Yoshida K, McCulloch AD, Omens JH, Holmes JW. Predictions of Hypertrophy and Its Regression In Response to Pressure Overload. Biomechanics and Modeling in Mechanobiology, Dec 2019.

Estrada AC, Yoshida K, Clarke SA, Holmes JW. Longitudinal Reinforcement of Acute Myocardial Infarcts Improves Function by Transmurally Redistributing Stretch and Stress. Journal of Biomechanical Engineering, June 2019.

Phung TN, Waters CD, Holmes JW. Open-Source Routines for Building Personalized Left Ventricular Models from Cardiac MRI Data. Journal of Biomechanical Engineering, May 2019.

Witzenburg CM, Holmes JW. The Impact of Hemodynamic Reflex Compensation Following Myocardial Infarction on Subsequent Ventricular Remodeling. Journal of Biomechanical Engineering, May 2019.

Lee JJ, Talman L, Peirce SM, Holmes JW. Spatial scaling in multiscale models: methods for coupling agent-based and finite-element models of wound healing. Biomechanics and modeling in mechanobiology, Apr 2019.

Holmes JW. Model First and Ask Questions Later: Confessions of a Reformed Experimentalist. Journal of Biomechanical Engineering, Apr 2019.

Cohen N, Deshpande VS, Holmes JW, McMeeking RM. A microscopically motivated model for the remodeling of cardiomyocytes. Biomechanics and modeling in mechanobiology, Mar 2019.

Salimova E, Nowak KJ, Estrada AC, Furtado MB, McNamara E, Nguyen Q, Balmer L, Preuss C, Holmes JW, Ramialison M, Morahan G, Rosental NA. Variable outcomes of human heart attack recapitulated in genetically diverse mice. NJP Regenerative medicine, Mar 2019.

French BA, Holmes JW. Implications of scar structure and mechanics for post-infarction cardiac repair and regeneration. Experimental Cell Research, Jan 2019.


Chen K, Hu X, Blemker SS, Holmes JW. Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading. PloS Comp Bio, Dec 2018; 14(12):e1006652.

Richardson WJ, Kegerreis BJ, Thomopoulos S, Holmes JW. Potential strain-dependent mechanisms defining matrix alignment in healing tendons. Biomech Model Mechanobiol, Dec 2018; 17(6):1569-1580.

Caggiano LR, Lee JJ, Holmes JW. Surgical reinforcement alters collagen alignment and turnover in healing myocardial infarcts. Am J Physiol, Jul 2018; 315(4):H1041-H1050.

Lindsey ML, Bolli R, Canty J, Du X, Frangogiannis NG, Frantz S, Gourdie R, Holmes JW, Jones SP, Kloner RA, Lefer D, Liao R, Murphy E, Ping P, Przyklenk K, Recchia FA, Longacre LS, Ripplinger CM, VanEyk J, Heusch G. Guidelines for experimental models of myocardial ischemia and infarction. Am J Physiol Heart Circ Physiol, Apr 2018; 314(4):H812-H838.

Witzenburg CM, Holmes JW. Predicting the time course of ventricular dilation and thickening using a rapid compartmental model. J Cardiovasc Transl Res, Apr 2018; 11(2):109-122.

Chen K, Vigliotti A, Bacca M, McMeeking RM, Deshpande VS, Holmes JW. Role of boundary conditions in determining cell alignment in response to stretch, Jan 2018; Proc Nat Acad Sci, 115(5):986-991.


Witzenburg CM, Holmes JW. A comparison of phenomenologic growth laws for myocardial hypertrophy. J Elasticity, 2017 Dec; 129(1-2): 257-281.

Phung TN, Moyer CB, Norton PT, Ferguson JD, Holmes JW. Effect of ablation pattern on mechanical function in the atrium. Pacing Clin Electrophysiol, 2017 June; 40(6): 648-654.

Auger DA, Bilchick KC, Gonzalez JA, Cui SX, Holmes JW, Kramer CM, Salerno M, Epstein FH. Imaging left-ventricular mechanical activation in heart failure patients using cine DENSE MRI: Validation and implications for cardiac resynchronization therapy. J Magn Reson Imaging, 2017.

