Publications

Note: *corresponding author(s); † undergraduate students; †† College of Wooster undergraduate students;

Preprints (BioRXiv and/or under review):
- Deritei D, Anamika WJ, Zhou X, Silverman EK*, Ravasz Regan E*, Glass K*, HHIP’s Dynamic Role in Epithelial Wound Healing Reveals a Potential Mechanism of COPD Susceptibility, BioRXiv:2024.09.05.611545, 2024.

Peer Reviewed Articles
1. Sizek H††, Deritei D, Fleig K††, Harris M††, Regan PL, Glass K, Ravasz Regan E*, Unlocking Mitochondrial Dysfunction-Associated Senescence (MiDAS) with NAD⁺ – a Boolean Model of Mitochondrial Dynamics and Cell Cycle Control, Translational Oncology 49:102084, 2024 (special issue “Non-genetic heterogeneity and adaptive mechanisms in cancer evolution and drug resistance“).
2. Sullivan E††, Harris M††, Bhatnagar A††, Guberman E††, Zonfa I††, Ravasz Regan E*, Boolean modeling of mechanosensitive Epithelial to Mesenchymal Transition and its reversal, iScience 26(4): 106321, 2023.
3. Zakirov B, Charalambous G, Thuret R, Aspalter I. M., Van-Vuuren K, Mead T., Harrington K., Ravasz Regan E, Herbert S. P., Bentley K., Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo, Philosophical Transactions of the Royal Society B, 376: 20190753, 2021.
4. Guberman E ††, H. Sherief H ††, Ravasz Regan E*, Boolean model of anchorage dependence and contact inhibition points to coordinated inhibition but semi-independent induction of proliferation and migration, Computational and Structural Biotechnology Journal 18, 2145-2165, 2020.
5. Deritei D, Rozum J, Ravasz Regan E, Albert R, A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpoint, Scientific Reports, 9, 16430, 2019.
6. Sizek H ††, Hamel A ††, Deritei D, Campbell S ††, Ravasz Regan E*, Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K. PLoS Computational Biology, 15(3): e1006402, 2019.
7. Wade A ††, Lin CH, Kurkul C, Ravasz Regan E, Johnson RM, Combined toxicity of insecticides and fungicides applied to California almond orchards to honey bee larvae and adults. Insects, 10(1), 20, 2019.
8. Venkatraman L, Ravasz Regan E, Bentley K, Time to Decide? Dynamical Analysis Predicts Partial Tip/Stalk Patterning States Arise during Angiogenesis, PLOS One, 11(11): e0166489, 2016.
9. Deritei D †, Aird WC, Ercsey-Ravasz MM, Ravasz Regan E*, Principles of dynamical modularity in biological regulatory networks, Scientific Reports 2016; 6:21957.
10. Yuan L, Chan GC, Beeler D, Janes L, Spokes KC, Dharaneeswaran H, Mojiri A, Adams WJ, Sciu- to T, Garcia-Cardeña G, Molema G, Kang PM, Jahroudi N, Marsden PA, Dvorak A, Regan ER, Aird WC, Ravasz Regan E*, Aird WC*, A role of stochastic phenotype switching in generating mosaic endothelial cell heterogeneity, Nature Communications 2016; 7:10160. (Citations: WoS – 4, Google Scholar – 7)
11. Moser J, Heeringa P, Jongman RM, Zwiers PJ, Niemarkt AE, Yan R, de Graaf IA, Li R, Ravasz Regan E, Kümpers P, Aird WC, van Nieuw Amerongen GP, Zijlstra JG, Molema G, van Meurs M, Intracellular RIG-I Signaling Regulates TLR4-independent Endothelial Inflammatory Responses to Endotoxin, Journal of Immunology 2016; 1501819.
12. Okada Y, Naruse H, Tanaka T, Funahashi N, Ravasz Regan E, Yamakawa K, Hino N, Ishimoto K, Doi T, Aird WC, Expression of the Robo4 receptor in endothelial cells is regulated by two AP-1 protein complexes, Biochemical and Biophysical Research Communications 2015; S0006-291X(15):30729-4.
13. H. Dharaneeswaran, R. Abid, L. Yuan, D. Dupuis, D. Beeler, KC Spokes, L. Janes, T. Sciuto, P. Kang, SC. Jaminet, A. Dvorak, M.A. Grant, E. Ravasz Regan, W. C. Aird, FoxO1-mediated Activation of Akt plays a critical role in vascular homeostasis, Circulation Research 115, 238-51, 2014;
14. Bentley K, Philippides A, Ravasz Regan E, Do Endothelial Cells Dream of Eclectic Shape?, Developmental Cell 29, 146-158 (2014);
15. Dávid Deritei † , Zsolt Lázár, István Papp †, Ferenc Járai-Szabó, Robert Sumi †, Levente Varga †, Erzsébet Ravasz Regan, Mária-Magdolna Ercsey-Ravasz, Community detection by graph Voronoi diagrams, New Journal of Physics 16, 063007, 2014; Video Abstract
16. K. Bentley, K. Harrington, E. Ravasz Regan, Can active perception generate bistability? Heterogeneous collective dynamics and vascular patterning, ALIFE 14: The Fourteenth International Conference on the Synthesis and Simulation of Living Systems14, 328-335, 2014;
17. C. Priolo, S. Pyne, J. Rose, E. Ravasz Regan, G. Zadra, C. Photopoulos, S. Cacciatore, D. Schultz, N. Scaglia, J. McDunn, A. De-Marzo, M. Loda, AKT1 and MYC Induce Distinctive Metabolic Fingerprints in Human Prostate Cancer, Cancer Research, 74:7198-204, 2014.
18. Kurniati NF, Jongman RM, von Hagen F, Spokes KC, Moser J, Ravasz Regan E, Krenning G, Moonen JRAJ, Harmsen MC, Struys MMRF, Hammes HP, Zijlstra JG, Aird WC, Heeringa P, Molema G, van Meurs M. The flow dependency of Tie2 expression in endotoxemia, Intensive Care Medicine 39, 1262-1271, 2013;
19. Ravasz Regan E*, Aird WC. Dynamical systems approach to endothelial heterogeneity, Circulation Research, 111, 110-130 (2012);
20. Liu J, Yuan L, Molema G, Regan E, Janes L, Beeler D, Spokes KC, Minami T, Oettgen P, Aird WC, Vascular bed-specific regulation of the von Willebrand factor promoter in the heart and skeletal muscle, Blood 117(1):342-51 (2011);
21. Jin E, Liu J, Suehiro J, Okada Y, Yuan L, Nikolova-Krstevski V, Yano K, Janes L, Beeler D, Spokes KC, Regan E, Shih SC, Oettgen P, Minami T, Aird WC. Differential Roles for ETS, CREB and EGR Binding Sites in Mediating VEGF Receptor 1 Expression in Vivo, Blood 114(27):5557-66 (2009).
22. E. Ravasz, A.-L. Barabási, Hierarchical organization in complex networks, Phys. Rev. E, 67, 026112 (2003);
23. S. Y. Gerdes, M. D. Scholle, J. W. Campbell, G. Balázsi, E. Ravasz, M. D. Daugherty, A. L. Somera, N. C. Kyrpides, I. Anderson, M. S. Gelfand, A. Bhattacharya, V. Kapatral, M. D’Souza, M. V. Baev, Y. Grechkin, F. Mseeh, M. Y. Fonstein, R. Overbeek, A.-L. Barabási, Z. N. Oltvai, and A. L. Osterman, Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655, Journal of Bacteriology, 185, 5673 (2003);
24. E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai and A.-L. Barabási, Hierarchical organization of modularity in metabolic networks, Science, 297, 1551 (2002); Supplementaty Material.
25. I. Farkas, I. Derényi, H. Jeong, Z. Néda, Z. N. Oltvai, E. Ravasz, A. Schubert, A.-L. Barabási and T. Vicsek, Networks in life: Scaling properties and eigenvalue spectra, Physica A, 314, 25 (2002);
26. A.-L. Barabási, H. Jeong, Z. Néda, E. Ravasz, A. Schubert and T. Vicsek, Evolution of the social network of scientific collaborations, Physica A, 311, 590 (2002);
27. A.-L. Barabási, E. Ravasz and T. Vicsek, Deterministic scale-free networks, Physica A, 299, 559 (2001);
28. Z. Néda, E. Ravasz, T. Vicsek, Y. Brechet, and A.-L. Barabási, The sound of many hands clapping, Nature, 403, 850 (2000);
29. Z. Néda, E. Ravasz, T. Vicsek, Y. Brechet, and A.-L. Barabási, Physics of the rhythmic applause, Phys. Rev. E, 61, 6987 (2000);
30. Z. Néda, Á. Rusz, E. Ravasz, P. Lakdawala, and P. M. Gade, Spatial stochastic resonance in one-dimensional Ising systems, Phys. Rev. E, 60, R3463 (1999);

