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Related Concept Videos

Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Cell Motility through Blebbing01:16

Cell Motility through Blebbing

Blebs are a type of membrane protrusion formed by the internal hydrostatic pressure of the cytoplasm. Blebs are observed in several cell types, including fibroblasts, immune cells, and single-celled organisms like the amoeba. The primary function of blebs is cell locomotion and apoptosis, but they are also found during necrosis and cell division. The life cycle of a bleb comprises an initiation phase followed by the expansion and retraction phases.
Blebbing Through the Matrix
In multicellular...
Relative Motion Analysis - Velocity01:24

Relative Motion Analysis - Velocity

A stroke engine has a slider-crank mechanism that converts rotational motion from the crank into linear motion of the slider or vice versa. This mechanism consists of three main parts: the crank, the connecting rod, and the slider.
When an external force is exerted, it sets the crank into a rotational movement. This, in turn, instigates the motion of the connecting rod, leading to what is referred to as a general plane motion. This process involves two key points - point A on the connecting rod...
Chemotaxis and Direction of Cell Migration01:21

Chemotaxis and Direction of Cell Migration

Cells can detect chemical cues in their environment and reorganize the cytoskeleton to migrate toward them or away from them. This directional migration, called chemotaxis, is essential during embryogenesis and development, immune response, tissue repair and regeneration, and reproduction. These chemical cues can either attract or repel the cell's movement. For example, axon development is determined by a combination of chemoattractants and chemorepellents that direct the growing axon towards...
Cell Migration01:19

Cell Migration

Cell migration is a process by which the cells move from one location to another, playing an essential role in embryological development, repair and regeneration, immune response, and metastasis. Cells migrate in response to chemical or mechanical signals generated by specific organs or tissues. The overall mechanism includes three steps - polarization, protrusion, and release. Polarization involves the formation of a distinct cell front and rear, which determines the direction of movement.
Cell Migration01:09

Cell Migration

Cell migration, the process by which cells move from one location to another, is essential for the proper development and viability of organisms throughout their life. When cells are not able to migrate properly to their ordained locations, various disorders may occur. For example, disruption in cell migration causes chronic inflammatory diseases such as arthritis.

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Related Experiment Video

Updated: May 8, 2026

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools
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Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools

Published on: December 16, 2015

Dissecting and steering cell dynamics using spatially-informed RNA velocity with veloAgent.

Vishvak Raghavan1,2,3, Brent Yoon1,2, Gregory J Fonseca4

  • 1School of Computer Science, McGill University, Montreal, QC, Canada.

Molecular Systems Biology
|May 6, 2026
PubMed
Summary

RNA velocity analysis now integrates spatial context using veloAgent, a novel framework that models cell state transitions in large datasets. This method enhances accuracy and enables in silico perturbations for predicting cell fate dynamics.

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Last Updated: May 8, 2026

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools
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Published on: December 16, 2015

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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Area of Science:

  • Single-cell transcriptomics
  • Systems biology
  • Computational biology

Background:

  • RNA velocity infers cell state transitions by modeling mRNA dynamics.
  • Current methods lack spatial context and scalability for large datasets.
  • Tissue organization and dynamic processes remain challenging to study.

Purpose of the Study:

  • Introduce veloAgent, a deep generative and agent-based framework.
  • Integrate spatial information into RNA velocity analysis.
  • Enable scalable and accurate inference of cell state transitions.

Main Methods:

  • Agent-based simulations of local microenvironments to integrate spatial data.
  • Deep generative modeling of transcriptional kinetics.
  • In silico perturbation module for simulating regulatory interventions.

Main Results:

  • veloAgent improves RNA velocity accuracy by integrating molecular and spatial cues.
  • Achieves sublinear memory scaling for efficient analysis of large, multi-batch spatial datasets.
  • Accurately estimates gene- and cell-specific transcriptional kinetics.

Conclusions:

  • veloAgent is a scalable and versatile framework for dissecting spatially resolved cellular dynamics.
  • Facilitates prediction of cell fate dynamics and regulatory intervention impacts.
  • Advances the study of tissue organization and dynamic biological processes.