A Sense of Life

Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes

Bhubaneswar Mishra, Vera Cherepinsky, Naomi Silver, William Casey, Carla Piazza, Marta Simeoni, Paolo Barbano, Marina Spivak, Jiawu Feng, Ofer Gill, Mysore Venkatesh, Raoul Sam Daruwala, Fang Cheng, Bing Sun, Iuliana Ioniata, Thomas Anantharaman, E. Jane Albert Hubbard, Amir Pnueli, David Harel, Vijay Chandru & 16 others Ramesh Hariharan, Michael Wigler, Yi Zhou, Frank Park, Shih Chieh Lin, Yuri Lazebnik, Franz Winkler, Charles R. Cantor, Alessandra Carbone, Mikhael Gromov, Nadia Ugel, Alberto Policriti, Marco Antoniotti, Salvatore Paxia, Marc Rejali, Mikhael Gromov

Research output: Contribution to journalArticle

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
StatePublished - 2003

Fingerprint

Biochemical Phenomena
Biological Phenomena
Noise
Cataloging
Psychological Techniques
Systems Biology
Research
Proteomics
Molecules
Experiments

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

A Sense of Life : Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes. / Mishra, Bhubaneswar; Cherepinsky, Vera; Silver, Naomi; Casey, William; Piazza, Carla; Simeoni, Marta; Barbano, Paolo; Spivak, Marina; Feng, Jiawu; Gill, Ofer; Venkatesh, Mysore; Daruwala, Raoul Sam; Cheng, Fang; Sun, Bing; Ioniata, Iuliana; Anantharaman, Thomas; Hubbard, E. Jane Albert; Pnueli, Amir; Harel, David; Chandru, Vijay; Hariharan, Ramesh; Wigler, Michael; Zhou, Yi; Park, Frank; Lin, Shih Chieh; Lazebnik, Yuri; Winkler, Franz; Cantor, Charles R.; Carbone, Alessandra; Gromov, Mikhael; Ugel, Nadia; Policriti, Alberto; Antoniotti, Marco; Paxia, Salvatore; Rejali, Marc; Gromov, Mikhael.

In: OMICS A Journal of Integrative Biology, Vol. 7, No. 3, 2003, p. 253-268.

Research output: Contribution to journalArticle

Mishra, B, Cherepinsky, V, Silver, N, Casey, W, Piazza, C, Simeoni, M, Barbano, P, Spivak, M, Feng, J, Gill, O, Venkatesh, M, Daruwala, RS, Cheng, F, Sun, B, Ioniata, I, Anantharaman, T, Hubbard, EJA, Pnueli, A, Harel, D, Chandru, V, Hariharan, R, Wigler, M, Zhou, Y, Park, F, Lin, SC, Lazebnik, Y, Winkler, F, Cantor, CR, Carbone, A, Gromov, M, Ugel, N, Policriti, A, Antoniotti, M, Paxia, S, Rejali, M & Gromov, M 2003, 'A Sense of Life: Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes', OMICS A Journal of Integrative Biology, vol. 7, no. 3, pp. 253-268.
Mishra, Bhubaneswar ; Cherepinsky, Vera ; Silver, Naomi ; Casey, William ; Piazza, Carla ; Simeoni, Marta ; Barbano, Paolo ; Spivak, Marina ; Feng, Jiawu ; Gill, Ofer ; Venkatesh, Mysore ; Daruwala, Raoul Sam ; Cheng, Fang ; Sun, Bing ; Ioniata, Iuliana ; Anantharaman, Thomas ; Hubbard, E. Jane Albert ; Pnueli, Amir ; Harel, David ; Chandru, Vijay ; Hariharan, Ramesh ; Wigler, Michael ; Zhou, Yi ; Park, Frank ; Lin, Shih Chieh ; Lazebnik, Yuri ; Winkler, Franz ; Cantor, Charles R. ; Carbone, Alessandra ; Gromov, Mikhael ; Ugel, Nadia ; Policriti, Alberto ; Antoniotti, Marco ; Paxia, Salvatore ; Rejali, Marc ; Gromov, Mikhael. / A Sense of Life : Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes. In: OMICS A Journal of Integrative Biology. 2003 ; Vol. 7, No. 3. pp. 253-268.
@article{5e3b1986485b4c8698675564b85c5439,
title = "A Sense of Life: Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes",
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.",
author = "Bhubaneswar Mishra and Vera Cherepinsky and Naomi Silver and William Casey and Carla Piazza and Marta Simeoni and Paolo Barbano and Marina Spivak and Jiawu Feng and Ofer Gill and Mysore Venkatesh and Daruwala, {Raoul Sam} and Fang Cheng and Bing Sun and Iuliana Ioniata and Thomas Anantharaman and Hubbard, {E. Jane Albert} and Amir Pnueli and David Harel and Vijay Chandru and Ramesh Hariharan and Michael Wigler and Yi Zhou and Frank Park and Lin, {Shih Chieh} and Yuri Lazebnik and Franz Winkler and Cantor, {Charles R.} and Alessandra Carbone and Mikhael Gromov and Nadia Ugel and Alberto Policriti and Marco Antoniotti and Salvatore Paxia and Marc Rejali and Mikhael Gromov",
year = "2003",
language = "English (US)",
volume = "7",
pages = "253--268",
journal = "OMICS A Journal of Integrative Biology",
issn = "1536-2310",
publisher = "Mary Ann Liebert Inc.",
number = "3",

}

TY - JOUR

T1 - A Sense of Life

T2 - Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes

AU - Mishra, Bhubaneswar

AU - Cherepinsky, Vera

AU - Silver, Naomi

AU - Casey, William

AU - Piazza, Carla

AU - Simeoni, Marta

AU - Barbano, Paolo

AU - Spivak, Marina

AU - Feng, Jiawu

AU - Gill, Ofer

AU - Venkatesh, Mysore

AU - Daruwala, Raoul Sam

AU - Cheng, Fang

AU - Sun, Bing

AU - Ioniata, Iuliana

AU - Anantharaman, Thomas

AU - Hubbard, E. Jane Albert

AU - Pnueli, Amir

AU - Harel, David

AU - Chandru, Vijay

AU - Hariharan, Ramesh

AU - Wigler, Michael

AU - Zhou, Yi

AU - Park, Frank

AU - Lin, Shih Chieh

AU - Lazebnik, Yuri

AU - Winkler, Franz

AU - Cantor, Charles R.

AU - Carbone, Alessandra

AU - Gromov, Mikhael

AU - Ugel, Nadia

AU - Policriti, Alberto

AU - Antoniotti, Marco

AU - Paxia, Salvatore

AU - Rejali, Marc

AU - Gromov, Mikhael

PY - 2003

Y1 - 2003

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=12444266788&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=12444266788&partnerID=8YFLogxK

M3 - Article

VL - 7

SP - 253

EP - 268

JO - OMICS A Journal of Integrative Biology

JF - OMICS A Journal of Integrative Biology

SN - 1536-2310

IS - 3

ER -