Author

D. P. Nickerson

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioengineering· 4 Biochemistry· 1 Cell Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell signaling & trafficking· 3 Approach:experimental assay· 3 Research Focus:software / tool· 3 Research Focus:benchmarking· 2 Approach:deep learning· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1 Organism:human· 1

Frequent Co-Authors

K. Tran· 3 shared M. Pan· 3 shared N. Shahidi· 3 shared E. Crampin· 2 shared S. Safaei· 2 shared A. J. Merz· 1 shared A. Lin· 1 shared A. Merz· 1 shared

Activity by Year

2017-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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3 shared papersBioengineering

K. Tran

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

SBML to bond graphs: from conversion to composition

N. Shahidi, M. Pan, K. Tran, E. Crampin, D. P. Nickerson

The paper presents a framework to convert SBML models into bond graphs to ensure physical plausibility and thermodynamic consistency in biochemical models.

bioRxiv · May 25, 2022Bioengineering

A semantics, energy-based approach to automate biomodel composition

N. Shahidi, M. Pan, K. Tran, E. Crampin, D. P. Nickerson

The paper proposes an automated method to compose biosimulation models using semantic annotations and bond graphs, demonstrating it by integrating Ras-MAPK and EGFR models.

bioRxiv · Nov 12, 2021Bioengineering

A modular and reusable model of epithelial transport in the proximal convoluted tubule

D. P. Nickerson, L. Noroozbabaee, P. J. Blanco, S. Safaei

The paper develops a modular mathematical model of epithelial transport in the proximal convoluted tubule, providing an open-source Python implementation for simulation and analysis.

bioRxiv · Nov 11, 2021Bioengineering

Hierarchical semantic composition of biosimulation models using bond graphs

N. Shahidi, M. Pan, S. Safaei, K. Tran, E. J. Crampin, D. P. Nickerson

This paper introduces a method to compose biosimulation models using bond graphs and semantic annotations, demonstrating it on a human arterial circulation model to improve modularity and physical consistency.

bioRxiv · Mar 9, 2021Bioengineering

Gatekeeper helix activates Golgi SM protein Sly1 and directly mediates close-range vesicle tethering

M. Duan, R. L. Plemel, T. Takenaka, A. Lin, B. M. Delgado, U. Nattermann, D. P. Nickerson, J. Mima, E. A. Miller, A. J. Merz

The paper identifies a gatekeeper helix in Sly1 that binds membranes to relieve autoinhibition and mediate close-range vesicle tethering in the early secretory pathway.

bioRxiv · Jan 16, 2020 · PreprintCell Biology

Sec17 (α-SNAP) And An SM-Tethering Complex Control The Outcome Of SNARE Zippering In Vitro And In Vivo

M. L. Schwartz, D. P. Nickerson, B. T. Lobingier, C. G. Angers, M. Zick, A. Merz

The paper investigates how Sec17 and SM-tethering complexes influence SNARE zippering, showing divergent effects on fusion depending on zippering states and demonstrating HOPS's role in controlling Sec17's impact.

bioRxiv · Apr 1, 2017Biochemistry