COPASI's Use In Computational Method

Matzko RO, Konur S (2024) BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering. Bioinformatics Advances 4:vbae046 Computational Method Software Link

1 publication
Diamataris IG, Peristeras LD, Papavasileiou KD, Melissas VS, Boulougouris GC (2023) Statistical Inference of Rate Constants in Chemical and Biochemical Reaction Networks Using an “Inverse” Event-Driven Kinetic Monte Carlo Method. Journal of Physical Chemistry B 127:9132–9143 Computational Method Link
Garay Ruiz D (2023) Unweaving complex reactivity: graph-based tools to handle chemical reaction networks. TDX (Tesis Doctorals en Xarxa). Ph.D. Thesis, Universitat Rovira i Virgili, Tarragona, Spain Computational Method Link
Lauterbach S, Dienhart H, Range J, Malzacher S, Spöring J-D, Rother D, Pinto MF, Martins P, Lagerman CE, Bommarius AS, Høst AV, Woodley JM, Ngubane S, Kudanga T, Bergmann FT, Rohwer JM, Iglezakis D, Weidemann A, Wittig U, Kettner C, Swainston N, Schnell S, Pleiss J (2023) EnzymeML: seamless data flow and modeling of enzymatic data. Nature Methods 20:400–402 Computational Method Enzymology Link
Maeda K, Kurata H (2023) Automatic Generation of SBML Kinetic Models from Natural Language Texts Using GPT. International Journal of Molecular Sciences 24:7296 Computational Method Link
Mendes P (2023) Reproducibility and FAIR principles: the case of a segment polarity network model. Frontiers in Cell and Developmental Biology 11:1201673 Genetics Signaling Computational Method Link
Mutsuddy A, Erdem C, Huggins JR, Salim M, Cook D, Hobbs N, Feltus FA, Birtwistle MR (2023) Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format. Bioinformatics Advances 3:vbad039 Computational Method Link
Niehren J, Lhoussaine C, Vaginay A (2023) Core SBML and its Formal Semantics. Paper presented at the CMSB 2023 - 21th International Conference on Formal Methods in Systems Biology. Luxembourg. Computational Method Link
Yuan S, Chen S, Yang Y (2023) Dimension Reduction for Dynamic Analysis of Gene Expression Data Using Variational Autoencoder. 2023 IEEE 13th International Conference on CYBER Technology in Automation, Control, and Intelligent Systems (CYBER), 988–991. Computational Method Link

8 publications
Bauerstätter P (2022) Compartment Modeling of Overweight in Toddler Age: Modeling and Simulating a Diets Effect with COPASI. SNE Simulation Notes Europe 32:221–224 Physiology Computational Method Link
Bergman D, Marazzi L, Chowkwale M, Maheshvare M D, Bidanta S, Mapder T, Li J (2022) PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell. Gigabyte 2022:1–11 Computational Method Pharmacology Link
Daas JCJ, Förster J, Pahle J (2022) Dynamic publication media with the COPASI R Connector (CoRC). Mathematical Biosciences 348:108822 Computational Method Link
Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR (2022) A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nature Communications 13:3555 Computational Method Signaling Link
Esposito M, Picchiami L (2022) A Comparative Study of AI Search Methods for Personalised Cancer Therapy Synthesis in COPASI. In: Bandini S, Gasparini F, Mascardi V, Palmonari M and Vizzari G (eds) AIxIA 2021 – Advances in Artificial Intelligence. Lecture Notes in Computer Science 13196:638–654 Pharmacology Physiology Computational Method Link
Garay-Ruiz D, Bo C (2022) Chemical reaction network knowledge graphs: the OntoRXN ontology. Journal of Cheminformatics 14:29 Software Computational Method Link
Greenyer H (2022) Evaluation of network inference algorithms and their effects on network analysis for the study of small metabolomic data sets. MS Thesis, University of Victoria, Canada. Computational Method Metabolism Link
Kumar S (2022) Compact, Causal and Multivariate Functional Statistics in Model-Free Discrete Pattern Discovery. Ph.D. Thesis, New Mexico State University, USA. Computational Method Link
Lee JY, Styczynski MP (2022) Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework. Scientific Reports 12:762 Computational Method Metabolism Link
Lo-Thong-Viramoutou O, Charton P, Cadet XF, Grondin-Perez B, Saavedra E, Damour C, Cadet F (2022) Non-linearity of Metabolic Pathways Critically Influences the Choice of Machine Learning Model. Frontiers in Artificial Intelligence 5:744755 Computational Method Link
Maestri S, Merelli E, Pettini M (2022) Agent-based models for detecting the driving forces of biomolecular interactions. Scientific Reports 12:1878 Computational Method Metabolism Link
Marazzi L, Shah M, Balakrishnan S, Patil A, Vera-Licona P (2022) NETISCE: a network-based tool for cell fate reprogramming. npj Systems Biology and Applications 8:21 Computational Method Link
Ramachandran K, König M, Scharm M, Nguyen TVN, Hermjakob H, Waltemath D, Sheriff RSM (2022) FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast. Preprints 2022060137 Computational Method Epidemiology Link
Range J, Halupczok C, Lohmann J, Swainston N, Kettner C, Bergmann FT, Weidemann A, Wittig U, Schnell S, Pleiss J (2022) EnzymeML-a data exchange format for biocatalysis and enzymology. FEBS Journal 289:5864–5874 Enzymology Computational Method Link
Santos JPG, Pajo K, Trpevski D, Stepaniuk A, Eriksson O, Nair AG, Keller D, Hellgren Kotaleski J, Kramer A (2022) A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience. Neuroinformatics 20:241–259 Computational Method Link
Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Malik-Sheriff RS, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep JL, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk DD, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR (2022) BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research 50: W108–W114 Computational Method Link
Wysocka EM, Page M, Snowden J, Simpson TI (2022) Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network. PeerJ 10:e14516 Computational Method Link
Yuan L, Wu C, Guo X, Yang C (2022) ParaCopasi: A package for parallel biochemical simulation and analysis. Journal of Computational Chemistry 43:144–154 Computational Method Software Link

