CURRICULUM VITAE

NAME

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P.S. THIAGARAJAN

DATE OF BIRTH

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09.11.1948

ADDRESS

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Laboratory of Systems Pharmacology Harvard Medical School Armenise 109A, 200 Longwood Avenue Boston, MA02115, USA Phone: (1)-650-305-9290 E-mail: [email protected]

RESEARCH INTERESTS: • Computational systems biology • Modeling and analysis of probabilistic, hybrid dynamical systems EDUCATION: (i) B.Tech. (Electronics), Indian Institute of Technology (IIT), Madras (1970). (ii) Ph.D. (Computer Science), Rice University, Houston, Texas, U.S.A. (1973). CAREER POSITIONS: • Research Associate, Laboratory for Computer Science, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, Mass., U.S.A. (1973-75). • Research Staff Scientist, Gesellschaft f¨ ur Mathematik and Datenverarbeitung, St. Augustin, Germany (1975-83) • Lektor (Associate Professor), Computer Science Department, Aarhus University, Aarhus, Denmark (1983-86). 1

• Associate Professor, The Institute of Mathematical Sciences, Chennai, India (1986-89). • Professor, Chennai Mathematical Institute (initially known as SPIC Mathematical Institute), Chennai, India (1989- 2001). • Professor, Dept. of Computer Science, National University of Singapore, Singapore (2001 -2015) Senior Faculty Member, NUS Graduate School for Integrative Sciences and Engineering (NGS) (2003 -2015) VISITING Professorships: • Leiden University, Leiden, The Netherlands • University of Canterbury, Christ Church, New Zealand • DIMACS Center (during the Special Year on Logic and Algorithms), Rutgers university, NJ, USA. • Aarhus University, Aarhus, Denmark. • Ecole Normale Superioure de Cachan, Paris, France. • Georgia Institute of Technology, Atlanta, Georgia, USA. • Systems biology department, Harvard Medical School, Boston, USA • Technical University of Munich, Munich, Germany • Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA (Current) MEMBERSHIP IN PROFESSIONAL SOCIETIES: • A Fellow of the Indian Academy of Sciences. • A Fellow of the Indian National Academy of Sciences.

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PH.D STUDENTS (PAST) • Madhavan Mukund, Aarhus University, Aarhus, Denmark Thesis: Logics and Models for Concurrency (1992) Co-Supervisor: M. Nielsen (Currently Professor and Dean of Studies, Chennai Mathematical Institute, Chennai, India) • Peter Hoogers, Leiden University Thesis: Behavioral Aspects of Petri Nets (1994) Co-Supervisor: G. Rozenberg • Jesper Gulmann Henriksen, BRICS, Aarhus University, Aarhus, Denmark Thesis: Logics and Automata for Verification: Expressiveness and Decidability Issues (2000). Co-Supervisor: M. Nielsen • P. Madhusudan,The Institute of Mathematical Sciences, Chennai Thesis: Control and Synthesis of Open Reactive Systems (2002). Co-Supervisor: R. Ramanujam (Currently a tenured Associate Professor at the University of Illinois, Urbana-Champagne) • Deepak D’Souza, Chennai Mathematical Institute, Chennai (2000) Thesis : A Logical Study of Distributed Timed Automata. (Currently a tenured Associate Professor at the Indian Institute of Science, Bangalore, India) • Yang Shaofa, School of Computing, National University of Singapore (2006) Thesis: Controller Synthesis for Reactive systems in Distributed, Real Time and Hybrid Settings. (Currently a tenured Associate Professor at the Institute for Software, The Chinese Academy of Sciences, Beijing, China) • Kathy Nguyen Dang (SOC, NUS) Thesis: A design framework for reactive and time-triggered embedded systems via the UML-SystemC bridge 3

