A Sense of Life: Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes

Bud Mishra, Raoul Sam Daruwala, Yi Zhou, Nadia Ugel, Alberto Policriti, Marco Antoniotti, Salvatore Paxia, Marc Rejali, Archisman Rudra, Vera Cherepinsky, Naomi Silver, William Casey, Carla Piazza, Marta Simeoni, Paolo Barbano, Marina Spivak, Jiawu Feng, Ofer Gill, Mysore Venkatesh, Fang ChengBing Sun, Iuliana Ioniata, Thomas Anantharaman, E. Jane Albert Hubbard, Amir Pnueli, David Harel, Vijay Chandru, Ramesh Hariharan, Michael Wigler, Frank Park, Shih Chieh Lin, Yuri Lazebnik, Franz Winkler, Charles R. Cantor, Alessandra Carbone, Mikhael Gromov

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Pages (from-to)253-268
Number of pages16
JournalOMICS A Journal of Integrative Biology
Volume7
Issue number3
DOIs
StatePublished - 2003

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Genetics

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