The aim of enumeration is to list all the feasible solutions of a given problem satisfying some constraints. Enumeration algorithms are particularly useful whenever the goal of a problem is not clear and all its solutions need to be checked. Since one peculiar property of biological networks is the uncertainty, a scenario in which enumeration algorithms can be helpful is biological network analysis. Modelling biological networks indeed introduce bias: arc dependencies are neglected and underlying hyper-graph behaviours are forced in simple graph representations to avoid intractability. Moreover regulatory interactions between all the biological networks are omitted, even if none of the different biological layers is truly isolated. Last but not least, the dynamical behaviours of biological networks are often not considered: indeed most of the currently available biological network reconstructions are potential networks, where all the possible connections are indicated, even if edges/arcs and vertices are hardly present all together at the same time.

Algorithms for Biological Graphs: Analysis and Enumeration / Marino A. - In: BULLETIN OF THE EUROPEAN ASSOCIATION FOR THEORETICAL COMPUTER SCIENCE. - ISSN 0252-9742. - ELETTRONICO. - (2014), pp. 1-6.

Algorithms for Biological Graphs: Analysis and Enumeration

Marino A
2014

Abstract

The aim of enumeration is to list all the feasible solutions of a given problem satisfying some constraints. Enumeration algorithms are particularly useful whenever the goal of a problem is not clear and all its solutions need to be checked. Since one peculiar property of biological networks is the uncertainty, a scenario in which enumeration algorithms can be helpful is biological network analysis. Modelling biological networks indeed introduce bias: arc dependencies are neglected and underlying hyper-graph behaviours are forced in simple graph representations to avoid intractability. Moreover regulatory interactions between all the biological networks are omitted, even if none of the different biological layers is truly isolated. Last but not least, the dynamical behaviours of biological networks are often not considered: indeed most of the currently available biological network reconstructions are potential networks, where all the possible connections are indicated, even if edges/arcs and vertices are hardly present all together at the same time.
2014
1
6
Marino A
File in questo prodotto:
Non ci sono file associati a questo prodotto.

I documenti in FLORE sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/1149272
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus ND
  • ???jsp.display-item.citation.isi??? ND
social impact