Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation.

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works

Hierarchical Organization of Modularity in Metabolic Networks

Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., & Barabási, A.-L. (2002) · Science · doi:10.1126/science.1073374 · Cited by 4,224 · see citing works

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg015 · Cited by 3,060 · see citing works

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

Pawson, T. J., & Nash, P. (2003) · Science · doi:10.1126/science.1083653 · Cited by 1,403 · see citing works

Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors

Schoeberl, B., Eichler-Jonsson, C., Gilles, E. D., & Müller, G. I. (2002) · Nature Biotechnology · doi:10.1038/nbt0402-370 · Cited by 952 · see citing works

Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

Le Novere, N. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj092 · Cited by 762 · see citing works

Reactome: a knowledge base of biologic pathways and processes

Västrik, I., D’Eustachio, P., Schmidt, E., Geeta, J.-T., Gopinath, G., Croft, D. W., de Bono, B., Gillespie, M. E., Jassal, B., Lewis, S., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-3-r39 · Cited by 656 · see citing works

Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor

Kholodenko, B. Ν., Demin, O. V., Moehren, G., & Hoek, J. B. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.42.30169 · Cited by 618 · see citing works

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

Karp, P. D. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki892 · Cited by 611 · see citing works

Domains, Motifs, and Scaffolds: The Role of Modular Interactions in the Evolution and Wiring of Cell Signaling Circuits

Bhattacharyya, R. P., Reményi, A., Yeh, B. J., & Lim, W. A. (2006) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.75.103004.142710 · Cited by 449 · see citing works

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

Blinov, M. L., Faeder, J. R., Goldstein, B., & Hlavacek, W. S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth378 · Cited by 430 · see citing works

The Virtual Cell: a software environment for computational cell biology

Loew, L. M., & Schaff, J. C. (2001) · Trends in biotechnology · doi:10.1016/s0167-7799(01)01740-1 · Cited by 406 · see citing works

Rules for Modeling Signal-Transduction Systems

Hlavacek, W. S., Faeder, J. R., Blinov, M. L., Posner, R. G., Hucka, M., & Fontana, W. (2006) · Science's STKE · doi:10.1126/stke.3442006re6 · Cited by 350 · see citing works

CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse

Li, Q.-J., Dinner, A. R., Qi, S., Irvine, D. J., Huppa, J. B., Davis, M. M., & Chakraborty, A. K. (2004) · Nature Immunology · doi:10.1038/ni1095 · Cited by 232 · see citing works

Investigation of Early Events in FcεRI-Mediated Signaling Using a Detailed Mathematical Model

Faeder, J. R., Hlavacek, W. S., Reischl, I. G., Blinov, M. L., Metzger, H., Redondo, A., Wofsy, C., & Goldstein, B. (2003) · The Journal of Immunology · doi:10.4049/jimmunol.170.7.3769 · Cited by 165 · see citing works

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity

Blinov, M. L., Faeder, J. R., Goldstein, B., & Hlavacek, W. S. (2005) · Biosystems · doi:10.1016/j.biosystems.2005.06.014 · Cited by 161 · see citing works

Automatic generation of cellular reaction networks with Moleculizer 1.0

Lok, L., & Brent, R. (2005) · Nature Biotechnology · doi:10.1038/nbt1054 · Cited by 159 · see citing works

Rule‐based modeling of biochemical networks

Faeder, J. R., Blinov, M. L., Goldstein, B., & Hlavacek, W. S. (2005) · Complexity · doi:10.1002/cplx.20074 · Cited by 120 · see citing works

PAX of mind for pathway researchers

Luciano, J. (2005) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03501-4 · Cited by 107 · see citing works

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology

Laibe, C., & Novère, N. G. L. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-58 · Cited by 102 · see citing works

Structure-Based Kinetic Models of Modular Signaling Protein Function: Focus on Shp2

Barua, D., Faeder, J. R., & Haugh, J. M. (2007) · Biophysical Journal · doi:10.1529/biophysj.106.093484 · Cited by 41 · see citing works

Mining Clinical Data with a Temporal Dimension: A Case Study

Berlingerio, M., Bonchi, F., Giannotti, F., & Turini, F. (2007) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2007.42 · Cited by 35 · see citing works

Intracellular Signaling: Spatial and Temporal Control

Moraru, I. I., & Loew, L. M. (2005) · Physiology · doi:10.1152/physiol.00052.2004 · Cited by 27 · see citing works