Witzenburg CM, Holmes JW. Biomechanics of Myocardial Ischemia and Infarction. Biomechanics: Trends in Modeling and Simulation, 2017; 233-269.


Holmes JW, Wagenseil JE. Special Issue: Spotlight on the Future of Cardiovascular Engineering: Frontiers and Challenges in Cardiovascular Biomechanics. J Biomech Eng. 2016 Nov; 138(11): 110301.

Spinale FG, Frangogiannis NG, Hinz B, Holmes JW, Kassiri Z, Lindsey ML. Crossing into the next frontier of cardiac extracellular matrix research. Circ Res. 2016 Oct; 119(10): 1040-1045.

Zeigler AC, Richardson WJ, Holmes JW, Saucerman JJ. A computational model of cardiac fibroblast signaling predicts context-dependent drivers of myofibroblast differentiation. J Mol Cell Cardiol. 2016 May; 94: 72-81.

Richardson WJ, Holmes JW. Emergence of collagen orientation heterogeneity in healing infarcts and an agent-based model. Biophys J. 2016 May; 110(10): 2266-2277.

Clarke SA, Richardson WJ, Holmes JW. Modifying the mechanics of healing infarcts: is better the enemy of good? J Mol Cell Cardiol. 2016 Apr; 93: 115-124.

Zeigler AC, Richardson WJ, Holmes JW, Saucerman JJ. Computational modeling of cardiac fibroblasts and fibrosis. J Mol Cell Cardiol. 2016 Apr; 93: 78-83.

Holmes JW, Laksman Z, Gepstein L. Making better scar: emerging approaches for modifying mechanical and electrical properties following infarction and ablation. Prog Biophys Mol Biol. 2016 Jan; 120(1): 134-148.


Richardson WJ, Holmes JW. Why is infarct expansion such an elusive therapeutic target? Cardiovasc Transl Res. 2015 Oct; 8(7):421-430.

Richardson WJ, Clarke SA, Quinn TA, Holmes JW. Physiological implications of myocardial scar structure. Comprehensive Physiology. 2015 Sep; 5(4):1877-1909.

Clarke SA, Goodman NC, Ailawadi G, Holmes JW. Effect of scar compaction on the therapeutic efficacy of anisotropic reinforcement following myocardial infarction in the dog. J Cardiovasc Transl Res. 2015 Aug; 8(6):353-361.

Moyer C, Norton PT, Ferguson JD, Holmes JW. Changes in global and regional mechanics due to atrial fibrillation: insights from a coupled finite-element and circulation model. Ann Biomed Eng. 2015 Jul; 43(7):1600-1613.

Parker KM, Clark AP, Goodman NC, Glover DK, Holmes JW. Comparison of quantitative wall motion analysis and strain for detection of coronary stenosis with three-dimensional dobutamine stress echocardiography. Echocardiography. 2015 Feb; 32(2):349-360.

Lin D, French BA, Xu Y, Hossack JA, Holmes JW. An ultrasound-driven kinematic model for deformation of the infarcted mouse heart incorporating a near-incompressibility constraint. Ultrasound Med Biol. 2015 Feb; 41(2):532-41.


Rouillard AD, Holmes JW. Coupled agent-based and finite-element models for predicting scar structure following myocardial infarction. Prog Biophys Mol Biol. 2014 Aug; 115(2-3):235-43.

Parker KM, Bunting E, Clarke SA, Mason P, Malhotra R, Darby AE, Kramer CM, Salerno M, Holmes JW, Bilchick KB. Post-Procedure mapping of cardiac resynchronization lead position using standard fluoroscopy systems: implications for the nonresponder with scar. Pacing Clin Electrophysiol. 2014 Jun; 37(6):757-67.

Parker KM, Clark AP, Goodman NC, Glover DK, Holmes JW. Comparison of quantitative wall motion analysis and strain for detection of coronary stenosis with three-dimensional dobutamine stress echocardiography. Echocardiography. 2014 May; doi:10.1111/echo.12636.

