Related papers: Toolbox model of evolution of prokaryotic metaboli…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…
Increased biological complexity is generally associated with the addition of new genetic information, which must be integrated into the existing regulatory network that operates within the cell. General arguments on network control, as well…
Networks exhibiting "accelerating" growth have total link numbers growing faster than linearly with network size and can exhibit transitions from stationary to nonstationary statistics and from random to scale-free to regular statistics at…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Much current network analysis is predicated on the assumption that important biological networks will either possess scale free or exponential statistics which are independent of network size allowing unconstrained network growth over time.…
Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
We propose and study a class-expansion/innovation/loss model of genome evolution taking into account biological roles of genes and their constituent domains. In our model numbers of genes in different functional categories are coupled to…
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. However, analogous equilibrium models do not perform as well in…
The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
Metabolic scaling is one of the most important patterns in biology. Theory explaining the 3/4-power size-scaling of biological metabolic rate does not predict the non-linear scaling observed for smaller life forms. Here we present a new…
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Genome length varies widely among organisms, from compact genomes of prokaryotes to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome…
Data on the number of Open Reading Frames (ORFs) coded by genomes from the 3 domains of Life show some notable general features including essential differences between the Prokaryotes and Eukaryotes, with the number of ORFs growing linearly…
Even closely related prokaryotes show an astounding diversity in their ability to grow in different nutritional environments. Mechanistically, this diversity arises predominantly through horizontal gene transfer, the exchange of DNA between…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…