Publications

Members of Vondriska lab appear in bold.

1. Hu S, Chapski DJ, Gehred N, Kimball TK, Gromova T, Flores A, Rowat AC, Chen J, Packard RRS, Olszewski E, Davis J, Rau CD, McKinsey TA, Rosa Garrido M, Vondriska TM. Histone H1.0 couples cellular mechanical behaviors to chromatin structure. Nature Cardiovascular Research. 2024. PMID: 38765203

2. Arrieta A, Chapski DJ, Reese A, Kimball T, Song K, Rosa-Garrido M, Vondriska TM. Circadian Control of Histone Turnover During Cardiac Development and Growth. J Biol Chem. 2024 PMID: 38830405.

3. Chen J, Chapski DJ, Jong J, Awada J, Wang Y, Slamon DJ, Vondriska TM, Packard RRS. Integrative transcriptomics and cell systems analyses reveal protective pathways controlled by Igfbp-3 in anthracycline-induced cardiotoxicity. FASEB J. 2023 Jun;37(6):e22977.

4. Langenbacher AD, Lu F, Crisman L, Huang ZYS, Chapski DJ, Vondriska TM, Wang Y, Gao C, Chen JN. Rtf1 Transcriptionally Regulates Neonatal and Adult Cardiomyocyte Biology. J Cardiovasc Dev Dis. 2023 May 20;10(5):221.

5. Gromova T, Gehred ND, Vondriska TM. Single-cell transcriptomes in the heart: when every epigenome counts. Cardiovasc Res. 2023 Mar 17;119(1):64-78.

6. Chapski DJ, Vondriska TM. Unwind to the beat: chromatin and cardiac conduction. J Clin Invest. 2023 Feb 1;133(3):e165663.

7. Fischer MA, Chapski DJ, Soehalim E, Montoya DJ, Grogan T, Pellegrini M, Cai H, Shemin RJ, Vondriska TM. Longitudinal profiling in patients undergoing cardiac surgery reveals postoperative changes in DNA methylation. Clin Epigenetics. 2022 Dec 30;14(1):195.

8. Arrieta A, Vondriska TM. Nucleosome proteostasis and histone turnover. Front Mol Biosci. 2022 Sep 30;9:990006.

9. Chen J, Zhu AJ, Packard RRS, Vondriska TM, Chapski DJ. genomeSidekick: A user-friendly epigenomics data analysis tool. Front Bioinform. 2022 Jul 18;2:831025.

10. Cabré N, Luciano-Mateo F, Chapski DJ, Baiges-Gaya G, Fernández-Arroyo S, Hernández-Aguilera A, Castañé H, Rodríguez-Tomàs E, París M, Sabench F, Castillo DD, Del Bas JM, Tomé M, Bodineau C, Sola-García A, López-Miranda J, Martín-Montalvo A, Durán RV, Vondriska TM, Rosa-Garrido M, Camps J, Menéndez JA, Joven J. Laparoscopic Sleeve Gastrectomy in Patients with Severe Obesity Restores Adaptive Responses Leading to Nonalcoholic Steatohepatitis. Int J Mol Sci. 2022 Jul 15;23(14):7830.

11. Cao Y, Vergnes L, Wang YC, Pan C, Chella Krishnan K, Moore TM, Rosa-Garrido M, Kimball TH, Zhou Z, Charugundla S, Rau CD, Seldin MM, Wang J, Wang Y, Vondriska TM, Reue K, Lusis AJ. Sex differences in heart mitochondria regulate diastolic dysfunction. Nat Commun. 2022 Jul 4;13(1):3850. 

12. Fischer MA, Mahajan A, Cabaj M, Kimball TH, Morselli M, Soehalim E, Chapski DJ, Montoya D, Farrell CP, Scovotti J, Bueno CT, Mimila NA, Shemin RJ, Elashoff D, Pellegrini M, Monte E, Vondriska TM. DNA Methylation-Based Prediction of Post-operative Atrial Fibrillation. Front Cardiovasc Med. 2022 May 10;9:837725.

