Flux balance analysis: A geometric perspective

Flux balance analysis: a geometric perspective.

Advances in the field of bioinformatics have led to reconstruction of genome-scale networks for a number of key organisms. The application of physicochemical constraints to these stoichiometric networks allows researchers, through methods such as flux balance analysis, to highlight key sets of reactions necessary to achieve particular objectives. The key benefits of constraint-based analysis li...

Advances in flux balance analysis.

Biology is going through a paradigm shift from reductionist to holistic, systems-based approaches. The complete genome sequence for a number of organisms is available and the analysis of genome sequence data is proving very useful. Thus, genome sequencing projects and bioinformatic analyses are leading to a complete 'parts catalog' of the molecular components in many organisms. The next challen...

Constrained Allocation Flux Balance Analysis

New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genom...

Birkhoff's Theorem from a geometric perspective: A simple example

‎From Hilbert's theorem of zeroes‎, ‎and from Noether's ideal theory‎, ‎Birkhoff derived certain algebraic concepts (as explained by Tholen) that have a dual significance in general toposes‎, ‎similar to their role in the original examples of algebraic geometry‎. ‎I will describe a simple example that illustrates some of the aspects of this relationship‎. The dualization from algebra to geometr...

Multivariate Statistical Analysis: a Geometric Perspective