Joseph L Hellerstein
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Explore the profile of Joseph L Hellerstein including associated specialties, affiliations and a list of published articles.
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10
Citations
32
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Recent Articles
1.
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...
2.
Kochen M, Hellerstein J, Sauro H
Interface Focus
. 2024 Feb;
14(1):20230045.
PMID: 38344405
Cellular signal transduction takes place through a network of phosphorylation cycles. These pathways take the form of a multi-layered cascade of cycles. This work focuses on the sensitivity of single,...
3.
Ma S, Fan L, Konanki S, Liu E, Gennari J, Smith L, et al.
Bioinformatics
. 2023 Dec;
39(12).
PMID: 38096590
Motivation: Developing biochemical models in systems biology is a complex, knowledge-intensive activity. Some modelers (especially novices) benefit from model development tools with a graphical user interface. However, as with the...
4.
Shin W, Gennari J, Hellerstein J, Sauro H
Bioinformatics
. 2023 Oct;
39(11).
PMID: 37882737
Motivation: Annotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations,...
5.
Kochen M, Hellerstein J, Sauro H
bioRxiv
. 2023 Oct;
PMID: 37781602
Signal transduction from a cell's surface to cytoplasmic and nuclear targets takes place through a complex network of interconnected pathways. Phosphorylation cycles are common components of many pathways and may...
6.
Shin W, Gennari J, Hellerstein J, Sauro H
bioRxiv
. 2023 Jul;
PMID: 37503075
Motivation: Annotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations,...
7.
Tatka L, Smith L, Hellerstein J, Sauro H
J Transl Med
. 2023 Jul;
21(1):501.
PMID: 37496031
Computational models are increasingly used in high-impact decision making in science, engineering, and medicine. The National Aeronautics and Space Administration (NASA) uses computational models to perform complex experiments that are...
8.
Tatka L, Luk W, Elston T, Hellerstein J, Sauro H
Biosystems
. 2023 Jan;
224:104836.
PMID: 36640942
New tools and software in systems biology require testing and validation on reaction networks with desired characteristics such as number of reactions or oscillating behaviors. Often, there is only a...
9.
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...
10.
Shin W, Hellerstein J
Bioinformatics
. 2020 Aug;
37(3):388-395.
PMID: 32790862
Motivation: The growing complexity of reaction-based models necessitates early detection and resolution of model errors. Considerable work has been done on the detection of mass balance errors, especially atomic mass...