18 publications
Acón M, Geiß C, Torres-Calvo J, Bravo-Estupiñan D, Oviedo G, Arias-Arias JL, Rojas-Matey LA, Baez E, Vásquez-Vargas G, Oses-Vargas Y, Guevara-Coto J, Segura-Castillo A, Siles-Canales F, Quirós-Barrantes S, Régnier-Vigouroux A, Mendes P, Mora-Rodríguez R (2021) MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer. iScience 24:103407 Genetics Biochemistry Computational Method Link
Bhalla US (2021) HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks. PLoS Computational Biology 17:e1009621 Computational Method Link
Esposito M, Picchiami L (2021) Intelligent Search for Personalized Cancer Therapy Synthesis: an Experimental Comparison. In: Benedictis RD, Maratea M, Micheli A, Scala E, Serina I, Vallati M, et al. (eds) Proceedings of the 9th Italian workshop on Planning and Scheduling (IPS’21) and the 28th International Workshop on “Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion” (RCRA’21) with CEUR-WS. Milan, Italy. Physiology Computational Method Link
Fischer S, Dinh M, Henry V, Robert P, Goelzer A, Fromion V (2021) BiPSim: a flexible and generic stochastic simulator for polymerization processes. Scientific Reports 11:14112 Computational Method Link
Koshy-Chenthittayil S, Dimitrova E, Jenkins EW, Dean BC (2021) A computational framework for finding parameter sets associated with chaotic dynamics. In Silico Biology 14:41–51 Computational Method Link
Lakhova TN, Kazantsev FV, Lashin SA, Matushkin YG (2021) The finding and researching algorithm for potentially oscillating enzymatic systems. Vavilov Journal of Genetics and Breeding 25:318–330 Computational Method Metabolism Link
Marchisio MA (2021) Modular Modeling of Genetic Circuits in SBML Level 3. Methods in Molecular Biology 2189:45–63 Synthethic Biology Computational Method Link
Mısırlı G, Yang B, James K, Wipat A (2021) Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology 10:3304–3315 Computational Method Synthetic Biology Link
Rampadarath AK, Nickerson DP (2021) Automated Execution of Simulation Studies in Systems Medicine Using SED-ML and COMBINE Archive. Systems Medicine 3:423–430 Computational Method Link
Ritis D, Boulougouris GC (2021) On the hierarchical design of biochemical-based digital computations. Computers in Biology and Medicine 135:104630 Computational Method Theory Link
Schmiester L, Schälte Y, Bergmann FT, Camba T, Dudkin E, Egert J, Fröhlich F, Fuhrmann L, Hauber AL, Kemmer S, Lakrisenko P, Loos C, Merkt S, Müller W, Pathirana D, Raimúndez E, Refisch L, Rosenblatt M, Stapor PL, Städter P, Wang D, Wieland F-G, Banga JR, Timmer J, Villaverde AF, Sahle S, Kreutz C, Hasenauer J, Weindl D (2021) PEtab-Interoperable specification of parameter estimation problems in systems biology. PLoS Computational Biology 17:e1008646 Computational Method Link
Städter P, Schälte Y, Schmiester L, Hasenauer J, Stapor PL (2021) Benchmarking of numerical integration methods for ODE models of biological systems. Scientific Reports 11:2696 Computational Method Link
Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif Shohan MU, Xavier A, Maire M, Zyoud A, Men J, Ng S, Nguyen TVN, Glont M, Hermjakob H, Malik-Sheriff RS (2021) Reproducibility in systems biology modelling. Molecular Systems Biology 17:e9982 Computational Method Link
Tomasoni D, Paris A, Giampiccolo S, Reali F, Simoni G, Marchetti L, Kaddi C, Neves-Zaph S, Priami C, Azer K, Lombardo R (2021) QSPcc reduces bottlenecks in computational model simulations. Communications Biology 4:1022 Computational Method Software Link
Vaginay A, Boukhobza T, Smaïl-Tabbone M (2021) From quantitative SBML models to boolean networks. CNA 2021 - 10th International Conference on Complex Networks and their Applications, Nov 2021, Madrid, Spain. Computational Method Link
Yeom J-S, Georgouli K, Blake R, Navid A (2021) Towards dynamic simulation of a whole cell model. In: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 1–4, 2021, Gainesville, FL, USA, pp. 1–10. DOI:10.1145/3459930.3471161 Computational Method Link