Kinetic Modeling Using BioPAX Ontology

Ruebenacker, O., Moraru, I. I., Schaff, J. C., & Blinov, M. L. (2007) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2007.55 · Cited by 15 · see citing works

Think Simulation - Think Experiment: The Virtual Cell Paradigm

Moraru, I. I., Schaff, J. C., & Loew, L. M. (2006) · Winter Simulation Conference · doi:10.1109/wsc.2006.322947 · Cited by 4 · see citing works

Think simulation - think experiment: the virtual cell paradigm

Moraru, I. I., Schaff, J. C., & Loew, L. M. (2006) · Winter Simulation Conference · doi:10.5555/1218112.1218423 · Cited by 3 · see citing works

XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes

Blinov, M. L., & Moraru, I. I. (2007) · IEEE International Conference on Bioinformatics and Bioengineering (BIBE) · doi:10.1109/bibe.2007.4375678 · Cited by 1 · see citing works

The Natural and Engineered 3D Microenvironment as a Regulatory Cue During Stem Cell Fate Determination

Lund, A. W., Yener, B., Stegemann, J. P., & Plopper, G. E. (2009) · Tissue Engineering Part B Reviews · doi:10.1089/ten.teb.2009.0270 · Cited by 178 · see citing works

Molecular machines or pleiomorphic ensembles: signaling complexes revisited

Mayer, B. J., Blinov, M. L., & Loew, L. M. (2009) · Journal of Biology · doi:10.1186/jbiol185 · Cited by 85 · see citing works

Compartmental rule-based modeling of biochemical systems

Harris, L. A., Hogg, J., & Faeder, J. R. (2009) · Winter Simulation Conference · doi:10.1109/wsc.2009.5429719 · Cited by 38 · see citing works

Physiologically Based Pharmacokinetic Modeling of Nanoparticle Biodistribution: A Review of Existing Models, Simulation Software, and Data Analysis Tools

Kutumova, E. O., Akberdin, I. R., Kiselev, I. N., Sharipov, R., Egorova, V. S., Syrocheva, A. O., Parodi, A., Zamyatnin, A. A., & Kolpakov, F. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232012560 · Cited by 38 · see citing works

Integrating BioPAX pathway knowledge with SBML models

Ruebenacker, O., Moraru, I. I., Schaff, J. C., & Blinov, M. L. (2009) · IET Systems Biology · doi:10.1049/iet-syb.2009.0007 · Cited by 30 · see citing works

Toward modular biological models: defining analog modules based on referent physiological mechanisms

Petersen, B. K., Ropella, G. E. P., & Hunt, C. A. (2014) · BMC Systems Biology · doi:10.1186/s12918-014-0095-1 · Cited by 25 · see citing works

Annotation of SBML Models Through Rule-Based Semantic IntegrationPreprint

Lister, A., Lord, P., Pocock, M., & Wipat, A. (2009) · Nature Precedings · doi:10.1038/npre.2009.3286.1 · Cited by 25 · see citing works

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization

Misirli, G., Cavaliere, M., Waites, W., Pocock, M. R., Madsen, C., Gilfellon, O., Honorato-Zimmer, R., Zuliani, P., Danos, V., & Wipat, A. (2015) · Bioinform. · doi:10.1093/bioinformatics/btv660 · Cited by 21 · see citing works

A Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle

Akberdin, I. R., Kiselev, I. N., Pintus, S. S., Sharipov, R., Vertyshev, A. Y., Виноградова, О. Л., Викторович, П. Д., & Kolpakov, F. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910353 · Cited by 19 · see citing works

Thoroughly Calibrated Modular Agent-Based Model of the Human Cardiovascular and Renal Systems for Blood Pressure Regulation in Health and Disease

Kutumova, E., Kiselev, I., Sharipov, R., Lifshits, G., & Kolpakov, F. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.746300 · Cited by 16 · see citing works

CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation

Michalski, P. J., & Loew, L. M. (2012) · Physical Biology · doi:10.1088/1478-3975/9/3/036010 · Cited by 17 · see citing works

A framework for multi-scale intervention modeling: virtual cohorts, virtual clinical trials, and model-to-model comparisons

Michael, C. T., Almohri, S. A., Linderman, J. J., & Kirschner, D. E. (2024) · Frontiers in Systems Biology · doi:10.3389/fsysb.2023.1283341 · Cited by 16 · see citing works