Bilchick KB, Hamirani Y, Kuruvilla S, Ramachandran R, Clarke SA, Parker KM, Stukenborg GJ, Mason P, Ferguson JD, Moorman R, Malhotra R, Mangrum M, Darby AE, DiMarco J, Holmes JW, Salerno M, Kramer CM, Epstein FH. Impact of mechanical activation, scar, and electrical timing on cardiac resynchronization therapy response and clinical outcomes. J Am Coll Cardiol. 2014 Apr; 63(16):1657-1666

Rouillard AD, Holmes JW. Mechanical boundary conditions bias fibroblast invasion in a collagen-fibrin wound model. Biophys J. 2014 Feb; 106(4):932-943.

Haggart CR, Ames EG, Lee JK, Holmes JW. Effects of stretch and shortening on gene expression in intact myocardium. Physiol Genomics. 2014 Jan; 46(2):57-65.

Clarke SA, Ghanta RK, Ailawadi G, Holmes JW. Cardiac restraint and support following myocardial infarction (book chapter). In: Cardiovascular and Cardiac Therapeutic Devices, ed. Franz T, Springer (Berlin), 2014.


Moyer C, Helm PA, Clarke CC, Kramer CM, Ferguson JD, Norton PT, Holmes JW. Wall-motion based analysis of global and regional left atrial mechanics. IEEE Trans Med Imag. 2013 Oct; 32(10):1765-1776.

Ames EG, Lawson MJ, Mackey AJ, Holmes JW. Sequencing of mRNA identifies re-expression of fetal splice variants in cardiac hypertrophy. J Mol Cell Cardiol. 2013 Sep; 62:99-107.


Rouillard AD, Holmes JW. Mechanical regulation of fibroblast migration and collagen remodeling in healing myocardial infarcts, J Physiol. 2012 Sep; 590(18):4585-4602.

Fomovsky GM, Clark SA, Parker KM, Ailawadi G, Holmes JW. Anisotropic reinforcement of acute anteroapical infarcts improves pump function, Circ Heart Fail. 2012 Jul; 5:515-522.

Chandran PL, Paik DC, Holmes JW. Structural mechanism for alteration of collagen gel mechanics by glutaraldehyde crosslinking. Conn Tiss Res. 2012 Jun; 53(4):285-297.

Fomovsky GM, Rouillard AD, Holmes JW. Regional mechanics determine collagen fiber structure in healing myocardial infarcts. J Mol Cell Cardiol. 2012 May; 52:1083-1090.

Ateshian GA, Morrison III B, Holmes JW, Hung CT. Mechanics of cell growth. Mech Res Commun. 2012 Jun; 42:118-125.


Holmes JW, Vandegeest JP. Cardiovascular solid mechanics grows and remodels. J Biomech. 2011 Dec 7.

Sharafi B, Ames EG, Holmes JW, Blemker SS. Strains at the myotendinous junction predicted by a micromechanical model. J Biomech. 2011 Nov 10;16:2795-801.

Fomovsky GM, Macadangdang JR, Ailawadi G, Holmes JW. Model-based design of mechanical therapies for myocardial infarction. J Cardiovasc Transl Res, 2011 Feb;1:82-91.


Fomovsky GM, Holmes JW. Evolution of scar structure, mechanics, and ventricular function after myocardial infarction in the rat. Am J Physiol Heart Circ Physiol, 298:H221-H228, 2010.

Fomovsky GM, Thomopoulos S, Holmes JW. Contribution of extracellular matrix to the mechanical properties of the heart. J Mol Cell Cardiol, 48:490-496, 2010.

Herz SL, Hasegawa T, Makaryus AN, Parker KM, Homma S, Wang J, Holmes JW. Quantitative three-dimensional wall motion analysis predicts ischemic region size and location. Ann Biomed Eng, 38:1367-1376, 2010.


