Kinetic Modeling using BioPAX ontology

Autor Ruebenacker, Oliver, Moraru, Ion. I., Schaff, James C., Blinov, Michael L.
Vydáno 2007

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling

Autor Brown, Sherry-Ann, Moraru, Ion I., Schaff, James C., Loew, Leslie M.
Vydáno 2011

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology

Autor Schaff, James C., Gao, Fei, Li, Ye, Novak, Igor L., Slepchenko, Boris M.
Vydáno v PLoS Comput Biol (2016)

Rule-based modeling with Virtual Cell

Autor Schaff, James C., Vasilescu, Dan, Moraru, Ion I., Loew, Leslie M., Blinov, Michael L.
Vydáno v Bioinformatics (2016)

Morphological Control of Inositol-1,4,5-Trisphosphate–Dependent Signals

Autor Fink, Charles C., Slepchenko, Boris, Moraru, Ion I., Schaff, James, Watras, James, Loew, Leslie M.
Vydáno 1999

Reaction-diffusion modeling in the NEURON simulator

Autor McDougal, Robert A, Skolnick, Yosef, Schaff, James C, Lytton, William W, Hines, Michael L
Vydáno 2012

Spatial Modeling of Cell Signaling Networks

Autor Cowan, Ann E., Moraru, Ion I., Schaff, James C., Slepchenko, Boris M., Loew, Leslie M.
Vydáno 2012

Diffusion on a Curved Surface Coupled to Diffusion in the Volume: Application to Cell Biology

Autor Novak, Igor L., Gao, Fei, Choi, Yung-Sze, Resasco, Diana, Schaff, James C., Slepchenko, Boris M.
Vydáno 2007

Virtual Cell: computational tools for modeling in cell biology

Autor Resasco, Diana C., Gao, Fei, Morgan, Frank, Novak, Igor L., Schaff, James C., Slepchenko, Boris M.
Vydáno 2011

Compartmental and Spatial Rule-Based Modeling with Virtual Cell

Autor Blinov, Michael L., Schaff, James C., Vasilescu, Dan, Moraru, Ion I., Bloom, Judy E., Loew, Leslie M.
Vydáno v Biophys J (2017)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Autor Hucka, Michael, Bergmann, Frank T., Hoops, Stefan, Keating, Sarah M., Sahle, Sven, Schaff, James C., Smith, Lucian P., Wilkinson, Darren J.
Vydáno v J Integr Bioinform (2015)

The Virtual Cell Modeling and Simulation Software Environment

Autor Moraru, Ion I., Schaff, James C., Slepchenko, Boris M., Blinov, Michael, Morgan, Frank, Lakshminarayana, Anuradha, Gao, Fei, Li, Ye, Loew, Leslie M.
Vydáno 2008

Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling

Autor Blinov, Michael L., Schaff, James C., Ruebenacker, Oliver, Wei, Xintao, Vasilescu, Dan, Gao, Fei, Morgan, Frank, Ye, Li, Lakshminarayana, Anuradha, Moraru, Ion I., Loew, Leslie M.
Vydáno 2014

Cell Shape and Negative Links in Regulatory Motifs Together Control Spatial Information Flow in Signaling Networks

Autor Neves, Susana R., Tsokas, Panayiotis, Sarkar, Anamika, Grace, Elizabeth A., Rangamani, Padmini, Taubenfeld, Stephen M., Alberini, Cristina M., Schaff, James C., Blitzer, Robert D., Moraru, Ion I., Iyengar, Ravi
Vydáno 2008

WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration

Autor Santella, Anthony, Catena, Raúl, Kovacevic, Ismar, Shah, Pavak, Yu, Zidong, Marquina-Solis, Javier, Kumar, Abhishek, Wu, Yicong, Schaff, James, Colón-Ramos, Daniel, Shroff, Hari, Mohler, William A., Bao, Zhirong
Vydáno v BMC Bioinformatics (2015)

A systems pharmacology model for gene therapy in sickle cell disease

Autor Zheng, Bo, Wille, Lucia, Peppel, Karsten, Hagen, David, Matteson, Andrew, Ahlers, Jeffrey, Schaff, James, Hua, Fei, Yuraszeck, Theresa, Cobbina, Enoch, Apgar, Joshua F., Burke, John M., Roberts, John, Das, Raibatak
Vydáno v CPT Pharmacometrics Syst Pharmacol (2021)

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Autor Hucka, Michael, Bergmann, Frank T., Dräger, Andreas, Hoops, Stefan, Keating, Sarah M., Le Novére, Nicolas, Myers, Chris J., Olivier, Brett G., Sahle, Sven, Schaff, James C., Smith, Lucian P., Waltemath, Dagmar, Wilkinson, Darren J.
Vydáno v J Integr Bioinform (2015)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

Autor Hucka, Michael, Bergmann, Frank T., Dräger, Andreas, Hoops, Stefan, Keating, Sarah M., Le Novère, Nicolas, Myers, Chris J., Olivier, Brett G., Sahle, Sven, Schaff, James C., Smith, Lucian P., Waltemath, Dagmar, Wilkinson, Darren J.
Vydáno v J Integr Bioinform (2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Autor Hucka, Michael, Bergmann, Frank T., Dräger, Andreas, Hoops, Stefan, Keating, Sarah M., Le Novère, Nicolas, Myers, Chris J., Olivier, Brett G., Sahle, Sven, Schaff, James C., Smith, Lucian P., Waltemath, Dagmar, Wilkinson, Darren J.
Vydáno v J Integr Bioinform (2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Autor Hucka, Michael, Bergmann, Frank T., Chaouiya, Claudine, Dräger, Andreas, Hoops, Stefan, Keating, Sarah M., König, Matthias, Novère, Nicolas Le, Myers, Chris J., Olivier, Brett G., Sahle, Sven, Schaff, James C., Sheriff, Rahuman, Smith, Lucian P., Waltemath, Dagmar, Wilkinson, Darren J., Zhang, Fengkai
Vydáno v J Integr Bioinform (2019)