Hierarchical approaches for systems modeling in cardiac development

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volumn 5, Issue 3, 2013, Pages 289-305

  Gould, Russell A ^a   Aboulmouna, Lina M ^a   Varner, Jeffrey D ^a   Butcher, Jonathan T ^a  

^a School of Operations Research and Industrial Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPHIBIA; BIOLOGICAL MODEL; BIRD; BLOOD FLOW; CELL FUNCTION; CELL POPULATION; CELL TRANSFORMATION; COMPUTER MODEL; COPY NUMBER VARIATION; DEVELOPMENTAL GENETICS; DIAGNOSTIC VALUE; DNA METHYLATION; DROSOPHILA; EMBRYO DEVELOPMENT; EMBRYONIC STEM CELL; EXCITATION CONTRACTION COUPLING; GAP JUNCTION; GENE REGULATORY NETWORK; GENETIC MANIPULATION; GENETIC REGULATION; HEART; HEART DEVELOPMENT; HEART FUNCTION; HEART MUSCLE METABOLISM; HEART VALVE; HISTONE MODIFICATION; HUMAN; HUMAN GENOME PROJECT; MATHEMATICAL MODEL; MOUSE; NONHUMAN; PLACENTA CIRCULATION; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RAT; REVIEW; TIGHT JUNCTION; ZEBRA FISH;

AMPHIBIANS; ANIMALS; BIRDS; DROSOPHILA; GENOMICS; HEART; HUMANS; MODELS, BIOLOGICAL; MYOCARDIUM; SYSTEMS BIOLOGY; TRANSCRIPTION FACTORS; ZEBRAFISH;

VERTEBRATA;

EID: 84876090388     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.1217     Document Type: Review

References (146)

1. Reiter JF, Alexander J, Rodaway A, Yelon D, Patient R, Holder N, Stainier DY. Gata5 is required for the development of the heart and endoderm in zebrafish. Genes Dev 1999, 13:2983-2995.
2. Manner J. Cardiac looping in the chick embryo: a morphological review with special reference to terminological and biomechanical aspects of the looping process. Anat Rec 2000, 259:248-262.
3. Stainier DY. Zebrafish genetics and vertebrate heart formation. Nat Rev Genet 2001, 2:39-48.
4. Zaffran S, Frasch M. Early signals in cardiac development. Circ Res 2002, 91:457-469.
5. Schlesinger J, Schueler M, Grunert M, Fischer JJ, Zhang Q, Krueger T, Lange M, Tonjes M, Dunkel I, Sperling SR. The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs. PLoS Genet 2011, 7:e1001313.
6. Brand T. Heart development: molecular insights into cardiac specification and early morphogenesis. Dev Biol 2003, 258:1-19.
7. Olson EN, Srivastava D. Molecular pathways controlling heart development. Science 1996, 272:671-676.
8. Palsson B. The challenges of in silico biology. Nat Biotechnol 2000, 18:1147-1150.
9. Hood L. Systems biology: integrating technology, biology, and computation. Mech Ageing Dev 2003, 124:9-16.
10. Crampin EJ, Halstead M, Hunter P, Nielsen P, Noble D, Smith N, Tawhai M. Computational physiology and the Physiome Project. Exp Physiol 2004, 89:1-26.
11. Bassingthwaighte J, Hunter P, Noble D. The Cardiac Physiome: perspectives for the future. Exp Physiol 2009, 94:597-605.
12. Hunter PJ, Borg TK. Integration from proteins to organs: the Physiome Project. Nat Rev Mol Cell Biol 2003, 4:237-243.
13. Yutzey KE, Robbins J. Principles of genetic murine models for cardiac disease. Circulation 2007, 115:792-799.
14. Williams R. Thanks be to zebrafish. Circ Res 2010, 107:570-572.
15. Sehnert AJ, Huq A, Weinstein BM, Walker C, Fishman M, Stainier DY. Cardiac troponin T is essential in sarcomere assembly and cardiac contractility. Nat Genet 2002, 31:106-10.
16. Fishman MC. Genomics. Zebrafish-the canonical vertebrate. Science 2001, 294:1290-1291.
17. Talbot WS, Hopkins N. Zebrafish mutations and functional analysis of the vertebrate genome. Genes Dev 2000, 14:755-762.
18. Wienholds E, van Eeden F, Kosters M, Mudde J, Plasterk RH, Cuppen E. Efficient target-selected mutagenesis in zebrafish. Genome Res 2003, 13:2700-2707.
