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Biomedical subjects

Larry Lok

Publications and source records attributed to Larry Lok.

5 recordsLinked to original sources
PubMed2005

Automatic generation of cellular reaction networks with Moleculizer 1.0.

Accurate simulation of intracellular biochemical networks is essential to furthering our understanding of biological system behavior. The number of protein complexes and of chemical interactions among them has traditionally posed significant problems for simulation algorithms. Here we describe an approach to the exact stochastic simulation of biochemical networks that emphasizes the contribution of protein complexes to these systems. This simulation approach starts from a description of monomeric proteins and specifications for binding, unbinding and other reactions. This manageable specification is reasonably intuitive for biologists. Rather than requiring the inclusion of all possible complexes and reactions from the outset, our approach incorporates new complexes and reactions only when needed as the simulation proceeds. As a result, the simulation generates much smaller reaction networks, which can be exported to other simulators for further analysis. We apply this approach to the automatic generation of reaction systems for the study of signal transduction networks.

Algorithms↗
PubMed2002

Software for signaling networks, electronic and cellular.

Cellular signaling networks have many similarities with electronic circuits. Therefore, the tools used to test and analyze electronic circuits can be adapted to analyze cellular signaling processes. Lok describes some of these signaling network analysis tools, their underlying principles, and their limitations.

Feedback, Physiological↗
PubMed2002

Pathfinder and other tools for analyzing signal transduction networks.

Many electronic design tools are, at their core, tools for analyzing interacting networks of components in which there is a definite causal sense of direction in each interaction: outputs affect inputs, but not vice versa. Simplifying or restricting a network of protein interactions so that this kind of directedness holds makes the same category of software tools applicable. In signal transduction cascades the direction is usually given by "kinase phosphorylates substrate." This paper examines a few kinds of directed network analysis tools in the context of signal transduction.

Algorithms↗