• Phan Thi Xuan Linh, SOC, NUS Thesis: Formal modeling and analysis of streaming applications. (Currently a Research Assistant Professor at the University of Pennsylvania, Philadelphia, USA) • Koh Yeow Nam, Geoffery, NGS, NUS Thesis: Pathway model decomposition and composition techniques for parameter estimation. (Currently Vice-President(Research Support), WorldQuant LLC, Singapore) • Liu Bing, NGS, NUS Thesis: Probabilistic approximation and analysis techniques for biopathways models. (Currently a Post-Doctoral Fellow at the University of Pittsburg, Pittsburgh, USA) • Ooi Nick Sern, Brandon, Graduate Programme in Bio-Engineering, NUS (Co-Supervised with Dr. Phan Toan Thang, Dept. of Surgery & Division of Bio-Engineering, NUS) Thesis: Molecular and Computational Approaches to Understanding Keloid Scarring. (Currently a Lecturer at the Republic Polytechnic, Singapore) • Sucheendra Palanippan, SOC, NUS Thesis: Probabilistic Verification Techniques for Bio-Pathways Models. (Currently a Post-Doctoral Fellow at IRISA, Rennes, France) • Wang Junjie, Singapore-MIT Alliance program (Co-Supervised with Hanry Yu, Dept. of Physiology, Faculty of Medicine and Jacob White, Dept. of Electrical Engineering and Computer Science, MIT). Thesis: A Diffusion Model for Plasmin-TSP1 Activation of TGF-β1 in Liver Fibrosis. (Currently involved in a start-up in Shangai, China as a co-founder). • Benjamin Gyori, NGS, NUS (Co-supervised with David Hsu, Dept. of Computer Science, NUS) Thesis: Probabilistic approaches to modeling uncertainty in biological 4

pathways. (Currently a Post-doctoral Fellow at Harvard Medical School, Systems Biology department (Sorger Lab)). • Gireedhar Venkatachalam, NGS, NUS (Co-supervised with Marie-Veronique Clement, Dept. of Biochemistry, Faculty of Medicine, NUS) Thesis: Deciphering the molecular dynamics involved in the induction of senescence in cells exposed to subtoxic levels of oxidative stress. (Currently a Post-doctoral Fellow at the Institute for Molecular Cell Biology, Singapore). PH.D STUDENTS (CURRENT) • Ramanathan Rajendiran, SOC, NUS Topic: Statistical model checking of multi-mode signaling pathways using GPU platforms. SELECTED UNIVERSITY ACTIVITIES • Served as the area leader for systems and networks; Chaired the recruitment committee of the department for many years; Served multiple terms on the faculty promotion and tenure committee; Served a 3-year term as Vice-Dean(Research) of SOC; Currently chairing the search committee (again), a member of the executive committee of the Dept. of Computer science and the teaching evaluation committee. • Was a member of the executive committee, of the Board of Examiners and the faculty selection committee of the NUS Graduate School for Integrative Sciences and Engineering (NGS) (www.nus.edu.sg/ngs/). This is a university level graduate school with approximately 430 PhD students devoted to inter-disciplinary research. SELECTED PROFESSIONAL ACTIVITIES • Returned to India in 1983 to found the computer science group at the Institute of Mathematical Sciences (IMSc), Chennai, India (www.imsc.res.in). 5

• Co-founded the Chennai Mathematical Institute (CMI) in 1986 and developed its computer science teaching and research programme (www.cmi.ac.in). At present, CMI is the best institution in India for undergraduate education in Mathematics. Further, IMSc and CMI (which work together closely) constitute the strongest grouping of faculty and PhD students in theoretical computer science in India. • Currently a member of the academic council of CMI. • Served long terms on the editorial boards of the journals Theoretical Compute Science and International Journal of Foundations of Computer Science. Currently a member of the editorial board of Real-Time Systems journal and Transactions on Petri Nets and Other Models of Concurrency.

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PUBLICATIONS Edited Volumes • Jean-Francois Raskin and P.S. Thiagarajan: Formal Modeling and Analysis of Timed Systems, Proc. of the 5th International Conference on Formal Modeling and Analysis of Timed Systems (FORMATS 2007), Springer Lecture Notes in Computer Science 4763 (2007) • S. Donatelli and P.S. Thiagarajan: Petri Nets and Other Models of Concurrency, Proc. of the 27th International Conference on the applications and Theory of Petri Nets (ICATPN’06), Springer Lecture Notes in Computer Science 4024, (2006). • P. S. Thiagarajan, Roland H. C. Yap: Advances in Computing Science, Proc. of the 5th Asian Computing Science Conference (Asian’99), Springer Lecture Notes in Computer Science (1999) • P. S. Thiagarajan: Foundations of Software Technology and Theoretical Computer Science, Proc. of the 15th FST&TCS Conference, Springer Lecture Notes in Computer Science 1026 (1995) • P. S. Thiagarajan: Foundations of Software Technology and Theoretical Computer Science, Proc. of the 14th FST&TCS Conference, Springer Lecture Notes in Computer Science 880 (1994) Journal Articles (Computational systems biology) • Junjie Wang, Lisa Tucker-Kellog, Inn Chuan Ng, Ruirui Jia, P.S. Thiagarajan, Jacob White, Hanry Yu: The self-limiting dynamics of TGF-β signaling in silico and in vitro, with negative feedback through PP1MA upregulation, PLOS Computational Biology, 10(6) (2014) • Benjamin M. Gyori, Gireedhar Venkatachalam, P.S. Thiagarajan, David Hsu, Marie-Veronique Clement: OpenComet: An automated tool for comet image analysis. Redox Biology 2014; 2 (2014).

