Related papers: Bridging physiological and evolutionary time scale…
Gene Regulatory Networks (GRNs) consisting of combinations of transcription factors (TFs) and their cis promoters are assumed to be sufficient to direct the development of organisms. Mutations in GRNs are assumed to be the primary drivers…
Systems biology is an emerging interdisciplinary area of research that focuses on study of complex interactions in a biological system, such as gene regulatory networks. The discovery of gene regulatory networks leads to a wide range of…
Biological networks exhibit intricate architectures deemed to be crucial for their functionality. In particular, gene regulatory networks, which play a key role in information processing in the cell, display non-trivial architectural…
The integration of photovoltaic (PV) systems into greenhouses not only optimizes land use but also enhances sustainable agricultural practices by enabling dual benefits of food production and renewable energy generation. However, accurate…
Gene regulatory networks (GRNs) represent the causal relationships between transcription factors (TFs) and target genes in single-cell RNA sequencing (scRNA-seq) data. Understanding these networks is crucial for uncovering disease…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Here, conservation…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
Do ecosystems primarily reflect evolutionary history or current environment? Predicting land-atmosphere exchange hinges on this unresolved question. Plant traits adapt to particular environments over evolutionary timescales, yet their…
In this work, we study a class of hybrid dynamical systems called hybrid gene regulatory networks (HGRNs) which was proposed to model gene regulatory networks. In HGRNs, there exist well-behaved trajectories that reach a fixed point or…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Gene regulation is a dynamic process that underlies all aspects of human development, disease response, and other key biological processes. The reconstruction of temporal gene regulatory networks has conventionally relied on regression…
Pollinators play a crucial role for plant reproduction, either in natural ecosystem or in human-modified landscape. Global change drivers,including climate change or land use modifications, can alter the plant-pollinator interactions. To…
Accurately reconstructing Gene Regulatory Networks (GRNs) is crucial for understanding gene functions and disease mechanisms. Single-cell RNA sequencing (scRNA-seq) technology provides vast data for computational GRN reconstruction. Since…
Complex biological functions are carried out by the interaction of genes and proteins. Uncovering the gene regulation network behind a function is one of the central themes in biology. Typically, it involves extensive experiments of…
Drought stress is a major threat to global crop productivity, making its early and precise detection essential for sustainable agricultural management. Traditional approaches, though useful, are often time-consuming and labor-intensive,…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…