13. Hu S, Vondriska TM. How Chromatin Stiffens Fibroblasts. Curr Opin Physiol. 2022 Apr;26:100537.

14. Gromova T, Gehred ND, Vondriska TM. Single-cell transcriptomes in the heart: when every epigenome counts. Cardiovasc Res. 2022 Mar 24:cvac040.

15. McKee CM, Chapski DJ, Wehling-Henricks M, Rosa-Garrido M, Kuro-O M, Vondriska TM, Tidball JG. The anti-aging protein Klotho affects early postnatal myogenesis by downregulating Jmjd3 and the canonical Wnt pathway. FASEB J. 2022 Mar;36(3):e22192. 

16. Pezhouman A, Nguyen NB, Sercel AJ, Nguyen TL, Daraei A, Sabri S, Chapski DJ, Zheng M, Patananan AN, Ernst J, Plath K, Vondriska TM, Teitell MA, Ardehali R. Transcriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte Maturation. Front Cell Dev Biol. 2021 Dec 17;9:787684.

17. Chapski DJ, Cabaj M, Morselli M, Mason RJ, Soehalim E, Ren S, Pellegrini M, Wang Y, Vondriska TM, Rosa-Garrido M. Early adaptive chromatin remodeling events precede pathologic phenotypes and are reinforced in the failing heart. J Mol Cell Cardiol. 2021 Jul 15;160:73-86.

18. Chapski DJ, Vondriska TM. Taking Data Science to Heart: Next Scale of Gene Regulation. Curr Cardiol Rep. 2021 Mar 15;23(5):46. doi: 10.1007/s11886-021-01467-6.

19. Fischer MA, Vondriska TM. Clinical epigenomics for cardiovascular disease: Diagnostics and therapies. J Mol Cell Cardiol. 2021 May;154:97-105. 

20. Kimball, T. H., & Vondriska, T. M. (2020). Metabolism, epigenetics, and causal inference in heart failure. Trends in Endocrinology & Metabolism, 31(3), 181-191.

21. Mason RJ, Vondriska TM. Chromatin is the same in a relative way (but you're older). Circ Res. 2019;125:209-211.

22. Karbassi E, Rosa-Garrido M, Chapski DJ, Wu Y, Ren S, Wang Y, Stefani E, Vondriska TM. Direct Visualization of cardiac transcription factories reveals regulatory principles of nuclear architecture during pathological remodeling. Journal of Molecular and Cellular Cardiology. 2019;128:198-211.

23. Chapski DJ, Rosa-Garrido M, Hua N, Alber F, Vondriska TM. Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation. Frontiers. 2018;5:186

24. McKinsey, TA, Vondriska, TM, Wang, Y. Epigenomic regulation of heart failure: integrating histone marks, long non-coding RNAs, and chromatin architecture. F1000 Research. 2018;7:1713

25. Rosa Garrido M, Chapski DJ, Vondriska TM. Epigenomes in Cardiovascular Disease. Circ Res. 2018;122(11):1586-1607.

26. Rau, CD, Vondriska, TM. DNA Methylation and Human Heart Failure: Mechanisms or Progrnostics. Circulation. 2017;136,16:1545-1547

27. Rosa Garrido M, Chapski DJ, Schmitt AD, Kimball TH, Karbassi E, Monte E, Balderas E, Pellegrini M, Shih TT, Soehalim E, Liem DA, Ping P, Galjart NJ, Ren S, Wang Y, Ren B, Vondriska TM. High resolution mapping of chromatin conformation in cardiac myocytes reveals structural remodeling of the epigenome in heart failure. Circulation. 2017.

28. Monte E, Fischer MA, Vondriska TM. Epigenomic disruption of cardiovascular care: what it will take. Circ Res. 2017;120:1692-1693.

