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Structural Identifiability of Dynamic Systems Biology Models

Alejandro F. Villaverde, Antonio Barreiro, Antonis Papachristodoulou, Satoru Miyano
2016 PLoS Computational Biology  
The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.  ...  We illustrate its applicability to systems biology models of genetic, signalling, metabolic, and pharmacokinetic networks, showing which of them are unidentifiable and how they can be made identifiable  ...  of X. doi:10.1371/journal.pcbi.1005153.g002 Fig 3 . 3 The NF-κB model. doi:10.1371/journal.pcbi.1005153.g003 Structural Identifiability of Dynamic Systems Biology Models Thus this model is unidentifiable  ... 
doi:10.1371/journal.pcbi.1005153 pmid:27792726 pmcid:PMC5085250 fatcat:4em4vknovfgl5ihdsdqdlrp2oi

Structural Properties of Dynamic Systems Biology Models: Identifiability, Reachability, and Initial Conditions

Alejandro F Villaverde, Julio R Banga
2017 Processes  
Reachability (controllability), observability, and structural identifiability are classical system-theoretic properties of dynamical models.  ...  Dynamic modelling is a powerful tool for studying biological networks.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/pr5020029 fatcat:riexdvy4pbghlklhu2aclqn45y

Systems biology – old concepts, new science, new challenges

Raina Robeva
2010 Frontiers in Psychiatry  
Developing methodologies for identifying the structure of complex networks in terms of their simpler functional components, together with identifying system responses predicated on the network topology  ...  Such models are typically parsimonious, including a minimal number of key functional elements and interactions that describe the structure or the principal dynamics of the system.  ...  Developing methodologies for identifying the structure of complex networks in terms of their simpler functional components, together with identifying system responses predicated on the network topology  ... 
doi:10.3389/fpsyt.2010.00001 pmid:21451740 pmcid:PMC3065319 fatcat:frpah3wzarfkjltf6idtw7omha

Korean Systems Biology and Biotechnology Research

Sang Yup Lee, Do Han Kim, Jin Sik Kim, Hyun Uk Kim, Hongseok Yun
2006 Asia-Pacific Biotech News  
Acknowledgements This study was supported by Korean Systems Biology Research grant from Korean Ministry of Science and Technology, and the Brain Korea 21 Project.  ...  Current systems biology is mainly focused on the understanding of complex and dynamic behaviors of organisms by using various x-omics data and computational models.  ...  Research Areas Of Systems Biology and Biotechnology in Korea In silico Modeling and Simulation of Biological Systems The approaches involved in the in silico modeling and simulation of biological systems  ... 
doi:10.1142/s0219030306001509 fatcat:nayftmu2ivd27exnntkqlgcibe

Systems Biology: A Brief Overview

H. Kitano
2002 Science  
To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism.  ...  However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential.  ...  For dynamic analysis of a cellular system, we need to create a model.  ... 
doi:10.1126/science.1069492 pmid:11872829 fatcat:sno2d45cazhklm4q6u4ajnrcwm

ABME Special Issue: Systems Biology, Bioinformatics, and Computational Biology

Gerald M. Saidel, Jie Liang
2007 Annals of Biomedical Engineering  
In the first two articles of the nine that relate to systems biology, analyses of large-scale system models of metabolism incorporate optimization and statistical methods.  ...  Effective computational methods for identifying substrate binding sites from enzyme structures are also reported.  ...  In the first two articles of the nine that relate to systems biology, analyses of large-scale system models of metabolism incorporate optimization and statistical methods.  ... 
doi:10.1007/s10439-007-9325-7 fatcat:ty4ola6vqndr5dsz56eumu7wem

Computational systems biology: integration of sequence, structure, network, and dynamics

Yong Wang, Xiang-Sun Zhang, Luonan Chen
2011 BMC Systems Biology  
This article has been published as part of BMC Systems Biology  ...  We also thank the Academy of Mathematics and Systems Science (AMSS) and National Natural Science Foundation of China (NSFC) to provide financial supports.  ...  Modelling dynamical biomolecular network Dynamic modeling is important in metabolic engineering with known metabolic network.  ... 
doi:10.1186/1752-0509-5-s1-s1 pmid:21689468 pmcid:PMC3121109 fatcat:damflyrqpzbd5an6obp3i7mtjq

On structural and practical identifiability

Franz-Georg Wieland, Adrian L. Hauber, Marcus Rosenblatt, Christian Tönsing, Jens Timmer
2021 Current Opinion in Systems Biology  
We discuss issues of structural and practical identifiability of partially observed differential equations, which are often applied in systems biology.  ...  We argue that practical identifiability is more challenging than structural identifiability when it comes to modeling experimental data.  ...  exist to assess structural identifiability of nonlinear dynamic models.  ... 
doi:10.1016/j.coisb.2021.03.005 fatcat:7qcky4hvsnbf3eepdqklmippme