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• Chuan Hock Koh, Sucheendra K. Palaniappan, P. S. Thiagarajan, and Limsoon Wong. Improved statistical model checking methods for pathway analysis, BMC Bioinformatics (2012) • (invited) Sucheendra Kumar Palaniappan, S. Akshay, Bing Liu, B. Genest and P.S. Thiagarajan: A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathways Application, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5) (2012), pp. 1352-1365 • Bing Liu, Andrei Hagiescu, Sucheendra K. Palaniappan, Bipasa Chattopadhyay, Zheng Cui, Weng-Fai Wong and P.S. Thiagarajan: Approximate Probabilistic Analysis of Biopathways Dynamics, Bioinformatics, 28(11) (2012), pp. 1508-11516 • Bing Liu and P.S. Thiagarajan: Modeling and Analysis of Biopathways Dynamics, (review article), Journal of Bioinformatics and Computational Biology, 10(4) (2012). • Bing Liu, Jing Zhang, Pei Yi Tan, David Hsu, Anna M. Blom, Benjamin Leong, Sunil Sethi, Bow Ho, Jeak Leak Ding and P.S. Thiagarajan: A Combined Computational and Experimental Study of the Regulatory Mechanisms of the Complement System, PLoS Computational Biology, 7(1) (2011). • Geoffrey Koh, David Hsu and P.S. Thiagarajan: Components based Construction of Bio-Pathways Models. Theoretical Computer Science (Invited paper in a special issue on “Biochemical Networks”), 412(26) (2011) • (invited) Bing Liu, David Hsu and P.S. Thiagarajan: Probabilistic Approximations ODEs-based biopathways dynamics. Theoretical Computer Science 412(21), (2011) • G. Koh , H.F.C. Teong , M.V. Clment , D. Hsu and P.S. Thiagarajan: A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk, Bioinformatics, 22(14), (2006) (Also presented at the 14th

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Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006)) Journal Articles (Computer science) • Manindra Agrawal, S. Akshay, Blaise Genest and P.S. Thiagarajan. Approximate verification of the symbolic dynamics of Markov chains, Journal of the Association for Computing Machinery (JACM), 62(1), 2-34 (2015) • P. S. Thiagarajan, Yang Shaofa: Rabin’s theorem in the concurrency setting: A conjecture, Theoretical Computer Science, 546:225-236(2014); • Andrei Hagiescu, Bing Liu, R. Ramanathan, Sucheendra K. Palaniappan, Zheng Cui, Bipasa Chatopadhyay, P.S. Thiagarajan, Weng-Fai Wong. GPU code generation for ODEs based applications with phased shared-data access patterns, ACM Transactions on Architecture and code optimization (ACM TACO), 10(4) (2013) • P.S. Thiagarajan and Shaofa Yang: Modular Discrete Time Approximations of Distributed Hybrid Automata. Theoretical Computer Science, 429 (2012), pp. 292-304. • M. Agrawal, F. Stephan, P.S. Thiagarajan and Shaofa Yang: Discrete Approximate Regular behaviors of Hybrid automata, In: Modern applications of Automata Theory, Eds. Deepak D’Souza and Priti Shankar, World Scientific, Singapore (2011) • (invited) Philippe Darondeau, Blaise Genest , P. S. Thiagarajan and Shaofa Yang: Quasi-Static Scheduling of Communicating Tasks, Information and Computation, 208(10), (2010). • Thomas Gazagnaire, Blaise Genest, Loic Helouet, P.S. Thiagarajan and Shaofa Yang: Causal Message Sequence Charts. Theoretical Computer Science, Vol. 410(41) (2009). • Ankit Goel, Abhik Roychaudhury and P.S. Thiagarajan: Interacting Process Classes, ACM Transactions on Software Engineering and Methodology (TOSEM), 18, 4, (2009) 9

