Author details

Full Name

David P Nickerson

Affiliation

ORCID

Career Start Year

2005

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36865672	CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities.		2023
36096376	SBML to bond graphs: From conversion to composition.		2022
35657966	A semantics, energy-based approach to automate biomodel composition.	PLoS ONE	2022
36176770	A novel modular modeling approach for understanding different electromechanics between left and right heart in rat.	Frontiers in Physiology	2022
36355848	A modular and reusable model of epithelial transport in the proximal convoluted tubule.	PLoS ONE	2022
35330701	The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.	Journal of integrative bioinformatics	2021
33983945	Hierarchical semantic composition of biosimulation models using bond graphs.	PLoS Computational Biology	2021
34248680	The SPARC DRC: Building a Resource for the Autonomic Nervous System Community.	Front Physiol	2021
34132740	libOmexMeta: enabling semantic annotation of models to support FAIR principles.	Bioinformatics	2021
34674411	Specifications of standards in systems and synthetic biology: status and developments in 2021.	J Integr Bioinform	2021
34668356	OMEX metadata specification (version 1.2).	J Integr Bioinform	2021
34950044	Computational Modelling of Glucose Uptake by SGLT1 and Apical GLUT2 in the Enterocyte.	Frontiers in Physiology	2021
32853539	Best Practices for Making Reproducible Biochemical Models.		2020
32427998	Improving reproducibility in computational biology research.	PLoS Comput Biol	2020
32547426	Insights From Computational Modeling Into the Contribution of Mechano-Calcium Feedback on the Cardiac End-Systolic Force-Length Relationship.	Frontiers in Physiology	2020
32598316	Specifications of standards in systems and synthetic biology: status and developments in 2020.	Journal of integrative bioinformatics	2020
32598315	The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).	J Integr Bioinform	2020
32589606	Open modeling and exchange (OMEX) metadata specification version 1.0.	J Integr Bioinform	2020
31031632	Computational Modeling of Glucose Uptake in the Enterocyte.	Frontiers in Physiology	2019
31602618	Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.	Methods Mol Biol	2019
30462164	Harmonizing semantic annotations for computational models in biology.	Brief Bioinform	2019
29688273	Community-driven roadmap for integrated disease maps.	Brief Bioinform	2019
31301675	Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.	J Integr Bioinform	2019
31492098	Model annotation and discovery with the Physiome Model Repository.	BMC Bioinformatics	2019
29596055	Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.	J Integr Bioinform	2018
30117501	Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).	Stand Genomic Sci	2018
29550789	Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).	J Integr Bioinform	2018
28049131	SED-ML web tools: generate, modify and export standard-compliant simulation studies.		2017
28679581	eSolv, a CellML-based simulation front-end for online teaching.	American Journal of Physiology - Advances in Physiology Education	2017
28187405	Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.	J Integr Bioinform	2016
27051515	The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.	Interface Focus	2016
27353233	Modular modelling with Physiome standards.	Journal of Physiology	2016
26528556	Specifications of Standards in Systems and Synthetic Biology.	J Integr Bioinform	2015
25759811	Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.	Front Bioeng Biotechnol	2015
25759670	The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units.	Frontiers in Physiology	2015
26528560	Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.	J Integr Bioinform	2015
26528557	The CellML 1.1 Specification.	Journal of integrative bioinformatics	2015
25601911	Using CellML with OpenCMISS to Simulate Multi-Scale Physiology.	Frontiers in Bioengineering and Biotechnology	2014
25494900	COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.	BMC Bioinformatics	2014
24110992	Standards and tools supporting collaborative development of the virtual physiological human.	Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference	2013
22570375	Myocardial twitch duration and the dependence of oxygen consumption on pressure-volume area: experiments and modelling.	Journal of Physiology	2012
22837173	Relating components of pressure-volume area in Suga's formulation of cardiac energetics to components of the stress-time integral.	Journal of Applied Physiology	2012
22879535	Comparison of the Gibbs and Suga formulations of cardiac energetics: the demise of "isoefficiency".	Journal of Applied Physiology	2012
21552546	Minimum Information About a Simulation Experiment (MIASE).	PLoS Comput Biol	2011
22670210	A tool for multi-scale modelling of the renal nephron.	Interface Focus	2011
21216774	The Physiome Model Repository 2.		2011
21235804	Revision history aware repositories of computational models of biological systems.	BMC Bioinformatics	2011
21762717	OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project.	Progress in Biophysics and Molecular Biology	2011
22172142	Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.	BMC Syst Biol	2011
20377909	An overview of the CellML API and its implementation.	BMC Bioinformatics	2010