Perturbation biophysics

  • What is a perturbation experiment in biology?

    Perturbation biology is an experimental-computational technology for inferring network models that predict the response of cells to perturbations, and that may be useful in the design of combinatorial therapy against cancer..

  • What is perturbation in biology?

    Perturbation (biology), an alteration of the function of a biological system, induced by external or internal mechanisms..

m-1. A higher perturbation is shown at acidic pH, in which pores were visualized by Brewster angle microscopy. These perturbations may 
Proof of pore formation and biophysical perturbations through a 2D amoxicillin-lipid membrane interaction approach. Biochim Biophys Acta 

Can a deep generative model predict the distribution of perturbations in cells?

Small molecule treatment and gene knockout or overexpression induce complex changes in the molecular states of cells, and the space of possible perturbations is too large to measure exhaustively.
We present PerturbNet, a deep generative model for predicting the distribution of cell states induced by unseen chemical or genetic perturbations.

How do organisms respond to lipid perturbation?

Organisms across the tree of life, from prokaryotes to ectothermic animals, respond to such perturbations by tuning membrane lipid composition, down-regulating tightly packing lipids (e.g. containing saturated acyl chains) and up-regulating more loosely packed ones containing unsaturations or methylations in their lipid tails 10, 11, 12.

What is Perturb-seq & how does it work?

Our key innovation is to use high-throughput perturbation response data such as:

  • Perturb-Seq to learn a continuous mapping between the space of possible perturbations and the space of possible cell states.

    • What is perturbnet & why is it important?

    PerturbNet holds great promise for understanding perturbation responses and ultimately designing novel chemical and genetic interventions.
    The University of Michigan has filed a United States Provisional Patent on techniques and methods disclosed within this paper.

    Method for measuring heat changes

    Pressure perturbation calorimetry (PPC) is a technique closely related to isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC).
    In brief, PPC measures heat changes associated with dilute aqueous solutions of proteins or other biomolecules in response to introduction of relatively small pressure perturbations.
    Importantly, such heat changes can be related to thermodynamic properties of proteins such as hydration and conformational transitions upon folding and/or ligand binding.

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