• L. Feng, M. Wonham and P.S. Thiagarajan : Designing Communicating Transaction Processes by Supervisory Control Theory. Formal methods in System Design, 30, 2 (2007) • J. G. Henriksen, M. Mukund, K. Narayan Kumar, M. Sohoni and P.S. Thiagarajan : A Theory of Regular MSC Languages. Information and Computation, 202-1, (2005) • K D Nguyen, Z Sun, P S Thiagarajan and W F Wong, Model-Driven SoC Design: The UML-SystemC Bridge. In UML for SOC Design, edited by G. Martin and W. Mueller. Springer, (2005) • D. Harel and P.S. Thiagarajan: Message Sequence Charts, In: UML for Real: Design of Embedded Real-time Systems, Eds.: Luciano Lavagno, Grant Martin and Bran Selic, Kluwer Academic Publishers (2003) • P. Madhusudan and P.S. Thiagarajan : Branching-time Controllers for Discrete Event Systems. Theoretical Computer Science 174 (1-2), (2002) • (invited) P.S. Thiagarajan and I. Walukiewicz : An Expressively Complete Linear Time Temporal Logic for Mazurkiewicz Traces. Information and Computation, Vol. 179, No. 2 (2002) • J.G. Henriksen and P.S. Thiagarajan : Dynamic Linear Time Temporal Logic , Annals of Pure and Applied Logic, 96, 1-3, (1999). • P.W. Hoogers, H.C.M. Kleijn and P.S. Thiagarajan: An Event Structure Semantics for General Petri Nets, Theoretical Computer Science, 153, (1996) • P.W. Hoogers, H.C.M. Kleijn and P.S. Thiagarajan: A Trace Semantics for Petri Nets, Information and Computation, Vol. 117, No. 1 (1995). • K. Lodaya , R. Parikh, R. Ramanujam and P.S. Thiagarajan.: A Logical Study of Distributed Transition Systems, Information and Computation, Vol. 119, No. 1, (1995). • M. Nielsen, G. Rozenberg and P.S. Thiagarajan: Transition Systems, Event Structures and Unfoldings, Information and Computation, Vol. 118, No. 2 (1995). 10

• K. Lodaya, M. Mukund, R. Ramanujam and P.S. Thiagarajan.: Models and Logics for True Concurrency, Sadhana, Vol.17, Part 1 (1992). • K. Lodaya, R. Ramanujam and P.S. Thiagarajan.: Temporal Logics for Communicating Sequential Agents I, International Journal of Foundations of Computer Science, Vol.3, No.2 (1992). • M. Nielsen, G. Rozenberg and Thiagarajan P.S.: Elementary Transition Systems and Refinement, Acta Informaticae, 29 (1992). • M. Nielsen, G. Rozenberg and P.S. Thiagarajan: Elementary Transition Systems, Theoretical Computer Science 96 (1992). • B. Rozoy and P.S. Thiagarajan.: Event Structures and Trace Monoids,Theoretical Computer Science, 91 (1991). • M. Nielsen, G. Rozenberg and P.S. Thiagarajan.: Behavioral Notions for Elementary Net Systems, Distributed Computing, 4, 1 (1990). • P.S. Thiagarajan.: Some Behavioral Aspects of Net Theory, Theoretical Computer Science, 71, (1990). • C. Fernandez, M. Nielsen and Thiagarajan P.S.: Notions of Realizable Non-sequential Processes, Fundamenta Informaticae, IX (1986). • P.S. Thiagarajan and K. Voss. : A Fresh Look at Free choice Nets, Information and Control, Vol. 61, No. 2, (1984) • H.J. Genrich and P.S. Thiagarajan. : A Theory of Bipolar Sychronization Schemes, Theoretical Computer Science, 30, (1984). • C. Fernandez and P.S. Thiagarajan. : D-Continuous Causal Nets: A Model of Non-Sequential Processes, Theoretical Computer Science, 28, (1984). • H.J. Genrich, D. Janssens, G. Rozenberg and P.S. Thiagarajan. : Generalized Handle Grammars and their Relation to Petri Nets, Elektr. Informationsverarbeitung und Kybernetik, EIK 20 (1984). • J.R. Jump and P.S. Thiagarajan.: On the Interconnection of Asynchronous Control Structures, Journal of the ACM, 22, 4 (1975). 11

