Multi-class and Multi-scale Models of Complex Biological Phenomena This Review Comes from a Themed Issue on Systems Biology Sciencedirect Classes and Scales of Computational Models Model Classification Molecular Protein Network Cellular
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Mark P. Styczynski | Neda Bagheri | Jessica S Yu | Jessica S. Yu | N. Bagheri | F. Theis | Jessica S. Yu | Neda Bagheri
[1] Chang Gong,et al. A multi-scale approach to designing therapeutics for tuberculosis. , 2015, Integrative biology : quantitative biosciences from nano to macro.
[2] M. J. Hatcher,et al. Modeling Biological Systems: Principles and Applications , 1997 .
[3] Paola Causin,et al. Blood flow mechanics and oxygen transport and delivery in the retinal microcirculation: multiscale mathematical modeling and numerical simulation , 2016, Biomechanics and modeling in mechanobiology.
[4] M. Figge,et al. Deciphering chemokine properties by a hybrid agent-based model of Aspergillus fumigatus infection in human alveoli , 2015, Front. Microbiol..
[5] Marie Oshima,et al. Numerical Study of Cerebroarterial Hemodynamic Changes Following Carotid Artery Operation: A Comparison Between Multiscale Modeling and Stand-Alone Three-Dimensional Modeling. , 2015, Journal of biomechanical engineering.
[6] Robert J Gillies,et al. Impact of metabolic heterogeneity on tumor growth, invasion, and treatment outcomes. , 2015, Cancer research.
[7] G. Holzapfel,et al. Constitutive modelling of arteries considering fibre recruitment and three-dimensional fibre distribution , 2015, Journal of The Royal Society Interface.
[8] R. Sanfelice,et al. Hybrid dynamical systems , 2009, IEEE Control Systems.
[9] Arman Rahmim,et al. The Vital Role of Blood Flow-Induced Proliferation and Migration in Capillary Network Formation in a Multiscale Model of Angiogenesis , 2015, PloS one.
[10] Fabian J. Theis,et al. Data-driven modelling of biological multi-scale processes , 2015, 1506.06392.
[11] C. Engwer,et al. Effective equations for anisotropic glioma spread with proliferation: a multiscale approach and comparisons with previous settings. , 2016, Mathematical medicine and biology : a journal of the IMA.
[12] Eric J Kunkel,et al. Systems biology in drug discovery. , 2006, Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference.
[13] P Vicini,et al. A Mechanistic, Multiscale Mathematical Model of Immunogenicity for Therapeutic Proteins: Part 1—Theoretical Model , 2014, CPT: pharmacometrics & systems pharmacology.
[14] P. Mendes,et al. Multi-scale modelling and simulation in systems biology. , 2011, Integrative biology : quantitative biosciences from nano to macro.
[15] R. M. Simpson,et al. Functional Analysis of Prognostic Gene Expression Network Genes in Metastatic Breast Cancer Models , 2014, PloS one.
[16] Aleksander S Popel,et al. An agent-based model of cancer stem cell initiated avascular tumour growth and metastasis: the effect of seeding frequency and location , 2014, Journal of The Royal Society Interface.
[17] Svetlana Bunimovich-Mendrazitsky,et al. Modeling and simulation of a low-grade urinary bladder carcinoma , 2013, Comput. Biol. Medicine.
[18] G. Odell,et al. The segment polarity network is a robust developmental module , 2000, Nature.
[19] Radek Erban,et al. Multiscale reaction-diffusion simulations with Smoldyn , 2015, Bioinform..
[20] L. Pismen,et al. Multiscale modeling of tumor growth induced by circadian rhythm disruption in epithelial tissue , 2015, Journal of biological physics.
[21] Walter de Back,et al. Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology , 2014, Bioinform..
[22] Barbara Di Ventura,et al. From in vivo to in silico biology and back , 2006, Nature.
[23] Richard Lonsdale,et al. A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes , 2014, PLoS Comput. Biol..
[24] R. Eisen,et al. Meteorological conditions associated with increased incidence of West Nile virus disease in the United States, 2004-2012. , 2015, The American journal of tropical medicine and hygiene.
