Publications

1. 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 journal : official publication of the Federation of American Societies for Experimental Biology, 2023.
2. 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.. Journal of cardiovascular development and disease, 2023.
3. Gromova T, Gehred ND, Vondriska TM. Single-cell transcriptomes in the heart: when every epigenome counts.. Cardiovascular research, 2023.
4. Chapski DJ, Vondriska TM. Unwind to the beat: chromatin and cardiac conduction.. The Journal of clinical investigation, 2023.
5. 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.. Clinical epigenetics, 2022.
6. Arrieta A, Vondriska TM. Nucleosome proteostasis and histone turnover.. Frontiers in molecular biosciences, 2022.
7. Chen J, Zhu AJ, Packard RRS, Vondriska TM, Chapski DJ. genomeSidekick: A user-friendly epigenomics data analysis tool.. Frontiers in bioinformatics, 2022.
8. 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.. International journal of molecular sciences, 2022.
9. 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.. Nature communications, 2022.
10. 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.. Frontiers in cardiovascular medicine, 2022.
11. Hu S, Vondriska TM. How Chromatin Stiffens Fibroblasts.. Current opinion in physiology, 2022.
12. 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 journal : official publication of the Federation of American Societies for Experimental Biology, 2022.
13. 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.. Frontiers in cell and developmental biology, 2021.
14. 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.. Journal of molecular and cellular cardiology, 2021.
15. 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, Del Castillo D, 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. Glutaminolysis-induced mTORC1 activation drives non-alcoholic steatohepatitis progression.. Journal of hepatology, 2021.
16. Chapski DJ, Vondriska TM. Taking Data Science to Heart: Next Scale of Gene Regulation.. Current cardiology reports, 2021.
17. Fischer MA, Vondriska TM. Clinical epigenomics for cardiovascular disease: Diagnostics and therapies.. Journal of molecular and cellular cardiology, 2021.
18. Kimball TH, Vondriska TM. Metabolism, Epigenetics, and Causal Inference in Heart Failure.. Trends in endocrinology and metabolism: TEM, 2019.
19. Foo RS, Anene-Nzelu CG, Rosa-Garrido M, Vondriska TM. Dissecting Chromatin Architecture for Novel Cardiovascular Disease Targets.. Circulation, 2019.
20. Mason RJ, Vondriska TM. Chromatin Is the Same in a Relative Way (But You're Older).. Circulation research, 2019.
21. 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.
22. Chapski DJ, Rosa-Garrido M, Hua N, Alber F, Vondriska TM. Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation.. Frontiers in cardiovascular medicine, 2019.
23. McKinsey TA, Vondriska TM, Wang Y. Epigenomic regulation of heart failure: integrating histone marks, long noncoding RNAs, and chromatin architecture.. F1000Research, 2018.
24. Rosa-Garrido M, Chapski DJ, Vondriska TM. Epigenomes in Cardiovascular Disease.. Circulation research, 2018.
25. Rau CD, Vondriska TM. DNA Methylation and Human Heart Failure: Mechanisms or Prognostics.. Circulation, 2017.
26. Rosa-Garrido M, Chapski DJ, Schmitt AD, Kimball TH, Karbassi E, Monte E, Balderas E, Pellegrini M, Shih TT, Soehalim E, Liem D, 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.
27. 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.
28. Monte E, Fischer MA, Vondriska TM. Epigenomic Disruption of Cardiovascular Care: What It Will Take.. Circulation research, 2017.
29. Wang JJ, Aboulhosn JA, Hofer IS, Mahajan A, Wang Y, Vondriska TM. Operationalizing Precision Cardiovascular Medicine: Three Innovations.. Circulation research, 2016.
30. Franklin S, Kimball T, Rasmussen TL, Rosa-Garrido M, Chen H, Tran T, Miller MR, Gray R, Jiang S, Ren S, Wang Y, Tucker HO, Vondriska TM. The chromatin-binding protein Smyd1 restricts adult mammalian heart growth.. American journal of physiology. Heart and circulatory physiology, 2016.
31. Monte E, Rosa-Garrido M, Vondriska TM, Wang J. Undiscovered Physiology of Transcript and Protein Networks.. Comprehensive Physiology, 2016.
