An introduction to NMR-based approaches for measuring protein dynamics

IR Kleckner, MP Foster - Biochimica et Biophysica Acta (BBA)-Proteins and …, 2011 - Elsevier
Proteins are inherently flexible at ambient temperature. At equilibrium, they are
characterized by a set of conformations that undergo continuous exchange within a …

[HTML][HTML] Kinetic models in industrial biotechnology–improving cell factory performance

J Almquist, M Cvijovic, V Hatzimanikatis, J Nielsen… - Metabolic …, 2014 - Elsevier
An increasing number of industrial bioprocesses capitalize on living cells by using them as
cell factories that convert sugars into chemicals. These processes range from the production …

The coefficient of determination R-squared is more informative than SMAPE, MAE, MAPE, MSE and RMSE in regression analysis evaluation

D Chicco, MJ Warrens, G Jurman - Peerj computer science, 2021 - peerj.com
Regression analysis makes up a large part of supervised machine learning, and consists of
the prediction of a continuous independent target from a set of other predictor variables. The …

Predicting perturbation patterns from the topology of biological networks

M Santolini, AL Barabási - Proceedings of the National …, 2018 - National Acad Sciences
High-throughput technologies, offering an unprecedented wealth of quantitative data
underlying the makeup of living systems, are changing biology. Notably, the systematic …

Structural identifiability of dynamic systems biology models

AF Villaverde, A Barreiro… - PLoS computational …, 2016 - journals.plos.org
A powerful way of gaining insight into biological systems is by creating a nonlinear
differential equation model, which usually contains many unknown parameters. Such a …

Universally sloppy parameter sensitivities in systems biology models

RN Gutenkunst, JJ Waterfall, FP Casey… - PLoS computational …, 2007 - journals.plos.org
Quantitative computational models play an increasingly important role in modern biology.
Such models typically involve many free parameters, and assigning their values is often a …

[HTML][HTML] The first five seconds in the life of a clathrin-coated pit

E Cocucci, F Aguet, S Boulant, T Kirchhausen - Cell, 2012 - cell.com
Coated pits assemble by growth of a clathrin lattice, which is linked by adaptors to the
underlying membrane. How does this process start? We used live-cell TIRF imaging with …

Stochastic modelling for quantitative description of heterogeneous biological systems

DJ Wilkinson - Nature Reviews Genetics, 2009 - nature.com
Two related developments are currently changing traditional approaches to computational
systems biology modelling. First, stochastic models are being used increasingly in …

Identifiability analysis for stochastic differential equation models in systems biology

AP Browning, DJ Warne, K Burrage… - Journal of the …, 2020 - royalsocietypublishing.org
Mathematical models are routinely calibrated to experimental data, with goals ranging from
building predictive models to quantifying parameters that cannot be measured. Whether or …

Cargo and dynamin regulate clathrin-coated pit maturation

D Loerke, M Mettlen, D Yarar, K Jaqaman… - PLoS …, 2009 - journals.plos.org
Total internal reflection fluorescence microscopy (TIR-FM) has become a powerful tool for
studying clathrin-mediated endocytosis. However, due to difficulties in tracking and …