相关论文: Analysis of biochemical mechanisms provoking diffe…
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
Transcription factor combinations determine gene locus activity and thereby cell identity. However, the precise link between concentrations of such activating transcription factors and target-gene activity is ambiguous. Here we investigate…
Biological systems are majorly dependent on their property of bistability in order to exhibit nongenetic heterogeneity in terms of cellular morphology and physiology. Spatial patterns of phenotypically heterogeneous cells, arising due to…
Genes are frequently regulated in complex manners, necessitating modelling approaches which go beyond simple (linear) gene-to-gene interactions and address the modularity of cis-regulatory regions and alternate transcription initiation…
We examine a spatially discrete reaction diffusion model based on the interactions that create a periodic pattern in the Drosophila eye imaginal disc. This model is capable of generating a regular hexagonal pattern of gene expression behind…
In early development, regulation of transcription results in precisely positioned and highly reproducible expression patterns that specify cellular identities. How transcription, a fundamentally noisy molecular process, is regulated to…
The concentration gradient of the Bicoid morphogen, which is established during the early stages of a Drosophila melanogaster embryonic development, determines the differential spatial patterns of gene expression and subsequent cell fate…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular,…
Spatiotemporal gene expression data of the human brain offer insights on the spa- tial and temporal patterns of gene regulation during brain development. Most existing methods for analyzing these data consider spatial and temporal profiles…
We explore the joint effect of the intrinsic noise and time delay on the spatial pattern formation within a multi-scale mobile lattice model of the epithelium. The protein fluctuations are driven by transcription/translation processes 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"…
We investigate a mechanism for the robust identification of the center of a developing biological system. We assume the existence of two morphogen gradients, an activator emanating from the anterior, and a co-repressor from the posterior.…
Since its introduction in 1952, Turing's (pre-)pattern theory ("the chemical basis of morphogenesis") has been widely applied to a number of areas in developmental biology. The related pattern formation models normally comprise a system of…
Hyperspectral image classification (HSIC) has gained significant attention because of its potential in analyzing high-dimensional data with rich spectral and spatial information. In this work, we propose the Differential Spatial-Spectral…
Objective: The reservoir of human immunodeficiency virus (HIV) latently infected cells is the major obstacle for eradication of acquired immunodeficiency syndrome (AIDS). Due to the noisy environment and multiple influencing factors in the…
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
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…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…