Publications

2024

1. Cao S, Buchholz KS, Tan P, Stowe JC, Wang A, Fowler A, Knaus KR, Khalilimeybodi A, Zambon AC, Omens KH, Saucerman JJ, McCulloch AD (2024) Differential sensitivity to longitudinal and transverse stretch mediates transcriptional responses in mouse neonatal ventricular myocytes. Am J Physiol-Heart Circ Physiol 2024;326:2, H370-H384 and Cover. (PMID 38063811)
2. Lisa Pankewitz, Kristian G Hustad, Sachin Govil, James C Perry, Sanjeet Hegde, Renxiang Tang, Jeffrey H Omens, Alistair A Young, Andrew D McCulloch*, Hermenegild J Arevalo (2024) A universal biventricular coordinate system incorporating valve annuli: Validation in congenital heart disease. Medical Image Analysis 2024; Volume 93, 103091, https://doi.org/10.1016/j.media.2024.103091.
3. Fox SR, Toomu A, Gu K, Kang J, Sung K, Han FT, Hoffmayer KS, Hsu JC, Raissi F, Feld GK, McCulloch AD, Ho G, Krummen DE (2024) Impact of Artificial Intelligence Arrhythmia Mapping on Time to First Ablation, Procedure Duration, and Fluoroscopy Use. J Cardiovasc Electrophysiol 2024;1-13 DOI: 10.1111/jce.16237 (Mar 4, 2024)
4. Fowler A, Knaus KR, Khuu S, Khalilimeybodi A, Schenk S, Ward SR, Fry AC, Rangamani P, McCulloch A D (2024) Network model of skeletal muscle cell signalling predicts differential responses to endurance and resistance exercise training. Experimental Physiology 109(6):939-955 doi.org/10.1113/EP091712
5. Gizzi A, McCulloch AD, Drapaca C (2024) Multiscale Modeling and Analysis in Biophysics. J Appl Physics 2024;135(21) DOI: 10.1063/5.0219187 (Editorial)
6. Stokely A, Votapka L, Hock M, Teitgen A, McCammon JA, McCulloch A, Amaro R (2024) NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. J Chemical Information and Modeling (doi: 10.1021/acs.jcim.4c00899), in press
7. Laura van Rosmalen, Jiaoyue Zhu, Geraldine Maier, Erica G. Gacasan, Terry Lin, Elena Zhemchuzhnikova, Vince Rothenberg, Swithin Razu, Shaunak Deota, Ramesh K. Ramasamy, Robert L. Sah, Andrew D. McCulloch, Roelof A. Hut, Satchidananda Panda (2024) Multi-organ transcriptome atlas of a mouse model of relative energy deficiency in sport, Cell Metabolism, Volume 36, Issue 9, 2024, Pages 2015-2037.e6
8. Abigail E. Teitgen, Marcus T. Hock, Kimberly J. McCabe, Matthew C. Childers, Gary A. Huber, Bahador Marzban, Daniel A. Beard, J. Andrew McCammon, Michael Regnier, Andrew D. McCulloch (2024) Multiscale Modeling Shows How 2′-deoxy-ATP Rescues Ventricular Function in Heart Failure. PNAS August 22, 2024;121(35):e2322077121 https://www.pnas.org/doi/10.1073/pnas.2322077121

9. Craine A, Krishnamurthy A, Villongco CT, Vincent K, Krummen DE, Narayan SM, Kerckhoffs RCP, Omens JH, Contijoch F, McCulloch AD (2024) Successful cardiac resynchronization therapy reduces negative septal work in patient-specific models of dyssynchronous heart failure. PLoS Comput Biol 20(10): e1012150. doi:10.1371/journal.pcbi.1012150

10. Yotam Voskoboynik, Andrew D. McCulloch, Debashis Sahoo (2024) Macrophages on the run: Exercise balances macrophage polarization for improved health. Molecular Metabolism, 2024-Dec-01;90:102058

2023

1. Govil S, Mauger C, Hegde S, Occleshaw CJ, Yu X, Perry JC, Young AA, Omens JH, McCulloch AD (2023) Biventricular shape modes discriminate pulmonary valve replacement in tetralogy of Fallot better than imaging indices. Scientific Reports 2023;13:2335 https://doi.org/10.1038/s41598-023-28358-w (PMC9911768)
2. Govil S, Crabb BT, Deng Y, Dal Toso L, Puyol-Anton E, Pushparajah K, Hegde S, Perry JC, Omens JH, Hsaio A, Young AA, McCulloch AD (2023) A deep learning approach for fully automated cardiac shape modeling in tetralogy of Fallot. J Cardiovasc Magn Reson 2023;25:15. https://doi.org/10.1186/s12968-023-00924-1 (PMC9969707)
3. McCulloch AD (2023) How Can AI Accelerate Advances in Physiology? J Gen Physiol 2023;155(6):e202313388

4. Marcus T. Hock, Abigail E. Teitgen, Kimberly J. McCabe, Sophia P. Hirakis, Gary A. Huber, Michael Regnier, Rommie E. Amaro, J. Andrew McCammon, Andrew D. McCulloch (2023) Multiscale computational modeling of the effects of 2’-deoxy-ATP on cardiac muscle calcium handling. J. Appl. Phys. 21 August 2023; 134 (7): 074905. https://doi.org/10.1063/5.0157935

2022

1. Andrew McCulloch, Kevin Patrick, Arthur A. Boni (2022) New Clinical and Commercial Opportunities in Digital Health. Journal of Commercial Biotechnology (2022) 27(1), 4–3. doi: 10.5912/jcb1022
2. Joseph D. Powers, Natalie J. Kirkland, Canzhao Liu, Swithin Razu, Xi Fang, Adam J. Engler, Ju Chen, Andrew D. McCulloch (2022) Subcellular remodeling in filamin C deficient mouse hearts impairs myocyte tension development during progression of dilated cardiomyopathy. Int J Mol Sci 2022;23(2):871; https://doi.org/10.3390/ijms23020871
3. Powers JD, McCulloch AD (2022) Biomechanical signals regulating the structure of the heart. Current Opinion in Physiology 2022;2:100482. https://doi.org/10.1016/j.cophys.2021.100482.
4. Elsayed A, Mauger CA, Ferdian E, Gilbert K, Scadeng M, Occleshaw CJ, Lowe BS, McCulloch AD, Omens J, Govil S, Pushparajah K and Young AA (2022) Right Ventricular Flow Vorticity Relationships With Biventricular Shape in Adult Tetralogy of Fallot. Front. Cardiovasc. Med. 21 January 2022; 8:806107.  https://doi.org/10.3389/fcvm.2021.806107
5. Mîra A, Lamata P, Pushparajah K, Abraham G, Mauger CA, McCulloch AD, Omens J, Bissell MM, Blair Z, Huffaker T, Tandon A, Engelhardt S, Koehler S, Pickardt T, Beerbaum P, Sarikouch S, Latus H, Greil G, Young AA, Hussain T (2022) Le Coeur en Sabot: Shape associations with adverse events in repaired tetralogy of Fallot. J Cardiovasc Magn Reson 24, 46 (2022). https://doi.org/10.1186/s12968-022-00877-x
6. Krummen DE, Villongco CT, Ho G, Schricker AA, Field ME, Sung K, Kacena KA, Martinson MS, Hoffmayer KS, Hsu JC, Raissi F, Feld GK, McCulloch AD, Han FT (2022) Forward-Solution Noninvasive Computational Arrhythmia Mapping: The VMAP Study. Circ Arrhythm Electrophysiol. 2022 Sep;15(9):e010857. doi: 10.1161/CIRCEP.122.010857. Epub 2022 Sep 7. PMID: 36069189; PMCID: PMC9509662.
7. Govil S, Hegde S, Perry JC, Omens JH, McCulloch AD (2022). An Atlas-Based Analysis of Biventricular Mechanics in Tetralogy of Fallot. In: Camara O, Puyol-Antón E, Qin C, Sermesant M, Suinesiaputra A, Wang S, Young A. Statistical Atlases and Computational Models of the Heart. Regular and CMRxMotion Challenge Papers. STACOM 2022. Lecture Notes in Computer Science, 2022 Sep;13593:112-122. doi: 10.1007/978-3-031-23443-9_11. Epub 2023 Jan 28. PMID: 37251544; PMCID: PMC10226763.
8. Ali Khalilimeybodi, Muhammad Riaz, Stuart G. Campbell, Jeffrey H. Omens, Andrew D. McCulloch, Yibing Qyang, Jeffrey J. Saucerman (2022) Signaling network model of cardiomyocyte morphological changes in familial cardiomyopathy. J Mol Cell Cardiol. 2023;174:1-14. doi:10.1016/j.yjmcc.2022.10.006

2021

1. McCulloch AD.  Grandi E, Saucerman JJ (2021) Computational models of cardiovascular regulatory mechanisms, J Mol Cell Cardiol (In Press, Journal Pre-proof, Available online 26 February 2021.
2. Vincent KP, Forsch NB, Govil S, Jablon JM, Omens JH, Perry JC, McCulloch AD (2021) Atlas-based methods for efficient characterization of patient-specific ventricular activation patterns. Europace 2021;23:i88-i95. doi:10.1093/europace/euaa397 (PMC7943357)
3. James D. Hocker, Olivier B. Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, Joshua Chiou, Tsui-Min Wang, Qingquan Zhang, Xiaomeng Hou, Yang E. Li, Yanxiao Zhang, Elie N. Farah, Allen Wang, Andrew D. Mcculloch, Kyle J. Gaulton, Bing Ren, Neil C. Chi, Sebastian Preissl (2021) Cardiac cell type–specific gene regulatory programs and disease risk association. Science Advances  14 May 2021;7(20):eabf1444. DOI: 10.1126/sciadv.abf1444 (PMC in process)
4. Nickolas Forsch, Sachin Govil, James C Perry, Sanjeet Hegde, Alistair A Young, Jeffrey H Omens, Andrew D McCulloch (2021) Computational analysis of cardiac structure and function in congenital heart disease: Translating discoveries to clinical strategies. Journal of Computational Science, 2021;52:101211 (NIHMSID 1699991)
5. Charlène Mauger, Sachin Govil, Radomir Chabiniok, Kathleen Gilbert, Sanjeet Hegde, Tarique Hussain, Andrew D McCulloch, Christopher J Occleshaw, Jeffrey Omens, James C Perry, Kuberan Pushparajah, Avan Suinesiaputra, Liang Zhong, Alistair Young (2021)Right-left ventricular shape variations in tetralogy of Fallot: associations with pulmonary regurgitation. J Cardiovasc Magn Reson 23, 105 (2021) https://doi.org/10.1186/s12968-021-00780-x.
6. Ho G, Atwood TF, Bruggeman AR, Moore KL, McVeigh E, Villongco CT, Han FT, Hsu JC, Hoffmayer KS, Raissi F, Lin GY, Schricker A, Woods CE, Cheung JP, Taira AV, McCulloch A, Birgersdotter-Green U, Feld GK, Mundt AJ, Krummen DE (2021) Computational ECG Mapping and Respiratory Gating to Optimize Stereotactic Ablative Radiotherapy Workflow for Refractory Ventricular Tachycardia, Heart Rhythm O2, Sept 2021, in press.
7. Yue Gu, Chunfeng Wang, Namheon Kim, Jingxin Zhang,Tsui Min Wang, Jennifer Stowe, Rohollah Nasiri, Jinfeng Li, Daibo Zhang, Albert Yang, Leo Huan-Hsuan Hsu, Xiaochuan Dai, Jing Mu, Natalie Lawence, Zheyuan Liu, Muyang Lin, Weixin Li, Chonghe Wang, Hua Gong, Yimu Chen, Yusheng Lei, Hongjie Hu, Yang Li, Lin Zhang, Zhenlong Huang, Xingcai Zhang, Samad Ahadian, Pooja Banik, Liangfang Zhang, Xiaocheng Jiang, Peter J. Burke, Ali Khademhosseini, Andrew D. McCulloch, and Sheng Xu (2021)Three-dimensional transistor arrays for intra- and inter-cellular recording. Nat. Nanotechnol. (2021). https://doi.org/10.1038/s41565-021-01040-w
8. Asuka Hatano, Makoto Someya, Hiroaki Tanaka, Hiroki Sakakima, Satoshi Izumi, Masahiko Hoshijima, Mark Ellisman, Andrew D. McCulloch (2021) Isolation and reconstruction of cardiac mitochondria from SBEM images using a deep learning-based method. Journal of Structural Biology, 2021, 107806, https://doi.org/10.1016/j.jsb.2021.107806

