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Multiscale Modeling of Information Conveyed by Gene-Regulatory Signaling

Michael Mayo, Kevin Pilkiewicz
2016 Proceedings of the 9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)  
In this paper we study the informationtransmission characteristics of a single gene-regulatory interaction by employing an exactly solvable master equation model for the production and degradation of individual  ...  Applying this same metric to gene-regulatory interactions can better clarify how these biological signaling systems mitigate environmental noise.  ...  Below we report a simple mathematical model of protein production stimulated by a transcriptional-regulatory interaction, and use it to understand characteristics of the information transmission via Eq  ... 
doi:10.4108/eai.3-12-2015.2262540 dblp:journals/sg/MayoP16 fatcat:gnotvn6djzbdndhwmarafizgvq

Empirical Multiscale Networks of Cellular Regulation

Benjamin de Bivort, Sui Huang, Yaneer Bar-Yam
2007 PLoS Computational Biology  
Grouping genes by similarity of expression across multiple cellular conditions enables the identification of cellular modules.  ...  In this paper, we use a high-throughput approach to identify the effective mutual regulatory interactions between modules composed of mouse genes from the Alliance for Cell Signaling (AfCS) murine B-lymphocyte  ...  From these groups and regulatory influences, we derived many results comprising a first multiscale analysis of global gene-regulatory influences.  ... 
doi:10.1371/journal.pcbi.0030207 pmid:17953478 pmcid:PMC2041980 fatcat:aoktsaz2tzhfjn7j743rk6fj7y

A multiscale systems perspective on cancer, immunotherapy, and Interleukin-12

David J Klinke
2010 Molecular Cancer  
However, understanding mechanisms by which tumors evade elimination by the immune system of the host presents a significant challenge for developing effective cancer immunotherapies.  ...  The objective of this review is to summarize interactions between the tumor and cell-mediated immunity from a multiscale perspective.  ...  Acknowledgements This work was supported by grants from the PhRMA Foundation, the National Cancer Institute R15CA132124, and the National Institute of Allergy and Infectious Diseases R56AI076221.  ... 
doi:10.1186/1476-4598-9-242 pmid:20843320 pmcid:PMC3243044 fatcat:aihkjfyycrhvtlo2enbc2q77qq

The Cardiac Physiome: perspectives for the future

James Bassingthwaighte, Peter Hunter, Denis Noble
2009 Experimental Physiology  
by the IUPS Physiome Project to help with the understanding of complex physiological systems through the use of biophysically based mathematical models that link genes to organisms.  ...  This requires linking together different types of modelling at the various levels.  ...  module, they need not be conveyed, so the information flow is minimized.  ... 
doi:10.1113/expphysiol.2008.044099 pmid:19098089 pmcid:PMC2854146 fatcat:fe3t4ebx6zfttitxnlpmud2pvm

Strategies and Tactics in Multiscale Modeling of Cell-to-Organ Systems

J.B. Bassingthwaighte, H.J. Chizeck, L.E. Atlas
2006 Proceedings of the IEEE  
The lowest levels concern gene signaling and the regulation of transcription and translation, then biophysical and biochemical events at the protein level, and extend through the levels of cells, tissues  ...  Modeling is essential to integrating knowledge of human physiology.  ...  order to create a parametric image conveying physiological information about the tissues.  ... 
doi:10.1109/jproc.2006.871775 pmid:20463841 pmcid:PMC2867355 fatcat:g5x23zq5qncbxmrotrqjbofuva

Bridging the genotype-phenotype gap: what does it take?

Arne B. Gjuvsland, Jon Olav Vik, Daniel A. Beard, Peter J. Hunter, Stig W. Omholt
2013 Journal of Physiology  
and multiscale modelling.  ...  Gjuvsland is a researcher at the Centre for Integrative Genetics at the Norwegian University of Life Sciences. He did his PhD on linking genetic theory and gene regulatory network models.  ...  Acknowledgements This work has been supported in part by The Research Council of Norway, project number 178901/V30, Bridging the gap: disclosure, understanding and exploitation of the genotype-phenotype  ... 
doi:10.1113/jphysiol.2012.248864 pmid:23401613 pmcid:PMC3634519 fatcat:brrjptrimjetpkayvleoc44ogy

A Multiscale Model to Investigate Circadian Rhythmicity of Pacemaker Neurons in the Suprachiasmatic Nucleus

Christina Vasalou, Michael A. Henson, Karl J. Friston
2010 PLoS Computational Biology  
framework which captured characteristics of the SCN at both the electrophysiological and gene regulatory levels.  ...  The model predicted a direct relationship between firing frequency and gene expression amplitudes, demonstrated the importance of intracellular pathways for single cell behavior and provided a novel multiscale  ...  Discussion We developed a multiscale mathematical model to investigate the association between the circadian gene regulatory pathway, electrophysiology and cytosolic calcium and to evaluate SCN single  ... 
doi:10.1371/journal.pcbi.1000706 pmid:20300645 pmcid:PMC2837390 fatcat:5gql4i2hpzd4jlybucwk3iaw54

