Why network approach can promote a new way of thinking in biology

This work deals with the particular nature of network-based approach in biology. We will comment about the shift from the consideration of the molecular layer as the definitive place where causative process start to the elucidation of the among elements (at any level of biological organization they are located) interaction network as the main goal of scientific explanation. This shift comes from the intrinsic nature of networks where the properties of a specific node are determined by its position in the entire network (top-down explanation) while the global network characteristics emerge from the nodes wiring pattern (bottom-up explanation). This promotes a “middle-out” paradigm formally identical to the time honored chemical thought holding big promises in the study of biological regulation.

[1]  M. McCarthy,et al.  Genome-wide association studies for complex traits: consensus, uncertainty and challenges , 2008, Nature Reviews Genetics.

[2]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[3]  Christopher R. Myers,et al.  Universally Sloppy Parameter Sensitivities in Systems Biology Models , 2007, PLoS Comput. Biol..

[4]  María Robbiano,et al.  Applications of a theorem by Ky Fan in the theory of graph energy , 2010 .

[5]  R. Macfarlane.  An Enzyme Cascade in the Blood Clotting Mechanism, and its Function as a Biochemical Amplifier , 1964, Nature.

[6]  A. Giuliani,et al.  Why so few drug targets: a mathematical explanation? , 2011, Current computer-aided drug design.

[7]  Jan Bressler,et al.  Epigenetics and human disease. , 2004, Annual review of genomics and human genetics.

[8]  An-Ping Zeng,et al.  Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph , 2004, Bioinform..

[9]  Donald C. Mikulecky,et al.  Network Thermodynamics and Complexity: A Transition to Relational Systems Theory , 2001, Comput. Chem..

[10]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[11]  Matthias Dehmer,et al.  Quantitative Network Measures as Biomarkers for Classifying Prostate Cancer Disease States: A Systems Approach to Diagnostic Biomarkers , 2013, PloS one.

[12]  Hawoong Jeong,et al.  Prediction of Protein Essentiality Based on Genomic Data , 2002, Complexus.

[13]  Jonathan M. Garibaldi,et al.  Parameter Estimation Using Metaheuristics in Systems Biology: A Comprehensive Review , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[14]  Péter Csermely,et al.  The efficiency of multi-target drugs: the network approach might help drug design. , 2004, Trends in pharmacological sciences.

[15]  Denis Noble,et al.  A theory of biological relativity: no privileged level of causation , 2012, Interface Focus.

[16]  A. Giuliani.  Collective motions and specific effectors: a statistical mechanics perspective on biological regulation , 2010, BMC Genomics.

[17]  Hiroaki Kitano,et al.  Deduction of intracellular sub-systems from a topological description of the network. , 2007, Molecular bioSystems.

[18]  Alfredo Colosimo,et al.  A recursive network approach can identify constitutive regulatory circuits in gene expression data , 2005 .

[19]  Roberto Todeschini,et al.  Handbook of Molecular Descriptors , 2002 .

[20]  Macfarlane Rg,et al.  AN ENZYME CASCADE IN THE BLOOD CLOTTING MECHANISM, AND ITS FUNCTION AS A BIOCHEMICAL AMPLIFIER , 1964 .

[21]  A. Giuliani,et al.  Functional essentiality from topology features in metabolic networks: A case study in yeast , 2005, FEBS letters.

[22]  Michael Small,et al.  Recurrence-based time series analysis by means of complex network methods , 2010, Int. J. Bifurc. Chaos.

[23]  A. Giuliani,et al.  Protein contact networks: an emerging paradigm in chemistry. , 2013, Chemical reviews.

[24]  Lan V. Zhang,et al.  Evidence for dynamically organized modularity in the yeast protein–protein interaction network , 2004, Nature.

[25]  Andreas Bender,et al.  A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication , 2005, J. Chem. Inf. Model..

[26]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[27]  H. Günthard,et al.  Zusammenhang von Graphentheorie und MO-Theorie von Molekeln mit Systemen konjugierter Bindungen , 1956 .

[28]  Martin Suter,et al.  Small World , 2002 .

[29]  A. Giuliani,et al.  Essentiality is an emergent property of metabolic network wiring , 2007, FEBS letters.

[30]  I. Gutman,et al.  Laplacian energy of a graph , 2006 .