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ProbOnto: ontology and knowledge base of probability distributions
Swat, Maciej J., Grenon, Pierre, Wimalaratne, Sarala
Published in Bioinformatics (Oxford, England) (01.09.2016)
Published in Bioinformatics (Oxford, England) (01.09.2016)
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Journal Article
libRoadRunner: a high performance SBML simulation and analysis library
Somogyi, Endre T., Bouteiller, Jean-Marie, Glazier, James A., König, Matthias, Medley, J. Kyle, Swat, Maciej H., Sauro, Herbert M.
Published in Bioinformatics (15.10.2015)
Published in Bioinformatics (15.10.2015)
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Journal Article
Filopodial-Tension Model of Convergent-Extension of Tissues
Belmonte, Julio M., Swat, Maciej H., Glazier, James A.
Published in PLoS computational biology (01.06.2016)
Published in PLoS computational biology (01.06.2016)
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Journal Article
BioModels: expanding horizons to include more modelling approaches and formats
Glont, Mihai, Nguyen, Tung V N, Graesslin, Martin, Hälke, Robert, Ali, Raza, Schramm, Jochen, Wimalaratne, Sarala M, Kothamachu, Varun B, Rodriguez, Nicolas, Swat, Maciej J, Eils, Jurgen, Eils, Roland, Laibe, Camille, Malik-Sheriff, Rahuman S, Chelliah, Vijayalakshmi, Le Novère, Nicolas, Hermjakob, Henning
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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Journal Article
Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell, Virtual-Tissue Model of Tumor Evolution Using CompuCell3D
Swat, Maciej H., Thomas, Gilberto L., Shirinifard, Abbas, Clendenon, Sherry G., Glazier, James A.
Published in PloS one (17.06.2015)
Published in PloS one (17.06.2015)
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Journal Article
Development of a coupled simulation toolkit for computational radiation biology based on Geant4 and CompuCell3D
Liu, Ruirui, Higley, Kathryn A, Swat, Maciej H, Chaplain, Mark A J, Powathil, Gibin G, Glazier, James A
Published in Physics in medicine & biology (21.02.2021)
Published in Physics in medicine & biology (21.02.2021)
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Journal Article
Virtual-tissue computer simulations define the roles of cell adhesion and proliferation in the onset of kidney cystic disease
Belmonte, Julio M., Clendenon, Sherry G., Oliveira, Guilherme M., Swat, Maciej H., Greene, Evan V., Jeyaraman, Srividhya, Glazier, James A., Bacallao, Robert L.
Published in Molecular biology of the cell (07.11.2016)
Published in Molecular biology of the cell (07.11.2016)
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Journal Article
Multi-Scale Modeling of Tissues Using CompuCell3D
Swat, Maciej H., Thomas, Gilberto L., Belmonte, Julio M., Shirinifard, Abbas, Hmeljak, Dimitrij, Glazier, James A.
Published in Computational Methods in Cell Biology (2012)
Published in Computational Methods in Cell Biology (2012)
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Book Chapter
Journal Article
3D Multi-Cell Simulation of Tumor Growth and Angiogenesis
Shirinifard, Abbas, Gens, J. Scott, Zaitlen, Benjamin L., Popławski, Nikodem J., Swat, Maciej, Glazier, James A.
Published in PloS one (16.10.2009)
Published in PloS one (16.10.2009)
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Journal Article
A Liver-Centric Multiscale Modeling Framework for Xenobiotics
Sluka, James P., Fu, Xiao, Swat, Maciej, Belmonte, Julio M., Cosmanescu, Alin, Clendenon, Sherry G., Wambaugh, John F., Glazier, James A.
Published in PloS one (16.09.2016)
Published in PloS one (16.09.2016)
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Journal Article
Cycle Network Model of Prostaglandin H Synthase-1
Goltsov, Alexey, Swat, Maciej, Peskov, Kirill, Kosinsky, Yuri
Published in Pharmaceuticals (Basel, Switzerland) (23.09.2020)
Published in Pharmaceuticals (Basel, Switzerland) (23.09.2020)
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Journal Article
Learn–confirm in model‐informed drug development: Assessing an immunogenicity quantitative systems pharmacology platform
Franssen, Linnea C., Swat, Maciej J., Kierzek, Andrzej M., Rose, Rachel H., Graaf, Piet H., Grimm, Hans Peter
Published in CPT: pharmacometrics and systems pharmacology (01.02.2023)
Published in CPT: pharmacometrics and systems pharmacology (01.02.2023)
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Journal Article
Computer Simulations of Cell Sorting Due to Differential Adhesion
Zhang, Ying, Thomas, Gilberto L., Swat, Maciej, Shirinifard, Abbas, Glazier, James A.
Published in PloS one (18.10.2011)
Published in PloS one (18.10.2011)
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Journal Article
A Quantitative Systems Pharmacology Consortium Approach to Managing Immunogenicity of Therapeutic Proteins
Kierzek, Andrzej M., Hickling, Timothy P., Figueroa, Isabel, Kalvass, J. Cory, Nijsen, Marjoleen, Mohan, Krithika, Veldman, Geertruida M., Yamada, Akihiro, Sayama, Hiroyuki, Yokoo, Sachiko, Gulati, Abhishek, Dhanikula, Renu S., Gokemeijer, Jochem, Leil, Tarek A., Thalhauser, Craig J., Giorgi, Mario, Swat, Maciej J., Chelliah, Vijayalakshmi, Small, Ben G., Benson, Neil, Walker, Michael, Gadkar, Kapil, Quarmby, Valerie, Deng, Rong, Ferrante, Andrea, Dickinson, Gemma L., Van Der Walt, Jan‐Stefan, Zhou, Lian, Chen, Xiaoying, Jones, Hannah M., Narula, Jatin, Tourdot, Sophie, Lavé, Thierry, Ribba, Benjamin, Graaf, Piet H.
Published in CPT: pharmacometrics and systems pharmacology (01.11.2019)
Published in CPT: pharmacometrics and systems pharmacology (01.11.2019)
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Journal Article
Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study
Shirinifard, Abbas, Glazier, James Alexander, Swat, Maciej, Gens, J. Scott, Family, Fereydoon, Jiang, Yi, Grossniklaus, Hans E.
Published in PLoS computational biology (01.05.2012)
Published in PLoS computational biology (01.05.2012)
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Journal Article
Data standards for model-informed drug development: an ISoP initiative
Radivojevic, Andrijana, Corrigan, Brian, Downie, Nicholas, Fox, Robert, Fiedler-Kelly, Jill, Liu, Huan, Melhem, Murad, Radke, David, Schaefer, Peter, Su, Jing, Swat, Maciej J., Teuscher, Nathan S., Thanneer, Neelima, Zong, Alice, Wilkins, Justin J.
Published in Journal of pharmacokinetics and pharmacodynamics (01.10.2018)
Published in Journal of pharmacokinetics and pharmacodynamics (01.10.2018)
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Journal Article
The Standard Output: A Tool‐Agnostic Modeling Storage Format
Terranova, Nadia, Smith, Mike K., Nordgren, Rikard, Comets, Emmanuelle, Lavielle, Marc, Harling, Kajsa, Hooker, Andrew C., Sarr, Celine, Mentré, France, Yvon, Florent, Swat, Maciej J.
Published in CPT: pharmacometrics and systems pharmacology (01.09.2018)
Published in CPT: pharmacometrics and systems pharmacology (01.09.2018)
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Journal Article