Modeling-Enabled Systems Nutritional Immunology

Meghna Verma, Raquel Hontecillas, Vida Abedi, Andrew Leber, Nuria Tubau-Juni, Casandra Philipson, Adria Carbo, Josep Bassaganya-Riera
2016 Frontiers in Nutrition  
We propose to investigate nutritional immunology as a massively interacting system of interconnected multistage and multiscale networks that encompass hidden mechanisms by which nutrition, microbiome,  ...  Emerging global mechanistic insights in the field of nutritional immunology cannot be gained through reductionist methods alone or by analyzing a single nutrient at a time.  ...  energy required during metabolic demands as well as regulatory signals that help in the maintenance of homeostasis.  ... 
doi:10.3389/fnut.2016.00005 pmid:26909350 pmcid:PMC4754447 fatcat:3xomgnn7pzhavmlrcqruyvgwta

Multi-omics integration reveals molecular networks and regulators of psoriasis

Yuqi Zhao, Deepali Jhamb, Le Shu, Douglas Arneson, Deepak K. Rajpal, Xia Yang
2019 BMC Systems Biology  
Funding The study was supported by research funds from GSK (XY).  ...  The funder has no role in the design of the study and collection, analysis, and interpretation of the data, and in writing the manuscript.  ...  Using a multiscale gene coexpression network modeling approach MEGENA [20] , we reconstructed a psoriatic network comprised of 228 co-expression modules and a normal skin network comprised of 165 modules  ... 
doi:10.1186/s12918-018-0671-x pmid:30642337 pmcid:PMC6332659 fatcat:vmcf3nify5hfhgo2obzcqakesy

The many faces of mathematical modelling in oncology

Pedro Victori, Francesca M Buffa
2018 British Journal of Radiology  
We will outline radiobiology models, examples of other anticancer therapy models, multiscale modelling, and we will discuss mechanistic and phenomenological approaches to modelling.  ...  The application of modelling to solve problems in biology and medicine, and specifically in oncology and radiation therapy, is increasingly established and holds big promise.  ...  to inform modelling of signalling network in normal and cancer cells.  ... 
doi:10.1259/bjr.20180856 pmid:30485129 pmcid:PMC6435080 fatcat:bnhrf575tvd2letx6oj6okon3u

Quantitative and logic modelling of molecular and gene networks

Nicolas Le Novère
2015 Nature reviews genetics  
Quantitative models Mathematical models in which the values of the variables are determined by numerical analysis of the variables and parameters in the system.  ...  Quantitative and logic modelling are among the main methods currently used to model molecular and gene networks. Each approach comes with inherent advantages and weaknesses.  ...  Froehlich for extensive reading and correction of the manuscript, to L. Stephens and S. Edelstein for their corrections and advice, and to C. Chaouiya, P. Mendes, J. Saez-Rodriguez and D.  ... 
doi:10.1038/nrg3885 pmid:25645874 pmcid:PMC4604653 fatcat:ewf5l5frsbfr3pu3ut5c4wcb6y

Systems biology of asthma and allergic diseases: A multiscale approach

Supinda Bunyavanich, Eric E. Schadt
2015 Journal of Allergy and Clinical Immunology  
High throughput molecular, cellular, and physiologic profiling of populations is coupled with bioinformatic and computational techniques to identify new functional roles for genes, regulatory elements,  ...  manifested by the system.  ...  By building networks, we create maps of potential connections among components that can suggest new functional roles for specific genes, regulatory elements, and metabolites. 107 Networks can place genes  ... 
doi:10.1016/j.jaci.2014.10.015 pmid:25468194 pmcid:PMC4289105 fatcat:ctikhelngjdvbgbc37tlm72j4y

The Physics of Cellular Decision Making During Epithelial–Mesenchymal Transition

Shubham Tripathi, Herbert Levine, Mohit Kumar Jolly
2020 Annual Review of Biophysics  
In this article, we review the key features and characteristics of EMT dynamics, with a focus on the mathematical modeling approaches that have been instrumental to obtaining various useful insights.  ...  Mathematical modeling has been at the forefront of this transformation for the field, not only providing a conceptual framework to integrate and analyze experimental data, but also making testable predictions  ...  Sustained TGF-β signaling, modeled by fixing the TGF-β node in the ON state, activated SMAD complex formation followed by the induction of MAPK and AKT signaling, finally leading to the network exhibiting  ... 
doi:10.1146/annurev-biophys-121219-081557 pmid:31913665 fatcat:mwe5o7t6fbfhpd5ueipcxm23om

Promising Role of Engineered Gene Circuits in Gene Therapy [chapter]

Wei-Dong Wang, Jinyi Lang
2011 Gene Therapy - Developments and Future Perspectives  
DNA-binding specificity of transcription factors. Design of signaling and regulatory networks Artificial signaling and regulatory gene networks will need to be assembled for synthetic biology.  ...  quantitative understanding of regulatory and signaling processes; (2) to develop effective rules (Wall et al.,2003) and standards for characterizing modules and (3) to improve multiscale simulation  ...  Gene Therapy -Developments and Future Perspectives The aim of this book is to cover key aspects of existing problems in the field of development and future perspectives in gene therapy.  ... 
doi:10.5772/17400 fatcat:d2pfmhudjzavrk4rd743l4esvq

Multiscale Modeling in Biology

Santiago Schnell, Ramon Grima, Philip Maini
2007 American Scientist  
Multiscale Modeling in Biology  ...  We now have a good deal of information about the genetic mutations underlying colon cancer and how activation of the mutated genes is affected by conditions of oxygen starvation (hypoxia) and overcrowding  ...  A multiscale model would allow us to explore the effects of combination therapies, approaches that attempt to stop cancer in its tracks by barricading multiple pathways.  ... 
doi:10.1511/2007.64.1018 fatcat:3uigwjvrrjaftcb4yflr2yp5ia
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