745 research outputs found
Identification of control targets in Boolean molecular network models via computational algebra
Motivation: Many problems in biomedicine and other areas of the life sciences
can be characterized as control problems, with the goal of finding strategies
to change a disease or otherwise undesirable state of a biological system into
another, more desirable, state through an intervention, such as a drug or other
therapeutic treatment. The identification of such strategies is typically based
on a mathematical model of the process to be altered through targeted control
inputs. This paper focuses on processes at the molecular level that determine
the state of an individual cell, involving signaling or gene regulation. The
mathematical model type considered is that of Boolean networks. The potential
control targets can be represented by a set of nodes and edges that can be
manipulated to produce a desired effect on the system. Experimentally, node
manipulation requires technology to completely repress or fully activate a
particular gene product while edge manipulations only require a drug that
inactivates the interaction between two gene products. Results: This paper
presents a method for the identification of potential intervention targets in
Boolean molecular network models using algebraic techniques. The approach
exploits an algebraic representation of Boolean networks to encode the control
candidates in the network wiring diagram as the solutions of a system of
polynomials equations, and then uses computational algebra techniques to find
such controllers. The control methods in this paper are validated through the
identification of combinatorial interventions in the signaling pathways of
previously reported control targets in two well studied systems, a p53-mdm2
network and a blood T cell lymphocyte granular leukemia survival signaling
network.Comment: 12 pages, 4 figures, 2 table
Reconstruction of biological networks by supervised machine learning approaches
We review a recent trend in computational systems biology which aims at using
pattern recognition algorithms to infer the structure of large-scale biological
networks from heterogeneous genomic data. We present several strategies that
have been proposed and that lead to different pattern recognition problems and
algorithms. The strenght of these approaches is illustrated on the
reconstruction of metabolic, protein-protein and regulatory networks of model
organisms. In all cases, state-of-the-art performance is reported
Generation of genetic networks from a small number of gene expression patterns under the Boolean network model.
There are lots of work for inferring genetic network architectures from state transition tables which correspond to time series of gene expression patterns, using the Boolean network model. Results of those computational experiments suggested that a small number of state transition (INPUT/OUTPUT) pairs are sufficient in order to infer the original Boolean network correctly. Tatsuya AKUTSU, Satoru MIYANO and Satoru KUHARA gave a mathematical proof for this. So there is possibility to devise an algorithm to generate all consistent genetic networks from a small number of gene expression patterns under the Boolean network model
- …