Balwierz, Piotr J, Carninci, Piero, Daub, Carsten O, Kawai, Jun, Hayashizaki, Yoshihide, Van Belle, Werner, ...
Abstract With the advent of ultra high-throughput sequencing technologies, increasingly researchers are turning to deep sequencing for gene expression studies. Here we present a set of rigorous...
Severin, Jessica, Waterhouse, Andrew M, Kawaji, Hideya, Lassmann, Timo, Van Nimwegen, Erik, Balwierz, Piotr J, ...
Abstract EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new...
Taddei, Angela, Van Houwe, Griet, Nagai, Shigeki, Erb, Ionas, Van Nimwegen, Erik, Gasser, Susan M.
Budding yeast telomeres and cryptic mating-type loci are enriched at the nuclear envelope, forming foci that sequester silent information regulators (SIR factors), much as heterochromatic...
The evolution of domain-content in bacterial genomes (2008)
Molina, Nacho, Van Nimwegen, Erik
Abstract Background Across all sequenced bacterial genomes, the number of domains n c in different functional categories c scales as a power-law in the total number of domains n , i.e. n c ∝ n α c...
Chern, Tzu-Ming, Paul, Nicodeme, Van Nimwegen, Erik, Zavolan, Mihaela
High-throughput sequencing studies revealed that the majority of human and mouse multi-exon genes have multiple splice forms. High-density oligonucleotide array-based measurements have further...
Universal patterns of purifying selection at noncoding positions in bacteria (2008)
Molina, Nacho, Van Nimwegen, Erik
To investigate the dependence of the number of regulatory sites per intergenic region on genome size, we developed a new method for detecting purifying selection at noncoding positions in clades of...
Finding regulatory elements and regulatory motifs: a general probabilistic framework (2007)
Abstract Over the last two decades a large number of algorithms has been developed for regulatory motif finding. Here we show how many of these algorithms, especially those that model binding...
Correction: Inference of miRNA targets using evolutionary conservation and pathway analysis (2007)
Gaidatzis, Dimos, Van Nimwegen, Erik, Hausser, Jean, Zavolan, Mihaela
No abstract available.
Inference of miRNA targets using evolutionary conservation and pathway analysis (2007)
Gaidatzis, Dimos, Van Nimwegen, Erik, Hausser, Jean, Zavolan, Mihaela
Abstract Background MicroRNAs have emerged as important regulatory genes in a variety of cellular processes and, in recent years, hundreds of such genes have been discovered in animals. In contrast,...
SwissRegulon: a database of genome-wide annotations of regulatory sites (2007)
Pachkov, Mikhail, Erb, Ionas, Molina, Nacho, Van Nimwegen, Erik
SwissRegulon (http://www.swissregulon.unibas.ch) is a database containing genome-wide annotations of regulatory sites in the intergenic regions of genomes. The regulatory site annotations are...
Identification of clustered microRNAs using an ab initioprediction method (2005)
Sewer, Alain, Paul, Nicodème, Landgraf, Pablo, Aravin, Alexei, Pfeffer, Sébastien, Brownstein, Michael J, ...
Abstract Background MicroRNAs (miRNAs) are endogenous 21 to 23-nucleotide RNA molecules that regulate protein-coding gene expression in plants and animals via the RNA interference pathway. Hundreds...
Scaling laws in the functional content of genomes: Fundamental constants of evolution? (2004)
With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In...
Scaling laws in the functional content of genomes (2003)
With the number of sequenced genomes now over one hundred, and the availability of rough functional annotations for a substantial proportion of their genes, it has become possible to study the...
Yang, Edward, Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Schroeder, Mark, Magnasco, Marcelo, ...
Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover...
A probabilistic method to detect regulatory modules (2003)
Sinha, Saurabh, Van Nimwegen, Erik, Siggia, Eric D.
Motivation: The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity. Results: We develop a computational method...
Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Siggia, Eric D.
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that...