Electronic characterisation of atomistic modelling based electrically doped nano bio p‐i‐n FET

Dey, D., Roy, P., & De, D. (2016) · IET Computers & Digital Techniques · doi:10.1049/iet-cdt.2015.0156 · Cited by 15 · see citing works

Compositional modelling of signalling pathways in timed concurrent constraint programming

Chiarugi, D., Falaschi, M., Olarte, C. A., & Catuscia Palamidessi, A. (2010) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/1854776.1854843 · Cited by 12 · see citing works

Advances in Rule-based Modeling: Compartments, Energy, and Hybrid Simulation, with Application to Sepsis and Cell Signaling

Hogg, J. (2013) · D-Scholarship@Pitt (University of Pittsburgh) · Cited by 11 · see citing works

Rule-based epidemic models

Waites, W., Cavaliere, M., Manheim, D., Panovska‐Griffiths, J., & Vincent Danos, A. (2021) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2021.110851 · Cited by 11 · see citing works

Model-driven engineering of supramolecular buffering by multivalency

Paffen, T. F. E., Teunissen, A. J. P., de Greef, T. F. A., & Meijer, E. W. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1710993114 · Cited by 9 · see citing works

Modular Representation of Physiologically Based Pharmacokinetic Models: Nanoparticle Delivery to Solid Tumors in Mice as an Example

Kutumova, E. O., Akberdin, I. R., Kiselev, I. N., Sharipov, R., & Kolpakov, F. (2022) · Mathematics · doi:10.3390/math10071176 · Cited by 4 · see citing works

Modeling without Borders: Creating and Annotating VCell Models Using the Web

Blinov, M. L., Ruebenacker, O., Schaff, J. C., & Moraru, I. I. (2010) · Lecture notes in computer science · doi:10.1007/978-3-642-13078-6_3 · Cited by 3 · see citing works

A Declarative View of Signaling Pathways

Chiarugi, D., Falaschi, M., Olarte, C. A., & Catuscia Palamidessi, A. (2015) · Lecture notes in computer science · doi:10.1007/978-3-319-25527-9_13 · Cited by 3 · see citing works

A Systems Biology Approach Towards a Comprehensive Understanding of Ferroptosis

Arbatskiy, M. S., Balandin, D. E., Akberdin, I. R., & Churov, A. V. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252111782 · Cited by 3 · see citing works

Using views of Systems Biology Cloud: application for model building

Ruebenacker, O., & Blinov, M. L. (2010) · Theory in Biosciences · doi:10.1007/s12064-010-0108-6 · Cited by 2 · see citing works

Annotations for Rule-Based Models

Cavaliere, M., Danos, V., Honorato-Zimmer, R., & Waites, W. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-9102-0_13 · Cited by 1 · see citing works

Scaling up epidemiological models with rule-based modellingPreprint

Waites, W., Cavaliere, M., Manheim, D., Panovska‐Griffiths, J., & Vincent Danos, A. (2020) · HAL · Cited by 1 · see citing works

Systems Biology Pathway Exchange (SBPAX)

Ruebenacker, O. (2013) · Springer eBooks · doi:10.1007/978-1-4419-9863-7_1112 · Cited by 1 · see citing works

Automatic generation of cellular reaction networks with Moleculizer 1.0

Lok, L., & Brent, R. (2005) · Nature Biotechnology · doi:10.1038/nbt1054 · Cited by 159 · see citing works

Using Rules & Pathway Databases to Create Quantitative Mechanistic Models in Virtual Cell

Blinov, M. L., Vasilescu, D. D., Schaff, J. C., Moraru, I. I., & Loew, L. M. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2014.11.2586

Large Scale, High Resolution Models of Receptor Tyrosine Kinase Signaling Networks

Stites, E. C., Creamer, M. S., Aziz, M., Hlavacek, W. S., & Posner, R. G. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2011.11.2812

Leveraging Modeling Approaches: Reaction Networks and Rules

Blinov, M. L., & Moraru, I. I. (2011) · Advances in experimental medicine and biology · doi:10.1007/978-1-4419-7210-1_30 · Cited by 7 · see citing works

Chapter 30 Leveraging Modeling Approaches: Reaction Networks and

Blinov, M. L., Moraru, I. I., Blinov, M. L., & Moraru, I. I. (2013)