Literature DB >> 21212391

Computational models reduce complexity and accelerate insight into cardiac signaling networks.

Jason H Yang1, Jeffrey J Saucerman.   

Abstract

Cardiac signaling networks exhibit considerable complexity in size and connectivity. The intrinsic complexity of these networks complicates the interpretation of experimental findings. This motivates new methods for investigating the mechanisms regulating cardiac signaling networks and the consequences these networks have on cardiac physiology and disease. Next-generation experimental techniques are also generating a wealth of genomic and proteomic data that can be difficult to analyze or interpret. Computational models are poised to play a key role in addressing these challenges. Computational models have a long history in contributing to the understanding of cardiac physiology and are useful for identifying biological mechanisms, inferring multiscale consequences to cell signaling activities and reducing the complexity of large data sets. Models also integrate well with experimental studies to explain experimental observations and generate new hypotheses. Here, we review the contributions computational modeling approaches have made to the analysis of cardiac signaling networks and forecast opportunities for computational models to accelerate cardiac signaling research.

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Year:  2011        PMID: 21212391      PMCID: PMC3076046          DOI: 10.1161/CIRCRESAHA.110.223602

Source DB:  PubMed          Journal:  Circ Res        ISSN: 0009-7330            Impact factor:   17.367


  127 in total

1.  PKA phosphorylation dissociates FKBP12.6 from the calcium release channel (ryanodine receptor): defective regulation in failing hearts.

Authors:  S O Marx; S Reiken; Y Hisamatsu; T Jayaraman; D Burkhoff; N Rosemblit; A R Marks
Journal:  Cell       Date:  2000-05-12       Impact factor: 41.582

2.  Network motifs: simple building blocks of complex networks.

Authors:  R Milo; S Shen-Orr; S Itzkovitz; N Kashtan; D Chklovskii; U Alon
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

Review 3.  Role of stretch-activated channels on the stretch-induced changes of rat atrial myocytes.

Authors:  Jae Boum Youm; Jin Han; Nari Kim; Yin-Hua Zhang; Euiyong Kim; Hyun Joo; Chae Hun Leem; Sung Joon Kim; Kyung A Cha; Yung E Earm
Journal:  Prog Biophys Mol Biol       Date:  2005-07-07       Impact factor: 3.667

4.  The ionic currents underlying pacemaker activity in rabbit sino-atrial node: experimental results and computer simulations.

Authors:  H F Brown; J Kimura; D Noble; S J Noble; A Taupignon
Journal:  Proc R Soc Lond B Biol Sci       Date:  1984-09-22

5.  Role of CaMKII in RyR leak, EC coupling and action potential duration: a computational model.

Authors:  Yasmin L Hashambhoy; Joseph L Greenstein; Raimond L Winslow
Journal:  J Mol Cell Cardiol       Date:  2010-07-23       Impact factor: 5.000

Review 6.  Calmodulin kinase signaling in heart: an intriguing candidate target for therapy of myocardial dysfunction and arrhythmias.

Authors:  Mark E Anderson
Journal:  Pharmacol Ther       Date:  2005-01-12       Impact factor: 12.310

7.  The neurohormonal hypothesis: a theory to explain the mechanism of disease progression in heart failure.

Authors:  M Packer
Journal:  J Am Coll Cardiol       Date:  1992-07       Impact factor: 24.094

Review 8.  What is the role of beta-adrenergic signaling in heart failure?

Authors:  Martin J Lohse; Stefan Engelhardt; Thomas Eschenhagen
Journal:  Circ Res       Date:  2003-11-14       Impact factor: 17.367

9.  Boolean network simulations for life scientists.

Authors:  István Albert; Juilee Thakar; Song Li; Ranran Zhang; Réka Albert
Journal:  Source Code Biol Med       Date:  2008-11-14

Review 10.  Multi-scale computational modelling in biology and physiology.

Authors:  James Southern; Joe Pitt-Francis; Jonathan Whiteley; Daniel Stokeley; Hiromichi Kobashi; Ross Nobes; Yoshimasa Kadooka; David Gavaghan
Journal:  Prog Biophys Mol Biol       Date:  2007-08-11       Impact factor: 3.667

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  24 in total

1.  Automated image analysis identifies signaling pathways regulating distinct signatures of cardiac myocyte hypertrophy.

Authors:  Gregory T Bass; Karen A Ryall; Ashwin Katikapalli; Brooks E Taylor; Stephen T Dang; Scott T Acton; Jeffrey J Saucerman
Journal:  J Mol Cell Cardiol       Date:  2011-12-01       Impact factor: 5.000

2.  Phospholemman is a negative feed-forward regulator of Ca2+ in β-adrenergic signaling, accelerating β-adrenergic inotropy.

Authors:  Jason H Yang; Jeffrey J Saucerman
Journal:  J Mol Cell Cardiol       Date:  2012-01-20       Impact factor: 5.000

3.  Modeling mitochondrial ROS: a great balancing act.

Authors:  Jeffrey J Saucerman
Journal:  Biophys J       Date:  2013-09-17       Impact factor: 4.033

4.  Genomes, proteomes, and the central dogma.

Authors:  Sarah Franklin; Thomas M Vondriska
Journal:  Circ Cardiovasc Genet       Date:  2011-10

Review 5.  Knowledge gaps to understanding cardiac macrophage polarization following myocardial infarction.

Authors:  Merry L Lindsey; Jeffrey J Saucerman; Kristine Y DeLeon-Pennell
Journal:  Biochim Biophys Acta       Date:  2016-05-27

Review 6.  Bigger, better, faster: principles and models of AKAP anchoring protein signaling.

Authors:  Eric C Greenwald; Jeffrey J Saucerman
Journal:  J Cardiovasc Pharmacol       Date:  2011-11       Impact factor: 3.105

7.  A computational model of cardiac fibroblast signaling predicts context-dependent drivers of myofibroblast differentiation.

Authors:  A C Zeigler; W J Richardson; J W Holmes; J J Saucerman
Journal:  J Mol Cell Cardiol       Date:  2016-03-23       Impact factor: 5.000

Review 8.  Biomechanics of infarcted left ventricle: a review of modelling.

Authors:  Wenguang Li
Journal:  Biomed Eng Lett       Date:  2020-06-10

9.  Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development.

Authors:  Kasper Lage; Steven C Greenway; Jill A Rosenfeld; Hiroko Wakimoto; Joshua M Gorham; Ayellet V Segrè; Amy E Roberts; Leslie B Smoot; William T Pu; Alexandre C Pereira; Sonia M Mesquita; Niels Tommerup; Søren Brunak; Blake C Ballif; Lisa G Shaffer; Patricia K Donahoe; Mark J Daly; Jonathan G Seidman; Christine E Seidman; Lars A Larsen
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-16       Impact factor: 11.205

10.  β-adrenergic stimulation activates early afterdepolarizations transiently via kinetic mismatch of PKA targets.

Authors:  Yuanfang Xie; Eleonora Grandi; Jose L Puglisi; Daisuke Sato; Donald M Bers
Journal:  J Mol Cell Cardiol       Date:  2013-02-26       Impact factor: 5.000

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