Erik van Nimwegen
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Computational biologist
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Biology Computer Science
Erik van Nimwegen's Degrees
- PhD Computational Biology University of Basel
- Masters Bioinformatics University of Basel
- Bachelors Biology University of Basel
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Why Is Erik van Nimwegen Influential?
(Suggest an Edit or Addition)According to Wikipedia, Erik van Nimwegen is a Dutch computational biologist and Professor at the Biozentrum of the University of Basel, Switzerland. Life Erik van Nimwegen studied theoretical physics at the University of Amsterdam. He performed his PhD studies at the Santa Fe Institute in Santa Fe New Mexico, receiving his PhD from the Faculty of Biology at Utrecht University in 1999. This was followed by a year of post-doc studies at the SFI, and three years as a fellow at the Center of Studies in Physics and Biology at the Rockefeller University, New York. Since 2003 he is Professor of Computational Biology at the Biozentrum of the University of Basel, and group leader at the Swiss Institute of Bioinformatics since 2004.
Erik van Nimwegen's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- The Transcriptional Landscape of the Mammalian Genome (2005) (3394)
- A promoter-level mammalian expression atlas (2014) (1664)
- Neutral evolution of mutational robustness. (1999) (596)
- An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (2010) (592)
- Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. (2003) (546)
- The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line (2009) (441)
- Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming. (2013) (408)
- Inference of miRNA targets using evolutionary conservation and pathway analysis (2007) (362)
- Scaling Laws in the Functional Content of Genomes (2003) (337)
- Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads (2014) (314)
- PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny (2005) (311)
- Identification of clustered microRNAs using an ab initio prediction method (2005) (268)
- Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity (2012) (260)
- ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs (2014) (239)
- Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop (2012) (238)
- A probabilistic method to detect regulatory modules (2003) (234)
- The frequency distribution of gene family sizes in complete genomes. (1998) (214)
- Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments (2010) (206)
- Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method (2008) (189)
- An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (2010) (165)
- Statistical Dynamics of the Royal Road Genetic Algorithm (1999) (164)
- SwissRegulon: a database of genome-wide annotations of regulatory sites (2006) (154)
- Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data (2009) (151)
- A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets (2013) (149)
- Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells (2014) (145)
- Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8) (2013) (142)
- SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates (2012) (142)
- The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion. (2009) (134)
- Metastable evolutionary dynamics: Crossing fitness barriers or escaping via neutral paths? (1999) (132)
- Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial–mesenchymal transition (2014) (125)
- Finite populations induce metastability in evolutionary search (1997) (121)
- Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting (2013) (121)
- MicroRNA-221–222 Regulate the Cell Cycle in Mast Cells1 (2009) (99)
- Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium (2013) (98)
- Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software (2018) (93)
- Investigate the origins of COVID-19 (2021) (88)
- Expression noise facilitates the evolution of gene regulation (2014) (85)
- MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences (2012) (84)
- A Simple Physical Model Predicts Small Exon Length Variations (2006) (79)
- Computational analysis of small RNA cloning data. (2008) (78)
- Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. (2002) (78)
- The Corepressor NCoR1 Antagonizes PGC-1α and Estrogen-Related Receptor α in the Regulation of Skeletal Muscle Function and Oxidative Metabolism (2012) (77)
- Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics (2002) (72)
- FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions (2009) (71)
- Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli (2013) (66)
- Universal patterns of purifying selection at noncoding positions in bacteria. (2007) (65)
- Scaling laws in functional genome content across prokaryotic clades and lifestyles. (2009) (64)
- Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory (1998) (63)
- Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation (2010) (61)
- Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels (2012) (57)
- Timescales and bottlenecks in miRNA-dependent gene regulation (2013) (55)
- Influenza Escapes Immunity Along Neutral Networks (2006) (52)
- Finding regulatory elements and regulatory motifs: a general probabilistic framework (2007) (48)
- The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015) (47)
- Dynamics of one-pass germinal center models: Implications for affinity maturation (2000) (46)
- The Evolutionary Unfolding of Complexity (1999) (45)
- Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC (2018) (43)
- A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development (2015) (40)
- Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation. (2014) (39)
- 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. (2008) (38)
- Transcriptional Network Analysis in Muscle Reveals AP-1 as a Partner of PGC-1α in the Regulation of the Hypoxic Gene Program (2014) (38)
- Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers (2013) (37)
- The evolution of domain-content in bacterial genomes (2008) (36)
- SPA: A Probabilistic Algorithm for Spliced Alignment (2006) (36)
- Correlating Gene Expression Variation with cis-Regulatory Polymorphism in Saccharomyces cerevisiae (2010) (35)
- Bayesian inference of gene expression states from single-cell RNA-seq data (2021) (35)
- Co-expression of FBN1 with mesenchyme-specific genes in mouse cell lines: implications for phenotypic variability in Marfan syndrome (2010) (35)
- Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism (2019) (34)
- Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways (2014) (33)
- Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine (2014) (33)
- Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters (2011) (32)
- The types and prevalence of alternative splice forms. (2006) (32)
- Tead transcription factors differentially regulate cortical development (2020) (29)