19. Love DR, Pichler FB, Dodd A, Copp BR, Greenwood DR. Technology for high-throughput screens: the present and future using zebrafish. Curr Opin Biotechnol 2004, 15:564-571.
20. Beis D, Bartman T, Jin SW, Scott IC, D'Amico LA, Ober EA, Verkade H, Frantsve J, Field HA, Wehman A, et al. Genetic and cellular analyses of zebrafish atrioventricular cushion and valve development. Development 2005, 132:4193-4204.
21. Scherz PJ, Huisken J, Sahai-Hernandez P, Stainier DY. High-speed imaging of developing heart valves reveals interplay of morphogenesis and function. Development 2008, 135:1179-1187.
22. Schroeder JA, Jackson LF, Lee DC, Camenisch TD. Form and function of developing heart valves: coordination by extracellular matrix and growth factor signaling. J Mol Med (Berl) 2003, 81:392-403.
23. Vandevelde S, Broekaert E, Yates R, Kooyman M. The development of the therapeutic community in correctional establishments: a comparative retrospective account of the 'democratic' Maxwell Jones TC and the hierarchical concept-based TC in prison. Int J Soc Psychiatry 2004, 50:66-79.
24. Heasman J. Morpholino oligos: making sense of antisense?. Dev Biol 2002, 243:209-214.
25. Chin AJ. Analysis of two aspects of left-right patterning of the vertebrate heart. Heart tube position and heart tube chirality. Methods Mol Biol 2000, 136:261-270.
26. Singh BN, Koyano-Nakagawa N, Garry JP, Weaver CV. Heart of newt: a recipe for regeneration. J Cardiovasc Transl Res 2010, 3:397-409.
27. Butcher JT, Markwald RR. Valvulogenesis: the moving target. Phil Trans R Soc Lond B Biol Sci 2007, 362:1489-503.
28. Wessels A, Sedmera D. Developmental anatomy of the heart: a tale of mice and man. Physiol Genomics 2003, 15:165-176.
29. Yalcin HC, Shekhar A, Rane AA, Butcher JT. An ex-ovo chicken embryo culture system suitable for imaging and microsurgery applications. J Vis Exp 2010, 44:e2154.
30. Stern CD. The chick; a great model system becomes even greater. Dev Cell 2005, 8:9-17.
31. Gilbert SF, Sarkar S. Embracing complexity: organicism for the 21st century. Dev Dyn 2000, 219:1-9.
32. Alsan BH, Schultheiss TM. Regulation of avian cardiogenesis by Fgf8 signaling. Development 2002, 129:1935-1943.
33. Yalcin HC, Shekhar A, Nishimura N, Rane AA, Schaffer CB, Butcher JT. Two-photon microscopy-guided femtosecond-laser photoablation of avian cardiogenesis: noninvasive creation of localized heart defects. Am J Physiol Heart Circ Physiol 2010, 299:H1728-H1735.
34. Voiculescu O, Papanayotou C, Stern CD. Spatially and temporally controlled electroporation of early chick embryos. Nat Protoc 2008, 3:419-426.
35. Tao Y, Schulz RA. Heart development in Drosophila. Semin Cell Dev Biol 2007, 18:3-15.
36. Ocorr K, Perrin L, Lim HY, Qian L, Wu X, Bodmer R. Genetic control of heart function and aging in Drosophila. Trends Cardiovasc Med 2007, 17:177-182.
37. Piazza N, Wessells RJ. Drosophila models of cardiac disease. Prog Mol Biol Transl Sci 2011, 100:155-210.
38. Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res 2011, 21:182-192.
39. Bader M. Rat models of cardiovascular diseases. Methods Mol Biol 2010, 597:403-414.
40. Marcela SG, Cristina RM, Angel PG, Manuel AM, Sofia DC, Patricia de LR, Bladimir RR, Concepcion SG. Chronological and morphological study of heart development in the rat. Anat Rec (Hoboken) 2012, 295:1267-1290.
41. Patten RD, Hall-Porter MR. Small animal models of heart failure: development of novel therapies, past and present. Circ Heart Fail 2009, 2:138-144.
42. Horsthuis T, Christoffels VM, Anderson RH, Moorman AF. Can recent insights into cardiac development improve our understanding of congenitally malformed hearts?. Clin Anat 2009, 22:4-20.
43. Piliszek A, Kwon GS, Hadjantonakis AK. Ex utero culture and live imaging of mouse embryos. Methods Mol Biol 2011, 770:243-257.