Iterative Systems Biology for Medicine – Time for advancing from network signatures to mechanistic equations

David Gomez-Cabrero, Jesper Tegnér
2017 Current Opinion in Systems Biology  
Here we review principal advances with regard to identification of structure, dynamics, control, and design of biological systems, following the structure in the visionary review from 2002 by Dr.  ...  The rise and growth of Systems Biology following the sequencing of the human genome has been astounding.  ...  In contrast, in biology we aspire to identify not only the structure of cellular networks but also their dynamics, in order to achieve engineered control of the system [14, 15] .  ... 
doi:10.1016/j.coisb.2017.05.001 fatcat:2jp3or3flvehpeei2kvhx55tpy

Dynamical compensation in biological systems as a particular case of structural non-identifiability [article]

Alejandro F. Villaverde, Julio R. Banga
2017 arXiv   pre-print
Dynamical compensation (DC) has been recently defined as the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters.  ...  Here we note the similitude between DC and Structural Identifiability (SI), and we argue that the former can be explained in terms of (lack of) the latter.  ...  Dynamical compensation and structural identifiability Some biological systems are capable of maintaining an approximatively constant output despite environmental fluctuations [1] .  ... 
arXiv:1701.02562v1 fatcat:gjxefqtrlrdc5nyrjbsoy27pcy

Analyzing the Biology on the System Level

Wei Tong
2004 Genomics, Proteomics & Bioinformatics  
four key fields of systems biology-systemic structures, dynamics, control methods, and design principles.  ...  Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis  ...  Bailin Hao in Institute of Theoretical Physics, China, the suggestions of Prof. Uri Alon in Weizmann Institute of Science, Israel, and the precious comments of the reviewers.  ... 
doi:10.1016/s1672-0229(04)02002-9 fatcat:3ctjwxye2nbhpfzjpm3pcpmwrq

GenSSI: a software toolbox for structural identifiability analysis of biological models

O. Chis, J. R. Banga, E. Balsa-Canto
2011 Bioinformatics  
Mathematical modeling has a key role in systems biology.  ...  Obviously, the structural identifiability of any tentative model should be checked at the beginning of the model building loop.  ...  The vast majority of models in current systems biology are non-linear and dynamic.  ... 
doi:10.1093/bioinformatics/btr431 pmid:21784792 pmcid:PMC3167050 fatcat:6qlhso5r6vc4dhn3j7e4bfbpdm

Mapping What They Know: Concept Maps as an Effective Tool for Assessing Students' Systems Thinking

Jaklin Tripto, Orit Ben-Zvi Assaraf, Miriam Amit
2013 American Journal of Operations Research  
To do this, we identified the extent to which the students understand three central elements of systems, namely hierarchy, homeostasis, and dynamism, and then analyzed this understanding according to its  ...  In 2006 a new biology curriculum called "Human Biology: Emphasizing the Role of Homeostasis" was introduced into the Israeli high school system.  ...  components of the STH model manifested amongst high school biology students?  ... 
doi:10.4236/ajor.2013.31a022 fatcat:kwop3qwd4necbba4whvnliclvu

GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models

Thomas S Ligon, Fabian Fröhlich, Oana T Chiş, Julio R Banga, Eva Balsa-Canto, Jan Hasenauer, Jonathan Wren
2017 Bioinformatics  
Motivation: Mathematical modeling using ordinary differential equations is used in systems biology to improve the understanding of dynamic biological processes.  ...  GenSSI 2.0 is the first toolbox for structural identifiability analysis to implement Systems Biology Markup Language import, state/parameter transformations and multi-experiment structural identifiability  ...  of structural identifiability analysis in systems biology.  ... 
doi:10.1093/bioinformatics/btx735 pmid:29206901 pmcid:PMC5905618 fatcat:ixzpfwm3x5f2niwbvgbhwos6li

Systems biology of complex symptom profiles: Capturing interactivity across behavior, brain and immune regulation

Gordon Broderick, Travis John Adrian Craddock
2013 Brain, behavior, and immunity  
Systems biology is an emerging branch of science that sits as a translational catalyst at the interface of the life and computational sciences.  ...  While there is no universally accepted definition of systems biology, we attempt to provide an overview of some the basic unifying concepts and current efforts in the field as they apply to illnesses where  ...  National Institutes of Health, the U.S. Department of Defense (CDMRP program), the U.S. Department of Veterans Affairs and the CFIDS Association of America.  ... 
doi:10.1016/j.bbi.2012.09.008 pmid:23022717 pmcid:PMC3554865 fatcat:rb7hqcaugnhmvifx4rxwn6sywu
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