16 publications
Ajjolli Nagaraja A, Charton P, Cadet XF, Fontaine N, Delsaut M, Wiltschi B, Voit A, Offmann B, Damour C, Grondin-Perez B, Cadet F (2020) A Machine Learning Approach for Efficient Selection of Enzyme Concentrations and Its Application for Flux Optimization. Catalysts 10:291 Computational Method Metabolism Link
Desoeuvres A, Trombettoni G, Radulescu O (2020) Interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity. In: Abate A, Petrov T and Wolf V (eds.) Computational Methods in Systems Biology. Springer International Publishing, 79–101 Computational Method Link
Dromms RA, Lee JY, Styczynski MP (2020) LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism. BMC Bioinformatics 21:93 Computational Method Metabolism Link
Glont M, Arankalle C, Tiwari K, Nguyen TVN, Hermjakob H, Malik-Sheriff RS (2020) BioModels Parameters: a treasure trove of parameter values from published systems biology models. Bioinformatics 36:4649–4654 Computational Method Link
Hinze T (2020) Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis. Journal of Membrane Computing 2:281–289 Computational Method Link
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H (2020) BioModels—15 years of sharing computational models in life science. Nucleic Acids Research 48:D407–D415 Computational Method Link
Mochão H, Barahona P, Costa RS (2020) KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. Database 2020:baaa093 Computational Method Link
Sotnikov DV, Byzova NA, Zvereva EA, Bartosh AV, Zherdev AV, Dzantiev BB (2020) Mathematical modeling of immunochromatographic test systems in a competitive format: Analytical and numerical approaches. Biochemical Engineering Journal 164:107763 Computational Method Laboratory Method Link
Vargas-Villamil LM, Tedeschi LO, Medina-Peralta S, Izquierdo-Reyes F, Navarro-Alberto J, González-Garduño R (2020) A multi-inverse approach for a holistic understanding of applied animal science systems. Animal 14:s238–s249 Computational Method Physiology Link

9 publications
Boba P (2019) Graphenrekonstruktion anhand abhängiger Zeitreihen in biologischen Netzwerken. Ph.D. Thesis, Technische Universität Darmstadt, Germany. Computational Method Link
Broto Vispe JM (2019) Adding new functionality to COPASI, a software for simulation of biological circuits in systems biology. Bachelors Thesis, Universitat de Lleida, Spain. Computational Method Link
Iancu B, Sanwal U, Gratie C, Petre I (2019) Refinement-based modeling of the ErbB signaling pathway. Computers in Biology and Medicine 106:91–96 Signaling Computational Method Link
Jahagirdar S, Suarez-Diez M, Saccenti E (2019) Simulation and Reconstruction of Metabolite-Metabolite Association Networks Using a Metabolic Dynamic Model and Correlation Based Algorithms. Journal of Proteome Research 18:1099–1113 Computational Method Metabolism Link
Koeman M, Engel J, Jansen J, Buydens L (2019) Critical comparison of methods for fault diagnosis in metabolomics data. Scientific Reports 9:1123 Metabolism Computational Method Link
Madec M (2019) Systemes heterogenes : outils CAO et applications a la biologie. Habilitation Thesis, Universite de Strasbourg, France. Computational Method Link
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H (2020) BioModels—15 years of sharing computational models in life science. Nucleic Acids Research 48:D407–D415 Software Computational Method Link
Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA (2019) Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB). Methods in Molecular Biology 1945:119–139 Computational Method Link
Pollice R (2019) A General Fitting Function to Estimate Apparent Reaction Orders of Kinetic Profiles. chemrxiv doi:10.26434/chemrxiv.7885760.v1 Computational Method Link
Revell JD (2019) Parameter inference for stochastic biological models. Ph.D. Thesis, Newcastle University, UK. Computational Method Link
Ruggiero S, Versypt A (2019) SMBLtoODEpy: A software program for converting SBML models into ODE models in Python. Journal of Open Source Software 4:1643 Computational Method Link
Stalidzans E, Landmane K, Sulins J, Sahle S (2019) Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs. Mathematical Biosciences 307:25–32 Computational Method Link
Stanbury DM, Harshman J (2019) Large-Scale Models of Radiation Chemistry and the Principle of Detailed Balancing. Journal of Physical Chemistry 123:10240–10245 Chemistry Computational Method Link
Yeoh JW, Ng KBI, Teh AY, Zhang J, Chee WKD, Poh CL (2019) An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs. ACS Synthetic Biology 8:1484–1497 Synthetic Biology Computational Method Link
Yvinec R, Ayoub MA, De Pascali F, Crépieux P, Reiter E, Poupon A (2019) Workflow Description to Dynamically Model β-Arrestin Signaling Networks. Methods in Molecular Biology 1957:195–215 Signaling Computational Method Link