32. Wang Z, Zhang XJ, Ji YX, Zhang P, Deng 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.. Nature medicine, 2016.
33. Karbassi E, Monte E, Chapski DJ, Lopez R, Rosa Garrido M, Kim J, Wisniewski N, 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.
34. 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 Hmgb and Ctcf: IMPLICATIONS FOR TRANSCRIPTIONAL REGULATION.. The Journal of biological chemistry, 2016.
35. Chen H, Orozco LD, 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.. Circulation research, 2016.
36. 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. RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure.. The Journal of clinical investigation, 2015.
37. Monte E, Lopez R, Vondriska TM. Not low hanging but still sweet: Metabolic proteomes in cardiovascular disease.. Journal of molecular and cellular cardiology, 2015.
38. Vondriska TM. Transcriptome and proteome dynamics in the cardiovascular system.. The Journal of physiology, 2015.
39. Shimizu H, Schredelseker J, Huang J, Lu K, Naghdi S, Lu F, Franklin S, Fiji HD, Wang K, Zhu H, Tian C, Lin B, Nakano H, Ehrlich A, Nakai J, Stieg AZ, Gimzewski JK, Nakano A, Goldhaber JI, Vondriska TM, Hajnóczky G, Kwon O, Chen JN. Mitochondrial Ca(2+) uptake by the voltage-dependent anion channel 2 regulates cardiac rhythmicity.. eLife, 2015.
40. 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.
41. Ubil E, Duan J, Pillai IC, Rosa-Garrido M, Wu Y, Bargiacchi F, Lu Y, Stanbouly S, Huang J, Rojas M, Vondriska TM, Stefani E, Deb A. Mesenchymal-endothelial transition contributes to cardiac neovascularization.. Nature, 2014.
42. Vondriska TM, Jensen ON. Proteomics in chromatin biology and epigenetics.. Proteomics, 2014.
43. Karbassi E, Vondriska TM. How the proteome packages the genome for cardiovascular development.. Proteomics, 2014.
44. Monte E, Vondriska TM. Epigenomes: the missing heritability in human cardiovascular disease?. Proteomics. Clinical applications, 2014.
45. Chapski DJ, Monte E, Vondriska TM. Positive feedback in cardioprotection: can more mechanism lead to translation?. Circulation research, 2014.
46. Monte E, Mouillesseaux K, Chen H, Kimball T, Ren S, Wang Y, Chen JN, Vondriska TM, Franklin S. Systems proteomics of cardiac chromatin identifies nucleolin as a regulator of growth and cellular plasticity in cardiomyocytes.. American journal of physiology. Heart and circulatory physiology, 2013.
47. Lu G, Ota A, Ren S, Franklin S, Rau CD, Ping P, Lane TF, Zhou ZH, Reue K, Lusis AJ, Vondriska T, 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.
48. Rosa-Garrido M, Karbassi E, Monte E, Vondriska TM. Regulation of chromatin structure in the cardiovascular system.. Circulation journal : official journal of the Japanese Circulation Society, 2013.
49. Chen H, Monte E, Vondriska TM, Franklin S. Systems proteomics of healthy and diseased chromatin.. Methods in molecular biology (Clifton, N.J.), 2013.
50. Monte E, Chen H, Kolmakova M, Parvatiyar M, Vondriska TM, Franklin S. Quantitative analysis of chromatin proteomes in disease.. Journal of visualized experiments : JoVE, 2012.
51. Chen H, Monte E, Parvatiyar MS, Rosa-Garrido M, Franklin S, Vondriska TM. Structural considerations for chromatin state models with transcription as a functional readout.. FEBS letters, 2012.
52. Mitchell-Jordan S, Chen H, Franklin S, Stefani E, Bentolila LA, Vondriska TM. Features of endogenous cardiomyocyte chromatin revealed by super-resolution STED microscopy.. Journal of molecular and cellular cardiology, 2012.
53. Picha B, Thompson M, Vondriska TM. Preclinical trials: Keep 'reproducibility' in context.. Nature, 2012.
54. Franklin S, Chen H, Mitchell-Jordan S, Ren S, Wang Y, Vondriska TM. Quantitative analysis of the chromatin proteome in disease reveals remodeling principles and identifies high mobility group protein B2 as a regulator of hypertrophic growth.. Molecular & cellular proteomics : MCP, 2012.
