Quantifying information of intracellular signaling: progress with machine learning

Y Tang, A Hoffmann - Reports on Progress in Physics, 2022 - iopscience.iop.org
Cells convey information about their extracellular environment to their core functional
machineries. Studying the capacity of intracellular signaling pathways to transmit information …

The genotype‐phenotype landscape of an allosteric protein

DS Tack, PD Tonner, A Pressman… - Molecular systems …, 2021 - embopress.org
Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling,
and metabolism. Yet a quantitative understanding of allosteric genotype‐phenotype …

Exploiting information and control theory for directing gene expression in cell populations

L Henrion, M Delvenne, F Bajoul Kakahi… - Frontiers in …, 2022 - frontiersin.org
Microbial populations can adapt to adverse environmental conditions either by appropriately
sensing and responding to the changes in their surroundings or by stochastically switching …

Precision engineering of biological function with large-scale measurements and machine learning

DS Tack, PD Tonner, A Pressman, ND Olson, SF Levy… - PloS one, 2023 - journals.plos.org
As synthetic biology expands and accelerates into real-world applications, methods for
quantitatively and precisely engineering biological function become increasingly relevant …

Robust topology optimization under loading uncertainties via stochastic reduced order models

AP Torres, JE Warner, MA Aguiló… - International Journal for …, 2021 - Wiley Online Library
An efficient approach for topology optimization under uncertainty is presented. Stochastic
reduced order models (SROMs) are leveraged for the modeling and propagation of …

Automated analysis of bacterial flow cytometry data with FlowGateNIST

D Ross - PLoS One, 2021 - journals.plos.org
Flow cytometry is commonly used to evaluate the performance of engineered bacteria. With
increasing use of high-throughput experimental methods, there is a need for automated …

[PDF][PDF] Method for reproducible automated bacterial cell culture and measurement

D Ross, PD Tonner, OB Vasilyeva - Synthetic Biology, 2022 - academic.oup.com
Microbial cell culture is one of the most commonly performed protocols for synthetic biology,
and laboratories are increasingly using 96-well plates and laboratory automation systems …

Decoding cellular communication: An information theoretic perspective on cytokine and endocrine signaling

F Schaper, T Jetka, A Dittrich - Current Opinion in Endocrine and Metabolic …, 2022 - Elsevier
Humoral communication is mediated by complex signaling pathways that are
heterogeneously activated in individual cells. According to Shannon's information theory …

Efficacy of information transmission in cellular communication

S Sarkar, MZ Ali, S Choubey - Physical Review Research, 2023 - APS
Cell signaling is essential for individual cells to execute various tasks and respond to
changes in their environment. It is carried out via diffusing molecules, whose transport is …

High content imaging for monitoring signalling dynamics in single cells

KL Garner - Journal of Molecular Endocrinology, 2020 - jme.bioscientifica.com
All living cells are sensors of their environment: they sense signals, hormones, cytokines,
and growth factors, among others. Binding of these signals to cell surface receptors initiates …