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

द्वारा Chylek, Lily A, Harris, Leonard A, Faeder, James R, Hlavacek, William S
में प्रकाशित Phys Biol (2015)

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

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

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

द्वारा Jones, Zack W., Leander, Rachel, Quaranta, Vito, Harris, Leonard A., Tyson, Darren R.
में प्रकाशित PLoS One (2018)

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

द्वारा Harris, Leonard A., Beik, Samantha, Ozawa, Patricia M. M., Jimenez, Lizandra, Weaver, Alissa M.
में प्रकाशित Curr Opin Syst Biol (2019)

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

द्वारा E Wenskovitch, John, Harris, Leonard A, Tapia, Jose-Juan, Faeder, James R, Marai, G Elisabeta
में प्रकाशित BMC Bioinformatics (2014)

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

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

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

द्वारा Lubbock, Alexander L R, Harris, Leonard A, Quaranta, Vito, Tyson, Darren R, Lopez, Carlos F
में प्रकाशित Nucleic Acids Res (2021)

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

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

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

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

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

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

GPU-powered model analysis with PySB/cupSODA

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

An unbiased metric of antiproliferative drug effect in vitro

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

BioNetGen 2.2: advances in rule-based modeling

द्वारा 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.
में प्रकाशित Bioinformatics (2016)

Quantifying drug combination synergy along potency and efficacy axes.

द्वारा 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
में प्रकाशित Cell Syst (2019)

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

द्वारा 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
में प्रकाशित PLoS Comput Biol (2017)

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

द्वारा 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
में प्रकाशित J Integr Bioinform (2020)