2020

2019

2018

1. Gilbert K, Forsch N, Hegde S, Mauger C, Omens J, Perry JC, Pontre B, Suinesiaputra A, Young AA, McCulloch AD (2018) Atlas-Based Computational Analysis of Heart Shape and Function in Congenital Heart Disease. J Cardiovasc Transl Res 11(2):123-132 (PMCID: 5910190) doi.org/10.1007/s12265-017-9778-5
2. Cranford JP, O’Hara TJ, Villongco CT, Hafez OM, Blake RC, Loscalzo J, Fattebert J-L, Richards DF, Zhang X, Glosli JN, McCulloch AD, Krummen DE, Lightstone FC, Wong SE (2018) Efficient Computational Modeling of Human Ventricular Activation and its Electrocardiographic Representation: A Sensitivity Study. Cardiovasc Eng Technol 9(3):447-467 (PMCID: 6095770) doi:10.1007/s13239-018-0347-0
3. Lye TH, Vincent KP, McCulloch AD, Hendon CP (2018) Tissue-specific optical mapping models of swine atria informed by optical coherence tomography. Biophys J 114(6):1477-1489 (PMCID: 5883619) doi:10.1016/j.bpj.2018.01.035
4. Lewalle A, Land S, Carruth E, Frank LR, Lamata P, Omens JH, McCulloch AD, Niederer SA, Smith NP (2018) Decreasing compensatory ability of concentric ventricular hypertrophy in aortic-banded rat hearts. Front Physiol 9:37 (PMCID: 5829063) doi: 10.3389/fphys.2018.00037
5. Erdemir A, Hunter PJ, Holzapfel GA, Loew LM, Middleton J, Jacobs CR, Nithiarasu P, Lohner R, Wei G, Winkelstein BA, Barocas VH, Guilak F, Ku J, Hicks JL, Delp S, Sacks M, Weiss JA, Ateshian GA, Maas SA, McCulloch AD, Peng GCY (2018) Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research. J Biomech Eng 140(2):024701 (PMCID: 5821103) doi:10.1115/1.4038768
6. Mauger C, Gilbert K, Suinesiaputra A, Pontré B, J. Omens J, McCulloch A, Young A (2018) An Iterative Diffeomorphic Algorithm for Registration of Subdivision Surfaces: Application to Congenital Heart Disease. Ann Int Conf IEEE Eng Med Biol Soc. 2018 Jul; 2018: 596–599. (PMC8175008)

    

2017

1. Tan PM, Buchholz KS, Omens JH, McCulloch AD, Saucerman JJ (2017) Predictive model identifies key network regulators of cardiomyocyte mechano-signaling. PLOS Comput Biol 13(11):e1005854 (PMCID: 5703578)  doi.org/10.1371/journal.pcbi.1005854

2. Timmermann V, Dejgaard LA, Haugaa KH, Edwards SG, Sundnes J, McCulloch AD, Wall ST (2017) An integrative appraisal of mechano-electric feedback mechanisms in the heart. Prog Biophys Mol Biol 130(Pt B):404-417 (PMCID: 5716869) doi:10.1016/j.pbiomolbio.2017.08.008

3. McCulloch AD (2017) The future of computational physiology and medicine. In Gupta J, Barman SM, Allen D, Lucion A, Belova N, Zelter M, Peltonen L, Csernoch L, Leem CH, Balaban P, Filaretova, Makaula S, Can J: Physiology-Current Trends and Future Challenges. (Report by the Board of the General Assembly of the International Union of Physiological Sciences and The Physiological Society)

4. Gan Z, Powell FL, Zambon AC, Buchholz KS, Fu Z, Ocorr K, Bodmer R, Haddad GG, Moya EA, Stowe JC, McCulloch AD (2017) Transcriptomic analysis identifies a role of PI3K/Akt signaling in the responses of skeletal muscle to acute hypoxia in vivo. J Physiol 595(17):5797-5813 (PMCID: 5577531) doi:10.1113/JP274556

5. Ho G, Villongco CT, Yousefian O, Faiwiszewski Y, Hayase J, Rappel W-J, McCulloch AD, Krummen DE (2017) Rotors exhibit greater surface ECG variation during ventricular fibrillation than focal sources due to wavebreak, secondary rotors, and meander. J Cardiovasc Electrophysiol 28(10):1158–1166 doi:10.1111/jce.13283

6. Herum KM, Lunde IG, McCulloch AD, Christensen G (2017) The Soft- and Hard-Heartedness of Cardiac Fibroblasts: Mechanotransduction Signaling Pathways in Fibrosis of the Heart. J Clin Med 6(5). pii:E53  (PMCID: 5447944) doi:10.3390/jcm6050053

7. Herum KM, Choppe J, Kumar A, Engler AJ, McCulloch AD (2017) Mechanical regulation of cardiac fibroblast pro-fibrotic phenotypes. Mol Biol Cell 28(14):1871-1882 (PMCID: 5541838) doi:mbc.E17-01-0014

8. Dewan S, McCabe KJ, Regnier M, McCulloch AD (2017) Insights and Challenges of Multi-scale Modeling of Sarcomere Mechanics in cTn and Tm DCM mutants – Genotype to Cellular Phenotype. Front Physiol 14;8:151 (PMCID: 5348544) doi:10.3389/fphys.2017.00151

9. Dewan S, Krishnamurthy A, Kole D, Conca G, Kerckhoffs R, Puchalski MD, Omens JH, Sun H, Nigam V, McCulloch AD (2017) Model of Human Fetal Growth in Hypoplastic Left Heart Syndrome: Reduced Ventricular Growth Due to Decreased Ventricular Filling and Altered Shape. Front Pediatr 22;5:25 (PMCID: 5319967) doi:10.3389/fped.2017.00025

10. Bradford WH, Omens JH, Sheikh F (2017) Vinculin at the heart of aging. Ann Transl Med 5(3):62 (PMCID: 5326649) doi:10.21037/atm.2017.01.65

11. McClymont D, Teh I, Carruth E, Omens J, McCulloch A, Whittington HJ, Kohl P, Grau V, Schneider JE (2017) Evaluation of non-Gaussian diffusion in cardiac MRI. Magn Reson Med 78(3):1174-1186 (PMCID: 5366286) doi:10.1002/mrm.26466

2016

1. Villongco CT, Krummen DE, Omens JH, McCulloch AD (2016) Non-invasive, model-based measures of ventricular electrical dyssynchrony for predicting CRT outcomes. Europace 18 (suppl 4): iv104-iv112 (PMCID: 5225967) doi:10.1093/europace/euw356

2. Carruth ED, McCulloch AD, Omens JH (2016) Transmural gradients of myocardial structure and mechanics: Implications for fiber stress and strain in pressure overload. Prog Biophys Mol Biol 122(3):215–226 (PMCID: 5161628) doi:10.1016/j.pbiomolbio.2016.11.004

3. Farrar G, Suinesiaputra A, Gilbert K, Perry KC, Hegde S, Marsden A, Young AA, Omens JH, McCulloch AD (2016) Atlas-Based Ventricular Shape Analysis for Understanding Congenital Heart Disease. Prog Pediatr Cardiol 43:61–69 (PMCID: 5222611) doi:10.1016/j.ppedcard.2016.07.010

4. Suinesiaputra A, McCulloch AD, Nash MP, Pontre B, Young AA (2016) Cardiac image modeling: Breadth and depth in heart disease. Med Imag Anal 33:38–43 (PMCID: 5123588) doi: 10.1016/j.media.2016.06.027

5. Yang P-C, Boras BW, Jeng M-T, Docken SS, Lewis TJ, McCulloch AD, Harvey RD, Clancy CE (2016) A computational modeling and simulation approach to investigate mechanisms of subcellular cAMP compartmentation. PLoS Comput Biol 12(7):e1005005 (PMCID:4943723) doi: 10.1371/journal.pcbi.1005005

6. Zhang K, Barocas V, Berceli S, Clancy C, Eckmann D, Garbe M, Kassab G, Lochner D, McCulloch A, Tran-Son-Tat R, Trayanova N (2016) Multi-scale Modeling of the Cardiovascular System: Disease Development, Progression,and Clinical Intervention. Ann Biomed Eng 44(9):2642–2660 (PMCID:4983486) doi:10.1007/s10439-016-1628-0

7. Mezzano V, Liang Y, Wright AT, Lyon RC, Pfeiffer ER, Song MY, Gu Y, Dalton ND, Scheinman M, Peterson KL, Evans SM, Fowler S, Cerrone M, McCulloch AD, Sheikh F (2016) Desmosomal junctions are necessary for adult sinus node function. Cardiovasc Res 111(3):274-86 (PMCID: 4957488) doi: 10.1093/cvr/cvw083

8. Cheng Y, Lindert S, Oxenford L, Tu AY, McCulloch AD, Regnier M. Effects of Cardiac Troponin I Mutation P83S on Contractile Properties and the Modulation by PKA-Mediated Phosphorylation. J Phys Chem B. 2016 Aug 25;120(33):8238-53. doi: 10.1021/acs.jpcb.6b01859. Epub 2016 May 18. (PMC5001945).

9. Morotti S, McCulloch AD, Bers DM, Edwards AG, Grandi E (2016) Atrial-selective targeting of arrhythmogenic phase-3 early afterdepolarizations in human myocytes. J Mol Cell Cardiol 96:63-71 (PMCID: 4734906) doi:10.1016/j.yjmcc.2015.07.030

10. Dewan S, McCabe K, Regnier M, McCulloch A, Lindert S (2016) Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation – An Integrated Multi-Scale Modeling Study J Phys Chem Part B 120(33):8264–8275 (PMCID: 5001916) doi:10.1021/acs.jpcb.6b01950

11. Tveito A, Lines G, Edwards AG, McCulloch A (2016) Computing rates of Markov models of voltage-gated ion channels by inverting partial differential equations governing the probability density functions of the conducting and non-conducting states. Math Biosci 277:126-135 (PMCID: 4894014) doi:10.1016/j.mbs.2016.04.011

12. McCulloch AD (2016) Systems biophysics: Multi-scale biophysical modeling of organ systems. Biophys J 110:1023-1027 (PMCID: 4788749) doi:10.1016/j.bpj.2016.02.007

13. Schilling JM, Horikawa YT, Zemljic-Harpf A, Vincent KP, Tyan L, Yu JK, McCulloch AD, Balijepalli RC, Patel HH, Roth DM (2016) Electrophysiology and metabolism of caveolin-3 over expressing mice. Bas Res Cardiol 111:28 (PMCID:5336321) doi:10.1007/s00395-016-0542-9

14. Krishnamurthy A, Gonzales M, Sturgeon G, Segars P, McCulloch AD (2016) Biomechanics simulations using cubic Hermite meshes with extraordinary nodes for isogeometric cardiac modeling. Comp Aid Geom Des 43:27–38 (PMCID: 4862616 ) doi:10.1016/j.cagd.2016.02.016

15. Sanna MG*, Vincent KP*, Repetto E*, Nhan N, Brown SJ, Abgaryan L, Riley SW, Leaf NB, Cahalan SM, Kiosses WB, Kohno Y, Brown JH, McCulloch AD, Rosen H, Gonzalez-Cabrera PK (2016) Bitopic S1P₃ Antagonist Rescue from Complete Heart Block: Pharmacological and Genetic Evidence for Direct S1P₃ Regulation of Mouse Cardiac Conduction. Mol Pharmacol 89(1):176-186 (PMCID: 4702096) doi:10.1124/mol.115.100222

