Translating time-course gene expression profiles into semi-algebraic hybrid automata via dimensionality reduction

Alberto Casagrande, Kevin Casey, Rachele Falchi, Carla Piazza, Benedetto Rupert, Giannina Vizzotto, Bhubaneswar Mishra

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Biotechnological innovations which sample gene expressions allow to measure the gene expression levels of a biological system with varying degree of accuracy, cost and speed. By repeating the measurement steps at different sampling rates, one can both infer relations among the genes and define a dynamic model of the underlying biological system. When a very large number of genes and measurements are involved, they raise several difficult algorithmic questions, as accurate model-building, checking and inference tasks. Semi-algebraic hybrid automata were proposed as a modeling formalism for biological systems (see, e.g., [17,6]), and demonstrated their abilities to handle complex biochemical pathways. This paper proposes an automatic procedure to build semi-algebraic hybrid automata from gene-expression profiles. In order to reduce the size of the resulting automata and to minimize their analysis computational complexity, our approach exploits various dimensionality reduction techniques. The paper concludes with several experimental results about peach fruit.

Original languageEnglish (US)
Title of host publicationAlgebraic Biology - Second International Conference, AB 2007, Proceedings
Pages51-65
Number of pages15
Volume4545 LNCS
StatePublished - 2007
Event2nd International Conference on Algebraic Biology, AB 2007 - Castle of Hagenberg, Austria
Duration: Jul 2 2007Jul 4 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4545 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other2nd International Conference on Algebraic Biology, AB 2007
CountryAustria
CityCastle of Hagenberg
Period7/2/077/4/07

Fingerprint

Hybrid Automata
Gene Expression Profile
Dimensionality Reduction
Biological systems
Transcriptome
Biological Systems
Gene expression
Gene Expression
Biological Models
Systems Analysis
Genes
Gene
Fruit
Fruits
Costs and Cost Analysis
Automata
Dynamic models
Computational complexity
Pathway
Dynamic Model

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Casagrande, A., Casey, K., Falchi, R., Piazza, C., Rupert, B., Vizzotto, G., & Mishra, B. (2007). Translating time-course gene expression profiles into semi-algebraic hybrid automata via dimensionality reduction. In Algebraic Biology - Second International Conference, AB 2007, Proceedings (Vol. 4545 LNCS, pp. 51-65). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4545 LNCS).

Translating time-course gene expression profiles into semi-algebraic hybrid automata via dimensionality reduction. / Casagrande, Alberto; Casey, Kevin; Falchi, Rachele; Piazza, Carla; Rupert, Benedetto; Vizzotto, Giannina; Mishra, Bhubaneswar.

Algebraic Biology - Second International Conference, AB 2007, Proceedings. Vol. 4545 LNCS 2007. p. 51-65 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4545 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Casagrande, A, Casey, K, Falchi, R, Piazza, C, Rupert, B, Vizzotto, G & Mishra, B 2007, Translating time-course gene expression profiles into semi-algebraic hybrid automata via dimensionality reduction. in Algebraic Biology - Second International Conference, AB 2007, Proceedings. vol. 4545 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4545 LNCS, pp. 51-65, 2nd International Conference on Algebraic Biology, AB 2007, Castle of Hagenberg, Austria, 7/2/07.
Casagrande A, Casey K, Falchi R, Piazza C, Rupert B, Vizzotto G et al. Translating time-course gene expression profiles into semi-algebraic hybrid automata via dimensionality reduction. In Algebraic Biology - Second International Conference, AB 2007, Proceedings. Vol. 4545 LNCS. 2007. p. 51-65. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Casagrande, Alberto ; Casey, Kevin ; Falchi, Rachele ; Piazza, Carla ; Rupert, Benedetto ; Vizzotto, Giannina ; Mishra, Bhubaneswar. / Translating time-course gene expression profiles into semi-algebraic hybrid automata via dimensionality reduction. Algebraic Biology - Second International Conference, AB 2007, Proceedings. Vol. 4545 LNCS 2007. pp. 51-65 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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