C&SP Summary

Collaboration & Service Projects Summary

C&SP # and title

Collaborator PI (s)
and co-Is

Institution of
Collaborator

TR&D

(a)

MMBioS Leader &

Co-Is

External Funding 

(source/grant code, title, and start-end dates)

5. Modeling immunoreceptor signaling, autophagy, and endocytosis

William Hlavacek

U of New Mexico, Los Alamos Natl lab

3

Faeder

NCI, 5R01-GM111510-02, Hardening Software for Rule-Based Modeling (Hlavacek)

8/1/14-4/30/18

7. Interfacing image-derived generative models with cell simulation engines

Michael Hucka,

Leslie M. Loew,

James C. Schaff

Caltech, U Conn

2, 3, 4

Murphy,

Faeder,

Bartol, Hood

5P41-GM103313-18:

National Resource for Cell Analysis and Modeling (Loew)

9/30/98-4/30/17

8. Using generative models of cell organization to investigate drug mechanisms and tumor cell heterogeneity

Steven J.

Altschuler,

Lani Wu

UCSF

4

Murphy

NCI: R01-CA133253-06:

Lung Cancer Heterogeneity and its Impact on Drug Resistance

8/1/10-5/31/16

15. Reconstructing zebrafish neural circuits controlling visually induced behaviors

Florian Engert,

David L. Hildebrand,

Harvard

2

Wetzel, Hood

NINDS: 5U01-NS090449

Neural Circuits in Zebrafish Form, Function and Plasticity (Engert) 9/30/14-7/31/17

16. Latent factor models for identification of novel neuroprotectives for Huntington’s Disease

Robert M.

Friedlander,

ME. Schurdak,

Andrew M. Stern, D. Lansing Taylor

U of Pittsburgh,

UPMC

1

Bahar

R01-NS077748-04:

Functional Role of Micro RNAS in Huntington’s Disease Pathogenesis (Friedlander) 2/15/12-1/31/17

17. NMJ Calcium signaling

Stephen D. Meriney

 Peter Wipf

U of Pittsburgh

1, 2

Bartol, Bahar,

Hood, Cheng,

Laghaei, Czech

NINDS, 5R01-NS090644-02,

CRCNS: Transmitter Release Site Organization in Plasticity and Disease at the NMJ 8/1/14-5/31/19

18.Effect of RNA-editing of ADAR1 on the activity of ionotropic glutamate receptors

QingDe Wang

UPMC

1

Bahar

NIH 5R21CA158650-02

Function of a novel molecule ADAR1 in endothelial cells for angiogenesis 4/15/2016 - 3/31/2018

19. Mapping the supramolecular organization of dendritic spines to model the regulation of synaptic signal transfer

Mark H. Ellisman

Andreas Herz

UCSD

Ludwig-Maximilians U, Munich, Germany

2, 4

Sejnowski

Bartol

NIDA: R01-DA038896-02:

CRCNS: Deciphering the dynamical multiscale structure-function of dendritic spines 7/1/14-6/30/19

20. Structural plasticity of chaperonins determined by cryo-electron microscopy: Modeling the machinery of GroEL and TRiC

Wah Chiu

Baylor College of Medicine

1, 4

Bahar

P01NS092525 “From structure to therapy: the TRiC chaperonin network in Huntington’s disease” (Chiu, Co-PI) 4/1/2016-31/3/2021

5P41-GM103832-31: 3D Electron Microscopy of

Macromolecules 12/1/96-12/31/19

22. Modeling T cell fate decisions

Penelope Morel, Robin E. C. Lee

U of Pittsburgh

3

Faeder

Juvenile Diabetes Research

Foundation 1-INO-2016-215-A-N

(Morel) 06/01/2016-05/31/2017

23. CaMKII structural dynamics

John Kuriyan

Berkeley

1, 2, 3

Bahar,

Faeder Sejnowski,

Bartol

 

24. Spatio-temporal cell biology

Alan Horwitz,

Gregory Johnson

Allen Institute

4

Murphy

The Allen Foundation has provided $100 million to create the Allen Institute for Cell Science to support the collection of cell images

26. GPCR signaling and interactions. Learning from

SILAC/ proteomics

Kunhong (Kevin) Xiao

U Pitt

1, 3

Bahar, Faeder

NHLBI: 2P01-HL07544311, Novel

Mechanisms and Therapies in Heart Failure (PI: Rockman, Duke U) Proteomics and Structure Core (PI: Xiao) 8/1/2015 7/31/2020

27. Circuit reconstruction of association cortex

Lee

Harvard

2

 

NIDCD: 5R03-DC013622-03: Network

Anatomy of Olfactory Processing

9/18/13-8/31/16

28. Dynamic modulation of interferon binding affinity as a mechanism to regulate interferon receptor signaling

Gideon Schreiber

Weizmann Institute, Israel

1, 3

Bahar, Faeder

ISF (Israel Science Foundation) Center of Research Excellence for

Integrated Structural Cell Biology,

2013-2018

29. Spatiotemporal models of autophagy

Joern Dengjel

University of Frieburg

4

Murphy

Swiss National Fund 31003A_ 166482/1 Stimulus and time dependent protein dynamics in autophagy analyzed by quantitative MS

30. Modeling of Tetrahymena basal body dynamics

Chad G. Pearson

University of Colorado,

Denver

4

Murphy

5R01GM099820-04, Mechanisms of Centriole Assembly and Stability 9/24/12-7/31/17

31. Receptor Clustering and the Kinetics of T Cell-Mediated Killing

Yuri Sykulev

Thomas Jefferson University

3

Faeder

5R21AI113819-02 Exploiting an Artificial APC to Induce Different T Subsets 1/1/15-12/31/16

32. Integrating compartmental rule-based modeling into VCell

Schaff,

Blinov, Moraru, Les Loew

U Connecticut Health Center

3

Faeder,

Bartol

5P41-GM103313-18: National Resource for Cell Analysis

and Modeling (Loew) 9/30/98-4/30/17

33. Integration of rule-based modeling capabilities with pySB modeling platform

Carlos F. Lopez

Vanderbilt

3

Faeder

 

34. Development of a high-level, rule-based whole-cell modeling language

Jonathan Karr

Mt. Sinai

3

Faeder

NSF 1548123L, ERASynBio:

MiniCell - A Model-driven approach to minimal cell engineering (Karr) 12/17/2015 - 7/31/2018

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