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cytoNet: Network Analysis of Cell Communities

36 Pages Posted: 19 Mar 2019 Sneak Peek Status: Review Complete

See all articles by Arun S. Mahadevan

Arun S. Mahadevan

University of Pennsylvania - Department of Bioengineering

Byron L. Long

University of Texas at San Antonio - Department of Biomedical Engineering

Chenyue Wendy Hu

Rice University - Department of Bioengineering

David T. Ryan

Rice University - Department of Bioengineering

George L. Britton

Rice University - Department of Systems, Synthetic, and Physical Biology Program

Andrew Ligeralde

University of California, Berkeley - Biophysics Graduate Program

Jacob T. Robinson

Rice University - Department of Bioengineering; Rice University - Department of Electrical and Computer Engineering

Aryeh Warmflash

Rice University - Department of Bioengineering; Rice University - Department of Systems, Synthetic, and Physical Biology Program; Rice University - Department of BioSciences

Amina Ann Qutub

University of Texas at San Antonio - Department of Biomedical Engineering; Rice University - Department of Systems, Synthetic, and Physical Biology Program

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Abstract

We introduce cytoNet, a method to characterize multicellular topology from microscopy images. Accessible through a web-based interface, cytoNet quantifies the spatial relationships in cell communities using principles of graph theory, and evaluates the effect of cell-cell interactions on individual cell phenotypes. We demonstrate cytoNet’s capabilities in two applications relevant to regenerative medicine: quantifying the morphological response of endothelial cells to neurotrophic factors present in the brain after injury, and characterizing cell cycle dynamics of differentiating neural progenitor cells. The framework introduced here can be used to study complex cell communities in a quantitative manner, leading to a deeper understanding of environmental effects on cellular behavior.

Suggested Citation

Mahadevan, Arun S. and Long, Byron L. and Hu, Chenyue Wendy and Ryan, David T. and Britton, George L. and Ligeralde, Andrew and Robinson, Jacob T. and Warmflash, Aryeh and Qutub, Amina Ann, cytoNet: Network Analysis of Cell Communities (March 15, 2019). Available at SSRN: https://ssrn.com/abstract=3353224 or http://dx.doi.org/10.2139/ssrn.3353224
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Arun S. Mahadevan

University of Pennsylvania - Department of Bioengineering

220 S 33rd St
Philadelphia, PA 19104
United States

Byron L. Long

University of Texas at San Antonio - Department of Biomedical Engineering

Applied Engineering Building (AET)
Room 1.102 One UTSA Circle
San Antonio, TX 78249
United States

Chenyue Wendy Hu

Rice University - Department of Bioengineering

6500 Main Street
Houston, TX 77030
United States

David T. Ryan

Rice University - Department of Bioengineering

6500 Main Street
Houston, TX 77030
United States

George L. Britton

Rice University - Department of Systems, Synthetic, and Physical Biology Program

6100 South Main Street
Houston, TX 77005-1892
United States

Andrew Ligeralde

University of California, Berkeley - Biophysics Graduate Program

CA
United States

Jacob T. Robinson

Rice University - Department of Bioengineering

6500 Main Street
Houston, TX 77030
United States

Rice University - Department of Electrical and Computer Engineering

6100 Main St
Houston, TX 77005-1892
United States

Aryeh Warmflash

Rice University - Department of Bioengineering

6500 Main Street
Houston, TX 77030
United States

Rice University - Department of Systems, Synthetic, and Physical Biology Program

6100 South Main Street
Houston, TX 77005-1892
United States

Rice University - Department of BioSciences

Houston, TX 77005
United States

Amina Ann Qutub (Contact Author)

University of Texas at San Antonio - Department of Biomedical Engineering ( email )

Applied Engineering Building (AET)
Room 1.102 One UTSA Circle
San Antonio, TX 78249
United States

Rice University - Department of Systems, Synthetic, and Physical Biology Program ( email )

6100 South Main Street
Houston, TX 77005-1892
United States

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