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NAR
2006
87views more  NAR 2006»
13 years 4 months ago
From genomics to chemical genomics: new developments in KEGG
The increasing amount of genomic and molecular information is the basis for understanding higherorder biological systems, such as the cell and the 15 organism, and their interacti...
Minoru Kanehisa, Susumu Goto, Masahiro Hattori, Ki...
ENTCS
2007
91views more  ENTCS 2007»
13 years 4 months ago
Timed Concurrent Constraint Programming for Analysing Biological Systems
In this paper we present our rst approach to model and verify biological systems using ntcc, a concurrent constraint process calculus. We argue that the partial information const...
Julian Gutierrez, Jorge A. Pérez, Camilo Ru...
ENTCS
2007
82views more  ENTCS 2007»
13 years 4 months ago
A Simple Calculus for Proteins and Cells
The use of process calculi to represent biological systems has led to the design of different formalisms such as brane calculi and κ-calculus. Both have proved to be useful to m...
Cosimo Laneve, Fabien Tarissan
JCB
2006
185views more  JCB 2006»
13 years 4 months ago
A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks
Biological systems are traditionally studied by focusing on a specific subsystem, building an intuitive model for it, and refining the model using results from carefully designed ...
Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Sh...
JAL
2008
74views more  JAL 2008»
13 years 4 months ago
Solving satisfiability in the tile assembly model with a constant-size tileset
Biological systems are far more complex and robust than systems we can engineer today. One way to increase the complexity and robustness of our engineered systems is to study how ...
Yuriy Brun
ENTCS
2006
155views more  ENTCS 2006»
13 years 4 months ago
Biomolecular Agents as Multi-behavioural Concurrent Objects
In recent years, there has been increasing interest in computational models of biological systems based on various calculi of communicating processes, such as the stochastic pi-ca...
Denys Duchier, Céline Kuttler
BMCBI
2006
179views more  BMCBI 2006»
13 years 4 months ago
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers
Background: Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuation...
Howard Salis, Vassilios Sotiropoulos, Yiannis N. K...
BMCBI
2010
136views more  BMCBI 2010»
13 years 4 months ago
A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles
Background: Many research results show that the biological systems are composed of functional modules. Members in the same module usually have common functions. This is useful inf...
Chia-Hao Chin, Shu-Hwa Chen, Chin-Wen Ho, Ming-Tat...
BIOSYSTEMS
2008
72views more  BIOSYSTEMS 2008»
13 years 4 months ago
The manipulation of calcium oscillations by harnessing self-organisation
This paper investigates how self-organisation might be harnessed for the manipulation and control of calcium oscillations. Calcium signalling mechanisms are responsible for a numb...
Cristina Costa Santini, Andy M. Tyrrell
BIOSYSTEMS
2007
109views more  BIOSYSTEMS 2007»
13 years 4 months ago
Complex adaptation and system structure
The structural organization of biological systems is one of nature’s most fascinating aspects, but its origin and functional role is not yet fully understood. For instance, basi...
Marc Toussaint, Werner von Seelen