From Cardiac Systems Biology Lab

Main: Downloads

Repositories

Saucerman lab on GitHub:[https://github.com/saucermanlab]

BioModels: [https://wwwdev.ebi.ac.uk/biomodels/search?query=saucerman]

Physiome Database: [https://models.physiomeproject.org/@@search?SearchableText=saucerman]

Image Analysis

Sutcliffe MD, Tan PM, Fernandez-Perez A, Nam YJ, Munshi NV, Saucerman JJ. High content analysis identifies unique morphological features of reprogrammed cardiomyocytes. Sci Rep. 2018 Jan 19;8(1):1258.

MATLAB code [download]
Images used for analysis [download]

Ryall KA, Saucerman JJ. Automated microscopy of cardiac myocyte hypertrophy: a case study on the role of intracellular α-adrenergic receptors. Methods Mol Biol. 2015;1234:123-34.

CellProfiler pipeline [download]

Laker RC, Xu P, Ryall KA, Sujkowski A, Kenwood BM, Chain KH, Zhang M, Royal MA, Hoehn KL, Driscoll M, Adler PN, Wessells RJ, Saucerman JJ, Yan Z. A novel MitoTimer reporter gene for mitochondrial content, structure, stress, and damage in vivo. J Biol Chem. 2014 Apr 25;289(17):12005-15.

MitoTimer analysis code (MATLAB) [download]
Example MitoTimer images [download]

Ryall KA, *Saucerman JJ. Automated imaging reveals a concentration-dependent delay in reversibility of cardiac myocyte hypertrophy. J Mol Cell Cardiol, 2012 53(2):282-90. PMCID: 3389167. [Pubmed]

CellProfiler pipeline [download]

Bass GT, Ryall KA, Katikapalli A, Taylor BE, Dang ST, Acton ST, Saucerman JJ. Automated image analysis identifies signaling pathways regulating distinct signatures of cardiac myocyte hypertrophy. J Mol Cell Cardiol. 2012; 52(5):923-30. PMCID: 3299901. [Link]

CellProfiler pipeline and example images [download]
CellProfiler is developed by Anne Carpenter at the Broad Institute and should be downloaded at [link]. Our data was processed using CellProfiler Developer build 1.0.7522 [download].

Amanfu, RK, Muller, J, Saucerman JJ. Automated image analysis of cardiac myocyte Ca2+ dynamics. Conf Proc IEEE Eng Med Biol Soc 2011. [Pubmed]

MATLAB code: [download]

Computational Models

Netflux: user-friendly software for logic-based modeling of biological networks

Windows version 1.0 installer: [Netflux_1p0_Windows.exe]
Mac version 1.0 installer: [Netflux_1p0_Mac.zip]
MATLAB source code: https://github.com/saucermanlab/Netflux
Note: during installation, the Windows and Mac versions will automatically download and install a ~250 MB MATLAB runtime. If you already have MATLAB, we recommend using the sourcecode version as the runtime is not needed.

Yang JH, Polanowska-Grabowska RK, Smith JS, Shields CW 4th, Saucerman JJ. PKA catalytic subunit compartmentation regulates contractile and hypertrophic responses to β-adrenergic signaling. J Mol Cell Cardiol. 2014 Jan;66:83-93. [Pubmed]

MATLAB code: [download]

Ryall KA, Holland DO, Delaney KA, Kraeutler MJ, Parker AJ, Saucerman JJ. Network reconstruction and systems analysis of cardiac myocyte hypertrophy signaling. J Biol Chem. 2012 Oct 22. [Pubmed]

MATLAB code and Netflux spreadsheet: [download]

Yang JH, Saucerman JJ. Phospholemman is a negative feed-forward regulator of Ca2+ in β-adrenergic signaling, accelerating β-adrenergic inotropy. J Mol Cell Cardiol. 2012; 52(5):1048-55. PMCID: 3327824. [Pubmed]

MATLAB code: [download]

Holland DO, Krainak NC, Saucerman JJ. Graphical approach to model reduction for nonlinear biochemical networks. PLoS One. 2011;6(8):e23795. Epub 2011 Aug 25. [Pubmed]

MATLAB code: [download]

Soltis AR, Saucerman JJ. "Synergy between CaMKII substrates and β-adrenergic signaling in regulation of cardiac myocyte Ca(2+) handling." Biophys J. 2010;99(7):2038-47. [Pubmed]. Selected as a “Must Read” 8/10 by [Faculty of 1000].

MATLAB code: [download]

Saucerman JJ, Bers DM. "Calmodulin mediates differential sensitivity of CaMKII and calcineurin to local Ca2+ in cardiac myocytes." Biophys J. 2008 Nov 15;95(10):4597-612. [Pubmed]

MATLAB code: [download]

Saucerman JJ, Zhang J, Martin JC, Peng LX, Stenbit AE, Tsien RY, McCulloch AD. "Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes." Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12923-8. [Pubmed]

Virtual Cell Public model user: jsaucer, model: AKARmyocyte

Saucerman JJ, Healy SN, Belik ME, Puglisi JL, McCulloch AD. "Proarrhythmic consequences of a KCNQ1 AKAP-binding domain mutation: computational models of whole cells and heterogeneous tissue." Circ Res. 2004 Dec 10;95(12):1216-24. [Pubmed]

MATLAB code: [download]

Saucerman JJ, McCulloch AD. "Mechanistic systems models of cell signaling networks: a case study of myocyte adrenergic regulation." Prog Biophys Mol Biol. 2004 Jun-Jul;85(2-3):261-78. [Pubmed]

MATLAB code: [download]

Saucerman JJ, Brunton LL, Michailova AP, McCulloch AD. "Modeling beta-adrenergic control of cardiac myocyte contractility in silico." J Biol Chem. 2003 Nov 28;278(48):47997-8003. [Pubmed]

MATLAB code: [download]

Don't see what you're looking for? Email Dr. Saucerman and we'll try to send it to your or get it posted.

Retrieved from http://bme.virginia.edu/saucerman/index.php?n=Main.Downloads
Page last modified on March 29, 2018, at 01:56 PM EST