Duan Q, Angelini ED, Herz SL, Ingrassia CM, Costa KD, Holmes JW, Homma S, Laine AF. Region-based endocardium tracking on real-time three-dimensional ultrasound. Ultrasound Med Biol 35:256-265, 2009.

George I, Morrow B, Xu K, Yi GH, Holmes J, Wu EX, Li Z, Protter AA, Oz MC, Wang J. Prolonged effects of B-type natriuretic peptide infusion on cardiac remodeling after sustained myocardial injury. Am J Physiol Heart Circ Physiol 297:h2 708-h2 717, 2009.

Quinn TA, Cabreriza SE, Richmond ME, Weinberg AD, Holmes JW, Spotnitz HM. Simultaneous variation of ventricular pacing site and timing with biventricular pacing in acute ventricular failure improves function by interventricular assist. Am J Physiol Heart Circ Physiol, 297:H2220-H2226, 2009.

Duan Q, Parker KM, Lorsakul A, Angelini ED, Hyodo E, Homma S, Holmes JW, Laine AF. Quantitative validation of optical flow based myocardial strain measures using sonomicrometry (conference paper). Proceedings International Symposium on Biomedical Imaging 2009, 454-457.

Duan Q, Angelini ED, Lorsakul A, Homma S, Holmes JW, Laine AF. Coronary occlusion detection with 4D optical flow based strain estimation on 4D ultrasound (conference paper). In: Functional Imaging and Modeling of the Heart 2009, eds. Ayachi N, Delingette H, Sermesant M. Lecture Notes In Computer Science v.5528, 2009.

Humphrey JD, Holmes JW. Style and Ethics of Communication in Science and Engineering (book). Morgan and Claypool, 2009.


Lee EJ, Holmes JW, Costa KD. Remodeling of engineered tissues in response to altered boundary conditions. Ann Biomed Eng 36:1322-1334, 2008.

Duan Q, Angelini ED, Gerard O, Costa KD, Holmes JW, Homma S, Laine AF. Cardiac motion analysis based on optical flow of real-time 3-D ultrasound data (book chapter). In: Advances in Diagnostic and Therapeutic Ultrasound Imaging, eds. Suri JS, Kathuria C, Chang RF, Fenster A. Artech House (Boston), Chapter 9: 227-246, 2008.


George I, Cheng Y, Yi GH, He KL, Li X., Oz MC, Holmes JW, Wang J. Effect of passive cardiac containment on ventricular synchrony and cardiac function in awake dogs. Eur J Cardiothorac Surg 31:55-64, 2007.

Cheng Y, George I, Yi GH, Reiken S, Gu A, Tao YK, Muraskin J, Qin S, He KL, Hay I, Yu K, Oz MC, Burkhoff D, Holmes J, Wang J. Bradycardic therapy improves left ventricular function and remodeling in dogs with coronary embolization-induced chronic heart failure. J Pharmacol Exp Ther 321:469-476, 2007.

Ingrassia CM, Usyk TP, Kerckhoffs RCP, McCulloch AD, Costa KD, Holmes JW. Model-based development of 4-dimensional wall motion measures. Comp Meth Appl Mech Eng 196:3061-3069, 2007.

Aarabi S, Bhatt KA, Shi Y, Paterno J, Chang EI, Loh SA, Holmes JW, Longaker MT, Yee H, Gurtner GC. Mechanical loading initiates hypertrophic scar formation through decreased cellular apoptosis. FASEB J 21:3250-3261, 2007.

Thomopoulos S, Fomovsky GM, Chandran PL, Holmes JW. Collagen fiber structure does not explain mechanical anisotropy in fibroblast populated collagen gels. J Biomech Eng 129:642-649,2007.

Lee W, Ingrassia CM, Fung-Kee-Fung SD, Costa KD, Holmes JW, Konofagou EE. Theoretical quality assessment of myocardial elastography with in vivo validation. IEEE Trans Ultrason Ferroelectr Freq Control 54:2233-2245, 2007.

