Formal Methods in Macro-Biology

This talk discusses the opportunities and research challenges faced in the modeling, analysis and control of the human heart. Consisting of more than 4 billion communication nodes, interconnected through a very sophisticated communication structure, this ultimate cyberphysical system achieves with an astonishing reliability, the electric synchronization and the mechanical contraction of all of its nodes, in order to pump blood, during what is commonly known as a heart beat. However, even this cyber-physical system, engineered by billion years of evolution is fallible. Predicting and controlling its failure is a great challenge for our society. Fast Enumeration of Smallest Metabolic Engineering Strategies in Genome-Scale Networks

[1]  Andrew C. Myers,et al.  Language-based information-flow security , 2003, IEEE J. Sel. Areas Commun..

[2]  S. Shankar Sastry,et al.  O-Minimal Hybrid Systems , 2000, Math. Control. Signals Syst..

[3]  Ashish Tiwari,et al.  Series of Abstractions for Hybrid Automata , 2002, HSCC.

[4]  Thomas A. Henzinger,et al.  The theory of hybrid automata , 1996, Proceedings 11th Annual IEEE Symposium on Logic in Computer Science.

[5]  M. Malim,et al.  Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection , 2013, Nature.

[6]  Nancy A. Lynch,et al.  Hybrid I/O automata , 1995, Inf. Comput..

[7]  J. Meseguer,et al.  Security Policies and Security Models , 1982, 1982 IEEE Symposium on Security and Privacy.

[8]  C. Granger,et al.  Intramuscular interferon beta‐1a for disease progression in relapsing multiple sclerosis , 1996, Annals of neurology.

[9]  François Fages,et al.  Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures , 2011, Theor. Comput. Sci..

[10]  Riccardo Focardi,et al.  Bisimulation and Unwinding for Verifying Possibilistic Security Properties , 2002, VMCAI.

[11]  Oded Maler,et al.  Robust Satisfaction of Temporal Logic over Real-Valued Signals , 2010, FORMATS.

[12]  F. Fages,et al.  Long-term model predictive control of gene expression at the population and single-cell levels , 2012, Proceedings of the National Academy of Sciences.

[13]  Thomas A. Henzinger,et al.  Hybrid Automata: An Algorithmic Approach to the Specification and Verification of Hybrid Systems , 1992, Hybrid Systems.

[14]  Carla Piazza,et al.  Unwinding biological systems , 2015, Theor. Comput. Sci..

[15]  Carla Piazza,et al.  Inclusion dynamics hybrid automata , 2008, Inf. Comput..

[16]  Robert E. Tarjan,et al.  Three Partition Refinement Algorithms , 1987, SIAM J. Comput..

[17]  Riccardo Focardi,et al.  Information flow security in dynamic contexts , 2006, J. Comput. Secur..

[18]  C. Tomlin,et al.  Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-Notch protein signalling. , 2004, Systems biology.

[19]  J. Manning,et al.  Alpha interferon for induction of remission in hairy-cell leukemia. , 1984, The New England journal of medicine.

[20]  K. Melén,et al.  Inflammatory responses in influenza A virus infection. , 2000, Vaccine.

[21]  Zohar Manna,et al.  From Timed to Hybrid Systems , 1991, REX Workshop.

[22]  Claire J. Tomlin,et al.  Lateral Inhibition through Delta-Notch Signaling: A Piecewise Affine Hybrid Model , 2001, HSCC.

[23]  Ezio Bartocci,et al.  On the Robustness of Temporal Properties for Stochastic Models , 2013, HSB.

[24]  Rajeev Alur,et al.  A Theory of Timed Automata , 1994, Theor. Comput. Sci..

[25]  F. Dianzani,et al.  Tissue culture models of in vivo interferon production and action. , 1978, Advances in experimental medicine and biology.

[26]  Roberto Gorrieri,et al.  A Taxonomy of Security Properties for Process Algebras , 1995, J. Comput. Secur..

[27]  H. Kitano.  Towards a theory of biological robustness , 2007, Molecular systems biology.

[28]  Andreas Handel,et al.  Neuraminidase Inhibitor Resistance in Influenza: Assessing the Danger of Its Generation and Spread , 2007, PLoS Comput. Biol..

[29]  Carla Piazza,et al.  Compositional information flow security for concurrent programs , 2007, J. Comput. Secur..

[30]  Robin Milner,et al.  A Calculus of Communicating Systems , 1980, Lecture Notes in Computer Science.

[31]  Fred Kröger,et al.  Temporal Logic of Programs , 1987, EATCS Monographs on Theoretical Computer Science.

[32]  Ashish Tiwari,et al.  Automated Symbolic Reachability Analysis; with Application to Delta-Notch Signaling Automata , 2003, HSCC.

[33]  Lubos Brim,et al.  Robustness Analysis for Value-Freezing Signal Temporal Logic , 2013, HSB.

[34]  Amir Pnueli.  The Temporal Semantics of Concurrent Programs , 1981, Theor. Comput. Sci..

[35]  Carla Piazza,et al.  Hybrid Automata and ε-Analysis on a Neural Oscillator , 2012, HSB.

[36]  Thomas Ferrère,et al.  Efficient Robust Monitoring for STL , 2013, CAV.

[37]  Peter Y. A. Ryan,et al.  Process algebra and non-interference , 1999, Proceedings of the 12th IEEE Computer Security Foundations Workshop.

[38]  George J. Pappas,et al.  Robustness of Temporal Logic Specifications , 2006, FATES/RV.

[39]  Stephan Merz,et al.  Model Checking , 2000 .

[40]  Niall Johnson,et al.  Updating the Accounts: Global Mortality of the 1918-1920 "Spanish" Influenza Pandemic , 2002, Bulletin of the history of medicine.

[41]  Jie-Hong Roland Jiang,et al.  On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models , 2013, CMSB.

[42]  J. Taubenberger,et al.  Influenza : the Mother of All Pandemics , 2022 .

[43]  Ann Cullinane,et al.  Dynamics of Influenza Virus Infection and Pathology , 2010, Journal of Virology.

[44]  Hiroaki Kitano,et al.  Biological robustness , 2008, Nature Reviews Genetics.