Literature DB >> 26013981

Fostering synergy between cell biology and systems biology.

James A Eddy1, Cory C Funk1, Nathan D Price2.   

Abstract

In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown
Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  cell biology; data integration; modeling; networks; systems biology

Mesh:

Year:  2015        PMID: 26013981      PMCID: PMC4758507          DOI: 10.1016/j.tcb.2015.04.005

Source DB:  PubMed          Journal:  Trends Cell Biol        ISSN: 0962-8924            Impact factor:   20.808


  46 in total

1.  KEGG: kyoto encyclopedia of genes and genomes.

Authors:  M Kanehisa; S Goto
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  Network biology: understanding the cell's functional organization.

Authors:  Albert-László Barabási; Zoltán N Oltvai
Journal:  Nat Rev Genet       Date:  2004-02       Impact factor: 53.242

Review 3.  Recent advances in reconstruction and applications of genome-scale metabolic models.

Authors:  Tae Yong Kim; Seung Bum Sohn; Yu Bin Kim; Won Jun Kim; Sang Yup Lee
Journal:  Curr Opin Biotechnol       Date:  2011-11-04       Impact factor: 9.740

4.  Explanation: a mechanist alternative.

Authors:  William Bechtel; Adele Abrahamsen
Journal:  Stud Hist Philos Biol Biomed Sci       Date:  2005-06

5.  A whole-cell computational model predicts phenotype from genotype.

Authors:  Jonathan R Karr; Jayodita C Sanghvi; Derek N Macklin; Miriam V Gutschow; Jared M Jacobs; Benjamin Bolival; Nacyra Assad-Garcia; John I Glass; Markus W Covert
Journal:  Cell       Date:  2012-07-20       Impact factor: 41.582

Review 6.  Boosting signal-to-noise in complex biology: prior knowledge is power.

Authors:  Trey Ideker; Janusz Dutkowski; Leroy Hood
Journal:  Cell       Date:  2011-03-18       Impact factor: 41.582

7.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

8.  Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality.

Authors:  Livnat Jerby-Arnon; Nadja Pfetzer; Yedael Y Waldman; Lynn McGarry; Daniel James; Emma Shanks; Brinton Seashore-Ludlow; Adam Weinstock; Tamar Geiger; Paul A Clemons; Eyal Gottlieb; Eytan Ruppin
Journal:  Cell       Date:  2014-08-28       Impact factor: 41.582

9.  Robust network topologies for generating switch-like cellular responses.

Authors:  Najaf A Shah; Casim A Sarkar
Journal:  PLoS Comput Biol       Date:  2011-06-23       Impact factor: 4.475

10.  A system-level model for the microbial regulatory genome.

Authors:  Aaron N Brooks; David J Reiss; Antoine Allard; Wei-Ju Wu; Diego M Salvanha; Christopher L Plaisier; Sriram Chandrasekaran; Min Pan; Amardeep Kaur; Nitin S Baliga
Journal:  Mol Syst Biol       Date:  2014-07-15       Impact factor: 11.429

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  1 in total

1.  SBMLmod: a Python-based web application and web service for efficient data integration and model simulation.

Authors:  Sascha Schäuble; Anne-Kristin Stavrum; Mathias Bockwoldt; Pål Puntervoll; Ines Heiland
Journal:  BMC Bioinformatics       Date:  2017-06-24       Impact factor: 3.169

  1 in total

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