Ryan Suderman
Overview
Explore the profile of Ryan Suderman including associated specialties, affiliations and a list of published articles.
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Articles
9
Citations
146
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0
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Recent Articles
1.
Mitra E, Suderman R, Colvin J, Ionkov A, Hu A, Sauro H, et al.
iScience
. 2019 Sep;
19:1012-1036.
PMID: 31522114
In systems biology modeling, important steps include model parameterization, uncertainty quantification, and evaluation of agreement with experimental observations. To help modelers perform these steps, we developed the software PyBioNetFit, which...
2.
Hlavacek W, Csicsery-Ronay J, Baker L, Ramos Alamo M, Ionkov A, Mitra E, et al.
Methods Mol Biol
. 2019 Apr;
1945:391-419.
PMID: 30945257
BioNetFit is a software tool designed for solving parameter identification problems that arise in the development of rule-based models. It solves these problems through curve fitting (i.e., nonlinear regression). BioNetFit...
3.
Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules
Suderman R, Fricke G, Hlavacek W
Methods Mol Biol
. 2019 Apr;
1945:33-42.
PMID: 30945241
RuleBuilder is a tool for drawing graphs that can be represented by the BioNetGen language (BNGL), which is used to formulate mathematical, rule-based models of biochemical systems. BNGL provides an...
4.
Erickson K, Rukhlenko O, Shahinuzzaman M, Slavkova K, Lin Y, Suderman R, et al.
PLoS Comput Biol
. 2019 Jan;
15(1):e1006706.
PMID: 30653502
Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding...
5.
Suderman R, Deeds E
Interface Focus
. 2018 Nov;
8(6):20180039.
PMID: 30443336
All living things have evolved to sense changes in their environment in order to respond in adaptive ways. At the cellular level, these sensing systems generally involve receptor molecules at...
6.
Civciristov S, Ellisdon A, Suderman R, Pon C, Evans B, Kleifeld O, et al.
Sci Signal
. 2018 Oct;
11(551).
PMID: 30301787
G protein-coupled receptors (GPCRs) are the largest class of cell surface signaling proteins, participate in nearly all physiological processes, and are the targets of 30% of marketed drugs. Typically, nanomolar...
7.
Suderman R, Mitra E, Lin Y, Erickson K, Feng S, Hlavacek W
Bull Math Biol
. 2018 Mar;
81(8):2822-2848.
PMID: 29594824
Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration of all reactions and all chemical species...
8.
Suderman R, Bachman J, Smith A, Sorger P, Deeds E
Proc Natl Acad Sci U S A
. 2017 May;
114(22):5755-5760.
PMID: 28500273
Signal transduction networks allow eukaryotic cells to make decisions based on information about intracellular state and the environment. Biochemical noise significantly diminishes the fidelity of signaling: networks examined to date...
9.
Suderman R, Deeds E
PLoS Comput Biol
. 2013 Oct;
9(10):e1003278.
PMID: 24130475
Despite the importance of intracellular signaling networks, there is currently no consensus regarding the fundamental nature of the protein complexes such networks employ. One prominent view involves stable signaling machines...