David P Nickerson
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Explore the profile of David P Nickerson including associated specialties, affiliations and a list of published articles.
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39
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443
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Recent Articles
11.
Shahidi N, Pan M, Tran K, Crampin E, Nickerson D
PLoS One
. 2022 Jun;
17(6):e0269497.
PMID: 35657966
Hierarchical modelling is essential to achieving complex, large-scale models. However, not all modelling schemes support hierarchical composition, and correctly mapping points of connection between models requires comprehensive knowledge of each...
12.
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Shaikh B, Smith L, Vasilescu D, Marupilla G, Wilson M, Agmon E, et al.
Nucleic Acids Res
. 2022 May;
50(W1):W108-W114.
PMID: 35524558
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating...
13.
Munarko Y, Sarwar D, Rampadarath A, Atalag K, Gennari J, Neal M, et al.
Front Physiol
. 2022 Mar;
13:820683.
PMID: 35283794
Semantic annotation is a crucial step to assure reusability and reproducibility of biosimulation models in biology and physiology. For this purpose, the COmputational Modeling in BIology NEtwork (COMBINE) community recommends...
14.
Afshar N, Safaei S, Nickerson D, Hunter P, Suresh V
Front Physiol
. 2021 Dec;
12:699152.
PMID: 34950044
It has been suggested that glucose absorption in the small intestine depends on both constitutively expressed SGLT1 and translocated GLUT2 in the brush border membrane, especially in the presence of...
15.
Schreiber F, Gleeson P, Golebiewski M, Gorochowski T, Hucka M, Keating S, et al.
J Integr Bioinform
. 2021 Oct;
18(3).
PMID: 34674411
This special issue of the contains updated specifications of COMBINE standards in systems and synthetic biology. The 2021 special issue presents four updates of standards: Synthetic Biology Open Language Visual...
16.
Gennari J, Konig M, Misirli G, Neal M, Nickerson D, Waltemath D
J Integr Bioinform
. 2021 Oct;
18(3).
PMID: 34668356
A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and...
17.
Osanlouy M, Bandrowski A, de Bono B, Brooks D, Cassara A, Christie R, et al.
Front Physiol
. 2021 Jul;
12:693735.
PMID: 34248680
The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical...
18.
Welsh C, Nickerson D, Rampadarath A, Neal M, Sauro H, Gennari J
Bioinformatics
. 2021 Jun;
37(24):4898-4900.
PMID: 34132740
Summary: As the number and complexity of biosimulation models grows, so do demands for tools that can help users better understand models and make those models more findable, shareable and...
19.
Shahidi N, Pan M, Safaei S, Tran K, Crampin E, Nickerson D
PLoS Comput Biol
. 2021 May;
17(5):e1008859.
PMID: 33983945
Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model...
20.
Porubsky V, Goldberg A, Rampadarath A, Nickerson D, Karr J, Sauro H
Cell Syst
. 2020 Aug;
11(2):109-120.
PMID: 32853539
Like many scientific disciplines, dynamical biochemical modeling is hindered by irreproducible results. This limits the utility of biochemical models by making them difficult to understand, trust, or reuse. We comprehensively...