutionary search

Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network

Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells

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

Identification of clustered microRNAs using an ab initio prediction method

Inference of miRNA targets using evolutionary conservation and pathway analysis

Inference of miRNA targets using evolutionary conservation and pathway analysis

Influenza Escapes Immunity Along Neutral Networks

Investigate the origins of COVID-19

Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8).

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

MicroRNA-221-222 regulate the cell cycle in mast cells

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

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

Neutral evolution of mutational robustness

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

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

Optimizing epochal evolutionary search: population-size independent theory

Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium

Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation

PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information

PhyloGibbs: A Gibbs Sampling Motif Finder that Incorporates Phylogeny

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny

Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics

Quantifying the strength of miRNA-target interactions

Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli

SPA: a probabilistic algorithm for spliced alignment

Scaling Laws in the Functional Content of Genomes

Scaling laws in functional genome content across prokaryotic clades and lifestyles

Scaling laws in the functional content of genomes

Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming

Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome

Statistical Dynamics of the Royal Road Genetic Algorithm

Subpopulations of sensorless bacteria drive fitness in fluctuating environments

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

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

Tead transcription factors differentially regulate cortical development

Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition

The Evolutionary Unfolding of Complexity

The corepressor NCoR1 antagonizes PGC-1α and estrogen-related receptor α in the regulation of skeletal muscle function and oxidative metabolism