15 publications
Beneš N, Brim L, Pastva S, Šafránek D, Troják M, Červenỳ J, Šalagovič J (2018) Fully Automated Attractor Analysis of Cyanobacteria Models. 2018 22nd International Conference on System Theory, Control and Computing (ICSTCC). pp. 354–359 Computational Method Link
Folch-Fortuny A, Teusink B, Hoefsloot HC, Smilde AK, Ferrer A (2018) Dynamic elementary mode modelling of non-steady state flux data. BMC Systems Biology 12:71 Computational Method Link
Gupta A, Mendes P (2018) An overview of network-based and-free approaches for stochastic simulation of biochemical systems. Computation 6:9 Computational Method Link
Jones Jr TC, Hoops S, Watson LT, Palmisano A, Tyson JJ, Shaffer CA (2018) JigCell Model Connector: building large molecular network models from components. SIMULATION 94:993–1008 Computational Method Software Link
Kim J, Woo SS, Sarpeshkar R (2018) Fast and precise emulation of stochastic biochemical reaction networks with amplified thermal noise in silicon chips. IEEE Transactions on Biomedical Circuits and Systems 12:379–389 Computational Method Link
Revell JD, Zuliani P (2018) Stochastic Rate Parameter Inference Using the Cross-Entropy Method. In: Češka M., Šafránek D. (eds.) Computational Methods in Systems Biology. CMSB2018. Lecture Notes in Computer Science, vol 11095. Springer, Cham pp.146–164 Computational Method Link
Šalagovič J (2018) Computational analysis and model integration of biorhythmic systems. Masters Thesis, Masaryk University, Faculty of Informatics, Czech Republic Metabolism Microbiology Computational Method Link
Scharm M (2018) Improving Reproducibility and Reuse of Modelling Results in the Life Sciences. Ph.D. Thesis, University of Rostock, Germany Computational Method Link
Welsh CM, Fullard N, Proctor CJ, Martinez-Guimera A, Isfort RJ, Bascom CC, Tasseff R, Przyborski SA, Shanley DP (2018) PyCoTools: A Python Toolbox for COPASI. Bioinformatics 34:3702–3710 Computational Method Software Link
Woo SS, Kim J, Sarpeshkar R (2018) A Digitally Programmable Cytomorphic Chip for Simulation of Arbitrary Biochemical Reaction Networks. IEEE Transactions on Biomedical Circuits and Systems 12:360–378 Computational Method Link

10 publications
Aguilera LU, Zimmer C, Kummer U (2017) A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study. BMC Systems Biology 11:26 Computational Method Immunology Link
Appleton E, Madsen C, Roehner N, Densmore D (2017) Design Automation in Synthetic Biology. Cold Spring Harbor Perspectives in Biology 9:a023978 Synthetic Biology Computational Method Link
Chua HE, Bhowmick SS, Tucker-Kellogg L (2017) Synergistic target combination prediction from curated signaling networks: Machine learning meets systems biology and pharmacology. Methods 129:60–80 Computational Method Software Link
Dalle Pezze P, Le Novère N (2017) SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology 11:46 Computational Method Software Link
Elsts A, Pentjuss A, Stalidzans E (2017) SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments. Bioinformatics 33:2966–2967 Software Computational Method Link
Fortuny AF (2017) Chemometric Approaches for Systems Biology. Ph.D. Thesis, Universitat Politècnica de València, Spain. Computational Method Link
Fribourg M, Logothetis DE, González-Maeso J, Sealfon SC, Galocha-Iragüen B, Andrés FL-H, Brezina V (2017) Elucidation of molecular kinetic schemes from macroscopic traces using system identification. PLoS Computational Biology 13:e1005376 Computational Method Link
Greene JL, Wäechter A, Tyo KE, Broadbelt LJ (2017) Acceleration Strategies to Enhance Metabolic Ensemble Modeling Performance. Biophysical Journal 113:1150–1162 Computational Method Link
Hendrickx DM, Souza T, Jennen DG, Kleinjans JC (2017) DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. Archives of Toxicology 91:2343–2352 Computational Method Toxicology Link
Ismail AM, Mohamad MS, Abdul Majid H, Abas KH, Deris S, Zaki N, Mohd Hashim SZ, Ibrahim Z, Remli MA (2017) An improved hybrid of particle swarm optimization and the gravitational search algorithm to produce a kinetic parameter estimation of aspartate biochemical pathways. BioSystems 162:81–89 Computational Method Link
Komasilovs V, Pentjuss A, Elsts A, Stalidzans E (2017) Total enzyme activity constraint and homeostatic constraint impact on the optimization potential of a kinetic model. BioSystems 162:128-134 Computational Method Biotechnology Link
Marchetti L, Lombardo R, Priami C (2017) HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks. Complexity 2017:1–12 Computational Method Link
Nakatani-Webster E, Nath A (2017) Inferring Mechanistic Parameters from Amyloid Formation Kinetics by Approximate Bayesian Computation. Biophysical Journal 112:868–880 Macromolecular Biochemistry Computational Method Link
Simak M, Yeang C-H, Lu HH-S (2017) Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae. PLoS One 12:e0185475 Computational Method Link
Stalidzans E, Mozga I, Sulins J, Zikmanis P (2017) Search for a Minimal Set of Parameters by Assessing the Total Optimization Potential for a Dynamic Model of a Biochemical Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14:978–985 Computational Method Biotechnology Link
Zimmer C, Yaesoubi R, Cohen T (2017) A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models. PLoS Computational Biology 13:e1005257 Computational Method Link

