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Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
1. In Bayesian Network Regression models, networks are considered the predictors of continuous responses. These models have been successfully used in brain research to identify regions in the brain that are associated with specific human…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network…
In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Recent multi-omic microbiome studies enable integrative analysis of microbes and metabolites, uncovering their associations with various host conditions. Such analyses require multivariate models capable of accounting for the complex…
The analysis of biological networks is characterized by the definition of precise linear constraints used to cumulatively reduce the solution space of the computed states of a multi-omic (for instance metabolic, transcriptomic and…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
The gut microbiome, crucial for human health, presents challenges in analyzing its complex metaomic data due to high dimensionality and sparsity. Traditional methods struggle to capture its intricate relationships. We investigate graph…
The large-scale shape and function of metabolic networks are intriguing topics of systems biology. Such networks are on one hand commonly regarded as modular (i.e. built by a number of relatively independent subsystems), but on the other…
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this…
We revisit the modeling of the diauxic growth of a pure microorganism on two distinct sugars which was first described by Monod. Most available models are deterministic and make the assumption that all cells of the microbial ecosystem…