Biomedical subjects

Alberto Policriti

Publications and source records attributed to Alberto Policriti.

3 recordsLinked to original sources

PubMed2005

Structured motifs search.

In this paper, we describe an algorithm for the localization of structured models, i.e. sequences of (simple) motifs and distance constraints. It basically combines standard pattern matching procedures with a constraint satisfaction solver, and it has the ability, not present in similar tools, to search for partial matches. A significant feature of our approach, especially in terms of efficiency for the application context, is that the (potentially) exponentially many solutions to the considered problem are represented in compact form as a graph. Moreover, the time and space necessary to build the graph are linear in the number of occurrences of the component patterns.

Algorithms↗

PubMed2003

A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes.

We collaborate in a research program aimed at creating a rigorous framework, experimental infrastructure, and computational environment for understanding, experimenting with, manipulating, and modifying a diverse set of fundamental biological processes at multiple scales and spatio-temporal modes. The novelty of our research is based on an approach that (i) requires coevolution of experimental science and theoretical techniques and (ii) exploits a certain universality in biology guided by a parsimonious model of evolutionary mechanisms operating at the genomic level and manifesting at the proteomic, transcriptomic, phylogenic, and other higher levels. Our current program in "systems biology" endeavors to marry large-scale biological experiments with the tools to ponder and reason about large, complex, and subtle natural systems. To achieve this ambitious goal, ideas and concepts are combined from many different fields: biological experimentation, applied mathematical modeling, computational reasoning schemes, and large-scale numerical and symbolic simulations. From a biological viewpoint, the basic issues are many: (i) understanding common and shared structural motifs among biological processes; (ii) modeling biological noise due to interactions among a small number of key molecules or loss of synchrony; (iii) explaining the robustness of these systems in spite of such noise; and (iv) cataloging multistatic behavior and adaptation exhibited by many biological processes.

Animals↗

PubMed2003

Model building and model checking for biochemical processes.

A central claim of computational systems biology is that, by drawing on mathematical approaches developed in the context of dynamic systems, kinetic analysis, computational theory and logic, it is possible to create powerful simulation, analysis, and reasoning tools for working biologists to decipher existing data, devise new experiments, and ultimately to understand functional properties of genomes, proteomes, cells, organs, and organisms. In this article, a novel computational tool is described that achieves many of the goals of this new discipline. The novelty of this system involves an automaton-based semantics of the temporal evolution of complex biochemical reactions starting from the representation given as a set of differential equations. The related tools also provide ability to qualitatively reason about the systems using a propositional temporal logic that can express an ordered sequence of events succinctly and unambiguously. The implementation of mathematical and computational models in the Simpathica and XSSYS systems is described briefly. Several example applications of these systems to cellular and biochemical processes are presented: the two most prominent are Leibler et al.'s repressilator (an artificial synthesized oscillatory network), and Curto- Voit-Sorribas-Cascante's purine metabolism reaction model.

Biochemical Phenomena↗