16. Wassenaar JW, Gaetani R, Garcia JJ, Braden RL, MS, Luo CG, Huang D, DeMaria, AN, Omens JH, Christman KL (2016) Evidence for mechanisms underlying the functional benefits of a myocardial matrix hydrogel for post-MI treatment. J Am Coll Cardiol 67(9):1074-86 (PMCID: 4779189) doi:10.1016/j.jacc.2015.12.035

17. Gan Z, Fu Z, Stowe JC, Powell FL, McCulloch AD (2016) A protocol to collect specific mouse skeletal muscles for metabolomics studies. Methods Mol Biol 1375:169-79. doi:10.1007/7651_2015_248

2015

1. Aung A, Bhullar IS, Theprungsirikul1 J, Davey SK, Lim HL, Chiu Y-J, Ma X, Dewan S, Lo Y-H, McCulloch AD, Varghese S (2015) 3D cardiac μtissues within a microfluidic device with real-time contractile stress readout. Lab Chip 16:153-162 (PMCID: 4681661) doi:10.1039/C5LC00820D

2. Krishnamurthy A, Coppola B, Tangney J, Kerckhoffs RCP, Omens JH, McCulloch AD (2016) A Microstructurally Based Multi-Scale Constitutive Model of Active Myocardial Mechanics. Chapter 22 in Kassab GS, Sacks MS (eds.), “Structure-Based Mechanics of Tissues and Organs: A Tribute to Yoram Lanir”. Springer DOI 10.1007/978-1-4899-7630-7_22

3. Cheng Y, Rao V, Tu A-Y, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M (2015) Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties and Modulation by PKA-mediated Phosphorylation. J Biol Chem 290(46):27749-66 (PMCID: 4646022) doi/10.1074/jbc.M115.683045

4. Boras BW, Hirakis SP, Votapka LW, Malmstrom RD, Amaro RE, McCulloch AD (2015) Bridging scales through multiscale modeling: A case study on Protein Kinase A. Front Physiol 6:250 (PMCID: 4563169) doi.org/10.3389/fphys.2015.00250

5. Vincent KP, Gonzales MJ, Gillette AK, Villongco CT, Pezzuto S, Omens JH, Holst MJ, McCulloch AD (2015) High-order finite element methods for cardiac monodomain simulations. Front Physiol. 6:217 (PMCID: 4525671) doi:10.3389/fphys.2015.00217

6. Suarez SL, Rane AA, Munoz A, Wright AT, Zhang SX, Braden RL, Almutairi A, McCulloch AD, Christman K (2015) Intramyocardial injection of hydrogel with high interstitial spread does not impact action potential propagation. Acta Biomaterialia pii:S1742-7061 (PMCID: 4734906) doi: 10.1016/j.actbio.2015.08.004

7. T Stobdan, D Zhou, E Ao-Ieong, D Ortiz, R Ronen, I Hartley, Z Gan, AD McCulloch, V Bafna, P Cabrales, GG Haddad (2015) Endothelin receptor B, a candidate gene from human studies at high altitude, improves cardiac tolerance to hypoxia in genetically engineered heterozygote mice. Proc Natl Acad Sci U S A 112(33):10425-30 (PMCID: 4547246) doi:10.1073/pnas.1507486112

8. de Oliveira BL, Pfeiffer ER, Sundnes J, Wall ST, McCulloch AD (2015) Increased cell membrane capacitance is the dominant mechanism of stretch-dependent conduction slowing in the rabbit heart: a computational study. Cell Mol Bioeng 8(2):237-246 (PMCID: 4830494) doi:10.1007/s12195-015-0384-9

9. Guimarães-Camboa N, Stowe J, Aneas I, Sakabe N, Cattaneo P, Henderson L, Kilberg MS, Johnson RS, Chen J, McCulloch AD, Nobrega M, Evans SM, Zambon AC (2015) HIF1α represses cell stress pathways to allow proliferation of hypoxic fetal cardiomyocytes. Dev Cell 33(5):507-21 (PMCID: 4509618) doi:10.1016/j.devcel.2015.04

10. Lyon RC, Zanella F, Omens JH, Sheikh F (2015) Mechanotransduction in cardiac hypertrophy and failure. Circ Res 116:1462-1476 (PMCID: 4394185) doi:10.1161/CIRCRESAHA.116.304937

11. Krishnamurthy A, Villongco C, Beck A, Omens J, McCulloch A (2015) Left ventricular diastolic and systolic material property estimation from image data: LV mechanics challenge. Stat Atlases Comput Models Heart 8896:63-73 (PMCID: 4339056) doi:10.1007/978-3-319-14678-2_7

12. Krummen DE, Hayase J, Vampola SP, Ho G, Schricker AA, Lalani GG, Baykaner T, Coe TM, Clopton P, Rappel WJ, Omens JH, Narayan SM (2015) Modifying ventricular fibrillation by targeted rotor substrate ablation: Proof-of-concept from experimental studies to clinical VF. J Cardiovasc Electrophysiol 26(10):1117-26. (PMCID: 4826737) doi:10.1111/jce.1275

13. Gilbert K, Farrar G, Cowan BR, Suinesiaputra A, Occleshaw C, Pontre B, Perry J, Hegde S, Marsden A, Omens J, McCulloch A, Young AA (2015) Creating shape templates for patient specific biventricular modeling in congenital heart disease. Conf Proc IEEE Eng Med Biol Soc 679-82. (PMCID: 5797697) doi:10.1109/EMBC.2015.7318453

2014

1. Pfeiffer ER*, Wright AT*, Edwards AG, Stowe JC, McNall K, Tan J, Niesman I, Patel HH, Roth DM, Omens JH, McCulloch AD (2014) Caveolae in ventricular myocytes are required for stretch-dependent conduction slowing. J Mol Cell Cardiol 76:265–274 (PMCID: 4023651) doi:10.1016/j.yjmcc.2014.09.014

2. Boras BW, Kornev A, Taylor SS, McCulloch AD (2014) Using Markov state models to develop a mechanistic understanding of protein kinase A-RIα activation in response to cAMP binding. J Biol Chem 289(43):30040-30051 (PMCID: 4208011) doi:10.1074/jbc.M114.568907

3. Edwards AG, Grandi E, Hake J, Patel S, Li P, Miyamoto S, Omens JH, Brown JH, Bers DM, McCulloch AD (2014) Non-equilibrium reactivation of Na⁺ current drives early afterdepolarizations in mouse ventricle. Circ Arrhythm Electrophysiol 7(6):1205-1213 (PMCID: 4301603) doi:10.1161/CIRCEP.113.001666

4. Cheng Y, Lindert S, Kekenes-Huskey P, Rao VS, Solaro RJ, Rosevear PR, Amaro R, McCulloch AD, McCammon JA, Regnier M (2014) Computational studies of the S23D/S24D troponin I mutation on cardiac troponin structural dynamics. Biophys J 107(7):1675-1685 (PMCID: 4190606) doi:10.1016/j.bpj.2014.08.008

5. Villongco CT, Krummen DE, Stark P, Omens JH, McCulloch AD (2014) Patient-specific modeling of ventricular activation pattern using surface ECG-derived vectorcardiogram in bundle branch block. Prog Biophys Mol Biol 115:305-313 (PMCID: 4254140) doi:10.1016/j.pbiomolbio.2014.06.011

6. Vincent KP, McCulloch AD, Edwards AG (2014) Toward a hierarchy of mechanisms in CaMKII-mediated arrhythmia. Front Pharmacol 5:110 (PMCID: 4062880) doi:10.3389/fphar.2014.00110

7. Gonzales MJ, Vincent KP, Rappel W-J, Narayan SM, McCulloch AD (2014) Structural contributions to fibrillatory rotors in a patient-derived computational model of the atria. Europace 16:iv3-iv10 (PMCID: 4565557) doi:10.1093/europace/euu251

8. Rao V, Cheng Y, Lindert S, Kekenes-Huskey P, Wang P, Oxenford L, McCulloch AD, McCammon JA, Arzberger P, Regnier M (2014) PKA phosphorylation of cardiac troponin I modulates activation and relaxation kinetics of ventricular myofibrils. Biophys J 107(5):1196-204 (PMCID: 4156663) doi:10.1016/j.bpj.2014.07.027

9. Tangney JR, Campbell SG, McCulloch AD, Omens JH (2014) Timing and magnitude of systolic stretch affect myofilament activation and mechanical work. Am J Physiol Heart Circ Physiol 307:H353-360 (PMCID: 4182292) doi:10.1152/ajpheart.00233.2014

10. Pfeiffer E, Tangney JR, Omens JH, McCulloch AD (2014) Biomechanics of cardiac electromechanical coupling and mechanoelectric feedback. J Biomech Eng 136(2), 021007 (PMCID: 4023651) doi:10.1115/1.4026221

11. Gan Z, Stowe JC, Altintas I, McCulloch AD, Zambon AC (2014) Using Kepler for tool integration in microarray analysis workflows. Procedia Comp Sci 29:2162–2167 (PMCID: 4655117) doi:10.1016/j.procs.2014.05.201

12. Gan Z, Wang J, Salomonis N, Stowe JC, Haddad GG, McCulloch AD, Altintas I, Zambon AC (2014) MAAMD: A workflow to standardize meta-analyses and comparison of Affymetrix microarray data. BMC Bioinformatics 15:69 (PMCID: 3975178) doi:10.1186/1471-2105-15-69

13. Hake J, Kekenes-Huskey PM, McCulloch AD (2014) Computational modeling of subcellular transport and signaling. Curr Opin Struct Biol 25C:92-97 (PMCID: 4040296) doi:10.1016/j.sbi.2014.01.006

14. Sundnes J, Wall S, Osnes H, Thorvaldsen T, McCulloch AD (2014) Improved discretization and linearization of active tension in strongly coupled cardiac electro-mechanics simulations. Comput Methods Biomech Biomed Engin 17:604-615 (PMCID: 4230300) doi:10.1080/10255842.2012.704368

15. Hohendanner F, McCulloch AD, Blatter LA, Michailova AP (2014) Calcium and IP3 dynamics in cardiac myocytes: Experimental and computational perspectives and approaches. Front Pharmacol, 5:35 (PMCID: 3944219) doi:10.3389/fphar.2014.00035

16. Morotti S, Edwards AG, McCulloch AD, Bers DM, Grandi E (2014) A novel computational model of mouse myocyte electrophysiology to assess the synergy between Na⁺ loading and CaMKII. J Physiol 592(Pt 6):1181-97 (PMCID: 3961080) doi:10.1113/jphysiol.2013.266676

17. Banerjee I, Zhang J, Moore-Morris T, Pfeiffer E, Buchholz K, Liu A, Ouyang K, Stroud M, Gerace L, Evans SM, McCulloch A, Chen J (2014) Targeted ablation of Nesprin 1 and Nesprin 2 from murine myocardium results in cardiomyopathy, altered nuclear morphology and inhibition of the biomechanical gene response. PLOS Genetics 10(2):e1004114 (PMCID: 3930490) doi:10.1371/journal.pgen.1004114

18. Lyon RC, Mezzano V, Wright A, Pfeiffer E, Chuang J, Banares K, Castaneda A, Ouyang K, Cui L, Gu Y, Evans SM, Omens JH, Peterson KL, McCulloch AD, Sheikh F (2014) Connexin defects underlie arrhythmogenic right ventricular cardiomyopathy in a novel mouse model. Hum Mol Gen 23:1134-50 (PMCID: 3919010) doi:10.1093/hmg/ddt508

2013

1. Kekenes-Huskey PM, Liao T, Gillette AK, Hake JE, Zhang Y, Michailova AP, McCulloch AD, McCammon JA (2013) Molecular and sub cellular-scale modeling of nucleotide diffusion in the cardiac myofilament lattice. Biophys J 105(9):2130-2140 (PMCID: 3835335) doi:10.1016/j.bpj.2013.09.020

2. Lo YH, Peachey T, Abramson D, McCulloch A, Michailova A (2013) Sensitivity of rabbit ventricular action potential and Ca2+ dynamics to small variations in membrane currents and ion diffusion coefficients. Biomed Res Int 2013:565431 (PMCID: 3814049) doi:10.1155/2013/565431