55. Franklin S, Vondriska TM. Genomes, proteomes, and the central dogma.. Circulation. Cardiovascular genetics, 2011.
56. Li Y, Franklin S, Zhang MJ, Vondriska TM. Highly efficient purification of protein complexes from mammalian cells using a novel streptavidin-binding peptide and hexahistidine tandem tag system: application to Bruton's tyrosine kinase.. Protein science : a publication of the Protein Society, 2011.
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.. Molecular & cellular proteomics : MCP, 2010.
58. 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 the ischemic myocardium.. American journal of physiology. Heart and circulatory physiology, 2010.
59. Paulsson AK, Franklin S, Mitchell-Jordan SA, Ren S, Wang Y, Vondriska TM. Post-translational regulation of calsarcin-1 during pressure overload-induced cardiac hypertrophy.. Journal of molecular and cellular cardiology, 2010.
60. 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).. Proceedings of the National Academy of Sciences of the United States of America, 2009.
61. Lu G, Sun H, She P, Youn JY, Warburton S, Ping P, Vondriska TM, Cai H, Lynch CJ, Wang Y. Protein phosphatase 2Cm is a critical regulator of branched-chain amino acid catabolism in mice and cultured cells.. The Journal of clinical investigation, 2009.
62. Singh H, Warburton S, Vondriska TM, Khakh BS. Proteomics to identify proteins interacting with P2X2 ligand-gated cation channels.. Journal of visualized experiments : JoVE, 2009.
63. Qu Z, Vondriska TM. The effects of cascade length, kinetics and feedback loops on biological signal transduction dynamics in a simplified cascade model.. Physical biology, 2009.
64. Vondriska TM, Wang Y. A new (heat) shocking player in cardiac hypertrophy.. Circulation research, 2008.
65. Mitchell-Jordan SA, Holopainen T, Ren S, Wang S, Warburton S, Zhang MJ, Alitalo K, Wang Y, Vondriska TM. Loss of Bmx nonreceptor tyrosine kinase prevents pressure overload-induced cardiac hypertrophy.. Circulation research, 2008.
66. Yang L, Vondriska TM, Han Z, Maclellan WR, Weiss JN, Qu Z. Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.. BMC bioinformatics, 2008.
67. Maclellan WR, Wang Y, Vondriska TM, Weiss JN, Ping P. Proteomic insights into cardiac cell death and survival.. Proteomics. Clinical applications, 2008.
68. Zhang J, Liem DA, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Korge P, Drews O, Maclellan WR, Honda H, Weiss JN, Apweiler R, Ping P. Altered proteome biology of cardiac mitochondria under stress conditions.. Journal of proteome research, 2008.
69. Wang GW, Guo Y, Vondriska TM, Zhang J, Zhang S, Tsai LL, Zong NC, Bolli R, Bhatnagar A, Prabhu SD. Acrolein consumption exacerbates myocardial ischemic injury and blocks nitric oxide-induced PKCepsilon signaling and cardioprotection.. Journal of molecular and cellular cardiology, 2008.
70. Zhang J, Li X, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Liem DA, Yang JI, Korge P, Honda H, Weiss JN, Apweiler R, Ping P. Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria.. Proteomics, 2008.
71. 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.
72. Gugiu BG, Mouillesseaux K, Duong V, Herzog T, Hekimian A, Koroniak L, Vondriska TM, Watson AD. Protein targets of oxidized phospholipids in endothelial cells.. Journal of lipid research, 2007.
73. Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, 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).. Nature biotechnology, 2007.
74. Han Z, Vondriska TM, Yang L, Robb MacLellan W, Weiss JN, Qu Z. Signal transduction network motifs and biological memory.. Journal of theoretical biology, 2007.
75. Ping P, Vondriska TM, Creighton CJ, Gandhi TK, Yang Z, Menon R, Kwon MS, Cho SY, Drwal G, Kellmann M, Peri S, Suresh S, Gronborg M, Molina H, Chaerkady R, Rekha B, Shet AS, Gerszten RE, Wu H, Raftery M, Wasinger V, Schulz-Knappe P, Hanash SM, Paik YK, Hancock WS, States DJ, Omenn GS, Pandey A. A functional annotation of subproteomes in human plasma.. Proteomics, 2005.
