Modeling for (physical) biologists: an introduction to the rule-based approach

od Chylek, Lily A, Harris, Leonard A, Faeder, James R, Hlavacek, William S
izdano v Phys Biol (2015)

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

od Hogg, Justin S., Harris, Leonard A., Stover, Lori J., Nair, Niketh S., Faeder, James R.
Izdano 2014

A drift-diffusion checkpoint model predicts a highly variable and growth-factor-sensitive portion of the cell cycle G1 phase

od Jones, Zack W., Leander, Rachel, Quaranta, Vito, Harris, Leonard A., Tyson, Darren R.
izdano v PLoS One (2018)

Modeling heterogeneous tumor growth dynamics and cell-cell interactions at single-cell and cell-population resolution

od Harris, Leonard A., Beik, Samantha, Ozawa, Patricia M. M., Jimenez, Lizandra, Weaver, Alissa M.
izdano v Curr Opin Syst Biol (2019)

MOSBIE: a tool for comparison and analysis of rule-based biochemical models

od E Wenskovitch, John, Harris, Leonard A, Tapia, Jose-Juan, Faeder, James R, Marai, G Elisabeta
izdano v BMC Bioinformatics (2014)

Unsupervised logic-based mechanism inference for network-driven biological processes

od Prugger, Martina, Einkemmer, Lukas, Beik, Samantha P., Wasdin, Perry T., Harris, Leonard A., Lopez, Carlos F.
izdano v PLoS Comput Biol (2021)

Thunor: visualization and analysis of high-throughput dose–response datasets

od Lubbock, Alexander L R, Harris, Leonard A, Quaranta, Vito, Tyson, Darren R, Lopez, Carlos F
izdano v Nucleic Acids Res (2021)

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

od Chylek, Lily A., Harris, Leonard A., Tung, Chang-Shung, Faeder, James R., Lopez, Carlos F., Hlavacek, William S.
Izdano 2013

An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability

od Hayford, Corey E., Tyson, Darren R., Robbins, C. Jack, Frick, Peter L., Quaranta, Vito, Harris, Leonard A.
izdano v PLoS Biol (2021)

A Nonquiescent “Idling” Population State in Drug-Treated, BRAF-Mutated Melanoma

od Paudel, B. Bishal, Harris, Leonard A., Hardeman, Keisha N., Abugable, Arwa A., Hayford, Corey E., Tyson, Darren R., Quaranta, Vito
izdano v Biophys J (2018)

GPU-powered model analysis with PySB/cupSODA

od Harris, Leonard A, Nobile, Marco S, Pino, James C, Lubbock, Alexander L R, Besozzi, Daniela, Mauri, Giancarlo, Cazzaniga, Paolo, Lopez, Carlos F
izdano v Bioinformatics (2017)

An unbiased metric of antiproliferative drug effect in vitro

od Harris, Leonard A., Frick, Peter L., Garbett, Shawn P., Hardeman, Keisha N., Paudel, B. Bishal, Lopez, Carlos F., Quaranta, Vito, Tyson, Darren R.
izdano v Nat Methods (2016)

BioNetGen 2.2: advances in rule-based modeling

od Harris, Leonard A., Hogg, Justin S., Tapia, José-Juan, Sekar, John A. P., Gupta, Sanjana, Korsunsky, Ilya, Arora, Arshi, Barua, Dipak, Sheehan, Robert P., Faeder, James R.
izdano v Bioinformatics (2016)

Quantifying drug combination synergy along potency and efficacy axes.

od Meyer, Christian T., Wooten, David J., Paudel, B. Bishal, Bauer, Joshua, Hardeman, Keisha N., Westover, David, Lovly, Christine M., Harris, Leonard A., Tyson, Darren R., Quaranta, Vito
izdano v Cell Syst (2019)

Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective

od Chifman, Julia, Arat, Seda, Deng, Zhiyong, Lemler, Erica, Pino, James C., Harris, Leonard A., Kochen, Michael A., Lopez, Carlos F., Akman, Steven A., Torti, Frank M., Torti, Suzy V., Laubenbacher, Reinhard
izdano v PLoS Comput Biol (2017)

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

od Zhang, Fengkai, Smith, Lucian P., Blinov, Michael L., Faeder, James, Hlavacek, William S., Juan Tapia, Jose, Keating, Sarah M., Rodriguez, Nicolas, Dräger, Andreas, Harris, Leonard A., Finney, Andrew, Hu, Bin, Hucka, Michael, Meier-Schellersheim, Martin
izdano v J Integr Bioinform (2020)