Related papers: Using biophotonics to study signaling mechanisms i…

In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently,…

Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…

Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…

Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…

Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…

Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…

This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…

The knowledge of cell molecular mechanisms implicated in human diseases is expanding and should be converted into guidelines for deciphering pathological cell signaling and suggesting appropriate treatment. The basic assumption is that…

This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…

Biophotonic techniques are growing in rapid rhythms enabling the monitoring of subcellular structures and non-invasive theranostic interventions in cancer and autoimmune diseases. The integration of Biophotonics with nanotechnology and…

Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data…

Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…

Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…

Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently…

The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…

Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…

In view of ever-changing conditions both in the external world and in intrinsic brain states, maintaining the robustness of computations poses a challenge, adequate solutions to which we are only beginning to understand. At the level of…

The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…

Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a…