76. Berhane BT, Zong C, Liem DA, Huang A, Le S, Edmondson RD, Jones RC, Qiao X, Whitelegge JP, Ping P, Vondriska TM. Cardiovascular-related proteins identified in human plasma by the HUPO Plasma Proteome Project pilot phase.. Proteomics, 2005.
77. Gomes AV, Zong C, Edmondson RD, Berhane BT, Wang GW, Le S, Young G, Zhang J, Vondriska TM, Whitelegge JP, Jones RC, Joshua IG, Thyparambil S, Pantaleon D, Qiao J, Loo J, Ping P. The murine cardiac 26S proteasome: an organelle awaiting exploration.. Annals of the New York Academy of Sciences, 2005.
78. Zhang J, Baines CP, Zong C, Cardwell EM, Wang G, Vondriska TM, Ping P. Functional proteomic analysis of a three-tier PKCepsilon-Akt-eNOS signaling module in cardiac protection.. American journal of physiology. Heart and circulatory physiology, 2004.
79. Wang G, Liem DA, Vondriska TM, Honda HM, Korge P, Pantaleon DM, Qiao X, Wang Y, Weiss JN, Ping P. Nitric oxide donors protect murine myocardium against infarction via modulation of mitochondrial permeability transition.. American journal of physiology. Heart and circulatory physiology, 2004.
80. MacLellan WR, Ping P, Vondriska T. Heart disease leaves its mark: proteomics-based biosignatures in acute coronary syndromes.. Journal of the American College of Cardiology, 2004.
81. Vondriska TM, Pass JM, Ping P. Scaffold proteins and assembly of multiprotein signaling complexes.. Journal of molecular and cellular cardiology, 2004.
82. Zhang J, Ping P, Wang GW, Lu M, Pantaleon D, Tang XL, Bolli R, Vondriska TM. Bmx, a member of the Tec family of nonreceptor tyrosine kinases, is a novel participant in pharmacological cardioprotection.. American journal of physiology. Heart and circulatory physiology, 2004.
83. Vondriska TM, Ping P. Multiprotein signaling complexes and regulation of cardiac phenotype.. Journal of molecular and cellular cardiology, 2003.
84. Zhang J, Ping P, Vondriska TM, Tang XL, Wang GW, Cardwell EM, Bolli R. Cardioprotection involves activation of NF-kappa B via PKC-dependent tyrosine and serine phosphorylation of I kappa B-alpha.. American journal of physiology. Heart and circulatory physiology, 2003.
85. Ping P, Baines CP, Gu Y, Prabhu SD, Zhang J, Tsai LL, Cardwell E, Zong NC, Vondriska TM, Korge P, Bhatnagar A, Wang GW. Cardiac toxic effects of trans-2-hexenal are mediated by induction of cardiomyocyte apoptotic pathways.. Cardiovascular toxicology, 2003.
86. Pass JM, Zhang J, Vondriska TM, Ping P. Functional proteomic analysis of the protein kinase C signaling system.. Methods in molecular biology (Clifton, N.J.), 2003.
87. Tang XL, Kodani E, Takano H, Hill M, Shinmura K, Vondriska TM, Ping P, Bolli R. Protein tyrosine kinase signaling is necessary for NO donor-induced late preconditioning against myocardial stunning.. American journal of physiology. Heart and circulatory physiology, 2002.
88. Edmondson RD, Vondriska TM, Biederman KJ, Zhang J, Jones RC, Zheng Y, Allen DL, Xiu JX, Cardwell EM, Pisano MR, Ping P. Protein kinase C epsilon signaling complexes include metabolism- and transcription/translation-related proteins: complimentary separation techniques with LC/MS/MS.. Molecular & cellular proteomics : MCP, 2002.
89. Ping P, Song C, Zhang J, Guo Y, Cao X, Li RC, Wu W, Vondriska TM, Pass JM, Tang XL, Pierce WM, Bolli R. Formation of protein kinase C(epsilon)-Lck signaling modules confers cardioprotection.. The Journal of clinical investigation, 2002.