44. Bult CJ, et al. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 2008, 36:D724-D728.
45. van der Weyden L, Adams DJ, Bradley A. Tools for targeted manipulation of the mouse genome. Physiol Genomics 2002, 11:133-164.
46. Guan C, Ye C, Yang X, Gao J. A review of current large-scale mouse knockout efforts. Genesis 2010, 48:73-85.
47. Chien KR. To Cre or not to Cre: the next generation of mouse models of human cardiac diseases. Circ Res 2001, 88:546-549.
48. Utomo AR, Nikitin AY, Lee WH. Temporal, spatial, and cell type-specific control of Cre-mediated DNA recombination in transgenic mice. Nat Biotechnol 1999, 17:1091-1096.
49. Van Vliet P, Wu SM, Zaffran S, Puceat M. Early cardiac development: a view from stem cells to embryos. Cardiovasc Res 2012, 96:352-362.
50. Nakamura H, Katahira T, Sato T, Watanabe Y, Funahashi J. Gain- and loss-of-function in chick embryos by electroporation. Mech Dev 2004, 121:1137-1143.
51. Chesnutt C, Niswander L. Plasmid-based short-hairpin RNA interference in the chicken embryo. Genesis 2004, 39:73-78.
52. Xia H, Mao Q, Paulson HL, Davidson BL. siRNA-mediated gene silencing in vitro and in vivo. Nat Biotechnol 2002, 20:1006-1010.
53. Yeung T, Georges PC, Flanagan LA, Marg B, Ortiz M, Funaki M, Zahir N, Ming W, Weaver V, Janmey PA. Effects of substrate stiffness on cell morphology, cytoskeletal structure, and adhesion. Cell Motil Cytoskeleton 2005, 60:24-34.
54. Khanafer K, Duprey A, Schlicht M, Berguer R. Effects of strain rate, mixing ratio, and stress-strain definition on the mechanical behavior of the polydimethylsiloxane (PDMS) material as related to its biological applications. Biomed Microdevices 2009, 11:503-508.
55. Kim DH, Wong PK, Park J, Levchenko A, Sun Y. Microengineered platforms for cell mechanobiology. Annu Rev Biomed Eng 2009, 11:203-233.
56. Gould RA, Chin K, Santisakultarm TP, Dropkin A, Richards JM, Schaffer CB, Butcher JT. Cyclic strain anisotropy regulates valvular interstitial cell phenotype and tissue remodeling in three-dimensional culture. Acta Biomater 2012, 8:1710-1719.
57. Lutolf MP, Hubbell JA. Synthetic biomaterials as instructive extracellular microenvironments for morphogenesis in tissue engineering. Nat Biotechnol 2005, 23:47-55.
58. Lencinas A, Tavares AL, Barnett JV, Runyan RB. Collagen gel analysis of epithelial-mesenchymal transition in the embryo heart: an in vitro model system for the analysis of tissue interaction, signal transduction, and environmental effects. Birth Defects Res C Embryo Today 2011, 93:298-311.
59. Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat Rev Genet 2010, 11:476-486.
60. Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 2010, 42:806-810.
61. Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10:669-680.
62. Wu J, Smith LT, Plass C, Huang TH. ChIP-chip comes of age for genome-wide functional analysis. Cancer Res 2006, 66:6899-6902.
63. Shibata Y, Crawford GE. Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip). Methods Mol Biol 2009, 556:177-190.
64. Palmke N, Santacruz D, Walter J. Comprehensive analysis of DNA-methylation in mammalian tissues using MeDIP-chip. Methods 2011, 53:175-184.
65. Barrans JD, Allen PD, Stamatiou D, Dzau VJ, Liew CC. Global gene expression profiling of end-stage dilated cardiomyopathy using a human cardiovascular-based cDNA microarray. Am J Pathol 2002, 160:2035-2043.
66. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 2011, 12:499-510.
67. Faita F, Vecoli C, Foffa I, Andreassi MG. Next generation sequencing in cardiovascular diseases. World J Cardiol 2012, 4:288-295.
68. Regalado ES, Guo DC, Villamizar C, Avidan N, Gilchrist D, McGillivray B, Clarke L, Bernier F, Santos-Cortez RL, Leal SM. Exome sequencing identifies SMAD3 mutations as a cause of familial thoracic aortic aneurysm and dissection with intracranial and other arterial aneurysms. Circ Res 2011, 109:680-686.
69. Gal-Yam EN, Saito Y, Egger G, Jones PA. Cancer epigenetics: modifications, screening, and therapy. Annu Rev Med 2008, 59:267-280.
