Zobrazeno 1 - 10
of 26
pro vyhledávání: '"Ryan, Suderman"'
Autor:
Eshan D. Mitra, Ryan Suderman, Joshua Colvin, Alexander Ionkov, Andrew Hu, Herbert M. Sauro, Richard G. Posner, William S. Hlavacek
Publikováno v:
iScience, Vol 19, Iss , Pp 1012-1036 (2019)
Summary: 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,
Externí odkaz:
https://doaj.org/article/758e396753f54cbcb6ef1980853409b4
Autor:
Keesha E Erickson, Oleksii S Rukhlenko, Md Shahinuzzaman, Kalina P Slavkova, Yen Ting Lin, Ryan Suderman, Edward C Stites, Marian Anghel, Richard G Posner, Dipak Barua, Boris N Kholodenko, William S Hlavacek
Publikováno v:
PLoS Computational Biology, Vol 15, Iss 1, p e1006706 (2019)
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 phosphot
Externí odkaz:
https://doaj.org/article/1ac9fae3f9c4494488487ff0d56be8a6
Autor:
Ryan Suderman, Eric J Deeds
Publikováno v:
PLoS Computational Biology, Vol 9, Iss 10, p e1003278 (2013)
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 with well-defined quater
Externí odkaz:
https://doaj.org/article/6e900a922a42410e9d5e795daece3bc7
Autor:
Song Feng, William S. Hlavacek, Keesha E. Erickson, Ryan Suderman, Yen Ting Lin, Eshan D. Mitra
Publikováno v:
Bull Math Biol
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 that may arise in the syste
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8238f534b34fb7c4050c23fc7a5e8d1f
https://doi.org/10.1007/s11538-018-0418-2
https://doi.org/10.1007/s11538-018-0418-2
Autor:
William S, Hlavacek, Jennifer A, Csicsery-Ronay, Lewis R, Baker, María Del Carmen, Ramos Álamo, Alexander, Ionkov, Eshan D, Mitra, Ryan, Suderman, Keesha E, Erickson, Raquel, Dias, Joshua, Colvin, Brandon R, Thomas, Richard G, Posner
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 1945
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 is compatible with determin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::6c762844ac2431104f0cd97998aadfb2
https://pubmed.ncbi.nlm.nih.gov/30945257
https://pubmed.ncbi.nlm.nih.gov/30945257
Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 1945
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 intuitive plain text, or string, representation of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::52176fd42ca163811a1c1e017b83100b
https://pubmed.ncbi.nlm.nih.gov/30945241
https://pubmed.ncbi.nlm.nih.gov/30945241
Autor:
William S. Hlavacek, Brandon R. Thomas, Ryan Suderman, Joshua Colvin, Keesha E. Erickson, Lewis R. Baker, Raquel Dias, Jennifer Csicsery-Ronay, Richard G. Posner, Eshan D. Mitra, María del Carmen Ramos Álamo, Alexander Ionkov
Publikováno v:
Modeling Biomolecular Site Dynamics ISBN: 9781493991006
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 is compatible with determin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::594098bdf27d8176bcfa5a448d0944aa
https://doi.org/10.1007/978-1-4939-9102-0_18
https://doi.org/10.1007/978-1-4939-9102-0_18
Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules
Publikováno v:
Modeling Biomolecular Site Dynamics ISBN: 9781493991006
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 intuitive plain text, or string, representation of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c4e8955dccee613d5378b0d5e7db2d17
https://doi.org/10.1007/978-1-4939-9102-0_2
https://doi.org/10.1007/978-1-4939-9102-0_2
Autor:
Ryan Suderman, Eric J. Deeds
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 the cell surface, which detect changes outside the cell an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4a0294ce5dc379510da2d62d8b020f30
https://europepmc.org/articles/PMC6227803/
https://europepmc.org/articles/PMC6227803/