16 publications
Bergmann FT, Sahle S, Zimmer C (2016) Piecewise parameter estimation for stochastic models in COPASI. Bioinformatics 32:1586–1588 Computational Method Link
Ganesan N, Li J, Sharma V, Jiang H, Compagnoni A (2016) Process Simulation of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively Parallel Computing Platforms. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13:365–379 Computational Method Link
Hamgini BB (2016) Petri net siphon analysis and network centrality measures for identifying combination therapies in signaling pathways. Ph.D. Thesis, Queen’s University, Kingston, Ontario, Canada Computational Method Link
Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D (2016) Notions of similarity for systems biology models. Briefings in Bioinformatics 19:77–88 Computational Method Link
Hoops S, Hontecillas R, Abedi V, Leber A, Philipson CW, Carbo A, Bassaganya-Riera J (2016) Chapter 5 - Ordinary Differential Equations (ODEs) Based Modeling. In: Bassaganya-Riera J (ed) Computational Immunology. Academic Press, 63–78. Computational Method Software Link
Julien-Laferrière A (2016) Models and algorithms applied to metabolism: From revealing the responses to perturbations towards the design of microbial consortia. Ph.D. Thesis, Université Lyon 1-Claude Bernard, France Computational Method Metabolism Microbiology Link
Michalak P, Sobral BW, Abedi V, Kim YB, Deng X, Philipson CW, Viladomiu M, Lu P, Wendelsdorf K, Hontecillas R, Bassaganya-Riera J (2016) From Big Data Analytics and Network Inference to Systems Modeling. In: Bassaganya-Riera J (ed) Computational Immunology, Academic Press, 113–144. Computational Method Immunology Link
Mizeranschi A, Swain MT, Scona R, Fazilleau Q, Bosak B, Piontek T, Kopta P, Thompson P, Dubitzky W (2016) MultiGrain/MAPPER: A distributed multiscale computing approach to modeling and simulating gene regulation networks. Future Generation Computer Systems 63:1–14 Computational Method Link
Panchal C, Azimi S, Petre I (2016) Generating the Logicome of a Biological Network. International Conference on Algorithms for Computational Biology. Springer, 38–49 Computational Method Signaling Link
Samal SS (2016) Analysis of biochemical reaction networks using tropical and polyhedral geometry methods. Ph.D. Thesis, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany Computational Method Theory Link
Scharm M, Waltemath D (2016) A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5:2421 Computational Method Link
Vinciotti V, Augugliaro L, Abbruzzo A, Wit EC (2016) Model selection for factorial Gaussian graphical models with an application to dynamic regulatory networks. Statistical Applications in Genetics and Molecular Biology 15:193–212 Computational Method Link
Walker MA, Madduri R, Rodriguez A, Greenstein JL, Winslow RL (2016) Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models. Biophysical Journal 110:1038–1043 Computational Method Link
Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PEP, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DFH, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knüpfer C, König M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song J-H, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F (2016) Toward Community Standards and Software for Whole-Cell Modeling. IEEE Transactions on Biomedical Engineering 63:2007–2014 Computational Method Whole-Cell Models Link
Woods ML, Barnes CP (2016) Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair. PLoS Computational Biology 12:e1005131 Computational Method Link
Zimmer C, Bergmann FT, Sahle S (2016) Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation. arXiv preprint arXiv:1601.04458 Computational Method Link
Zimmer C (2016) Experimental Design for Stochastic Models of Nonlinear Signaling Pathways Using an Interval-Wise Linear Noise Approximation and State Estimation. PLoS One 11:e0159902 Computational Method Link
Zimmer C, Sahle S (2016) Comparison of approaches for parameter estimation on stochastic models: Generic least squares versus specialized approaches. Computational Biology and Chemistry 61:75–85 Computational Method Link