Book chapters:
1. Ravasz Regan E, Stochastic phenotypic switching in endothelial cell heterogeneity. In: Levine H (ed). Phenotypic Switching: Implications in Biology and Medicine; Academic Press; 2020, 0128179961 (ISBN-13: 978-0-128-17996-3).
2. Ravasz Regan E. Hierarchical Modularity in Biological Networks. In: Buchanan, Calderelli, De Los Rios, Rao and Vendruscolo (eds). Networks in Cell Biology. Cambridge University Press; 2010 (SBN-13: 978-0-521-88273-6).
3. Ravasz Regan E. Networks: Structure and Dynamics. In: Meyers RA, editor in chief. Encyclopedia of Complexity and System Science. Springer; 2009 (SBN-13: 978-0-387-75888-6).
4. Ravasz E. Detecting hierarchical modularity in biological networks. In: McDermott J, Samudrala R, Bumgarner R, Montgomery K, editors. Computational Systems Biology. Humana Press; 2009. p. 145-160 (SBN-10: 1588299058).
5. S. Wuchty, Ravasz E. and A.-L. Barabási, The Architecture of Biological Networks, in: T.S. Deisboeck, J. Yasha Kresh and T.B. Kepler (eds.), Complex Systems in Biomedicine, Kluwer Academic Publishing, New York (2005), ISBN: 0306477874.

Proceedings:
1. A.-L. Barabási, Z. Dezső, Ravasz E., S. H. Yook, and Z. N. Oltvai, Scale-free and hierarchical structures in complex networks, AIP Conf. Proc. 661, 1 (2003); MODELING OF COMPLEX SYSTEMS: Seventh Granada Lectures, Granada, Spain, 2002, Melville, New York;
2. A.-L. Barabási, Ravasz E., and Z. N. Oltvai, Hierarchical Organization of Modularity in Complex Networks, Lecture Notes in Physics 625, 46 (2003); R. Pastor-Satorras, J.M. Rubi,and A. Diaz-Guilera (eds.), Proc. of the XVIII Sitges Conference on Statistical Mechanics, Sitges, Barcelona, Spain, 2002, Springer, Berlin;

Archives

Meta