Related papers: Constrained Allocation Flux Balance Analysis
This paper introduces a new optimisation algorithm, called Adaptive Bacterial Colony Optimisation (ABCO), modelled after the foraging behaviour of E. coli bacteria. The algorithm follows three stages--explore, exploit and reproduce--and is…
We show, in this report, how a population balance model differential equation describing batch crystal growth from solution can be solved in closed form for the case of diffusion limited growth with and without modeling the effects of…
The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular…
Quantitative Fitness Analysis (QFA) is a high-throughput experimental and computational methodology for measuring the growth of microbial populations. QFA screens can be used to compare the health of cell populations with and without a…
Theoretical analyses of evolution strategies are indispensable for gaining a deep understanding of their inner workings. For constrained problems, rather simple problems are of interest in the current research. This work presents a…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large…
Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells, is, however, a wide open question. We present a…
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…
In distributed computing frameworks like MapReduce, Spark, and Dyrad, a coflow is a set of flows transferring data between two stages of a job. The job cannot start its next stage unless all flows in the coflow finish. To improve the…
When data on treatment assignment, outcomes, and covariates from a randomized trial are available, a question of interest is to what extent covariates can be used to optimize treatment decisions. Statistical hypothesis testing of…
In model-based clustering and classification, the cluster-weighted model constitutes a convenient approach when the random vector of interest constitutes a response variable Y and a set p of explanatory variables X. However, its…
Despite growth being fundamental to all aspects of cell biology, we do not yet know its organizing principles in eukaryotic cells. Classic models derived from the bacteria E. coli posit that protein-synthesis rates are set by mass-action…
One of the major characteristics of living organisms is metabolic rate, which is the amount of energy produced per unit of time. When the mass of organisms increases, the metabolic rate also increases (usually as a power function of mass),…
Production of energy (metabolism) and its distribution is vital for living organisms, both at individual level - between different functions of an organism, as well as between species of communities at different organizational levels,…
High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…
Cancer cells are often seen to prefer glycolytic metabolism over oxidative phosphorylation even in the presence of oxygen-a phenomenon termed the Warburg effect. Despite significant strides in the decades since its discovery, a clear basis…
Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux…
We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications typically there is insufficient history to compute a sample covariance matrix (SCM) for a large number of alphas. To…