29. Chai H, Diaz-Castro B, Shigetomi E, Monte E, Octeau JC, Yu X, Cohn W, Rajendran PS, Vondriska TM, Whitelegge JP, Coppola G, Khakh BS. Neural circuit-specialized astrocytes: transcriptomic, proteomic, morphological and functional evidence. Neuron. 2017;95:531-549.

30. Wang J, Aboulhosn JA, Hofer IS, Mahajan A, Wang Y, Vondriska TM. Operationalizing precision cardiovascular medicine: three innovations. Circ Res. 2016. 119:984-987. 

31. Wang Z, Zhang XJ, Ji YX, Zhang P, Den KQ, Gong J, Ren S, Wang X, Chen I, Wang H, Gao C, Yokota T, Ang YS, Li S, Cass A, Vondriska TM, Li G, Deb A, Srivastava D, Yang HT, Xiao X, Li H, Wang Y. The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy. Nat Med. 2016;22:1131-39.

32. Franklin S, Kimball T, Rasmussen T, Rosa Garrido M, Chen H, Tran T,  Miller M, Gray R, Jiang S, Ren S, Wang Y, Tucker H, Vondriska TM. The chromatin binding protein Smyd1 restricts adult mammalian heart growth. American Journal of Physiology - Heart and Circulatory Physiology. 2016;311:H1234-47.

33. Karbassi E, Monte E, Chapski DJ, Lopez R, Rosa Garrido M, Kim J, Wisniewski NA, Rau CD, Wang JJ, Weiss JN, Wang Y, Lusis AJ, Vondriska TM. Relationship of disease-associated gene expression to cardiac phenotype is buffered by genetic diversity and chromatin regulation. Physiological Genomics. 2016. 48:601-615.

34. Jiang, S, Vondriska, TM. (Agnetti et al. Editors). Sensing and remembering cellular states through chromatin. Manual of Cardiac Proteomics. (2016).

35. Monte E, Rosa Garrido M, Karbassi E, Chen H, Lopez R, Rau CD, Wang J, Nelson SF, Wu Y, Stefani E, Lusis AJ, Wang Y, Kurdistani SK, Franklin S, Vondriska TM. Reciprocal regulation of the cardiac epigenome by chromatin structural proteins HMBG and CTCF: implications for transcriptional regulation. J Biol Chem. 2016. 291:15428-46.

36. Monte E, Rosa Garrido M, Vondriska TM, Wang J. Undiscovered physiology of transcript and protein networks. Comprehensive Physiology. 2016;6:1851-1872.

37. Chen H, Orozco L, Wang J, Rau CD, Rubbi L, Ren S, Wang Y, Pellegrini M, Lusis AJ, Vondriska TM. DNA methylation indicates susceptibility to isoproterenol-induced cardiac pathology and is associated with chromatin states. Circ Res. 2016;118:786-797.

38. Gao C, Ren S, Lee JH, Qiu J, Chapski DJ, Rau CD, Zhou Y, Abdellatif M, Nakano A, Vondriska TM, Xiao X, Fu XD, Chen JN, Wang Y. REFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure. J Clin Invest. 2015;126:195-206.

39. Monte E, Lopez R, Vondriska TM. Not low hanging but still sweet: metabolic proteomes in cardiovascular disease. J Mol Cell Cardiol. 2015;90:70-73.

40. Vondriska TM. Transcriptome and proteome dynamics in the cardiovascular system. J Physiol. 2015;593:1773-5.

41. Shimizu H, Schredelseker J, Huang J, Lu K, Naghdi S, Lu F, Franklin S, Fiji HD, Zhu H, Tian C, Lin B, Nakano H, Ehrlich A, Nakai J, Stieg AZ, Gimzewski JK, Nakano A, Goldhaber JI, Vondriska TM, Hajnoczky G, Kwon O, Chen JN. Mitochondrial Ca(2+) uptake by the voltage-dependent anion channel 2 regulates cardiac rhythmicity. Elife. 2015;4. PMID: 25588501