- Transformation fingerprint: induced STAT3-C, v-Src and Ha-Ras cause small initial changes but similar established profiles in mRNA (2004) (27)
- Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8) (2013) (25)
- An epigenetic profile of early T‐cell development from multipotent progenitors to committed T‐cell descendants (2014) (23)
- Inference of miRNA targets using evolutionary conservation and pathway analysis (2007) (23)
- Quantifying the strength of miRNA-target interactions. (2015) (22)
- Statistical Features of Yeast ’ s Transcriptional Regulatory Code (2006) (21)
- Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species (2021) (21)
- The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells. (2016) (20)
- The statistical dynamics of epochal evolution (1999) (20)
- Single‐cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction (2018) (20)
- Epidemiology. Influenza escapes immunity along neutral networks. (2006) (20)
- Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network (2021) (18)
- Analysis of Human Immunodeficiency Virus Cytopathicity by Using a New Method for Quantitating Viral Dynamics in Cell Culture (2005) (17)
- Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion (2014) (16)
- Finding regulatory elements and regulatory motifs: a general probabilistic framework (2007) (15)
- Whole genome phylogenies reflect long-tailed distributions of recombination rates in many bacterial species (2019) (15)
- Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? (2016) (14)
- PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information (2004) (14)
- Detecting regulatory sites using PhyloGibbs. (2007) (13)
- Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support (2014) (13)
- Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria (2019) (12)
- Subpopulations of sensorless bacteria drive fitness in fluctuating environments (2020) (12)
- Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements (2022) (10)
- Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors (2016) (10)
- Corrigendum: DNA-binding factors shape the mouse methylome at distal regulatory regions (2012) (10)
- Bayesian inference of the gene expression states of single cells from scRNA-seq data (2019) (10)
- Computational Analysis of Full-length cDNAs Reveals Frequent Coupling Between Transcriptional and Splicing Programs (2008) (9)
- Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium (2013) (8)
- No evidence that synonymous mutations in yeast genes are mostly deleterious (2022) (7)
- Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs (2018) (6)
- Scaling laws in the functional content of genomes. (2003) (5)
- Noise propagation shapes condition-dependent gene expression noise in Escherichia coli (2019) (4)
- ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data. (2015) (4)
- Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? (2016) (4)
- Tracking single-cell gene regulation in dynamically controlled environments using an integrated microfluidic and computational setup (2016) (4)
- Power Laws in the Size Distribution of Gene Families in Complete Genomes: Biological Interpretations (1997) (3)
- Growth rate controls the sensitivity of gene regulatory circuits (2022) (3)
- Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli (2013) (3)
- The ISMARA client (2016) (3)
- Crunch: Completely Automated Analysis of ChIP-seq Data (2016) (3)
- Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (2021) (2)
- Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis (2022) (2)
- Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99]. (2016) (2)
- Frequent co-regulation of splicing and polyadenylation by RNA-binding proteins inferred with MAPP (2022) (2)
- Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs (2023) (2)
- Inferring intrinsic and extrinsic noise from a dual fluorescent reporter (2016) (2)
- Authors' Reply (2006) (2)
- of regulatory motifs ISMARA : automated modeling of genomic signals as a democracy Material Supplemental (2014) (2)
- Ewing sarcoma breakpoint region 1 prevents transcription-associated genome instability (2015) (2)
- ISMARA: Completely automated inference of gene regulatory networks from high-throughput data (2017) (2)
- Effective bet-hedging through growth rate dependent stability (2023) (1)
- Coupling phenotype stability to growth rate overcomes limitations of bet-hedging strategies (2022) (1)
- Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets (2015) (1)
- Influenza Escapes Immunity Along Neutral Networks (2006) (1)
- Supporting Material Response to : Alternative splicing at NAGNAG acceptors : Simply noise or noise and more ? (2006) (1)
- PLOS Computational Biology 2017 Reviewer and Editorial Board Thank You (2018) (1)
- The Evolutionary Unfolding of Complexity James P Crutch (2001) (1)
- O47 PEGYLATED INTERFERON-ALPHA INDUCES SUSTAINED TRANSCRIPTIONAL RESPONSE IN LIVER INFILTRATING IMMUNE CELLS BUT NOT IN HEPATOCYTES IN THE LIVER OF PATIENTS WITH CHRONIC HEPATITIS C (2014) (0)
- Inferring intrinsic and extrinsic noise from a dual fluorescent reporter (2016) (0)
- Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements (2022) (0)
- The ISMARA client [ version 1 ; peer review : 2 approved ] (2020) (0)
- Supporting Information : Universal patterns of purifying selection at non-coding positions in bacteria (2007) (0)
- Power-laws in the size distribution of genefamilies in complete genomes : biologicalinterpretationsMartijn (1997) (0)
- Decision letter: Predicting bacterial promoter function and evolution from random sequences (2021) (0)
- Single-cell data on lac operon induction by lactose in E. coli (2020) (0)
- A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks (2006) (0)
- Report on the ESF exploratory workshop EW06-069 ”Computational approaches to the role of epigenetic marks in transcription regulation” (2008) (0)
- Author response: Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species (2021) (0)
- Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (2022) (0)
- The protooncogene Ski regulates the neuron-glia switch during development of the mammalian cerebral cortex (2022) (0)
- Tead transcription factors differentially regulate cortical development (2020) (0)
- 105PLONG-TERM EFFECTS OF EARLY PREGNANCY ON THE GENE EXPRESSION AND PROPERTIES OF MAMMARY EPITHELIAL CELL SUBPOPULATIONS IN MICE (2013) (0)
- Preclinical (epi)genomics – identifying safety biomarkers for the prediction of non-genotoxic carcinogenesis (2013) (0)
- Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC (2017) (0)
- How do prokaryotic genomes evolve (2017) (0)
- Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software (2018) (0)
- Discovery of global regulators of 3′ untranslated region processing in cancers with KAPAC (2017) (0)
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