18 publications
Azimi S, Czeizler E, Gratie C, Gratie D, Iancu B, Ibssa N, Petre I, Rogojin V, Shadbahr T, Shokri F (2015) An Excursion Through Quantitative Model Refinement. Lecture Notes in Computer Science 9504:25-47 Computational Method Software Link
Bodei C, Bortolussi L, Chiarugi D, Guerriero ML, Policriti A, Romanel A (2015) On the impact of discreteness and abstractions on modelling noise in gene regulatory networks. Computational Biology and Chemistry 56:98-1089 Computational Method Link
Dromms RA, Styczynski MP (2015) Improved metabolite profile smoothing for flux estimation. Molecular BioSystems 11:2394-2405 Computational Method Laboratory Method Link
Hinze T, Kirkici K, Sauer P, Sauer P, Behre J (2015) Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential. Lecture Notes in Computer Science 9504:215-235 Computational Method Link
Koutsouradis E, Provelengios G, Kouskoumvekakis E, Manolakos ES (2015) Scalable FPGA Accelerator of the NRM Algorithm for Efficient Stochastic Simulation of Large-Scale Biochemical Reaction Networks. in 2015 Euromicro Conference on Digital System Design (DSD) pp.583-590 Computational Method Link
Lu P, Abedi V, Mei Y, Hontecillas R, Hoops S, Carbo A, Bassaganya-Riera J (2015) Supervised learning methods in modeling of CD4+ T cell heterogeneity. BioData Mining 8:1-21 Computational Method Immunology Link
Madsen C, Shmarov F, Zuliani P (2015) BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models. Proceedings 13th International Conference, CMSB 2015 (Roux O, Bourdon J, Eds.), Springer pp182-94 Computational Method Link
Phelix CF, Feltus FA (2015) Plant stress biomarkers from biosimulations: the Transcriptome-To-Metabolome(TTM) technology-effects of drought stress on rice. Plant Biology 17:63-73 Computational Method Plant Biology Link
Rezgui A, Madec M, Lallement C, Haiech J (2015) Integration of SBML models for the description of biological system in a lab-on-chip. Proceedings of the 22nd International Conference Mixed Design of Integrated Circuits & Systems 165-70 Computational Method Laboratory Method Link
Šalagovič J (2015) Formální modely oscilací v biologii a jejich analýza. Ph.D. Thesis, Masarykova univerzita, Czech Republic. Computational Method Link
Samal SS, Grigoriev D, Fröhlich H, Weber A, Radulescu O (2015) A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions. Bulletin of Mathematical Biology 77:2180-211. Computational Method Theory Link
Tummler K, Kühn C, Klipp E (2015) Dynamic metabolic models in context: biomass backtracking. Integrative Biology 7:940-51 Computational Method Link
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR (2015) BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology 9:8 Computational Method Link
Zimmer C (2015) Reconstructing the hidden states in time course data of stochastic models. Mathematical Biosciences 269:117-29 Computational Method Link
Zimmer C, Sahle S (2015) A termination criterion for parameter estimation in stochastic models in systems biology. BioSystems 9:181-92 Computational Method Link

15 publications
Bellini M, Besozzi D, Cazzaniga P, Mauri G, Nobile MS (2014) Simulation and analysis of the blood coagulation cascade accelerated on GPU. 2014 22nd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), IEEE, 590–593 Computational Method Link
Boba P, Gries S, Hamacher K (2014) R as an Integration Tool in High Performance Computing - Lessons Learned. GI-Jahrestagung. Lecture Notes in Informatics 232:138–148 Computational Method Software Link
Castaldi DF (2014) Network Based Simulation on HPC for Translational Medicine: an Application to Anticoagulation. Ph.D. Thesis, University of Milano-Bicocca, Milan, Italy. Computational Method Link
Cazzaniga P, Nobile MS, Besozzi D, Bellini M, Mauri G (2014) Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. BioMed Research International 2014:863298 Computational Method Link
Figueredo GP, Siebers P-O, Owen MR, Reps J, Aickelin U (2014) Comparing stochastic differential equations and agent-based modelling and simulation for early-stage cancer. PLoS One 9:e95150 Computational Method Link
Ivan ANY (2014) Assisted Design of DNA Computing Systems: the DNA Toolbox and Beyond. Ph.D. Thesis, University of Tokyo, Japan. Synthetic Biology Computational Method Link
Liao C, Cai Y (2014) Towards Modeling Automation for Synthetic Biology. In: Kulkarni V., Stan GB., Raman K. (eds.) A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems. Springer, Dordrecht, 201–217 Synthetic Biology Computational Method Link
Meyer P, Cokelaer T, Chandran D, Kim KH, Loh P-R, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Sauro HM, Stolovitzky G, Saez-Rodriguez J (2014) Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Systems Biology 8:13 Computational Method Link
Mozga I, Stalidzans E (2014) Reduction of Combinatorial Space of Adjustable Kinetic Parameters of Biochemical Network Models in Optimisation Task. Baltic Journal of Modern Computing 150:150–159 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Mauri G (2014) GPU-accelerated simulations of mass-action kinetics models with cupSODA. Journal of Supercomputing 69:17-24 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Pescini D, Mauri G (2014) cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems. PLoS One 9:e91963. Computational Method Link
Palmisano A, Hoops S, Watson LT, Jones Jr TC, Tyson JJ, Shaffer CA (2014) Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. BMC Systems Biology 8:42 Software Computational Method Link
Phelix CF, Villareal G, LeBaron RG, Roberson DJ (2014) Biomarkers from biosimulations: Transcriptome-to-reactome™ Technology for individualized medicine. 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 3452–3455 Computational Method Link
Rao S, van der Schaft A, van Eunen K, Bakker BM, Jayawardhana B (2014) A model reduction method for biochemical reaction networks. BMC Systems Biology 8:52 Computational Method Link
Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK (2014) Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Research 42:7539-7552 Computational Method Link
Zimmer C, Sahle S, Pahle J (2014) Exploiting intrinsic fluctuations to identify model parameters. IET Systems Biology 9:64-73 Computational Method Link

