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

21. Functional significance of the dynamics of AMPAR extracellular region

Ingo Greger

MRC Lab of

Mol Biology, Cambridge,

UK

1, 2

Bahar, Bartol, Sejnowski

MRC Research Institute (Cambridge) Core Funds (2003 -)

BBSRC Synaptic Role of the AMPA

receptor N-terminal domain

(4/2016 - 4/2019)

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

25. Efficient parallel sampling at multiple scales using the weighted ensemble strategy

Lillian T. Chong

U of

Pittsburgh

1

Zuckerman

R01 GM115805- 01

High performance weighted ensemble software for simulation of complex bioevents (MPI: Chong & Zuckerman) 1/8/2015- 30/6/2019

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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