70. Akazawa H, Komuro I. Cardiac transcription factor Csx/Nkx2-5: Its role in cardiac development and diseases. Pharmacol Ther 2005, 107:252-268.
71. Chen H, Shi S, Acosta L, Li W, Lu J, Bao S, Chen Z, Yang Z, Schneider MD, Chien KR, et al. BMP10 is essential for maintaining cardiac growth during murine cardiogenesis. Development 2004, 131:2219-2231.
72. Chakraborty S, Cheek J, Sakthivel B, Aronow BJ, Yutzey KE. Shared gene expression profiles in developing heart valves and osteoblast progenitor cells. Physiol Genomics 2008, 35:75-85.
73. Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, et al. The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res 2008, 36:D768-D772.
74. Darnell DK, Kaur S, Stanislaw S, Davey S, Konieczka JH, Yatskievych TA, Antin PB. GEISHA: an in situ hybridization gene expression resource for the chicken embryo. Cytogenet Genome Res 2007, 117:30-35.
75. Smith CM, Finger JH, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The mouse gene expression database (GXD): 2007 update. Nucleic Acids Res 2007, 35:D618-D623.
76. Velculescu VE, Vogelstein B, Kinzler KW. Analysing uncharted transcriptomes with SAGE. Trends Genet 2000, 16:423-425.
77. Xie F, Qu Z, Yang J, Baher A, Weiss JN, Garfinkel A. A simulation study of the effects of cardiac anatomy in ventricular fibrillation. J Clin Invest 2004, 113:686-693.
78. Clayton RH, Bernus O, Cherry EM, Dierckx H, Fenton FH, Mirabella L, Panfilov AV, Sachse FB, Seemann G, Zhang H. Models of cardiac tissue electrophysiology: progress, challenges and open questions. Prog Biophys Mol Biol 2011, 104:22-48.
79. Dal-Bianco JP, Aikawa E, Bischoff J, Guerrero JL, Handschumacher MD, Sullivan S, Johnson B, Titus JS, Iwamoto Y, Wylie-Sears J, et al. Active adaptation of the tethered mitral valve: insights into a compensatory mechanism for functional mitral regurgitation. Circulation 2009, 120:334-342.
80. Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. Ensembl 2007. Nucleic Acids Res 2007, 35:D610-D617.
81. Joyce AR, Palsson BO. The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 2006, 7:198-210.
82. Ghosh S, Matsuoka Y, Asai Y, Hsin KY, Kitano H. Software for systems biology: from tools to integrated platforms. Nat Rev Genet 2011, 12:821-832.
83. Hong SE, Rho SH, Yeom YI, Kim do H. HCNet: a database of heart and calcium functional network. Bioinformatics 2006, 22:2053-2054.
84. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, et al. ArrayExpress update-trends in database growth and links to data analysis tools. Nucleic Acids Res 2013, 41:D987-D990.
85. Brazma A. Minimum information about a microarray experiment (MIAME)-successes, failures, challenges. Sci World J 2009, 9:420-423.
86. Isserlin R, El-Badrawi RA, Bader GD. The biomolecular interaction network database in PSI-MI 2.5. Database (Oxford) 2011.baq037.
87. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano, et al. The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010, 28:935-942.
88. Stromback L, Lambrix P. Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics 2005, 21:4401-4407.
89. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531.
90. Lloyd CM, Halstead MD, Nielsen PF. CellML: its future, present and past. Prog Biophys Mol Biol 2004, 85:433-450.
91. Christie GR, Nielsen PM, Blackett SA, Bradley CP, Hunter PJ. FieldML: concepts and implementation. Phil Trans A Math Phys Eng Sci 2009, 367:1869-1884.
92. Bergmann FT, Sauro HM. Comparing Simulation Results of SBML Capable Simulators. Bioinformatics 2008, 24:1963-1965. (Accessed February 8, 2013).
93. Kohl C, Tessarz P, von der Malsburg K, Zahn R, Bukau B, Mogk A. Cooperative and Independent Activities of Sgt2 and Get5 in the Targeting of Tail-anchored Proteins. Biological chemistry 2011, 392:601-608. (Accessed February 8, 2013).
94. Wierling C, Herwig R, Lehrach H. Resources, standards and tools for systems biology. Brief Funct Genomic Proteomic 6:240-251.
95. Klipp E, Liebermeister W, Helbig A, Kowald A, Schaber J. Systems biology standards-the community speaks. Nat Biotechnol 2007, 25:390-391.