3. Liao T, Zhang Y, Kekenes-Huskey P, Cheng Y, Michailova A, McCulloch AD, Holst M, McCammon JA (2013) Multi-core CPU or GPU-accelerated multiscale modeling for biomolecular complexes. Mol Based Math Biol 1:164–179 (PMCID: 3858848) doi:10.2478/mlbmb-2013-0009

4. Westenbrink BD, Edwards AG, McCulloch AD, Heller Brown J (2013) The promise of CaMKII inhibition for heart disease: preventing heart failure and arrhythmias. Exp Opin Ther Targ 17(8):889-903 doi:10.1517/14728222.2013.809064

5. Tang T, Lai NC, Wright AT, Gao MH, Lee P, Guo T, Tang R, McCulloch AD, Hammond HK (2013) Adenylyl cyclase 6 deletion increases mortality during sustained beta-Adrenergic receptor stimulation. J Mol Cel Cardiol 60:60-67 (PMCID: 3987812) doi:10.1016/j.yjmcc.2013.04.005

6. Gonzales MJ, Sturgeon G, Krishnamurthy A, Hake J, Jonas R, Stark P, Rappel W-J, Narayan SM, Zhang Y, Segars WP, McCulloch AD (2013) A three-dimensional finite element model of human atrial anatomy: New methods for cubic Hermite meshes with extraordinary vertices. Med Image Anal 17:525–537 (PMCID: 3660421) doi:10.1016/j.media.2013.03.005

7. Tangney JR, Chuang JS, Janssen MS, Krishnamurthy A, Liao P, Hoshijima M, Wu X, Meininger GA, Muthuchamy M, Zemljic-Harpf A, Ross RS, Frank LR, McCulloch AD, Omens JH (2013) Novel role for vinculin in ventricular myocyte mechanics and dysfunction. Biophys J 104:1623-33 (PMCID: 3617425) doi:10.1016/j.bpj.2013.02.021

8. Howard EJ, Kerckhoffs RCP, Vincent KP, Krishnamurthy A, Villongco CT, Mulligan LJ, McCulloch AD, Omens JH (2013) Myofiber prestretch magnitude determines regional systolic function during ectopic activation in the tachycardia-induced failing canine heart. Am J Physiol Heart Circ Physiol 305:H192-202 (PMCID: 3726954) doi:10.1152/ajpheart.00186.2012

9. Krishnamurthy A, Villongco CT, Chuang J, Frank LR, Nigam V, Belezzuoli E, Stark P, Krummen DE, Narayan S, Omens JH, McCulloch AD, Kerckhoffs RCP (2013) Patient-specific models of cardiac biomechanics. J Comput Physics 244:4-21 (PMCID: 3667962) doi:10.1016/j.jcp.2012.09.015

2012

1. Meng P, Irturk A, Kastner R, McCulloch A, Omens J, Wright A (2012) GPU acceleration of optical mapping algorithm for cardiac electrophysiology. Conf Proc IEEE Eng Med Biol Soc 2012:1558-61 (PMCID: 3651586)

2. Smith NP, McCulloch AD, Paterson DJ (2012) What can modelling provide to cardiac physiology? J Physiol 590:4401-4402 (PMCID: 3477748)

3. Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP (2012) Modeling effects of L-type Ca²⁺ current and Na⁺-Ca²⁺ exchanger on Ca²⁺ trigger flux in rabbit myocytes with realistic t-tubule geometries. Front Physiol 3:351 (PMCID: 3463892)

4. Berger T, Meng E, George S, Khoo M, Marmarelis V, McCulloch A, Cauwenberghs G, Ohno-Machado L, Schultz J (2012) Southern California: a hotbed of biomedical engineering: nine bioengineers describe their research and why Southern California has the biotech market cornered. Interviews by Jessica P. Johnson. IEEE Pulse 3:14-21

5. Kerckhoffs RCP, Omens JH, McCulloch AD (2012) Mechanical discoordination increases continuously after onset of left bundle branch block despite constant electrical dyssynchrony in a computational model of cardiac electromechanics and growth. Europace 14:v65-v72 (PMCID: 3482618)

6. Tveito A, Lines GT, Edwards AG, Maleckar MM, Michailova AP, Hake J, McCulloch AD (2012) Slow calcium-depolarization-calcium waves may initiate fast local depolarization waves in ventricular tissue. Prog Biophys Molec Biol 110(2–3):295–304 (PMCID: 3484180)

7. Raskin A, Lange S, Banares K, Lyon RC, Zieseniss A, Lee LK, Yamazaki KG, Granzier HL, Gregorio CC, McCulloch AD, Omens JH, Sheikh F (2012) A novel mechanism involving four-and-a-half LIM domain protein-1 and extracellular signal-regulated kinase-2 regulates titin phosphorylation and mechanics. J Biol Chem 287:29273-29284 (PMCID: 3436149)

8. Zhang Y, Liang X, Ma J, Jing Y, Gonzales MJ, Villongco C, Krishnamurthy A, Frank LR, Nigam V, Stark P, Narayan SM, McCulloch AD (2012) An atlas-based geometry pipeline for cardiac hermite model construction and diffusion tensor reorientation. Med Imag Anal 16:1130-1141 (PMCID: 3443263)

9. Ashikaga H, Omens JH (2012) In vivo validation of longitudinal-circumferential area change ratio to estimate myofiber shortening in the heart. IEEE Trans Biomed Eng 59:1391-1397 (PMCID: 4247784)

10. Hake J, Edwards AG, Yu Z, Kekenes-Huskey PM, Michailova AP, McCammon JA, Holst MJ, Hoshijima M, McCulloch AD (2012) Modeling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol 590:4403-4422 (PMCID: 3477749)

11. Kerckhoffs RCP, Omens JH, McCulloch AD (2012) A single strain-based growth law predicts concentric and eccentric cardiac growth during pressure and volume overload. Mech Res Commun 42:40-50 (PMCID: 3358801)

12. Hunt DL, Campbell PH, Zambon AC, Vranizan K, Evans SM, Kuo H-C, Yamaguchi KD, Omens JH, McCulloch AD (2012) Early post-myocardial infarction survival in MRL mice is mediated by attenuated apoptosis and inflammation but depends on genetic background. Exp Physiol 97:102-114 (PMCID: 3253239)

13. Sheikh F, Ouyang K, Campbell SG, Lyon RC, Chuang J, Fitzsimons D, Tangney J, Hidalgo CG, Chung CS, Cheng H, Dalton ND, Gu Y, Kasahara H, Ghassemian M, Omens JH, Peterson KL, Granzier HL, Moss RL, McCulloch AD, Chen J (2012) Mouse and computational models link Mlc2V dephosphorylation to altered myosin kinetics in early cardiac disease. J Clin Invest 122:1209-1221 (PMCID: 3314469)

14. Cheng Y, Kekenes-Huskey P, Hake J, Holst MJ, McCammon AJ, Michailova AP (2012) Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction. Comp Sci Discov 5:015002

15. Feala JD, Cortes J, Duxbury PM, McCulloch AD, Piermarocchi C, Paternostro G (2012) Statistical properties and robustness of biological controller­-target networks. PLoS ONE 7:e29374 (PMCID: 3250441)

16. Kerckhoffs, RCP (2012) Computational modeling of cardiac growth in the post-natal rat with a strain-based growth law. J Biomech 45:865–871 (PMCID: 3294007)

2011

1. Meyer GA, McCulloch AD, Lieber RL (2011) A nonlinear model of passive muscle viscosity. J Biomech Eng 133: 0910071

2. Viceconti M, McCulloch AD (2011) Policy needs and options for a common approach towards modelling and simulation of human physiology and diseases with a focus on the Virtual Physiological Human. Stud Health Technol Inform 170:49-82

3. Campbell SG, McCulloch AD (2011) Multi-scale computational models of familial hypertrophic cardiomyopathy: genotype to phenotype. J R Soc Interface 8:1550–1561 (PMCID: 3177620)

4. Howard EJ, Covell JW, Mulligan LJ, McCulloch AD, Omens JH and Kerckhoffs RCP (2011) Improvement in pump function with endocardial biventricular pacing increases with activation time at the left ventricular pacing site in failing canine hearts. Am J Physiol Heart Circ Physiol 301:H1447-H1455 (PMCID: 3197362)

5. Aguado-Sierra J, Krishnamurthy A, Villongco C, Chuang J, Howard E, Gonzales MJ, Omens J, Krummen DE, Narayan S, Kerckhoffs RCP, McCulloch AD (2011) Patient-specific modeling of dyssynchronous heart failure: A case study. Prog Biophys Molec Biol 107:147-155 (PMCID: 3190065)

6. Frangi AF, Coatrieux JL, Peng GC, D’Argenio DZ, Marmarelis VZ, Michailova A (2011) Editorial: Special issue on multiscale modeling and analysis in computational biology and medicine — Part-1. IEEE Trans Biomed Eng 58:2936-2942

7. Frangi AF, Coatrieux JL, Peng GC, D’Argenio DZ, Marmarelis VZ, Michailova A (2011) Editorial: TBME Letters special issue on multiscale modeling and analysis in computational biology and medicine — Part-2. IEEE Trans Biomed Eng 58:3434-3439

8. Yu Z, Yao G, Hoshijima M, Michailova A, Holst M (2011) Multi-Scale modeling of calcium dynamics in entricular myocytes with realistic transverse tubules. IEEE Trans Biomed Eng 58:2947-2951 (PMCID: 3179564)

9. Trumble DR, McGregor WE, Kerckhoffs RCP, Waldman LK (2011) Cardiac Assist with a Twist: Apical Torsion as a Means to Improve Failing Heart Function. J Biomech Eng 133:101003

10. Quinn TA, Granite S, Allessie MA, Antzelevitch C, Bollensdorff C, Bub G, Burton RAB, Cerbai E, Chen PS, Delmar M, DiFrancesco D, Earm YE, Efimov IR, Egger M, Entcheva E, Fink M, Fischmeister R, Franz MR, Garny A, Giles WR, Hannes T, Harding SE, Hunter PJ, Iribe G, Jalife J, Johnson CR, Kass RS, Kodama I, Koren G, Lord P, Markhasin VS, Matsuoka S, McCulloch AD, Mirams GR, Morley GE, Nattel S, Noble D, Olesen SP, Panfilov AV, Trayanova NA, Ravens U, Richard S, Rosenbaum DS, Rudy Y, Sachs F, Sachse FB, Saint DA, Schotten U, Solovyova O, Taggart P, Tung L, Varró A, Volders PG, Wang K, Weiss JN, White E, Wilders R, Winslow RL, Kohl P (2011) Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised Reporting for Model Reproducibility, Interoperability, and Data Sharing. Prog Biophys Molec Biol 107:4-10 (PMCID: 3190048)

11. Rane AA, Chuang JS, Shah A, Hu DP, Dalton ND, Gu Y, Peterson KL, Omens JH, Christman KL (2011) Increased infarct wall thickness by a bio-inert material is insufficient to prevent negative left ventricular remodeling after myocardial infarction. PLoS One 6:e21571 (PMCID: 3121880)

12. Tvieto A, Lines GT, Li P, McCulloch A (2011) Defining candidate drug characteristics for long-QT (LQT3) syndrome. Math Biosci Eng 8:861-73

13. Mills RW, Wright AT, Narayan SM, McCulloch AD (2011) The effects of wall stretch on ventricular conduction and refractoriness in the whole heart. In: Kohl P, Sachs F, Franz MR (Eds) Cardiac Mechno-Electric Feedback and Arrhythmias. Oxford: Oxford University Press, Pages 180-186

14. Howard EJ, Omens JH (2011) Distributions of myocyte stress, strain, and work in normal and infarcted ventricles. In: Kohl P, Sachs F, Franz MR (Eds) Cardiac Mechno-Electric Feedback and Arrhythmias. Oxford: Oxford University Press, Pages 442-449

2010

1. Cheng Y, Yu Z, Hoshijima M, Holst MJ, McCulloch AD, McCammon JA, Michailova AP (2010) Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. PLoS Comp Biol 6:e1000972 (PMCID: 2965743)

