Systems biology of signal transduction in cancer
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Department of Chemistry
Towards theoretical systems biology and a system view of medicine we seek to provide a description of molecular -e.g., kinase-signaling networks that is intermediate between biochemical components and a global view and that highlights predictive ability. It is desired to present not only a steady state but also a time evolving portrayal of the network dynamics. The approach inherently allows for the inevitable cellular fluctuations and offers different levels of coarse graining -e.g., proteins, pathways, networks - of the description. At each level we provide the minimal set of informative constraints that recover the state of the components. Such quantitative insight into the state of diseased cells is intended to aid the development of effective diagnostics and tailored intervention. As a practical consideration, the input takes advantage of the large volumes of data produced by the current methods of systems biology. A secondary objective of our program is the use of signal transduction networks as models for robust and error correcting concatenated logic networks.
Gross Ayelet, Levine Raphael D Surprisal analysis of transcripts expression levels in the presence of noise: a reliable determination of the onset of a tumor phenotype. PloS one. 2013; 8(4): e61554.
Wang Jun, Tham Douglas, Wei Wei, Shin Young Shik, Ma Chao, Ahmad Habib, Shi Qihui, Yu Jenkan, Levine Raphael D, Heath James R Quantitating cell-cell interaction functions with applications to glioblastoma multiforme cancer cells. Nano letters. 2012; 12(12): 6101-6.
Kravchenko-Balasha N, Remacle, F. Gross, A., Rotter, Varda, Levitzki Alexander, Levine, R.D. On a fundamental structure of gene networks in living cells. :. Proceedings of the National Academy of Sciences of the United States of America 2012; 109(12): 4702-4707..
Remacle F, Graeber TG, Levine RD (2011) Whose Entropy: A Maximal Entropy Analysis of Phosphorylation Signaling. . Journal of Statistical Physics 2011; 144((2)): 429-442.
Shin Young Shik, Remacle F, Fan Rong, Hwang Kiwook, Wei Wei, Ahmad Habib, Levine R D, Heath James R Protein signaling networks from single cell fluctuations and information theory profiling. Biophysical journal. 2011; 100(10): 2378-86.
Kravchenko-Balasha Nataly, Remacle F, Gross Ayelet, Rotter Varda, Levitzki Alexander, Levine R D Convergence of logic of cellular regulation in different premalignant cells by an information theoretic approach. BMC systems biology. 2011; 5(17): 42.
Muskatel B H, Remacle F, Thiemens Mark H, Levine R D On the strong and selective isotope effect in the UV excitation of N2 with implications toward the nebula and Martian atmosphere. Proceedings of the National Academy of Sciences of the United States of America. 2011; 108(15): 6020-5.
F. Remacle, Nataly Kravchenko-Balasha, Alexander Levitzki, and R. D. Levine Information-theoretic analysis of phenotype changes in early stages of carcinogenesis. PNAS. 2010; 107(22): 10324-9.
Graeber TG, Heath JR, Skaggs BJ, Phelps ME, Remacle F, Levine RD Maximal entropy inference of oncogenicity from phosphorylation signaling. Proc Natl Acad Sci U S A. 2010; 107(13): 6112-7.
Periyasamy G., Levine R. D., Remacle F. Redox-Executed Logic Operations through the Reversible Voltammetric Response Characteristics of Electroactive Self-Assembled Monolayers . Australian Journal of Chemistry. 2010; 63(2): 173-183 .
Klein M., Mol J. A., Verduijn J., Levine R. D., et al. Ternary logic implemented on a single dopant atom field effect silicon transistor. APPLIED PHYSICS LETTERS. 2010; 96(4): .
Elbaz Johann, Lioubashevski Oleg, Wang Fuan, Remacle FranÃ§oise, Levine Raphael D, Willner Itamar DNA computing circuits using libraries of DNAzyme subunits. Nature nanotechnology. 2010; 5(6): 417-22.
Klein, M. Lansbergen, G. P. Mol, J. A. Rogge, S. Levine, R. D. Remacle, F. Reconfigurable Logic Devices on a Single Dopant Atom-Operation up to a Full Adder by Using Electrical Spectroscopy. Chemphyschem. 2009; 10(1): 162-173.
Kuznetz, O. Salman, H. Eichen, Y. Remacle, F. Levine, R. D. Speiser, S. All optical full adder based on intramolecular electronic energy transfer in the rhodamine-azulene bichromophoric system. Journal of Physical Chemistry C. 2008; 112(40): 15880-15885.
Torres, E. A. Kompa, K. L. Remacle, F. Levine, R. D. Ultrafast vibrational spectroscopy and relaxation in polyatomic molecules: Potential for molecular parallel computing. Chemical Physics. 2008; 347(1-3): 531-545.
Remacle, F. Kienberger, R. Krausz, F. Levine, R. D. On the feasibility of an ultrafast purely electronic reorganization in lithium hydride. Chemical Physics. 2007; 338(2-3): 342-347.
Remacle, F. Levine, R. D. Time-resolved electrochemical spectroscopy of charge migration in molecular wires: Computational evidence for rich electronic dynamics. Journal of Physical Chemistry C. 2007; 111(5): 2301-2309.
Remacle, F. Levine, R. D. Towards parallel computing: representation of a linear finite state digital logic machine by a molecular relaxation process. European Physical Journal D. 2007; 42(1): 49-59.
Klein, M. Rogge, S. Remacle, F. Levine, R. D. Transcending binary logic by gating three coupled quantum dots. Nano Letters. 2007; 7(9): 2795-2799.
Gross, A. Levine, R. D. A mechanical representation of entropy for a large finite system. Journal of Chemical Physics. 2006; 125(14): 9.
Remacle, F. Levine, R. D. An electronic time scale in chemistry. Proceedings of the National Academy of Sciences of the United States of America. 2006; 103(18): 6793-6798.
Remacle, F. Heath, J. R. Levine, R. D. Electrical addressing of confined quantum systems for quasiclassical computation and finite state logic machines. Proceedings of the National Academy of Sciences of the United States of America. 2005; 102(16): 5653-5658.
Somorjai, G. A. Levine, R. D. The changing landscape of physical chemistry at the beginning of the 21st century. Journal of Physical Chemistry B. 2005; 109(19): 9853-9854.