Related papers: An Enrichment Method for Obtaining Biologically Si…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…
We are interested in the comparison of transcript boundaries from cells which originated in different environments. The goal is to assess whether this phenomenon, called differential splicing, is used to modify the transcription of the…
Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying…
Genome-wide gene expression profiles, as measured with microarrays or RNA-Seq experiments, have revolutionized biological and biomedical research by providing a quantitative measure of the entire mRNA transcriptome. Typically, researchers…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in…
Epigenetic modifications to histones may promote either activation or repression of the transcription of nearby genes. Recent experimental studies show that the promoters of many lineage-control genes in stem cells have "bivalent domains"…
Gene regulation in higher eukaryotes involves a complex interplay between the gene proximal promoter and distal genomic elements (such as enhancers) which work in concert to drive spatio-temporal expression. The experimental…
Understanding the morphological changes of primary neuronal cells induced by chemical compounds is essential for drug discovery. Using the data from a single high-throughput imaging assay, a classification model for predicting the…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…
The emergence of acquired drug resistance in cancer represents a major barrier to treatment success. While research has traditionally focused on genetic sources of resistance, recent findings suggest that cancer cells can acquire transient…
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
A prespecified set of genes may be enriched, to varying degrees, for genes that have altered expression levels relative to two or more states of a cell. Knowing the enrichment of gene sets defined by functional categories, such as gene…
Even under constant external conditions, the expression levels of genes fluctuate. Much emphasis has been placed on the components of this noise that are due to randomness in transcription and translation; here we analyze the role of noise…
Life science is entering a new era of petabyte-level sequencing data. Converting such big data to biological insights represents a huge challenge for computational analysis. To this end, we developed DeepMetabolism, a biology-guided deep…
Phenotypic drug discovery has attracted widespread attention because of its potential to identify bioactive molecules. Transcriptomic profiling provides a comprehensive reflection of phenotypic changes in cellular responses to external…