[25] Gregory A Voth,et al. Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.
[26] M. Eremets,et al. Ammonia as a case study for the spontaneous ionization of a simple hydrogen-bonded compound , 2014, Nature Communications.
[27] Cheng Luo,et al. Computational drug discovery , 2012, Acta Pharmacologica Sinica.
[28] Leng Han,et al. Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types , 2014, Nature Communications.
[29] A. Hoffmann,et al. A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins. , 2015, Journal of theoretical biology.
[30] M. Marathe,et al. Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection , 2013, PloS one.
[31] L. Preziosi,et al. A hybrid mathematical model for self-organizing cell migration in the zebrafish lateral line , 2013, Journal of mathematical biology.
[32] Lawrence H. Schwartz,et al. Survival and Death Signals Can Predict Tumor Response to Therapy After Oncogene Inactivation , 2011, Science Translational Medicine.
[33] Alissa M. Weaver,et al. Tumor Morphology and Phenotypic Evolution Driven by Selective Pressure from the Microenvironment , 2006, Cell.
[34] Alexey Solovyev,et al. A Multiscale Agent-Based in silico Model of Liver Fibrosis Progression , 2014, Front. Bioeng. Biotechnol..
[35] Ming Yang,et al. Modelling and simulating reaction-diffusion systems using coloured Petri nets , 2014, Comput. Biol. Medicine.
[36] Aravind Srinivasan,et al. Modelling disease outbreaks in realistic urban social networks , 2004, Nature.
[37] Alessandro Vespignani,et al. Spatiotemporal spread of the 2014 outbreak of Ebola virus disease in Liberia and the effectiveness of non-pharmaceutical interventions: a computational modelling analysis. , 2015, Lancet. Infectious Diseases (Print).
[38] W. Sloan,et al. Probabilistic Models to Describe the Dynamics of Migrating Microbial Communities , 2015, PloS one.
[39] Brittany E. Bannish,et al. Modelling fibrinolysis: a 3D stochastic multiscale model. , 2014, Mathematical medicine and biology : a journal of the IMA.
[40] E J Rayfield,et al. What makes an accurate and reliable subject-specific finite element model? A case study of an elephant femur , 2014, Journal of The Royal Society Interface.
[41] Joseph D Butner,et al. Simulating cancer growth with multiscale agent-based modeling. , 2015, Seminars in cancer biology.
[42] Peter Sorger,et al. New approaches to modeling complex biochemistry , 2011, Nature Methods.
[43] Peter Szolovits,et al. Text Mining in Cancer Gene and Pathway Prioritization , 2014, Cancer informatics.
[44] G. Braus,et al. One Juliet and four Romeos: VeA and its methyltransferases , 2015, Front. Microbiol..
[45] Nicholas A Cilfone,et al. Strategies for Efficient Numerical Implementation of Hybrid Multi-scale Agent-Based Models to Describe Biological Systems , 2014, Cellular and Molecular Bioengineering.
[46] Blerta Shtylla,et al. A Stochastic Multiscale Model That Explains the Segregation of Axonal Microtubules and Neurofilaments in Neurological Diseases , 2015, PLoS Comput. Biol..
[47] I. Kohane,et al. An Epidemiological Network Model for Disease Outbreak Detection , 2007, PLoS medicine.
[48] Didier Gonze,et al. A Model for the Epigenetic Switch Linking Inflammation to Cell Transformation: Deterministic and Stochastic Approaches , 2014, PLoS Comput. Biol..
[49] P. R. Buenzli,et al. A multiscale mechanobiological model of bone remodelling predicts site-specific bone loss in the femur during osteoporosis and mechanical disuse , 2015, Biomechanics and modeling in mechanobiology.
[50] P. Bentley,et al. The Role of Chromosome Missegregation in Cancer Development: A Theoretical Approach Using Agent-Based Modelling , 2013, PloS one.
