Filters








17,822 Hits in 5.0 sec

A Compositional Approach to the Stochastic Dynamics of Gene Networks [chapter]

Luca Cardelli
2005 Lecture Notes in Computer Science  
We propose a compositional approach to the dynamics of gene regulatory networks based on the stochastic π-calculus, and develop a representation of gene network elements which can be used to build complex  ...  To demonstrate the power of the approach we apply it to several artificial networks, such as the repressilator and combinatorial gene circuits first studied in Combinatorial Synthesis of Genetic Networks  ...  To conclude, we believe that the compositional approach we propose for the formulation of stochastic models of gene networks will allow a useful path for more detailed, quantitative studies of regulatory  ... 
doi:10.1007/11539452_3 fatcat:quz57kg64jfr5ll2b7nbt6z4gu

A Compositional Approach to the Stochastic Dynamics of Gene Networks [chapter]

Ralf Blossey, Luca Cardelli, Andrew Phillips
2006 Lecture Notes in Computer Science  
We propose a compositional approach to the dynamics of gene regulatory networks based on the stochastic π-calculus, and develop a representation of gene network elements which can be used to build complex  ...  To demonstrate the power of the approach we apply it to several artificial networks, such as the repressilator and combinatorial gene circuits first studied in Combinatorial Synthesis of Genetic Networks  ...  To conclude, we believe that the compositional approach we propose for the formulation of stochastic models of gene networks will allow a useful path for more detailed, quantitative studies of regulatory  ... 
doi:10.1007/11732488_10 fatcat:ltpdxuylv5ahxftd6gdraynkpa

Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation

Ralf Blossey, Luca Cardelli, Andrew Phillips
2008 HFSP Journal  
Here, we propose a compositional approach to models of gene regulatory network dynamics whose underlying philosophy derives from process calculi developed in the application of programming language methods  ...  We present an approach to compose dynamic models of gene regulatory networks from simple computational elements.  ...  RB wishes to thank the Microsoft Research -University of Trento Centre of Computational Systems Biology for its hospitality during a stay, and François Fages, Leon Glass and Marc Lefranc for illuminating  ... 
doi:10.2976/1.2804749 pmid:19404450 pmcid:PMC2640994 fatcat:jqudie7kcnawvepflvofo7ozcq

Compositionality, stochasticity and cooperativity in dynamic models of gene regulation [article]

R.Blossey, L.Cardelli, A. Phillips
2007 arXiv   pre-print
We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements.  ...  While the ode-approach requires fixing the system's topology before its correct implementation, expressing them in stochastic pi-calculus leads to a fully compositional scheme: network elements become  ...  RB wishes to thank the Microsoft Research -University of Trento Centre of Computational Systems Biology for its hospitality during a stay, and François Fages, Leon Glass and Marc Lefranc for illuminating  ... 
arXiv:q-bio/0702016v2 fatcat:vsxkgncy2beedfpbuhtbarwx5e

Modeling and Dynamical Analysis of Molecular Networks [chapter]

Ruiqi Wang, Xing-Ming Zhao, Zengrong Liu
2009 Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering  
Instead of analyzing individual molecules, systems biology is to study dynamical networks of interacting molecules which give rise to life.  ...  This paper presents a brief survey on recent developments on modeling and analyzing complex molecular networks mainly from global and dynamical properties of complex molecular networks.  ...  Acknowledgements This work was supported by the National Natural Science Foundation of China (Youth Research Grant 10701052), Shanghai Pujiang Program, and the Innovation Fund of Shanghai University.  ... 
doi:10.1007/978-3-642-02469-6_90 fatcat:57tnb4skmvas3a4hppbti63ftu

Toward integration of systems biology formalism: the gene regulatory networks case

Raffaella Gentilini
2005 Genome Informatics Series  
Specifically, we define automatic procedures for translating stochastic pi-calculus descriptions of gene regulatory networks to S-systems differential equations.  ...  We consider the problem of integrating different systems biology formalisms, namely, the process calculi based formalism, the modeling approach based on systems of differential equations, and the one relying  ...  Note that, within the network of genes defined by a compositional approach in [6] , the production of a protein following a gene transcription can only regulate the synthesis (either positively or negatively  ... 
pmid:16901104 fatcat:lxbpaqpf4vbzlkq57mm6swprpq

Complex microbial systems across different levels of description

Benedikt von Bronk, Alexandra Götz, Madeleine Opitz
2018 Physical Biology  
In this review paper, we focus on microbial communities, and first, summarize a general hierarchy of relevant scales and description levels to understand these complex systems: (1) genetic networks, (2  ...  Complex biological systems offer a variety of interesting phenomena at the different physical scales.  ...  Acknowledgment BvB was supported by a DFG Fellowship through the Graduate School of Quantitative Biosciences Munich (QBM).  ... 
doi:10.1088/1478-3975/aac473 pmid:29757151 fatcat:yaabxc7i4babpnxfogiq3b2jca

Perspective: Engineering noise in biological systems towards predictive stochastic design