2. Chuang JS, Zemljic-Harpf A, Ross RA, Frank LR, McCulloch AD, Omens JH (2010) Determination of three-dimensional ventricular strain distributions in gene-targeted mice using tagged MRI. Magnetic Resonance in Medicine 64:1281-8 (PMCID: 3272305)

3. Abramson D, Bethwaite B, Enticott C, Garic S, Peachey T, Michailova A, Amirriazi S (2010) Embedding Optimization Computational Science Workflows. J Computat Sci, 1: 41-47

4. Abramson D, Bethwaite B, Enticott C, Garic S, Peachey T, Michailova A, Amirriazi S (2010) Automatic Design Optimization using Parallel Workflows. Procedia Comp Sci, 1: 2159-2168

5. Lionetti FV, McCulloch AD, Baden SB (2010) Source-to-source optimization of CUDA C for GPU-accelerated cardiac cell modeling. The Sixteenth International Conference on Parallel Computing, EuroPar 2010, Ischia, Italy, Pages 38-49

6. Jacot JG, Martin JC, Hunt DL (2010) Mechanobiology of cardiomyocyte development. J Biomech 43:93-98 (PMCID: 2813357)

7. Kerckhoffs RCP, Omens JH, McCulloch AD, Mulligan LJ (2010) Ventricular dilation and electrical dyssynchrony synergistically increase regional mechanical non-uniformity but not mechanical dyssynchrony: A computational model. Circ Heart Fail 3:528-536 (PMCID: 3050711)

8. Campbell SG, Lionetti FV, Campbell KS, McCulloch AD (2010) Coupling of adjacent tropomyosins enhances cross-bridge-mediated cooperative activation in a Markov model of the cardiac thin filament. Biophys J 98:2254-2264 (PMCID: 2872217)

9. Neal ML, Kerckhoffs RCP (2010) Current Progress in Patient-Specific Modeling. Briefings in Bioinformatics 11, 111-126

10. Jacot JG, Kita-Matsuo H, Wei KA, Chen HSV, Omens JH, Mercola M, McCulloch AD (2010) Cardiac myocyte force development during differentiation and maturation. Ann NY Acad Sci 1188:121-127 (PMCID: 2920416)

11. Jacot JG, Raskin AJ, Omens JH, McCulloch AD, Tung L (2010) Mechanotransduction in Cardiac and Stem Cell Derived Cardiac Cells. In: Kamkin A, Kiseleva I (Eds) Mechanosensitivity in Cells and Tissues, Vol 3, Part 2 New York: Springer, Pages 99-139

12. Kerckhoffs RCP (Ed) (2010) Patient-Specific Modeling of the Cardiovascular System: Technology-Driven Personalized Medicine. New York: Springer.

13. Aguado-Sierra J, Kerckhoffs RCP, Lionetti F, Hunt D, Villongco C, Gonzales M, Campbell SG, McCulloch AD (2010) A computational framework for patient-specific multi-scale cardiac modeling. In: Roy Kerckhoffs (Ed) Patient-Specific Modeling of the Cardiovascular System: Technology-Driven Personalized Medicine New York: Springer, Pages 203-224

14. Kerckhoffs RCP, Mulligan LJ (2010) Computational modeling of heart failure with application to cardiac resynchronization therapy. In: Guccione JM, Kassab GS, Ratcliffe M (Eds) Computational Cardiovascular Mechanics: Modeling and Applications in Heart Failure New York: Springer, Pages 239-254

2009

1. Feala JD, Coquin L, Zhou D, Haddad GG, Paternostro G, McCulloch AD (2009) Metabolism as means for hypoxia adaptation: Metabolic profiling and flux balance analysis. BMC Syst Biol 3:91 (PMCID: 2749811)

2. Feala JD, Cortes J, Duxbury PM, Piermarocchi C, McCulloch AD, Paternostro G (2009) Systems approaches and algorithms for discovery of combinatorial therapeutics. WIREs Syst Biol Med 2:181-193

3. Kita-Matsuo H, Barcova M, Prigozhina N, Salomonis N, Wei K, Jacot JG, Nelson B, Spiering S, Haverslag R, Kim C, Talantova M, Bajpai R, Calzolari D, McCulloch AD, Price JH, Conklin BR, Chen HSV, Mercola M (2009) Lentiviral vectors and protocols for creation of stable hESC lines for fluorescent tracking and drug resistance selection of cardiomyocytes. PLoS One 4:e5046. (PMCID: 2662416)

4. Campbell SG, Howard EJ, Aguado-Sierra J, Coppola BA, Omens JH, Mulligan LJ, McCulloch AD, Kerckhoffs RCP (2009) Effect of transmurally heterogeneous myocyte excitation-contraction coupling on canine left ventricular electromechanics. Exp Physiol 94:541-552 (PMCID: 2744637)

5. Ashikaga H, van der Spoel TI, Coppola BA, Omens JH (2009) Transmural myocardial mechanics during isovolumic contraction. JACC Cardiovasc Imaging 2:202-211 (PMCID: 2821599)

6. Lu S, Michailova A, Saucerman J, Cheng Y, Yu Z, Kaiser T, Li W, Bank RE, Holst M, McCammon JA, Hayashi T, Hoshijima M, Arzberger P, McCulloch AD (2009) Multi-scale modeling in rodent ventricular myocytes: Contributions of structural and functional heterogeneities to excitation-contraction coupling. IEEE Eng Med Biol Mag 28:65 (PMCID: 3197248)

7. Raskin AM, Hoshijima M, Swanson E, McCulloch AD, Omens JH (2009) Hypertrophic gene expression induced by chronic stretch of excised mouse heart muscle. Mol Cell Biomech 6:145-59 (PMCID: 3272304)

8. Raskin AM, McCulloch AD, Omens JH (2009) Role of Structural and Signaling Molecules in Cardiac Mechanotransduction . In: Chien S, Chen PC, Schmid-Schönbein, G, Tong P, Woo SL (Eds). Biomechanics: From Molecules to Man. Hackensack, NJ: World Scientific Publishing Co., Pages 65-80

2008

1. Calzolari D, Bruschi S, Coquin L, Schofield J, Feala JD, Reed JC, McCulloch AD, Paternostro G (2008) Search algorithms as a framework for the optimization of drug combinations. PLoS Comput Biol 4:e1000249 (PMCID: 2590660)

2. Coquin L, Feala JD, McCulloch AD, Paternostro G (2008) Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue. Mol Syst Biol 4:233 (PMCID: 2615305)

3. Sheikh F, Raskin A, Chu PH, Lange S, Domenighetti AA, Zheng M, Liang X, Zhang T, Yajima T, Gu Y, Dalton ND, Mahata SK, Dorn GW 2nd, Heller-Brown J, Peterson KL, Omens JH, McCulloch AD, Chen J (2008) An FHL1-containing complex within the cardiomyocyte sarcomere mediates hypertrophic biomechanical stress responses in mice. J Clin Invest 118:3870-3880 (PMCID: 2575833)

4. Mills RW, Narayan SM, McCulloch AD Mechanisms of Conduction Slowing During Myocardial Stretch by Ventricular Volume Loading in Rabbit. Am J Physiol Heart Circ Physiol 295:H1270-H1278 (PMCID: 2544493)

5. Rudy Y, Ackerman MJ, Bers DM, Clancy CE, Houser SR, London B, McCulloch AD, Przywara DA, Rasmusson R, Solaro J, Trayanova N, Van Wagoner DR, Varro A, Weiss JN, Lathrop DA (2008) Systems approach to understanding electromechanical activity in the human heart: A National Heart, Lung, and Blood Institute workshop summary. Circulation 118:1202-1211 (PMCID: 2908516)

6. Jacot JG, McCulloch AD, Omens JH (2008) Substrate stiffness affects the functional maturation of neonatal rat ventricular myocytes. Biophys J 95:3479-3487 (PMCID: 2547444)

7. Lim B-K, Xiong D, Dorner A, Youn T-J, Yung A, Liu TI, Gu Y, Dalton ND, Wright AT, Evans SM, Chen J, Peterson KL, McCulloch AD, Yajima T, Knowlton KU (2008) Coxsackievirus and adenovirus receptor (CAR) in the heart is essential for atrioventricular-node function and localization of connexin 45. JCI 118:2758-2770 (PMCID: 2467382)

8. Cai CL, Martin JC, Sun Y, Cui L, Wang L, Ouyang K, Yang L, Bu L, Liang X, Zhang X, Stallcup WB, Denton CP, McCulloch AD, Chen J, Evans SM (2008) A myocardial lineage derives from Tbx18 epicardial cells. Nature 454:104-108

9. Campbell SG, Flaim SN, Leem CH, McCulloch AD (2008) Mechanisms of transmurally-varying myocyte electromechanics in an integrated computational model. Phil Trans Royal Soc A 2008 366:3361-3380

10. Kerckhoffs RCP, Narayan SM, Omens JH, Mulligan LJ, McCulloch AD (2008) Computational modeling for bedside application. Heart Failure Clinics 4:371-378 (PMCID: 2518746)

11. Michailova A, McCulloch A (2008) Effects of Mg²⁺, pH and PCr on cardiac excitation-metabolic coupling. Magnes Res 21:16-28

12. Kerckhoffs RCP, McCulloch AD, Omens JH, Mulligan LJ (2008) Effects of biventricular pacing and scar size in a computational model of the failing heart with left bundle branch block. (2009) Med Imag Anal 13:362-369

13. Ashikaga H, Coppola BA, Yamazaki KG, Villarreal FJ, Omens JH, Covell JW (2008) Changes in regional myocardial volume during the cardiac cycle: implications for transmural blood flow and cardiac structure. Am J Physiol Heart Circ Physiol 295:H610-H618 (PMCID: 2519196)

14. Coppola BA, Omens JH (2008) Role of tissue structure on ventricular wall mechanics. Mol Cell Biomech 5:183-196 (PMCID: 2698048)

15. Coppola BA, Omens JH (2008) Use of larger species such as dog and pig as model systems to study cardiac disease. Drug Discov Today 5:195-200

16. Kerckhoffs RCP, Lumens J, Vernooy K, Omens JH, Mulligan LJ, Delhaas T, Arts T, McCulloch AD, Prinzen FW (2008) Cardiac Resynchronization: insight from experimental and computational models. Prog Biophy Mol Biol 97:543-561 (PMCID: 2676869)

17. Campbell PH, Hunt DL, Jones Y, Harwood F, Amiel D, Omens JH, McCulloch AD (2008) Effects of biglycan deficiency on myocardial infarct structure and mechanics. Mol Cell Biomech 5:27-36 (PMCID: 2679639)

18. Li W, Gurev V, McCulloch AD, Trayanova NA (2008) The role of mechanoelectric feedback in vulnerability to electric shock. Prog Biophys Mol Biol 97:461-478

19. Zhang Y, Sekara RB, McCulloch AD, Tung L (2008) Cell cultures as models of cardiac mechanoelectric feedback. Prog Biophys Mol Biol 97:367–382

20. Feala JD, Omens JH, Paternostro G, McCulloch AD (2008) Discovering regulators of the drosophila cardiac hypoxia response using automated phenotyping technology. Ann NY Acad Sci 1123:169-177

21. Feala J, McCulloch AD, Coquin L, Paternostro G (2008) Integrating metabolomics and phenomics with systems models of cardiac hypoxia. Prog Biophys Mol Biol 96:209-225

2007

1. Flaim SN, McCulloch AD (2007) Acetylcholine-induced shortening of the epicardial APD may increase repolarization gradients and LQT3 arrhythmic risk. J Electrocardiol 40:S66-S69

2. Zemljic-Harpf AE, Miller JC, Henderson SA, Wright AT, Manso AM, Elsherif L, Dalton ND, Thor AK, Perkins GA, McCulloch AD, Ross RS (2007) Cardiac-myocyte-specific excision of the vinculin gene disrupts cellular junctions, causing sudden death or dilated cardiomyopathy. Mol Cell Biol 27:7522-37