Yan W, George S, Fotadar U, Kamer A, Yost MJ, Price RL, Haggart CR, Holmes JW, Terracio L. Tissue engineering of skeletal muscle. Tissue Engineering 13:2781-2790, 2007.

Guterl KA, Haggart CR, Janssen PML, Holmes JW. Isometric contraction induces rapid myocyte remodeling in cultured rat right ventricular papillary muscles. Am J Physiol Heart Circ Physiol 293:H3707-H3712, 2007.

Bupha-Intr T, Holmes JW, Janssen PML. Induction of hypertrophy in vitro by mechanical loading in adult rabbit myocardium. Am J Physiol Heart Circ Physiol 293:H3759-H3767, 2007.


Holmes JW. Heart biomechanics. Enc Biomat Biomed Eng, published online March 27, 2006; doi:10.1081/E-EBBE-120041892.

Paik DC, Saito LY, Sugirtharaj DD, Holmes JW. Nitrite induced cross-linking alters remodeling and mechanical properties of collagenous engineered tissues. Conn Tiss Res 47(3):163-176, 2006.

Holmes JW. Teaching from classic papers: Hill’s model of muscle contraction. Adv Physiol Educ 30(2):67-72, 2006.

Quinn TA, Berberian G, Cabreriza SE, Curtis LJ, Weinberg AD, Holmes JW, Spotnitz HM. Effects of sequential biventricular pacing during right ventricular pressure overload. Am J Physiol Heart Circ Physiol 291:H2380-2387, 2006.

Freed LE, Guilak F, Guo EX, Gray ML, Tranquillo R, Holmes JW, Radisic M, Sefton MV, Kaplan D, Vunjak-Novakovic G. Advanced tools: scaffolds, bioreactors, signaling. Tissue Engineering 12:3285-3305, 2006.

Herz SL, Ingrassia CM, Costa KD, Holmes JW. Model-based screening of wall motion measures for detection of ischemia in three-dimensional cardiac images (conference paper). Conf Proc IEEE Eng Med Biol Soc 2006, 1:628-631.

Holmes JW, Costa KD. Imaging cardiac mechanics: what information do we need to extract from cardiac images (conference paper)? Conf Proc IEEE Eng Med Biol Soc 2006, 1:1545-1547.


Klotz S, Barbone A, Reiken S, Holmes JW, Naka Y, Oz MC, Marks AR, Burkhoff D. Left ventricular assist device support normalizes left and right ventricular β-adrenergic pathway properties. J Am Coll Cardiol 45(5):668-676, 2005.

Holmes JW, Borg TK, Covell JW. Structure and mechanics of healing myocardial infarcts. Annu Rev Biomed Eng 7:223-253, 2005.

Herz SL, Ingrassia CM, Homma S, Costa KD, Holmes JW. Parameterization of left ventricular wall motion for detection of regional ischemia. Ann Biomed Eng 33(7):920-927, 2005.

Derderian CA, Bastidas N, Lerman OZ, Bhatt KA, Lin SE, Voss J, Holmes JW, Levine JP, Gurtner GC. Mechanical strain alters gene expression in an in vitro model of hypertrophic scarring. Ann Plast Surg 55(1):69-75, 2005.

Angelini ED, Homma S, Pearson G, Holmes JW, Laine AF. Segmentation of real-time three-dimensional ultrasound for quantification of ventricular function: a clinical study on right and left ventricles. Ultrasound Med Biol 31(9):1143-1158, 2005.

Thomopoulos S, Fomovsky GM, Holmes JW. The development of structural and mechanical anisotropy in fibroblast populated collagen gels. J Biomech Eng 127(5):742-750, 2005.

Duan Q, Angelini ED, Herz SL, Gerard O, Allain P, Ingrassia CM, Costa KD, Holmes JW, Homma S, Laine AF. Tracking of LV endocardial surface on real-time three-dimensional ultrasound with optical flow (conference paper). In: Functional Imaging and Modeling of the Heart 2005, eds. Frangi AF, Radeva PI, Santos A, Hernandez M. Lecture Notes In Computer Science v.3504:434-445, 2005.