42. Ren S, Lu G, Ota A, Zhou ZH, Vondriska TM, Lane TF, Wang Y. IRE1 phosphatase PP2Ce regulates adaptive ER stress response in the postpartum mammary gland. PLoS One. 2014;9:e111606. PMID: 25369058

43. Monte E, Vondriska TM. Epigenomes: the missing heritability in cardiovascular disease? Proteomics ClinicalApplications. 2014; 8:480487.PMID: 24957631

44. Ubil E, Duan J, Pillai I, Rosa-Garrido M, Wu Y, Lu Y, Bargiacchi F, Rojas M, Vondriska TM, Stefani E, Deb A.Mesenchymal-endothelial transition contributes to neovascularization afterheart injury. Nature. 2014; InPress. PMID: 25317562

45. Karbassi E, Vondriska TM. How theproteome packages the genome for cardiovascular development. Proteomics.2014; 14:2115-2126. PMID: 25074278

46. Chapski D, Monte E, Vondriska TM. Positive feedback in cardioprotection: can more mechanism lead to translation? Circ Res. 2014;114:1225-1227. PMID: 24723653

47. Monte E, Mouillesseaux K, Chen H, Kimball T, Ren S, Wang Y, Chen J-N, Vondriska TM, Franklin S. Systems proteomics of cardiac chromatin identifies nucleolin as a regulator of growth and cellular plasticity in cardiomyocytes. Am J Physiol. 2013; 305:H1624-38. PMID: 24077883

48. Lu G, Ota A, Ren S, Franklin S, Rau CD, Ping P, Lane TF, Zhou H, Reue K, Lusis AJ, Vondriska TM, Wang Y. PPM1l encodes an inositol requiring protein 1 (IRE1) specific phosphatase that regulates the functional outcome of the ER stress response. Molecular Metabolism. 2013;2:405-416. PMID: 24327956

49. Chen H, Monte E, Parvatiyar M, Rosa-Garrido M, Franklin S, Vondriska TM. Structural considerations for chromatin state models with transcription as a functional readout. FEBS Lett. 2012. 586:3548-54. PMID: 22940112

50. Rosa-Garrido M, Karbassi E, Monte E, Vondriska TM. Regulation of chromatin structure in the cardiovascular system. Circ J. 2013;77:1389-98. PMID: 23575346

51. Chen H, Monte E, Vondriska TM, Franklin S. Systems proteomics of healthy and diseased chromatin. Heart Proteomics: Methods and Protocols. Humana Press; New Jersey, USA (2013); MIMB 1005:77-94. PMID: 23606250

52. Picha B, Thompson M, Vondriska TM. Preclinical trials: keep "reproducibility" in context. (Comment) Nature. 2012; 485:41. PMID: 22552083

53. Monte E, Chen H, Kolmakova M, Parvatiyar M, Vondriska TM, Franklin S. Quantitative analysis of chromatin proteomes in disease. J Vis Exp. 2012;70. PMID: 2329952

54. Mitchell-Jordan S, Chen H, Franklin S, Stefani E, Bentolila LA, Vondriska TM. Features of endogenous cardiomyocyte chromatin revealed by super resolution STED microscopy. J Mol Cell Cardiol. 2012. 53:552-8. PMID: 22846883

55. Franklin S, Chen H, Mitchell-Jordan SA , Ren S, Wang Y, Vondriska TM . Quantitative analysis of the chromatin proteome in disease reveals remodeling principles and identifies HMGB2 as a regulator of hypertrophic growth. Mol Cell Proteomics. 2012; 11:M111.014258. PMID: 22270000

56. Franklin S, Vondriska TM . Genomes, proteomes and the central dogma. Circulation Cardiovasc Genet. 2011; 4:576. PMID: 22010165

57. Franklin S, Zhang MJ , Chen H, Paulsson AK , Mitchell-Jordan SA , Li Y, Ping P, Vondriska TM . Specialized compartments of cardiac nuclei exhibit distinct proteomic anatomy. Mol Cell Proteomics. 2011; 10.PMID:20807835.