96. Stromback L, Hall D, Lambrix P. A review of standards for data exchange within systems biology. Proteomics 2007, 7:857-867.
97. Armstrong EJ, Bischoff J. Heart valve development: endothelial cell signaling and differentiation. Circ Res 2004, 95:459-470.
98. Nakajima Y, Mironov V, Yamagishi T, Nakamura H, Markwald RR. Expression of smooth muscle alpha-actin in mesenchymal cells during formation of avian endocardial cushion tissue: a role for transforming growth factor beta3. Dev Dyn 1997, 209:296-309.
99. Person AD, Klewer SE, Runyan RB. Cell biology of cardiac cushion development. Int Rev Cytol 2005, 243:287-335.
100. Moorman AF, Christoffels VM. Cardiac chamber formation: development, genes, and evolution. Physiol Rev 2003, 83:1223-1267.
101. Thiery JP. Epithelial-mesenchymal transitions in development and pathologies. Curr Opin Cell Biol 2003, 15:740-746.
102. Abdulla TA, Imms R, Schleich JM and Summers R. Multiscale Information Modelling for Heart Morphogenesis. Journal of Physics 2010. Conference Series, 238.
103. Ahmed S, Nawshad A. Complexity in interpretation of embryonic epithelial-mesenchymal transition in response to transforming growth factor-beta signaling. Cells Tissues Organs 2007, 185:131-145.
104. Cline M, Cerami SM, Kuchinsky E, Landys A. N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2:2366-2382.
105. Shannon P, Ozier MA, Baliga O, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
106. Brown KR, Otasek D, Ali M, McGuffin MJ, Xie W, Devani B, Toch IL, Jurisica I. NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. Bioinformatics 2009, 25:3327-3329.
107. Nikitin A, Daraselia ESN, Mazo I. Pathway studio-the analysis and navigation of molecular networks. Bioinformatics 2003, 19:2155-2157.
108. Kitano H, Matsuoka FAY, Oda K. Using process diagrams for the graphical representation of biological networks. Nat Biotechnol 2005, 23:961-966.
109. Funahashi A, Jouraku MY, Morohashi A, Kikuchi M, Kitano N. H CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proc IEEE 2008, 96:1254-1265.
110. Aguado-Sierra J, Kerckhoffs RCP, Lionetti F, Villongco C, Hunt D, Gonzales M, Campbell S, McCulloch AD. In: Kerckhoffs RCP, ed. A Computational Framework for Patient-Specific Multi-Scale Cardiac Modeling, in Patient-Specific Modeling of the Cardiovascular System: Technology-Driven Personalized Medicine. ©Springer Science+Business Media, 2010, 203-223.
111. Kohler S, Bauer S, Horn D, Robinson PN. Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 2008, 82:949-958.
112. Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 2007, 25:309-316.
113. Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, et al. Gene prioritization through genomic data fusion. Nat Biotechnol 2006, 24:537-544.
114. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL. The human disease network. Proc Natl Acad Sci USA 2007, 104:8685-8690.
115. Schuster-Bockler B, Bateman A. Protein interactions in human genetic diseases. Genome Biol 2008, 9:R9.
116. Barriot R, Breckpot J, Thienpont B, Brohee S, Van Vooren S, Coessens B, Tranchevent LC, Van Loo P, Gewillig M, Devriendt K, et al. Collaboratively charting the gene-to-phenotype network of human congenital heart defects. Genome Med 2010, 2:16.
117. McGary KL, Lee I, Marcotte EM. Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol 2007, 8:R258.
118. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet 2005, 37(suppl):S11-S17.
119. Ku CS, Cooper DN, Polychronakos C, Naidoo N, Wu M, Soong R. Exome sequencing: dual role as a discovery and diagnostic tool. Ann Neurol 2012, 71:5-14.
120. Complexity in biological information processing. Proceedings of a symposium. Berlin, Germany, 4-6 July 2000. Novartis Found Symp 2001, 239:1-250.
121. Bruggeman FJ, Westerhoff HV. The nature of systems biology. Trends Microbiol 2007, 15:45-50.
122. Noble D. Modeling the heart-from genes to cells to the whole organ. Science 2002, 295:1678-1682.
123. Hake J, Edwards AG, Yu Z, Kekenes-Huskey PM, Michailova AP, McCammon JA, Holst MJ, Hoshijima M, McCulloch AD. Modeling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol 2012, 590: 4403-4422.
