Related papers: Inferring maps of forces inside cell membrane micr…
Protein mobility is conventionally analyzed in terms of an effective diffusion. Yet, this description often fails to properly distinguish and evaluate the physical parameters (such as the membrane friction) and the biochemical interactions…
Trajectory inference is used to order single-cell omics data along a path that reflects a continuous transition between cells. This approach is useful for studying processes like cell differentiation, where a stem cell matures into a…
In the course of animal development, the shape of tissue emerges in part from mechanical and biochemical interactions between cells. Measuring stress in tissue is essential for studying morphogenesis and its physical constraints.…
We devise a method to detect and estimate forces in a heterogeneous environment based on experimentally recorded stochastic trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here,…
A very common strategy to penetrate the cell membrane and access the internal compartment, consists of using sharp tips or nano needles. However recent experiments of cell penetration by atomic force microscopy tips show, contrary to…
Network inference, the task of reconstructing interactions in a complex system from experimental observables, is a central yet extremely challenging problem in systems biology. While much progress has been made in the last two decades,…
During morphogenesis, the shape of a tissue emerges from collective cellular behaviors, which are in part regulated by mechanical and biochemical interactions between cells. Quantification of force and stress is therefore necessary to…
The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the…
As an effective method to deliver external materials into biological cells, microinjection has been widely applied in the biomedical field. However, the cognition of cell mechanical property is still inadequate, which greatly limits the…
Targeting signaling pathways that drive cancer cell migration or proliferation is a common therapeutic approach. A popular experimental technique, the scratch assay, measures the migration and proliferation-driven cell closure of a defect…
The measurement of cellular traction forces on soft elastic substrates has become a standard tool for many labs working on mechanobiology. Here we review the basic principles and different variants of this approach. In general, the…
Inspired by its central role in many biological processes, the transport of biopolymers across nanoscale pores is at the heart of a single-molecule sensing technology aimed at nucleic acid and protein sequencing, as well as biomarker…
Statistical inference of genetic regulatory networks is essential for understanding temporal interactions of regulatory elements inside the cells. For inferences of large networks, identification of network structure is typical achieved…
Investigating the cellular internalization pathways of single molecules or single nano-objects is important to understanding cell-matter interactions and to applications in drug delivery and discovery. Imaging and tracking the motion of…
Capturing data from dynamic processes through cross-sectional measurements is seen in many fields, such as computational biology. Trajectory inference deals with the challenge of reconstructing continuous processes from such observations.…
Neuroscience has recently made much progress, expanding the complexity of both neural-activity measurements and brain-computational models. However, we lack robust methods for connecting theory and experiment by evaluating our new big…
We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combinatorial therapy against cancer. The experiments are…
Migration of cells can be characterized by two, prototypical types of motion: individual and collective migration. We propose a statistical-inference approach designed to detect the presence of cell-cell interactions that give rise to…
Membrane organization is essential for cellular functions such as signal transduction and membrane trafficking. A major challenge is to understand the lateral heterogeneous structures in membranes and membrane fluidity in the presence of…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…