58. Li Y, Franklin S, Zhang MJ, Vondriska TM . Purification of protein complexes from mammalian cells using a novel streptavidin-binding peptide and hexahistidine tandem tag system: application to Btk. Protein Science. 2011; 20:140-149. PMID:21080425.

59. Zhang MJ , Franklin S, Li Y, Wang S, Ru X, Mitchell-Jordan SA , Mano H, Stefani E, Ping P, Vondriska TM . Stress signaling by Tec tyrosine kinase in ischemic myocardium. Am J Physiol. 2010; 299:H713–733.PMID: 20543088.

60. Paulsson AK , Franklin S, Mitchell-Jordan SA , Ren S, Wang Y, Vondriska TM . Post-translational regulation of calsarcin-1 in cardiac pressure overload. J Mol Cell Cardiol. 2010; 48:1206–1214.

61. Lomenick B, Hao R, Jonai N, Chin RM, Aghajan M, Warburton S, Wang J, Wu RP, Gomez F, Loo JA, Wohlschlegel JA, Vondriska TM , Pelletier J, Herschman HR, Clardy J, Clarke CF, Huang J. Target identification using drug affinity responsive target stability (DARTS). Proc Natl Acad Sci USA. 2009; 106:21984–21989.

62. Lu G, Sun H, She P, Youn J-Y, Warburton S, Ping P, Vondriska TM , Cai H, Lynch CJ, Wang Y. Protein phosphatase 2Cm regulates branched chain amino acid catabolism through dephosphorylation of the branched chain a-ketoacid-dehydrogenase complex in mice and cultured cells. J Clin Invest. 2009; 119:1678–1687.

63. Singh H, Warburton S, Vondriska TM , Khakh BS. Proteomics to identify proteins interacting with P2X2ligand-gated cation channels. J Vis Exp. 2009; 27:pii 1178.

64. Mitchell-Jordan SA , Holopainen T, Ren S, Warburton S, Zhang M, Wang S, Alitalo K, Wang Y, Vondriska TM . Loss of Bmx non-receptor tyrosine kinase prevents pressure overload-induced cardiac hypertrophy. Circ Res. 2008; 103:1359–1362.

65. Qu Z, Vondriska TM . Effects of cascade length, kinetics and feedback on signal transduction dynamics in a simplified cascade model. Phys Biol. 2009; 6:16007.

66. MacLellan WR, Wang Y, Vondriska TM , Weiss JN, Ping P. Proteomic insights into cardiac cell death and survival. Proteomics Clin Appl. 2008; 2:837–844.

67. Vondriska TM , Wang Y. A new (heat) shocking player in cardiac hypertrophy. Circ Res. 2008; 103:1194–1196.

68. Yang L, Vondriska TM , Han Z, MacLellan WR, Weiss JN, Qu Z. Deducing topology of protein-protein interaction networks from experimentally measured subnetworks. BMC Bioinformatics. 2008; 9:301.

69. Warburton S, White MY, Van Eyk JE, Cotter RJ, Ping P, Dunn MJ, Vondriska TM . Cardiovascular Initiative of the Human Proteome Organisation, 5th Workshop October 2007, Seoul, Korea. Proteomics. 2008; 8:924–926.

70. Gugiu BG, Mouillesseaux K, Duong V, Herzog T, Hekimian A, Koroniak L, Vondriska TM , Watson AD. Protein targets of oxidized phospholipids in endothelial cells. J Lipid Res. 2008; 49:510–520.

71. Han Z, Vondriska TM , Yang L, MacLellan WR, Weiss JN, Qu Z. Signal transduction network motifs and biological memory. J Theor Biol. 2007; 246:755–761.

72. Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJR, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM , Whitelegge JP, Wilkins MR, Xenarios I, Yates JR, Hermjakob H. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007; 25:887–893.

A PubMed search for "Vondriska TM" collects additional publications from prior to independent career.