124. Srivastava D, Olson EN. A genetic blueprint for cardiac development. Nature 2000, 407:221-226.
125. Faustino RS, Behfar A, Perez-Terzic C, Terzic A. Genomic chart guiding embryonic stem cell cardiopoiesis. Genome Biol 2008, 9:R6.
126. Clark KL, Yutzey KE, Benson DW. Transcription factors and congenital heart defects. Annu Rev Physiol 2006, 68:97-121.
127. Lickert H, Takeuchi JK, Von Both I, Walls JR, McAuliffe F, Adamson SL, Henkelman RM, Wrana JL, Rossant J, Bruneau BG. Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature 2004, 432:107-112.
128. Mazloom AR, Basu K, Mandal SS, Das SK. Chromatin remodeling in silico: a stochastic model for SWI/SNF. Biosystems 2010, 99:179-191.
129. Lage K, Mollgard K, Greenway S, Wakimoto H, Gorham JM, Workman CT, Bendsen E, Hansen NT, Rigina O, Roque FS, et al. Dissecting spatio-temporal protein networks driving human heart development and related disorders. Mol Syst Biol 2010, 6:381.
130. Lage K, Greenway SC, Rosenfeld JA, Wakimoto H, Gorham JM, Segre AV, Roberts AE, Smoot LB, Pu WT, Pereira AC, et al. Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development. Proc Natl Acad Sci USA 2012, 109:14035-14040.
131. Nath AK, Krauthammer M, Li P, Davidov E, Butler LC, Copel J, Katajamaa M, Oresic M, Buhimschi I, Buhimschi C, et al. Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects. PLoS One 2009, 4:e4221.
132. Toenjes M, Schueler M, Hammer S, Pape UJ, Fischer JJ, Berger F, Vingron M, Sperling S. Prediction of cardiac transcription networks based on molecular data and complex clinical phenotypes. Mol Biosyst 2008, 4:589-598.
133. Oka C, Matsuda H, Sarai N, Noma A. Modeling the calcium gate of cardiac gap junction channel. J Physiol Sci 2006, 56:79-85.
134. Cortassa S, et al. An integrated model of cardiac mitochondrial energy metabolism and calcium dynamics. Biophys J 2003, 84:2734-2755.
135. Varner VD, Taber LA. Not just inductive: a crucial mechanical role for the endoderm during heart tube assembly. Development 2012, 139:1680-1690.
136. Buskohl PR, Jenkins JT, Butcher JT. Computational simulation of hemodynamic-driven growth and remodeling of embryonic atrioventricular valves. Biomech Model Mechanobiol 2012, 11:1205-1217.
137. Nordsletten DA, Niederer SA, Nash MP, Hunter PJ, Smith NP. Coupling multi-physics models to cardiac mechanics. Prog Biophys Mol Biol 104:77-88.
138. Bishop MJ, Plank G, Burton RA, Schneider JE, Gavaghan DJ, Grau V, Kohl P. Development of an anatomically detailed MRI-derived rabbit ventricular model and assessment of its impact on simulations of electrophysiological function. Am J Physiol Heart Circ Physiol 2010, 298:H699-H718.
139. Kerckhoffs RC, Neal ML, Gu Q, Bassingthwaighte JB, Omens JH, McCulloch AD. Coupling of a 3D finite element model of cardiac ventricular mechanics to lumped systems models of the systemic and pulmonic circulation. Ann Biomed Eng 2007, 35:1-18.
140. Vetter FJ, McCulloch AD. Three-dimensional analysis of regional cardiac function: a model of rabbit ventricular anatomy. Prog Biophys Mol Biol 1998, 69:157-183.
141. Bassingthwaighte JB, Chizeck HJ, Atlas LE. Strategies and tactics in multiscale modeling of cell-to-organ systems. Proc IEEE Inst Electr Electron Eng 2006, 94:819-830.
142. Hunter PJ, Crampin EJ, Nielsen PM. Bioinformatics, multiscale modeling and the IUPS Physiome Project. Brief Bioinform 2008, 9:333-343.
143. Kitano H. Systems biology: a brief overview. Science 2002, 295:1662-1664.
144. Land S, Niederer SA, Smith NP. Efficient computational methods for strongly coupled cardiac electromechanics. IEEE Trans Biomed Eng 2012, 59:1219-1228.
145. McCulloch AD, Paternostro G. Cardiac systems biology. Ann N Y Acad Sci 2005, 1047:283-295.
146. Csete ME, Doyle JC. Reverse engineering of biological complexity. Science 2002, 295:1664-1669.