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
Citations
443
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Recent Articles
1.
Sauro H, Agmon E, Blinov M, Gennari J, Hellerstein J, Heydarabadipour A, et al.
ArXiv
. 2025 Mar;
PMID: 40034129
Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data...
2.
Smith L, Malik-Sheriff R, Nguyen T, Hermjakob H, Karr J, Shaikh B, et al.
bioRxiv
. 2025 Feb;
PMID: 39896466
The BioModels Repository contains over 1000 manually curated mechanistic models drawn from published literature, most of which are encoded in the Systems Biology Markup Language (SBML). This community-based standard formally...
3.
Hunter P, Ai W, Nickerson D
Biophys J
. 2024 Dec;
124(2):316-335.
PMID: 39644093
The SLC (solute carrier) superfamily mediates the passive transport of small molecules across apical and basolateral cell membranes in nearly all tissues. In this paper, we employ bond-graph approaches to...
4.
Golebiewski M, Bader G, Gleeson P, Gorochowski T, Keating S, Konig M, et al.
J Integr Bioinform
. 2024 Jul;
21(1).
PMID: 39026464
No abstract available.
5.
Gamage T, Elsayed A, Lin C, Wu A, Feng Y, Yu J, et al.
Annu Int Conf IEEE Eng Med Biol Soc
. 2023 Dec;
2023:1-4.
PMID: 38083471
Clinical translation of personalised computational physiology workflows and digital twins can revolutionise healthcare by providing a better understanding of an individual's physiological processes and any changes that could lead to...
6.
Konig M, Gleeson P, Golebiewski M, Gorochowski T, Hucka M, Keating S, et al.
J Integr Bioinform
. 2023 Mar;
20(1).
PMID: 36989443
This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2022 special issue presents three updates to the standards:...
7.
Munarko Y, Rampadarath A, Nickerson D
Front Bioinform
. 2023 Mar;
3:1107467.
PMID: 36865672
Maximising FAIRness of biosimulation models requires a comprehensive description of model entities such as reactions, variables, and components. The COmputational Modeling in BIology NEtwork (COMBINE) community encourages the use of...
8.
Noroozbabaee L, Blanco P, Safaei S, Nickerson D
PLoS One
. 2022 Nov;
17(11):e0275837.
PMID: 36355848
We review a collection of published renal epithelial transport models, from which we build a consistent and reusable mathematical model able to reproduce many observations and predictions from the literature....
9.
Kim N, Pronto J, Nickerson D, Taberner A, Hunter P
Front Physiol
. 2022 Sep;
13:965054.
PMID: 36176770
While ion channels and transporters involved in excitation-contraction coupling have been linked and constructed as comprehensive computational models, validation of whether each individual component of a model can be reused...
10.
Shahidi N, Pan M, Tran K, Crampin E, Nickerson D
Math Biosci
. 2022 Sep;
352:108901.
PMID: 36096376
The Systems Biology Markup Language (SBML) is a popular software-independent XML-based format for describing models of biological phenomena. The BioModels Database is the largest online repository of SBML models. Several...