3. Ingrassia CM, Usyk TP, Kerckhoffs RCP, McCulloch AD, Costa KD, Holmes JW (2007) Model-based development of four-dimensional wall motion measures. Comput Meth Appl Mech Eng 196:3061-3069

4. Flaim SN, Giles WR, McCulloch AD (2007) Arrhythmogenic consequences of Na⁺ channel mutations in the transmurally heterogeneous mammalian left ventricle: An analysis of the I1768V SCN5A mutation. Heart Rhythm 4:768-778

5. Broderick K, Potluri P, Feala J, McCulloch AD, Bigby T, Belke D, Boss G (2007) The cobalamin precursor cobinamide detoxifies nitroprusside-generated cyanide. Exp Biol and Med 232:789-798

6. Coppola BA, Covell JW, McCulloch AD, Omens JH (2007) Asynchrony of ventricular activation affects magnitude and timing of fiber stretch in late-activated regions of the canine heart. Am J Physiol Heart Circ Physiol 293:H754-H761 (PMCID: 3328414)

7. Costandi PN, McCulloch AD, Omens JH, Frank LR (2007) High-resolution longitudinal MRI of the transition to heart failure. Magn Reson Med 57:714-720 (PMCID: 4482467)

8. Feala J, Coquin L, McCulloch AD, Paternostro G (2007) Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis. Mol Syst Biol 3:99

9. Michailova AP, Lorentz W, McCulloch AD (2007) Modeling transmural heterogeneity of K_ATP current in rabbit ventricular myocytes. Am J Physiol Cell Physiol, 293:542-557

10. Kerckhoffs RCP, Neal M, Gu Q, Bassingthwaighte JBB, Omens JH, McCulloch AD (2007) Coupling of a three-dimensional finite element model of cardiac ventricular mechanics to lumped systems models of the systemic and pulmonic circulation. Ann Biomed Eng 35:1-18 (PMCID: 2872168)

11. Ashikaga H, Coppola BA, Hopenfeld B, Leifer ES, McVeigh ER, Omens JH (2007) Transmural dispersion of myofiber mechanics: Implications for Electrical Heterogeneity In Vivo. J Am Coll Cardiol 49:909-916 (PMCID: 2572715)

12. Means CK, Xiao CY, Li Z, Zhang T, Omens JH, Ihsii I, Chun J, Brown JH (2007) Sphingosine 1-phosphate S1P2 and S1P3 receptor-mediated Akt activation protects against in vivo myocardial ischemia-reperfusion injury. Am J Physiol Heart Circ Physiol 292:H2944-51

13. Kerckhoffs RCP, McCulloch AD (2007) Cardiac Electromechanics in the Healthy Heart. In: Chien S, Chen PCY, Fung YC (Eds). An Introductory Text to Bioengineering. Singapore: World Scientific Publishing Co., Pages 37-52.

14. Omens JH (2007) Cardiac Biomechanics and Disease In: Chien S, Chen PCY, Fung YC (Eds). An Introductory Text to Bioengineering. Singapore: World Scientific Publishing Co., Pages 53-68

15. Omens JH, McCulloch AD, Lorenzen-Schmidt I (2007) Mechanotransduction in cardiac remodeling and heart failure. In: Weckström M, Pavi T (Eds) Cardiac Mechanotransduction. Austin TX: Landes Bioscience, Pages 78-92

2006

1. Kerckhoffs RCP, Healy SN, Usyk TP, McCulloch AD (2006) Computational methods for modeling cardiac electromechanics. Proc IEEE 94:769-783

2. Hunter PJ, Li W, McCulloch AD, Noble D (2006) Multiscale modeling: Physiome project standards, tools, and databases. IEEE Computer 39:48-54

3. Camelliti P, Gallagher JO, Kohl P, McCulloch AD (2006) Micropatterned cell cultures on elastic membranes as an in-vitro model of myocardium. Nat Protoc 1:1379-1391

4. Saucerman JJ, McCulloch AD (2006) Cardiac β-adrenergic signaling: from subcellular microdomains to heart failure. Ann NY Acad Sci 1080:348-361

5. Flaim SN, Giles WR, McCulloch AD (2006) Contributions of sustained I_Na and I_Kv4.3 to transmural heterogeneity of early repolarization and arrhythmogenesis in canine left ventricular myocytes. Am J Physiol Heart Circ Physiol 291:H2617-H2629

6. Costandi PN, Frank LR, McCulloch AD, Omens JH (2006) Role of diastolic properties in the transition to failure in a mouse model of cardiac dilatation. Am J Physiol Heart Circ Physiol 291:H2971-H2979 (PMCID: 3334322)

7. Saucerman JJ, Zhang J, Martin JC, Peng LX, Stenbit AE, Tsien RY, McCulloch AD (2006) Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes. Proc Nat Acad Sci 103:12923-12928

8. Li W, Baker N, Baldridge K, McCammon JA, Ellisman MH, Gupta A, Holst M, McCulloch AD, Michailova AP, Papadopoulos P, Olson A, Sanner M, Arzbereger PW (2006) National Biomedical Computation Resource (NBCR): Developing End-to-End Cyberinfrastructure for Multiscale Modeling in Biomedical Research. CTWatch Quarterly August, 2(3)

9. Lorenzen-Schmidt I, Schmid-Schönbein GW, Giles WR, McCulloch AD, Chien S, Omens JH (2006) Chronotropic response of cultured neonatal rat ventricular myocytes to short-term fluid shear. Cell Biochem Biophys 46:113-122 (PMCID: 3310206)

10. Broderick KE, Feala J, McCulloch A, Paternostro G, Sharma VS, Pilz RB, Boss GR (2006) The nitric oxide scavenger cobinamide profoundly improves survival in a Drosophila melanogaster model of bacterial sepsis. FASEB J 20:1865-1873

11. McCulloch AD, Arzberger P, Hunter P (2006) Computational Physiology: From Genome to Physiome. The Physiologist 49:94-95

12. McCulloch AD, Omens JH (2006) Myocyte shearing, myocardial sheets, and microtubules. Circ Res 98:1-3

2005

1. Healy SN, McCulloch AD (2005) An ionic model of stretch-activated currents in rabbit ventricular myocytes. Europace 7:S128-S134

2. Lorenzen-Schmidt I, Stuyvers BD, ter Keurs HEDJ, Date M, Hoshijima M, Chien KR, McCulloch AD, Omens JH (2005) Young MLP deficient mice show diastolic dysfunction before the onset of dilated cardiomyopathy. J Molec Cell Cardiol 39:241-250 (PMCID: 4484861)

3. Lorenzen-Schmidt I, McCulloch AD, Omens JH (2005) Deficiency of actinin-associated LIM protein alters regional right ventricular function and hypertrophic remodeling. Ann Biomed Eng 33:888-896 (PMCID: 4482468)

4. Camelliti P, McCulloch AD, Kohl P (2005) Microstructured cocultures of cardiomyocytes and fibroblasts: a two-dimensional in vitro model of cardiac tissue. Microsc Microanal 11:249-259

5. Weis SM, Zimmerman SD, Shah M, Covell JW, Omens JH, Ross J, Jr., Dalton N, Jones Y, Reed CC, Iozzo RV, McCulloch AD (2005) A role for decorin in the remodeling of myocardial infarction. Matrix Biol 24:313-324

6. McCulloch AD, Paternostro G (2005) Cardiac systems biology. Ann NY Acad Sci 1047:283-295

7. Michailova AP, Saucerman JJ, Belik ME, McCulloch AD (2005) Modeling regulation of cardiac K_ATP and L-type Ca²⁺ currents by ATP, ADP and Mg²⁺. Biophys J 88:2234-2249

8. Ferrarini L, Bertelli L, Feala J, McCulloch AD, Paternostro G (2005) A more efficient search strategy for aging genes based on connectivity. Bioinformatics 21:338-48

9. Ashikaga H, Covell JW, Omens JH (2005) Diastolic dysfunction in volume overload hypertrophy is associated with abnormal shearing of myolaminar sheets. Am J Physiol Heart Circ Physiol 288:H2603-2610 (PMCID: 2822838)

10. Gurantz D, Yndestad A, Halvorsen B, Lunde OV, Omens JH, Ueland T, Moore CD, Kjekshus J, Greenberg GH (2005) Etanercept or intravenous immunoglobulin attenuates expression of genes involved in post-myocardial infarction remodeling. Cardiovasc Res 67:106-15

11. Usyk T, Kerckhoffs R (2005) Three dimensional electromechanical model of porcine heart with penetrating wound injury. Stud Health Technol Inform 111:568-73

12. Mills RW, Narayan SM, McCulloch AD (2005) The effects of wall stretch on ventricular conduction and refractoriness in the whole heart. In Kohl P, Sachs F, Franz MR (Eds) Cardiac Mechano-Electric Feedback and Arrhythmias: From Pipette To Patient. Philadelphia: Elsevier Saunders, Pages 127-136

2004

1. McCulloch AD (2004) Functionally and structurally integrated computational modeling of ventricular physiology. Jpn J Physiol 54:531-539

2. Saucerman JJ, Healy SN, Belik ME, Puglisi JL, McCulloch AD (2004) Proarrhythmic consequences of a KCNQ1 AKAP-binding domain mutation: computational models of whole cells and heterogeneous tissue. Circ Res 95:1216-1224

3. Chen L, McCulloch AD, May-Newman KD (2004) Nonhomogeneous deformation in the anterior leaflet of the mitral valve. Ann Biomed Eng 32:1599-606

4. Buckberg GD, Weisfeldt ML, Ballester M, Beyar R, Burkhoff D, Coghlan HC, Doyle M, Epstein ND, Gharib M, Ideker RE, Ingels NB, LeWinter MM, McCulloch AD, Pohost GM, Reinlib LJ, Sahn DJ, Spinale FG, Spotnitz HM, Sopko G, Torrent-Guasp F, Shapiro EP (2004) Left Ventricular Form and Function: Scientific Priorities and Strategic Planning for Development of New Views of Disease. Circulation 110:e333-e336

5. Michailova AP, Belik ME, McCulloch AD (2004) Effects of magnesium on cardiac excitation-contraction coupling. J Am Coll Nutr 23:514S-517S

6. Saucerman JJ, McCulloch AD (2004) Mechanistic systems models of cell signaling networks: a case study of myocyte adrenergic regulation. Prog Biophys Molec Biol 85:261-278

7. Shah S, Davis J, Weisleder N, Kostavassili I, McCulloch AD, Ralston E, Capetanaki Y, Lieber RL (2004) Structural and functional roles of desmin in mouse skeletal muscle during passive deformation. Biophys J 86:2993-3008

8. Ashikaga H, Criscione JC, Omens JH, Covell JW, Ingels Jr NB (2004) Transmural left ventricular mechanics underlying torsional recoil during relaxation. Am J Physiol Heart Circ Physiol 286:H640-H647 (PMCID: 2954110)

9. Villarreal FJ, Omens JH, Nguyen J, Dillmann W, Risteli J, Covell JW (2004) Early degradation and serum appearance of type I collagen fragments after myocardial infarction. J Mol Cell Cardiol 36:597-601

10. Ashikaga H, Omens JH, Ingels Jr NB, Covell JW (2004) Transmural mechanics at left ventricular epicardial pacing site. Am J Physiol Heart Circ Physiol 286:H2401-H2407 (PMCID: 2965026)

11. Ashikaga H, Omens JH, Covell JW (2004) Time-dependent remodeling of transmural architecture underlying abnormal ventricular geometry in chronic volume overload heart failure. Am J Physiol Heart Circ Physiol 287:H1994-2002 (PMCID: 2842928)

12. Belik ME, Usyk TP, McCulloch AD (2004) Computational methods for cardiac electrophysiology. In: Ayache N, Guest Ed (Eds) Computational Models for the Human Body, Special Volume of Handbook of Numerical Analysis, Volume XII. Philadelphia: Elsevier, Pages 129-188

2003

1. Usyk TP, McCulloch AD (2003) Electromechanical model of cardiac resynchronization in the dilated failing heart with left bundle branch block. J Electrocardiol 36(Suppl):57-61