[51] David Basanta,et al. Microenvironmental Variables Must Influence Intrinsic Phenotypic Parameters of Cancer Stem Cells to Affect Tumourigenicity , 2013, bioRxiv.
[52] John J. Tyson,et al. A Stochastic Model Correctly Predicts Changes in Budding Yeast Cell Cycle Dynamics upon Periodic Expression of CLN2 , 2014, PloS one.
[53] C. Tomlin,et al. Biology by numbers: mathematical modelling in developmental biology , 2007, Nature Reviews Genetics.
[54] W. L. Jorgensen. The Many Roles of Computation in Drug Discovery , 2004, Science.
[55] J. Bassaganya-Riera,et al. Multiscale modeling of mucosal immune responses , 2015, BMC Bioinformatics.
[56] Winston A Hide,et al. Big data: The future of biocuration , 2008, Nature.
[57] J. Glazier,et al. 3D Multi-Cell Simulation of Tumor Growth and Angiogenesis , 2009, PloS one.
[58] J. Fisher,et al. Emergent Stem Cell Homeostasis in the C. elegans Germline Is Revealed by Hybrid Modeling , 2015, Biophysical journal.
[59] Dirk Brockmann,et al. Spatial and Functional Heterogeneities Shape Collective Behavior of Tumor-Immune Networks , 2015, PLoS Comput. Biol..
[60] Athanassios Iliadis,et al. Mathematical modeling of tumor growth and metastatic spreading: validation in tumor-bearing mice. , 2014, Cancer research.
[61] Adilson E Motter,et al. Control of Stochastic and Induced Switching in Biophysical Networks. , 2015, Physical review. X.
[62] Stephanie R. Taylor,et al. Synchrony and entrainment properties of robust circadian oscillators , 2008, Journal of The Royal Society Interface.
[63] P. de Vos,et al. Immunological and Technical Considerations in Application of Alginate-Based Microencapsulation Systems , 2014, Front. Bioeng. Biotechnol..
[64] Peng Zhang,et al. Multiscale Particle-Based Modeling of Flowing Platelets in Blood Plasma Using Dissipative Particle Dynamics and Coarse Grained Molecular Dynamics , 2014, Cellular and molecular bioengineering.
[65] G. An,et al. Agent‐based models in translational systems biology , 2009, Wiley interdisciplinary reviews. Systems biology and medicine.
[66] Tamar Schlick,et al. Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study. , 2015, Journal of the American Chemical Society.
[67] Alfonso Caiazzo,et al. Multiscale modelling of palisade formation in gliobastoma multiforme. , 2014, Journal of theoretical biology.
[68] J. Carson. Introduction to modeling and simulation , 2005, Proceedings of the Winter Simulation Conference, 2005..
[69] James R. Faeder,et al. Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems , 2013, PLoS Comput. Biol..
[70] Robert B. Bourret,et al. Computer-Aided Resolution of an Experimental Paradox in Bacterial Chemotaxis , 1998, Journal of bacteriology.
[71] Adelinde M. Uhrmacher,et al. Rule-based multi-level modeling of cell biological systems , 2011, BMC Systems Biology.
[72] Edward W. Lowe,et al. Computational Methods in Drug Discovery , 2014, Pharmacological Reviews.
[73] Shayn M Peirce,et al. Multiscale computational models of complex biological systems. , 2013, Annual review of biomedical engineering.
[74] Kazuyuki Aihara,et al. A partial differential equation model and its reduction to an ordinary differential equation model for prostate tumor growth under intermittent hormone therapy , 2014, Journal of mathematical biology.
[75] O. Gandrillon,et al. The role of spatial organization of cells in erythropoiesis , 2013, Journal of mathematical biology.
[76] G. Nolan,et al. Computational solutions to large-scale data management and analysis , 2010, Nature Reviews Genetics.
[77] J Walpole,et al. Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks. , 2015, Integrative biology : quantitative biosciences from nano to macro.
[78] T. Elston,et al. Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.
[79] Andrew B. Goryachev,et al. Transition to Quorum Sensing in an Agrobacterium Population: A Stochastic Model , 2005, PLoS Comput. Biol..