Roy D. Dar, Ron Weiss
2018 APL Bioengineering  
However, our ability to engineer systems that begin to approach the complexity of natural pathways is severely limited by important challenges, e.g. due to noise, or the fluctuations in gene expression  ...  Here we highlight studies of an emerging discipline that collectively strives to engineer noise towards predictive stochastic design using interdisciplinary approaches at multiple-scales in diverse living  ...  The authors demonstrated that tuning noise across a defined noise phase space can modulate the dynamics of a positively auto-regulated gene circuit between unimodal and bimodal regimes of gene expression  ... 
doi:10.1063/1.5025033 pmid:31069294 pmcid:PMC6481707 fatcat:hezyv4g4u5eatgqteu3r55kv2y

Mean-field versus stochastic models for transcriptional regulation

R. Blossey, C. V. Giuraniuc
2008 Physical Review E  
We introduce a minimal model description for the dynamics of transcriptional regulatory networks.  ...  We elucidate the different results both approaches can deliver, depending on the network under study, and in particular depending on the level of detail retained in the respective description.  ...  In fact, the syntax and semantics of the π-calculus is perfectly adapted to a 'compositional' build-up of the transcriptional networks, a technical advantage of this approach.  ... 
doi:10.1103/physreve.78.031909 pmid:18851067 fatcat:j6kkgj3pofdvlj7ko3gh4qhlrq

Deterministic and Stochastic Models of Genetic Regulatory Networks [chapter]

Ilya Shmulevich, John D. Aitchison
2009 Methods in Enzymology  
We discuss four classes of dynamical systems used to model genetic regulatory networks.  ...  Traditionally molecular biology research has tended to reduce biological pathways to composite units studied as isolated parts of the cellular system.  ...  Thus, the stochastic dynamics of the Markov chain were able to mimic biological regulation.  ... 
doi:10.1016/s0076-6879(09)67013-0 pmid:19897099 pmcid:PMC3230268 fatcat:lmxdnkc6yrcb7kruo2zn2bdxtm

Toward Integration of Systems Biology Formalism: The Gene Regulatory Networks Case

Raffaella Gentilini
2005 Genome Informatics Series  
Specifically, we define automatic procedures for translating stochastic 7r-calculus descriptions of gene regulatory networks to S-systems differential equations .  ...  We consider the problem of integrating different systems biology formalisms , namely, the process calculi based formalism, the modeling approach based on systems of differential equations , and the one  ...  We start from [6], where the authors defined a compositional approach for process calculi descriptions of simple systems of genes, in which the translation of each gene can be inhibited/enhanced by the  ... 
doi:10.11234/gi1990.16.2_215 fatcat:frirnia6crarxmk7nyexxljtsa

Stochastic Simulation for Biochemical Reaction Networks in Infectious Disease [chapter]

Shailza Singh, Sonali Shinde
2012 Medicinal Chemistry and Drug Design  
Using this approach, a base is formulated for the appropriate selection of an inhibitor, taking into account the dynamics of the enzyme kinetics.  ...  Thus, we say graphical approaches simplify the process of transforming a network diagram into a set of linked equations.  ...  We hope that the textbook will enhance the knowledge of scientists in the complexities of some medicinal approaches; it will stimulate both professionals and students to dedicate part of their future research  ... 
doi:10.5772/38245 fatcat:ljlddzjemzayzd6yk3xfn4pwku

Mathematical Modelling of Gene Regulatory Networks [chapter]

Ana Tuek, elimir Kurtanjek
2012 Applied Biological Engineering - Principles and Practice  
Acknowledgment This work was supported by Ministry of Science, Education and Sport of Republic of Croatia grant MZOŠ 0589.  ...  According to Rosenfeld, 2007 for mathematical description of stochastic dynamics of gene regulatory networks two approaches can be used: 1. non-linear dynamics paradigm -treats the biochemical components  ...  According to Bruggeman & Westerholl, 2007 a complete systems biology approach requires (i) characterisation of organism molecular composition, (ii) components dynamics (spatial and temporal) and (iii  ... 
doi:10.5772/31388 fatcat:vbvytqbmnra7ndxtnb6fjofye4

Shaping development by stochasticity and dynamics in gene regulation

Peng Dong, Zhe Liu
2017 Open Biology  
These approaches outline next-generation experiments to decipher general principles bridging gaps between molecular dynamics in single cells and robust gene regulations in the embryo.  ...  and (ii) highly coordinated gene expression dynamics in the embryo.  ...  The authors apologize to those relevant studies that have not been cited in this review due to space constraints.  ... 
doi:10.1098/rsob.170030 pmid:28469006 pmcid:PMC5451542 fatcat:izfql5vqubfzfmp6po454cnf4m

On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models [chapter]

Katherine Chiang, François Fages, Jie-Hong Jiang, Sylvain Soliman
2013 Lecture Notes in Computer Science  
standard way to give meaning to the hybrid composition of heterogeneous models of biochemical processes.  ...  This is illustrated by a hybrid stochastic-differential model of bacteriophage T7 infection, and by a reconstruction of the hybrid model of the mammalian cell cycle regulation of Singhania et al. as the  ...  Acknowledgements This work has been supported by the French OSEO Biointelligence and ANR BioTempo projects, and by the European Eranet Sysbio C5Sys project.  ... 
doi:10.1007/978-3-642-40708-6_15 fatcat:uqkzd65tyzd25plimiodgoen4e
« Previous Showing results 1 — 15 out of 17,822 results