A semantics, energy-based approach to automate biomodel composition von Shahidi, Niloofar, Pan, Michael, Tran, Kenneth, Crampin, Edmund J, Nickerson, David P

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A modular and reusable model of epithelial transport in the proximal convoluted tubule von Noroozbabaee, Leyla, Blanco, Pablo J, Safaei, Soroush, Nickerson, David P

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Hierarchical semantic composition of biosimulation models using bond graphs von Shahidi, Niloofar, Pan, Michael, Safaei, Soroush, Tran, Kenneth, Crampin, Edmund J, Nickerson, David P

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Model annotation and discovery with the Physiome Model Repository von Sarwar, Dewan M, Kalbasi, Reza, Gennari, John H, Carlson, Brian E, Neal, Maxwell L, Bono, Bernard de, Atalag, Koray, Hunter, Peter J, Nickerson, David P

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A novel modular modeling approach for understanding different electromechanics between left and right heart in rat von Kim, Nari, Pronto, Julius D., Nickerson, David P., Taberner, Andrew J., Hunter, Peter J.

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The Physiome Model Repository 2 von YU, Tommy, LLOYD, Catherine M, NIELSEN, Poul M. F, NICKERSON, David P, COOLING, Michael T, MILLET, Andrew K, GARNY, Alan, TERKILDSEN, Jonna R, LAWSON, James, BRITTEN, Randall D, HUNTER, Peter J

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An overview of the CellML API and its implementation von Miller, Andrew K, Marsh, Justin, Reeve, Adam, Garny, Alan, Britten, Randall, Halstead, Matt, Cooper, Jonathan, Nickerson, David P, Nielsen, Poul F

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CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities von Munarko, Yuda, Rampadarath, Anand, Nickerson, David P

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Computational Modelling of Glucose Uptake by SGLT1 and Apical GLUT2 in the Enterocyte von Afshar, Nima, Safaei, Soroush, Nickerson, David P, Hunter, Peter J, Suresh, Vinod

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The SPARC DRC: Building a Resource for the Autonomic Nervous System Community von Osanlouy, Mahyar, Bandrowski, Anita, de Bono, Bernard, Brooks, David, Cassarà, Antonino M, Christie, Richard, Ebrahimi, Nazanin, Gillespie, Tom, Grethe, Jeffrey S, Guercio, Leonardo A, Heal, Maci, Lin, Mabelle, Kuster, Niels, Martone, Maryann E, Neufeld, Esra, Nickerson, David P, Soltani, Elias G, Tappan, Susan, Wagenaar, Joost B, Zhuang, Katie, Hunter, Peter J

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NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories von Munarko, Yuda, Sarwar, Dewan M, Rampadarath, Anand, Atalag, Koray, Gennari, John H, Neal, Maxwell L, Nickerson, David P

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Computational Modeling of Glucose Uptake in the Enterocyte von Afshar, Nima, Safaei, Soroush, Nickerson, David P, Hunter, Peter J, Suresh, Vinod

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OMEX metadata specification (version 1.2) von Gennari, John H., König, Matthias, Misirli, Goksel, Neal, Maxwell L., Nickerson, David P., Waltemath, Dagmar

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Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024 von Golebiewski, Martin, Bader, Gary, Gleeson, Padraig, Gorochowski, Thomas E., Keating, Sarah M., König, Matthias, Myers, Chris J., Nickerson, David P., Sommer, Björn, Waltemath, Dagmar, Schreiber, Falk

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CellML 2.0 von Clerx, Michael, Cooling, Michael T., Cooper, Jonathan, Garny, Alan, Moyle, Keri, Nickerson, David P., Nielsen, Poul M. F., Sorby, Hugh

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Insights From Computational Modeling Into the Contribution of Mechano-Calcium Feedback on the Cardiac End-Systolic Force-Length Relationship von Guidry, Megan E., Nickerson, David P., Crampin, Edmund J., Nash, Martyn P., Loiselle, Denis S., Tran, Kenneth

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Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022 von König, Matthias, Gleeson, Padraig, Golebiewski, Martin, Gorochowski, Thomas E., Hucka, Michael, Keating, Sarah M., Myers, Chris J., Nickerson, David P., Sommer, Björn, Waltemath, Dagmar, Schreiber, Falk

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CellML and associated tools and techniques von Garny, Alan, Nickerson, David P, Cooper, Jonathan, Santos, Rodrigo Weber dos, Miller, Andrew K, McKeever, Steve, Nielsen, Poul M.F, Hunter, Peter J

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Open modeling and exchange (OMEX) metadata specification version 1.0 von Neal, Maxwell L., Gennari, John H., Waltemath, Dagmar, Nickerson, David P., König, Matthias

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Specifications of standards in systems and synthetic biology: status and developments in 2021 von Schreiber, Falk, Gleeson, Padraig, Golebiewski, Martin, Gorochowski, Thomas E., Hucka, Michael, Keating, Sarah M., König, Matthias, Myers, Chris J., Nickerson, David P., Sommer, Björn, Waltemath, Dagmar

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