Metastable Evolutionary Dynamics: Crossing Fitness Barriers or Escaping via Neutral Paths? (1999)
Van Nimwegen, Erik, Crutchfield, James P.
We analytically study the dynamics of evolving populations that exhibit metastability on the level of phenotype or fitness. In constant selective environments, such metastable behavior is caused by...
Neutral Evolution of Mutational Robustness (1999)
Van Nimwegen, Erik, Crutchfield, James P., Huynen, Martijn
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population's limit distribution on the neutral network is solely...
The Evolutionary Unfolding of Complexity (1999)
Crutchfield, James P., Van Nimwegen, Erik
We analyze the population dynamics of a broad class of fitness functions that exhibit epochal evolution---a dynamical behavior, commonly observed in both natural and artificial evolutionary...
Optimizing Epochal Evolutionary Search: Population-Size Independent Theory (1998)
Van Nimwegen, Erik, Crutchfield, James P.
Epochal dynamics, in which long periods of stasis in population fitness are punctuated by sudden innovations, is a common behavior in both natural and artificial evolutionary processes. We use a...
Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory (1998)
Van Nimwegen, Erik, Crutchfield, James P.
Epochal dynamics, in which long periods of stasis in an evolving population are punctuated by a sudden burst of change, is a common behavior in both natural and artificial evolutionary processes. We...
Neutral evolution of mutational robustness
Van Nimwegen, Erik, Crutchfield, James P., Huynen, Martijn
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population’s limit distribution on the neutral network is solely...
Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Siggia, Eric D.
Genome-wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene-by-gene basis that need to be clustered into regulons. Using the assumption that...
Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome
Zavolan, Mihaela, Van Nimwegen, Erik, Gaasterland, Terry
We mapped the collection of The Institute of Physical and Chemical Research (Japan) (RIKEN) 21,076 full-length mouse cDNA clone sequences and the mouse RefSeq sequences to the recently completed...
Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence Attributes
Yang, Edward, Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Schroeder, Mark, Magnasco, Marcelo, ...
Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover...
Speirs, Christina, Van Nimwegen, Erik, Bolton, Diane, Zavolan, Mihaela, Duvall, Melody, Angleman, Sara, ...
Human immunodeficiency virus (HIV) causes complex metabolic changes in infected CD4+ T cells that lead to cell cycle arrest and cell death by necrosis. To study the viral functions responsible for...
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
Siddharthan, Rahul, Siggia, Eric D, Van Nimwegen, Erik
A central problem in the bioinformatics of gene regulation is to find the binding sites for regulatory proteins. One of the most promising approaches toward identifying these short and fuzzy sequence...
Identification of clustered microRNAs using an ab initio prediction method
Sewer, Alain, Paul, Nicodème, Landgraf, Pablo, Aravin, Alexei, Pfeffer, Sébastien, Brownstein, Michael J, ...
SPA: A Probabilistic Algorithm for Spliced Alignment
Van Nimwegen, Erik, Paul, Nicodeme, Sheridan, Robert, Zavolan, Mihaela
Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of...
A Simple Physical Model Predicts Small Exon Length Variations
Chern, Tzu-Ming, Van Nimwegen, Erik, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, ...
One of the most common splice variations are small exon length variations caused by the use of alternative donor or acceptor splice sites that are in very close proximity on the pre-mRNA. Among...
Neutral evolution of mutational robustness
Van Nimwegen, Erik, Crutchfield, James P., Huynen, Martijn
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population’s limit distribution on the neutral network is solely...
Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Siggia, Eric D.
Genome-wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene-by-gene basis that need to be clustered into regulons. Using the assumption that...
Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome
Zavolan, Mihaela, Van Nimwegen, Erik, Gaasterland, Terry
We mapped the collection of The Institute of Physical and Chemical Research (Japan) (RIKEN) 21,076 full-length mouse cDNA clone sequences and the mouse RefSeq sequences to the recently completed...
Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence Attributes
Yang, Edward, Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Schroeder, Mark, Magnasco, Marcelo, ...
Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover...
Speirs, Christina, Van Nimwegen, Erik, Bolton, Diane, Zavolan, Mihaela, Duvall, Melody, Angleman, Sara, ...
Human immunodeficiency virus (HIV) causes complex metabolic changes in infected CD4+ T cells that lead to cell cycle arrest and cell death by necrosis. To study the viral functions responsible for...
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
Siddharthan, Rahul, Siggia, Eric D, Van Nimwegen, Erik
A central problem in the bioinformatics of gene regulation is to find the binding sites for regulatory proteins. One of the most promising approaches toward identifying these short and fuzzy sequence...
Identification of clustered microRNAs using an ab initio prediction method
Sewer, Alain, Paul, Nicodème, Landgraf, Pablo, Aravin, Alexei, Pfeffer, Sébastien, Brownstein, Michael J, ...
SPA: A Probabilistic Algorithm for Spliced Alignment
Van Nimwegen, Erik, Paul, Nicodeme, Sheridan, Robert, Zavolan, Mihaela
Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of...
A Simple Physical Model Predicts Small Exon Length Variations
Chern, Tzu-Ming, Van Nimwegen, Erik, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, ...
One of the most common splice variations are small exon length variations caused by the use of alternative donor or acceptor splice sites that are in very close proximity on the pre-mRNA. Among...
SwissRegulon: a database of genome-wide annotations of regulatory sites
Pachkov, Mikhail, Erb, Ionas, Molina, Nacho, Van Nimwegen, Erik
SwissRegulon () is a database containing genome-wide annotations of regulatory sites in the intergenic regions of genomes. The regulatory site annotations are produced using a number of recently...
Inference of miRNA targets using evolutionary conservation and pathway analysis
Gaidatzis, Dimos, Van Nimwegen, Erik, Hausser, Jean, Zavolan, Mihaela
Inference of miRNA targets using evolutionary conservation and pathway analysis
Gaidatzis, Dimos, Van Nimwegen, Erik, Hausser, Jean, Zavolan, Mihaela
Finding regulatory elements and regulatory motifs: a general probabilistic framework
Over the last two decades a large number of algorithms has been developed for regulatory motif finding. Here we show how many of these algorithms, especially those that model binding specificities of...
Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method
Burger, Lukas, Van Nimwegen, Erik
Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian...
Universal patterns of purifying selection at noncoding positions in bacteria
Molina, Nacho, Van Nimwegen, Erik
To investigate the dependence of the number of regulatory sites per intergenic region on genome size, we developed a new method for detecting purifying selection at noncoding positions in clades of...
Schlecht, Ulrich, Erb, Ionas, Demougin, Philippe, Robine, Nicolas, Borde, Valérie, Van Nimwegen, Erik, ...
The autonomously replicating sequence binding factor 1 (Abf1) was initially identified as an essential DNA replication factor and later shown to be a component of the regulatory network controlling...
Chern, Tzu-Ming, Paul, Nicodeme, Van Nimwegen, Erik, Zavolan, Mihaela
High-throughput sequencing studies revealed that the majority of human and mouse multi-exon genes have multiple splice forms. High-density oligonucleotide array-based measurements have further...
Severin, Jessica, Waterhouse, Andrew M, Kawaji, Hideya, Lassmann, Timo, Van Nimwegen, Erik, Balwierz, Piotr J, ...
EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets.
Balwierz, Piotr J, Carninci, Piero, Daub, Carsten O, Kawai, Jun, Hayashizaki, Yoshihide, Van Belle, Werner, ...
A set of methods is presented for normalization, quantification of noise and co-expression analysis for gene expression studies using deep sequencing.
Taddei, Angela, Van Houwe, Griet, Nagai, Shigeki, Erb, Ionas, Van Nimwegen, Erik, Gasser, Susan M.
Budding yeast telomeres and cryptic mating-type loci are enriched at the nuclear envelope, forming foci that sequester silent information regulators (SIR factors), much as heterochromatic...