SBML Level 3: an extensible format for the exchange and reuse of biological models
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …
complexity of computational models. To reproduce simulation results and reuse models …
Parameter estimation and uncertainty quantification for systems biology models
ED Mitra, WS Hlavacek - Current opinion in systems biology, 2019 - Elsevier
Mathematical models can provide quantitative insights into immunoreceptor signaling, and
other biological processes, but require parameterization and uncertainty quantification …
other biological processes, but require parameterization and uncertainty quantification …
Control of cell state transitions
Understanding cell state transitions and purposefully controlling them is a longstanding
challenge in biology. Here we present cell state transition assessment and regulation …
challenge in biology. Here we present cell state transition assessment and regulation …
PEtab—Interoperable specification of parameter estimation problems in systems biology
L Schmiester, Y Schälte, FT Bergmann… - PLoS computational …, 2021 - journals.plos.org
Reproducibility and reusability of the results of data-based modeling studies are essential.
Yet, there has been—so far—no broadly supported format for the specification of parameter …
Yet, there has been—so far—no broadly supported format for the specification of parameter …
Co-regulation of the transcription controlling ATF2 phosphoswitch by JNK and p38
Transcription factor phosphorylation at specific sites often activates gene expression, but
how environmental cues quantitatively control transcription is not well-understood. Activating …
how environmental cues quantitatively control transcription is not well-understood. Activating …
Best practices for making reproducible biochemical models
VL Porubsky, AP Goldberg, AK Rampadarath… - Cell systems, 2020 - cell.com
Like many scientific disciplines, dynamical biochemical modeling is hindered by
irreproducible results. This limits the utility of biochemical models by making them difficult to …
irreproducible results. This limits the utility of biochemical models by making them difficult to …
Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry
Most of the fascinating phenomena studied in cell biology emerge from interactions among
highly organized multimolecular structures embedded into complex and frequently dynamic …
highly organized multimolecular structures embedded into complex and frequently dynamic …
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
ZB Haiman, DC Zielinski, Y Koike… - PLoS computational …, 2021 - journals.plos.org
Mathematical models of metabolic networks utilize simulation to study system-level
mechanisms and functions. Various approaches have been used to model the steady state …
mechanisms and functions. Various approaches have been used to model the steady state …
Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes
E Salazar-Cavazos, CF Nitta, ED Mitra… - Molecular Biology of …, 2020 - Am Soc Cell Biol
Differential epidermal growth factor receptor (EGFR) phosphorylation is thought to couple
receptor activation to distinct signaling pathways. However, the molecular mechanisms …
receptor activation to distinct signaling pathways. However, the molecular mechanisms …
Bayesian inference of state-level COVID-19 basic reproduction numbers across the United States
Although many persons in the United States have acquired immunity to COVID-19, either
through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to …
through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to …