16 publications
Berestovsky N, Nakhleh L (2013) An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data. PLoS One 8:e66031 Computational Method Link
Bulipopa N, Sulins J (2013) Automatic termination of parallel optimization runs of global stochastic optimization methods by upper limit criterion. Biosystems and Information Technology 2:15-18 Computational Method Link
Challenger JD (2013) The stochastic dynamics of biochemical systems. Ph.D. Thesis, University of Manchester, UK Computational Method Metabolism Link
Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G (2013) An online model composition tool for system biology models. BMC Systems Biology 7:88 Computational Method Link
Jensen MV, Hay JO (2013) Systems Biology Markup Language formulation of a dynamic kinetic model and its uses in quantitative and computational metabolic modeling. In (Stegman M, Morris M. and Blackburn N, eds.) A Compilation of Internship Reports. Brookhaven National Laboratory, Office of Educational Programs. pp. 108–112 Computational Method Link
Kennedy N, Mizeranschi A, Thompson P, Zheng H, Dubitzky W (2013) Reverse engineering of gene regulation models from multi-condition experiments. Proceedings of the 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pp.112-119 Computational Method Link
Kent E, Neumann S, Kummer U, Mendes P (2013) What Can We Learn from Global Sensitivity Analysis of Biochemical Systems? PLoS One 8:e79244 Computational Method Link
LeBaron R, Villareal G, Roberson DJ, Phelix CF (2013) Abstract 5224: Breast cancer biomarkers from biosimulations: transcriptome-to-reactome™ technology. Cancer Research 73:5224 Genomics Computational Method Link
Marchisio MA, Colaiacovo M, Whitehead E, Stelling J (2013) Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. BMC Systems Biology 7:42 Computational Method Link
Mednis M, Vigants A (2013) Automatic comparison of metabolites names: impact of criteria thresholds. Biosystems and Information Technology 2:1-5 Computational Method Link
Mei Y, Carbo A, Hontecillas R, Bassaganya-Riera J (2013) ENISI SDE: a novel web-based stochastic modeling tool for computational biology. 2013 Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 392-397 Computational Method Software Link
Mei Y, Hontecillas R, Zhang X, Carbo A, Bassaganya-Riera J (2013) Neural network models for classifying immune cell subsets. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 18-21 Dec. 2013, pp.5-11 Computational Method Link
Mozga I (2013) Determinition of best set of adjustable parameters with full search and limited search methods. Biosystems and Information Technology 2:11–14 Computational Method Link
Nobile MS , Besozzi D, Cazzaniga P, Mauri G, Pescini D (2013) cupSODA: a CUDA-powered simulator of mass-action kinetics. Parallel Computing Technologies Proceedings of the 12th International Conference, PaCT 2013, St. Petersburg, pp.344-357 Computational Method Link
Palaniappan SK (2013) Probabilistic verification and analysis of biopathway dynamics. Ph.D. Thesis School of Computing, National University of Singapore Computational Method Link
Roberts E, Stone JE, Luthey-Schulten Z (2013) Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. Journal of Computational Chemistry 34:245-255 Computational Method Link
Sharma V (2013) Language design for computational modeling, simulation, and visualization. Proceedings of the 2013 Winter Simulation Conference: Simulation: Making Decisions in a Complex World. Washington, D.C.: IEEE Press, 3934–3935 Computational Method Link
Sharma V, Compagnoni A (2013) Computational and mathematical models of the JAK-STAT signal transduction pathway. Proceedings of the 2013 Summer Computer Simulation Conference 15 Computational Method Signaling Link
Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W (2013) Systematic construction of kinetic models from genome-scale metabolic networks. PLoS One 8:e79195 Computational Method Whole-Cell Models Link
Tapinos A, Mendes P (2013) A Method for Comparing Multivariate Time Series with Different Dimensions. PLoS One 8:e54201 Computational Method Theory Link