2. Omens JH, McCulloch AD, Criscione JC (2003) Complex distributions of residual stress and strain in the mouse left ventricle: experimental and theoretical models. Biomech Model Mechanobiol 1:267-277

3. Usyk TP, McCulloch AD (2003) Relationship between regional shortening and asynchronous electrical activation in a three-dimensional model of ventricular electromechanics. J Cardiovasc Electrophysiol 14(suppl):S196-S202

4. Saucerman JJ, Brunton LL, Michailova AP, McCulloch AD (2003) Modeling β-adrenergic control of cardiac myocyte contractility in silico. J Biol Chem 278:47997–48003

5. Sung D, Mills RW, Schettler J, Narayan SM, Omens JH, McCulloch AD (2003) Ventricular filling slows epicardial conduction and increases action potential duration in an optical mapping study of the isolated rabbit heart. J Cardiovasc Electrophysiol 14:739-749

6. Herrmann KL, McCulloch AD , Omens JH (2003) Glycated collagen cross-linking alters cardiac mechanics in volume-overload hypertrophy. Am J Physiol Heart Circ Physiol 284:H1277-84 (PMCID: 3325795)

7. Gopalan SM, Flaim C, Bhatia SN, Hoshijima M, Knoell R, Chien KR, Omens JH, McCulloch AD (2003) Anisotropic stretch-induced hypertrophy in neonatal ventricular myocytes micropatterned on deformable elastomers. Biotechnol Bioeng 81:578-587

8. Villarreal FJ, Griffin M, Omens J, Dillmann W, Nguyen J, Covell J (2003) Early short-term treatment with doxycycline modulates postinfarction left ventricular remodeling. Circulation 108:1487-1492

9. Usyk TP, McCulloch AD (2003) Computational methods for soft tissue biomechanics. In: Holzapfel GA, Ogden RW (Eds) Biomechanics of Soft Tissue in Cardiovascular Systems. New York: Springer (CISM Courses and Lectures No. 441, International Center for Mechanical Sciences), Pages 273-342

10. Humphrey JD, McCulloch AD (2003) The cardiovascular system – anatomy, physiology and cell biology. In: Holzapfel GA, Ogden RW (Eds) Biomechanics of Soft Tissue in Cardiovascular Systems. New York: Springer (CISM Courses and Lectures No. 441, International Center for Mechanical Sciences), Pages 1-14

2002

1. Knöll R, Hoshijima M, Hoffman HM, Person V, Lorenzen-Schmidt I, Bang M-L, Hayashi T, Shiga N, Yasukawa H, Schaper W, McKenna W, Yokoyama M, Schork NJ, Omens JH, McCulloch AD, Kimura A, Gregorio CC, Poller W, Schaper J, Schultheiss HP, Chien KR (2002) The cardiac mechanical stretch sensor machinery involves a Z disc complex that is defective in a subset of human dilated cardiomyopathy. Cell 111:943–955

2. Sussman MA, McCulloch A, Borg TK (2002) Dance band on the Titanic: biomechanical signaling in cardiac hypertrophy. Circ Res 91:888-898

3. Stuyvers BD, McCulloch AD, Guo J, Duff HJ, ter Keurs HEDJ (2002) Effect of stimulation rate, sarcomere length and Ca2+ on force generation of mouse cardiac muscle. J Physiol (Lond) 544.3:817-830

4. Omens JH, Usyk TP, Li Z, McCulloch AD (2002) Muscle LIM protein deficiency leads to alterations in passive ventricular mechanics. Am J Physiol Heart Circ Physiol 282:H680-H687

5. Usyk TP, LeGrice IJ, McCulloch AD (2002) Computational model of three-dimensional cardiac electromechanics. Comput Visual Sci 4:249-257

6. Criscione JC, McCulloch AD, Hunter WC (2002) Constitutive framework optimized for myocardium and other high-strain, laminar materials reinforced with one family of fibers. J Mech Phys Solids 50:1681-1702

7. McCulloch AD, Huber G (2002) Integrative biological modelling in silico. In: Bock G, Goode JA (Eds) ‘In silico’ simulation of biological processes. Chichester: Wiley (Novartis Foundation Symposium 247), Pages 4-25

2001

1. Gregersen H, Weis SM, McCulloch AD (2001) Oesophageal morphometry and residual strain in a mouse model of osteogenesis imperfecta. Neurogastroenterol Motil 13:457-464

2. Baxter WW, McCulloch AD (2001) Finite element model-based image analysis of pacemaker lead mechanics in vivo. Med Image Anal 5:255-270

3. Sung D, Somayajula-Jagai J, Cosman P, Mills RW, McCulloch AD (2001) Phase-shifting prior to spatial filtering enhances optical recordings of cardiac action potential propagation. Ann Biomed Eng 29:854-861

4. Michailova A, McCulloch AD (2001) Model study of ATP and ADP buffering, transport of Ca2+ and Mg2+, and regulation of ion pumps in ventricular myocytes. Biophys J 81:614-629

5. Young AA, Dokos S, Powell KA, Sturm B, McCulloch AD, Randall C. Starling RC, McCarthy PM, White RD (2001) Regional heterogeneity of function in nonischemic dilated cardiomyopathy. Cardiovasc Res 49:308-318

6. Mazhari R, Omens JH, Pavelec RS, Covell JW, McCulloch AD (2001) Transmural distribution of three-dimensional systolic strains in stunned myocardium. Circulation 104:336-341

7. Usyk TP, Omens JH, McCulloch AD (2001) Regional septal dysfunction in a three-dimensional computational model of focal myofiber disarray. Am J Physiol Heart Circ Physiol 281:H506-H514

8. McCulloch AD, Mazhari R (2001) Regional ventricular mechanics: Integrative computational models of myocardial flow-function relations. J Nucl Cardiol 8:506-19

9. Vetter FJ, McCulloch AD (2001) Mechanoelectric feedback in a model of the passively inflated left ventricle. Ann Biomed Eng 29:414-426 (and cover)

10. Costa KD, Holmes JW, McCulloch AD (2001) Modeling cardiac mechanical properties in three dimensions. Phil Trans R Soc Lond A 359:1233-1250

11. Paternostro G, Vignola C, Bartsch DU, Omens JH, McCulloch AD, Reed JC (2001) Age-associated cardiac dysfunction in Drosophila melanogaster: Implications for genetic screening. Circ Res 88:1053-1058

12. Arts T, Costa KD, Covell JW, McCulloch AD (2001) Relating myocardial laminar architecture to shear strain and muscle fiber orientation. Am J Physiol Heart Circ Physiol 280:H2222-H2229

13. Ramakrishna R, Edwards JS, McCulloch AD, Palsson BO (2001) Flux balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am J Physiol Regul Integr Comp Physiol 280:R695-R704

14. McCulloch AD (2001) Regional stress and strain in healthy and diseased ventricular myocardium. In: Amini AA, Prinz JL (Eds) Measurement of Cardiac Deformations from MRI: Physical and Mathematical Models. New York: Kluwer Academic Publishers, Pages 1-15

15. McCulloch AD, Sung D, Thomas ME, Michailova M (2001) Experimental and Computational Modeling of Cardiac Electromechanical Coupling. In: Katila T, Magnin IE, Clarysse P, Montagnet J, Nenonen J, (Eds) Functional Imaging and Modeling of the Heart. Lecture Notes in Computer Science 2230. Berlin: Springer-Verlag, Pages 113-119

16. McCulloch AD, Sung D, Thomas ME, Michailova M (2001) Computational and Experimental Modeling of Ventricular Electromechanical Interactions. In: Virag N, Blanc O, Kappenberger L (Eds) Computer Simulation and Experimental Assessment of Cardiac Electrophysiology. Armonk NY: Futura Publishing, Pages 89-96

2000

1. Usyk TP, Mazhari R, McCulloch AD (2000) Effect of laminar orthotropic myofiber architecture on regional stress and strain in the canine left ventricle. J Elasticity 61:143-164

2. McCulloch AD (2000) Modeling the human cardiome in silico. J Nucl Cardiol 7(5):496-499 (Editorial)

3. Sung D, Omens JH, McCulloch AD (2000) Model-based analysis of optically mapped epicardial activation patterns and conduction velocity. Ann Biomed Eng 28(9):1085-1092

4. Mazhari R, McCulloch AD (2000) Integrative models for understanding the structural basis of regional mechanical dysfunction in ischemic myocardium. Ann Biomed Eng 28(8):979-990

5. Weis SM, Emery JL, Becker KD, McBride DJ Jr, Omens JH, McCulloch AD (2000) Myocardial mechanics and collagen structure in the osteogenesis imperfecta murine. Circ Res 87:663-669

6. Vetter FJ, McCulloch AD (2000) Three-dimensional stress and strain in passive rabbit left ventricle: A model study. Ann Biomed Eng 28:781-792

7. O’Dell WG, McCulloch AD (2000) Imaging three-dimensional cardiac function. Annu Rev Biomed Eng 2:431-456

8. Mazhari R, Omens JH, Covell JW, McCulloch AD (2000) Structural basis of regional dysfunction in acutely ischemic myocardium. Cardiovasc Res 47:284-293

9. Zimmerman SD, Karlon WJ, Holmes JW, Omens JH, Covell JW (2000) Structural and mechanical factors influencing infarct scar collagen organization. Am J Physiol 278:H194-H200

10. Karlon WJ, McCulloch AD, Covell JW, Hunter JJ, Omens JH (2000) Regional dysfunction correlates with myofiber disarray in transgenic mice with ventricular expression of ras. Am J Physiol: Heart Circ Physiol 278(3): H898-H906 (PMCID: 3328188)

11. McCulloch AD (2000) Cardiac Biomechanics. In: Bronzino JD (Ed) The Biomedical Engineering Handbook, 2nd Edition, Vol I. Boca Raton: CRC Press, pages 28-46.

1999

1. Karlon WJ, Hsu PP, Li S, Chien S, McCulloch AD, Omens JH (1999) Measurement of orientation and distribution of cellular alignment and cytoskeletal organization. Ann Biomed Eng 27(6): 712-20

2. Lee AA, Delhaas T, McCulloch AD, Villarreal FJ (1999) Differential responses of adult cardiac fibroblasts to biaxial strain patterns. J Mol Cell Cardiol 31(10):1833-43

3. Costa KD, Takayama Y, McCulloch AD, Covell JW (1999) Laminar fiber architecture and three-dimensional systolic mechanics of canine ventricular myocardium. Am J Physiol 276:H595-H607

4. Villarreal FJ, Hong D, Omens JH (1999) Nicotine modified postinfarction left ventricular remodeling. Am J Physiol 276:H1103-H1106 (PMCID: 3343001)

1998

1. Emery JL, Omens JH, Mathieu-Costello OA, McCulloch AD (1998) Structural mechanisms of acute ventricular strain softening. Int J Cardiovasc Med Sci 1(3/4):241-250

2. Omens JH, Vaplon SM, Fazeli B, McCulloch AD (1998) Left ventricular geometric remodeling and residual stress in the rat heart. J Biomech Eng 120(6):715-719

3. Summerour SR, Emery JL, Fazeli B, Omens JH, McCulloch AD (1998) Residual strain in ischemic ventricular myocardium. J Biomech Eng 120(6):710-714

4. Bluhm WF, Sung D, Lew WY, Garfinkel A, McCulloch AD (1998) Cellular mechanisms for the slow phase of the Frank-Starling response. J Electrocardiol 31:13-22

5. McCulloch AD, Bassingthwaighte JB, Hunter PJ, Noble D (1998) Computational biology of the heart: from structure to function. Prog Biophys Mol Biol 69:153-155

6. Vetter FJ, McCulloch AD (1998). Three-dimensional analysis of regional cardiac anatomy. Prog Biophys Mol Biol 69:157-184

7. Hunter PJ, McCulloch AD, ter Keurs HEDJ (1998) Modelling the mechanical properties of cardiac muscle. Prog Biophys Mol Biol 69: 289-332

8. May-Newman KD, McCulloch AD (1998) Homogenization modeling for the mechanics of perfused myocardium. Prog Biophys Mol Biol 69:463-482

