Chemistry and Biochemistry,
Molecular & Medical Pharmacology
Biochemistry, Biophysics & Structural Biology GPB Home Area,
California NanoSystems Institute,
JCCC Signal Transduction and Therapeutics Program Area,
Molecular Pharmacology GPB Home Area
Work Email Address:
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
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.
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.
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
Remacle F, Graeber TG, Levine RD (2011) Whose Entropy: A Maximal Entropy Analysis of Phosphorylation Signaling. .
Journal of Statistical Physics
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.
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
F. Remacle, Nataly Kravchenko-Balasha, Alexander Levitzki, and R. D. Levine Information-theoretic analysis of phenotype changes in early stages of carcinogenesis.
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
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
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
Elbaz Johann, Lioubashevski Oleg, Wang Fuan, Remacle Françoise, Levine Raphael D, Willner Itamar DNA computing circuits using libraries of DNAzyme subunits.
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.
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
Torres, E. A. Kompa, K. L. Remacle, F. Levine, R. D. Ultrafast vibrational spectroscopy and relaxation in polyatomic molecules: Potential for molecular parallel computing.
Remacle, F. Kienberger, R. Krausz, F. Levine, R. D. On the feasibility of an ultrafast purely electronic reorganization in lithium hydride.
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
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
Klein, M. Rogge, S. Remacle, F. Levine, R. D. Transcending binary logic by gating three coupled quantum dots.
Gross, A. Levine, R. D. A mechanical representation of entropy for a large finite system.
Journal of Chemical Physics
Somorjai, G. A. Levine, R. D. The changing landscape of physical chemistry at the beginning of the 21st century.
Journal of Physical Chemistry B