20 publications
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ (2012) The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. Journal of Biological Rhythms 27:328–332 Computational Method Link
Challenger JD, McKane AJ, Pahle J (2012) Multi-compartment linear noise approximation. Journal of Statistical Mechanics: Theory and Experiment 2012:P11010 Computational Method Link
Chua HE, Bhowmick SS, Tucker-Kellogg L, Forbes Dewey C (2012) STEROID: in silico heuristic target combination identification for disease-related signaling networks. Proceedings of the 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine BCB'12 pp. 4-11 Computational Method Link
Georgoulas A, Clark A, Ocone A, Gilmore S, Sanguinetti G (2012) A subsystems approach for parameter estimation of ODE models of hybrid systems. Electronic Proceedings in Theoretical Computer Science 92:30-41 Computational Method Link
Holcombe M, Adra S, Bicak M, Chin S, Coakley S, Graham AI, Green J, Greenough C, Jackson D, Kiran M, MacNeil S, Maleki-Dizaji A, McMinn P, Pogson M, Poole R, Qwarnstrom E, Ratnieks F, Rolfe MD, Smallwood R, Sun T, Worth D (2012) Modelling complex biological systems using an agent-based approach. Integrative Biology 4:53–64 Computational Method Link
Kleessen S, Nikoloski Z (2012) Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology 6:16 Computational Method Plant Biology Metabolism Link
Kostromins A, Mozga I, Stalidzans E (2012) ConvAn: A convergence analyzing tool for optimization of biochemical networks. BioSystems 108:73-77 Software Computational Method Link
Pahle J, Challenger JD, Mendes P, McKane AJ (2012) Biochemical fluctuations, optimisation and the linear noise approximation. BMC Systems Biology 6:86 Computational Method Software Link
Schaber J (2012) Easy parameter identifiability analysis with COPASI. BioSystems 110:183-185 Computational Method Link
Stalidzans E, Kostromins A, Sulins J (2012) Two stage optimization of biochemical pathways using parallel runs of global stochastic optimization methods. 13th IEEE International Symposium on Computational Intelligence and Informatics (CINTI 2012), IEEE, 365–369 Computational Method Link
Sulins J, Mednis M (2012) Automatic termination of parallel optimization runs of stochastic global optimization methods in consensus or stagnation cases. Biosystems and Information Technology 1:1-5 Software Computational Method Link
Surovtsova I, Simus N, Hübner K, Sahle S, Kummer U (2012) Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. BMC Systems Biology 6:14 Software Computational Method Link
Tagore S, De RK (2012) SAGPAR: Structural Grammar-based automated pathway reconstruction. Interdisciplinary Sciences: Computational Life Sciences 4:116-127 Software Computational Method Link
Warren PB, Allen RJ (2012) Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting. Journal of Chemical Physics 136:104106 Computational Method Link
Zimmer C (2012) Parameter estimation for stochastic models of biochemical reactions. Ph.D. Thesis, Heidelberg University, Germany. Computational Method Link

15 publications
Baker SM, Poskar CH, Junker BH (2011) Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models. EURASIP Journal on Bioinformatics & Systems Biology 2011:7 Computational Method Link
Bandaru P, Bansal M, Nemenman I (2011) Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data. Journal of Computational Biology 18:147-154 Laboratory Method Computational Method Link
Berestovsky N (2011) On the modeling of signaling networks with petri nets. MS Thesis, Rice University, Houston, Texas, USA. Computational Method Link
DasGupta B, Vera-Licona P, Sontag E (2011) Reverse engineering of molecular networks from a common combinatorial approach. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, M. Elloumi and A. Zomaya (editors). John Wiley & Sons, Inc. Computational Method Link
Gauges R (2011) Standards and Tools for Model Exchange and Analysis in Systems Biology. Ph.D. Thesis, Heidelberg University, Germany Software Computational Method Link
Koh G, Hsu D, Thiagarajan PS (2011) Component-based construction of bio-pathway models: The parameter estimation problem. Theoretical Computer Science 412:2840–2853 Computational Method Link
Mauch S, Stalzer M (2011) Efficient formulations for exact stochastic simulation of chemical systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8:27-35 Computational Method Link
Mozga I, Stalidzans E (2011) Convergence dynamics of biochemical models to the global optimum. Paper presented at the 2011 E-Health and Bioengineering Conference (EHB). IEEE: Iaşi, Romania, 1–4 Computational Method Metabolism Link
Schaber J, Flöttmann M, Li J, Tiger C-F, Hohmann S, Klipp E (2011) Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway. PLoS One 6:e14791 Signaling Computational Method Software Link
Waltemath D, Adams RR, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru II, Nickerson DP, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N (2011) Minimum Information About a Simulation Experiment (MIASE). PLoS Computational Biology 7:e1001122 Computational Method Link

10 publications