9. Omens JH (1998) Stress and Strain as Regulators of Myocardial Growth. Prog Biophys Mol Biol 69:559-572

10. Gregersen H, Emery JL, McCulloch AD (1998) History-dependent mechanical behavior of guinea-pig small intestine. Ann Biomed Eng 26:850-858

11. Mazhari R, Omens JH, Waldman LK, McCulloch AD (1998) Regional myocardial perfusion and mechanics: a model-based method of analysis. Ann Biomed Eng 26:743-755 (and cover)

12. Hennighausen H, Feldman ST, Bille JF, McCulloch AD (1998) Anterior-posterior strain variation in normally hydrated and swollen rabbit cornea. Invest Ophthal Vis Sci 39:253-62

13. Trost SU, Omens JH, Karlon WJ, Meyer M, Mestril R, Covell JW, Dillmann WH (1998) Protection against myocardial stunning in transgenic mice expressing inducible heat shock protein 70. J Clin Invest 101:855-862 (PMCID: 508634)

14. McCulloch AD, Sung D, Wilson JM, Pavelec RS, Omens JH (1998) Flow-function relations during graded coronary occlusions in the dog: effects of transmural location and segment orientation. Cardiovasc Res 37:636-645

15. Bluhm WF, Lew WYW, Garfinkel AJ, McCulloch AD (1998). Mechanisms of length-history dependent tension in an ionic model of the cardiac myocyte. Am J Physiol 274:H1032-H1040

16. Karlon WJ, Covell JW, McCulloch AD, Hunter JJ, Omens JH (1998) Automated measurement of myofiber disarray in transgenic mice with ventricular expression of ras. Anat Rec 252:612-625

1997

1. Lee AA, McCulloch AD (1997) Multiaxial myocardial mechanics and extracellular matrix remodeling: mechanochemical regulation of cardiac fibroblast function. Adv Exp Med Biol 430:227-240

2. Costa KD, May-Newman KD, Farr DD, O’Dell WG, McCulloch AD, Omens JH (1997) Three-dimensional residual strain and stress in canine left ventricle. Am J Physiol 273: H1968-1976 (PMCID: 3343007)

3. MacKenna DA, Vaplon SM, McCulloch AD (1997) Microstructural model of perimysial collagen fibers for myocardial mechanics during ventricular filling. Am J Physiol 273:H1576-H1586

4. Emery JL, Omens JH, McCulloch AD (1997) Biaxial mechanics of the passively overstretched left ventricle. Am J Physiol 272:H2299-H2305

5. Omens JH, Miller TR, Covell JW (1997) Relationship between passive tissue strain and collagen uncoiling in infarcted myocardium. Cardiovasc Res 33:351-358

6. Emery JL, Omens JH, McCulloch AD (1997) Strain softening in rat left ventricular myocardium. J Biomech Eng 119(1):6-12

7. Guccione JM, O’Dell WG, McCulloch AD, Hunter WC (1997) Anterior and posterior left ventricular sarcomere lengths behave similarly during ejection. Am J Physiol 272:H469-H477

8. Gallagher AM, Omens JH, Chu LL, Covell JW (1997) Alterations in collagen fibrillar structure and mechanical properties of the healing scar following myocardial infarction. Cardiovasc Pathobiol 2(1): 25-36

9. Emery JL, Omens JH (1997) Mechanical regulation of myocardial growth during volume-overload hypertrophy in the rat. Am J Physiol 273:H1198-H1204

1996

1. Costa KD, Hunter PJ, Rogers JM, Guccione JM, Waldman LK, McCulloch AD (1996) A three-dimensional finite element method for large elastic deformations of ventricular myocardium: Part I – Cylindrical and spherical polar coordinates. J Biomech Eng 118:452-463

2. Costa KD, Hunter PJ, Wayne JS, Waldman LK, Guccione JM, McCulloch AD (1996) A three-dimensional finite element method for large elastic deformations of ventricular myocardium: Part II – Prolate spheroidal coordinates. J Biomech Eng 118: 464-472

3. Lee AA, Delhaas T, Waldman LK, MacKenna DA, Villarreal FJ, McCulloch AD (1996) An equibiaxial strain system for cultured cells. Am J Physiol 271: C1400-C1408

4. Omens JH, Rodriguez EK, McCulloch AD (1996) Transmural changes in stress-free myocyte morphology during pressure overload hypertrophy in the rat. J Mol Cell Cardiol 28:1975-1983

5. Omens JH, Farr DD, McCulloch AD, Waldman LK (1996) Comparison of two techniques for measuring two-dimensional strain in rat left ventricles. Am J Physiol 271:H1256-1261

6. MacKenna DA, Omens JH, Covell JW (1996) Left ventricular perimysial collagen fibers uncoil rather than stretch during diastolic filling. Bas Res Cardiol 91:111-122

7. MacKenna DA, Omens JH (1996) A semi-automated method for measuring collagen area fraction and size distribution using picrosirius red. Cardiovasc Pathobiol 1:104-117

8. Waldman LK, Allen JJ, Pavelec RS, McCulloch AD (1996) Distributed mechanics of the canine right ventricle: effects of varying preload. J Biomech 29(3):373-382.

9. Rogers JM, Courtemanche M, McCulloch AD (1996) Finite element methods for modeling impulse propagation in the heart. In: Panfilov AV, Holden AV (Eds) Computational Biology of the Heart. Sussex: John Wiley and Sons, Ltd.

1995

1. May-Newman KD, Mathieu-Costello OA, Omens JH, Klumb K, McCulloch AD (1995) Transmural distribution of capillary morphology as a function of coronary perfusion pressure in the resting canine heart. Microvasc Res 50:381-396

2. Lee AA, Dillmann WH, McCulloch AD, Villarreal FJ (1995) Angiotensin II stimulates the autocrine production of transforming growth factor-β1 in adult rat cardiac fibroblasts. J Mol Cell Cardiol 27:2347-2357

3. Guccione JM, KD Costa, McCulloch AD (1995) Finite element stress analysis of left ventricular mechanics in the beating dog heart. J Biomech 28(10):1167-1177

4. Villarreal FJ, MacKenna DA, Omens JH, Dillmann WH (1991) Myocardial remodeling in hypertensive Ren-2 transgenic rats. Hypertension 25:98-104

5. Omens JH, Milkes DA, Covell JW (1995) Effects of pressure overload on the passive mechanics of the rat left ventricle. Ann Biomed Eng 23:152-163

6. McCulloch AD (1995) Cardiac Biomechanics. In: Bronzino JD (Ed) The Biomedical Engineering Handbook. Boca Raton: CRC Press, pages 418-439

7. MacKenna DA, McCulloch AD (1995) Contribution of the collagen extracellular matrix to ventricular mechanics. In: Ingels NB, Daughters GT, Baan J, Covell JW, Reneman RS, Yin FC-P (Eds) Systolic and Diastolic Function of the Heart. Tokyo: IOS Press, Pages 35-46

1994

1. Van Leuven SL, Waldman LK, McCulloch AD, Covell JW (1994) Gradients of epicardial strain across the perfusion boundary during acute myocardial ischemia. Am J Physiol 267:H2348-H2362

2. Bluhm WF, McCulloch AD, Lew WYW (1994) Active force in rabbit ventricular myocytes. J Biomech 28:1119-1122

3. Rogers JM, McCulloch AD (1994) Nonuniform muscle fiber orientation causes spiral wave drift in a finite element model of cardiac action potential propagation. J Cardiovasc Electrophysiol 5:496-509

4. May-Newman KD, Omens JH, Pavelec RS, McCulloch AD (1994) Three-dimensional transmural mechanical interaction between the coronary vasculature and the passive myocardium in the dog. Circ Res 74:1166-1178

5. Rogers JM, McCulloch AD (1994) A collocation-Galerkin finite element model of cardiac action potential propagation. IEEE Trans Biomed Eng 41:743-757

6. MacKenna DA, Omens JH, McCulloch AD, Covell JW (1994) Contribution of the endomysial collagen matrix to passive left ventricular mechanics in the isolated rat heart. Am J Physiol 266:H1007-H1018

7. Rodriguez EK, Hoger A, McCulloch AD (1994) Stress-dependent finite growth in soft elastic tissues. J Biomech 27:455-467

8. Omens JH, Rockman HA, Covell JW (1994) Passive ventricular mechanics in tight-skin mice. Am J Physiol 266:H1169-H1176.

1993

1. Waldman LK, McCulloch AD (1993) Nonhomogeneous ventricular wall strain: analysis of errors and accuracy. J Biomech Eng 115:497-502

2. Rodriguez EK, Omens JH, McCulloch AD (1993) Effect of residual stress on transmural sarcomere length distribution in rat left ventricle. Am J Physiol 33:H1048-1056

3. Omens JH, MacKenna DA, McCulloch AD (1993) Measurement of strain and analysis of stress in resting rat ventricular myocardium. J Biomech 26:665-676

4. Guccione JM, McCulloch AD (1993) Mechanics of active contraction in cardiac muscle: Part I. Constitutive relations for fiber stress that describe deactivation. J Biomech Eng 115:72-81

5. Guccione JM, Waldman LK, McCulloch AD (1993) Mechanics of active contraction in cardiac muscle: Part II. Cylindrical models of the systolic left ventricle. J Biomech Eng 115:82-90.

6. Hashima AR, Waldman LK, Young AA, McCulloch AD (1993) Nonhomogeneous analysis of epicardial strain distributions during acute myocardial ischemia in the dog. J Biomech 26:19-35

1992

1. McCulloch AD, Guccione JM, Waldman LK, Rogers JM (1992) Large-scale finite element analysis of the beating heart. Crit Rev Biomed Eng 20:427-449

2. McCulloch AD, Hunter PJ, Smaill BH (1992) Mechanical effects of coronary perfusion in the passive canine left ventricle. Am J Physiol 262:H523-530

3. McCulloch AD, Guccione JM, Waldman LK, Rogers JM (1992) Large-scale finite element analysis of the beating heart. In: Pilkington TC, Loftis B, Thompson JF, Woo SL-Y, Palmer TC, Budinger TF (Eds) High-Performance Computing in Biomedical Research. Boca Raton: CRC Press, Pages 27-49.

1991

1. Omens JH, May KD, McCulloch AD (1991) Transmural distribution of three-dimensional strain in isolated arrested canine left ventricle. Am J Physiol 261:H918-928

2. McCulloch AD, Omens JH (1991) Non-homogeneous analysis of three-dimensional transmural finite deformation in canine ventricular myocardium. J Biomech 24:539-548

3. Guccione JM, McCulloch AD, Waldman LK (1991) Passive material properties of intact ventricular myocardium determined from a cylindrical model. J Biomech Eng 113:42-55

4. Omens JH, Covell JW (1991) Transmural distribution of myocardial tissue growth induced by volume overload hypertrophy in the dog. Circulation 84:1235-1245

5. Glass L, Hunter PJ, McCulloch AD (Eds) (1991) Theory of Heart: Biomechanics, Biophysics and Nonlinear Dynamics of Cardiac Function. New York: Springer-Verlag.

6. Guccione JM, McCulloch AD (1991) Finite element models of ventricular mechanics. In: Glass L, Hunter PJ, McCulloch AD (Eds) Theory of Heart: Biomechanics, Biophysics and Nonlinear Dynamics of Cardiac Function. New York: Springer-Verlag, pages 121-145

7. McCulloch AD, Omens JH (1991) Factors affecting the regional mechanics of the diastolic heart. In: Glass L, Hunter PJ, McCulloch AD (Eds) Theory of Heart: Biomechanics, Biophysics and Nonlinear Dynamics of Cardiac Function. New York: Springer-Verlag, pages 85-120

Before 1991

1. 1. Omens JH, Fung YC (1990) Residual strain in rat left ventricle. Circ Res 66:37-45

   2. McCulloch AD, Smaill BH, Hunter PJ (1989) Regional left ventricular epicardial deformation in the passive dog heart. Circ Res 64:721-733

   3. McCulloch AD, Smaill BH, Hunter PJ (1987) Left ventricular epicardial deformation in the isolated arrested dog heart. Am J Physiol 252:H233-H241