• J.R. Jump and P.S. Thiagarajan: On the Equivalence of Asynchronous Control Structures, SIAM Journal on Computing, 2, 2(1973). Refereed Conference Papers (Computational systems biology) • Benjamin M. Gyori, Bing Liu, Soumya Paul, R. Ramanathan and P.S. Thiagarajan. Approximate Probabilistic Verification of Hybrid Systems, 4th International Workshop on Hybrid Systems Biology (HSB’2015), Springer Lecture Notes in Computer Science, 9271 (2016) • R. Ramanathan, Yan Zhang, Jun Zhou, Benjamin M. Gyori, WengFai Wong and P.S. Thiagarajan. Parallelized Parameter Estimation of Biological Pathway Models, 4th International Workshop on Hybrid Systems Biology (HSB’2015), Springer Lecture Notes in Computer Science, 9271 (2016) • Sucheendra K Palaniappan, Benjamin M. Gyori, Bing Liu, David Hsu and P. S. Thiagarajan. Statistical model checking based calibration and analysis of bio-pathway models, Proceedings of the 11th international conference on computational methods in systems biology (CMSB’2013), Springer Lecture Notes in Computer Science 8130 (2013). • Sucheendra Kumar Palaniappan, S. Akshay, B. Genest and P.S. Thiagarajan: A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Network models of Biopathways. Proceedings of the 9th Conference on Computational Methods in Systems Biology (CMSB 2011), Paris, France (2011). • Geoffrey Koh, David Hsu and P.S. Thiagarajan: Incremental Signaling Pathway Modeling by Data Integration. Proceedings of the 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010), Springer Lecture Notes in Computer Science 6044 (2010). • Bing Liu, David Hsu and P.S. Thiagarajan: Probabilistic Approximations of Signaling Pathway Dynamics, Proceedings of the 7th Conference on Computational Methods in Systems Biology (CMSB 2009), Springer Lecture Notes in Computer Science 5688 (2009).

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• G. Koh, L. Tucker-Kellog, D. Hsu and P.S. Thiagarajan: Composing Globally Consistent Pathway Parameter Estimates through Belief Propagation, Proceedings of the 7th Workshop on Algorithms in Bioinformatics (WABI 2007), Springer Lecture Notes in Bioinformatics 4645 (2007) Refereed Conference Papers (Computer science) • Ratul Saha, Javier Esparza, Sumit Jha, Madhavan Mukund, P.S. Thiagarajan. Distributed Markov chains, Proc. of 16th International Conference on Verification, Model Checking, Abstract Interpretation(VMCAI’2015), Springer Lecture Notes in Computer Science, Vol. 8931, 117-134 (2015). • M. Agrawal, S. Akshay, B. Genest and P.S. Thiagarajan: Approximate Verification of the Symbolic Dynamics of Markov Chains, Proceedings of the 27th ACM/IEEE Symposium on Logic in Computer Science (LICS 2012), Dubrovnik, Croatia (2012) • P. S. Thiagarajan and Shaofa Yang: Succinct Discrete Time Approximations of Distributed Hybrid Automata. Proc. of the 13th ACM International Conference on Hybrid Systems: Computation and Control (HSCC 2010), ACM Press (2010). • Linh Thi Xuan Phan, Samarjit Chakraborty and P S Thiagarajan: A Multi Mode Real Time Calculus, Proc. Of the 29th IEEE Real Time Systems Symposium (RTSS’08), IEEE Press (2008) • Philippe Darondeau, Blaise Genest , P. S. Thiagarajan and Shaofa Yang: Quasi-Static Scheduling of Communicating Tasks, Proc. of the 19th International Conference on Concurrency Theory (CONCUR 2008), Springer lecture Notes in Computer Science 5201, (2008). • Kathy Dang Nguyen, P.S. Thiagarajan and Weng-Fai Wong: A UMLbased Design Framework for Time-triggered Applications, Proc. Of the 28th IEEE Real Time Systems Symposium (RTSS’07), IEEE Press (2007) • Linh Thi Xuan Phan, Lothar Thiele, Samarjit Chakraborty and P S Thiagarajan: A Compositional Approach for the performance Analysis 13

of Heterogeneous Real-Time Systems, Proc. Of the 28th IEEE Real Time Systems Symposium (RTSS’07), IEEE Press (2007) • T. Gazagnaire, B. Genest, L. Helelouet, P.S. Thiagarajan and Shaofa Yang: Causal Message Sequence Charts, Proc. of the 18th International Conference on Concurrency Theory (CONCUR 2007), Springer lecture Notes in Computer Science 4703 (2007) • J. Mekie, S. Chakraborty, G. Venkataramani, P. S. Thiagarajan and D. K. Sharma: ”Interface Design for Rationally Clocked GALS Systems”, Proc. of International Symposium on Advanced Research in Asynchronous Circuits and Systems (ASYNC 2006), IEEE Press (2006) • A. Goel, S. Meng , A. Roychoudhury and P. S. Thiagarajan: Interacting Process Classes. Proc. of 28th International Conference on Software Engineering (ICSE 2006), ACM Press (2006) • Samarjit Chakraborty, T.X.L. Phan and P.S. Thiagarajan: Event Count Automata: A State-based Model for Stream Processing Systems. Proc. of the 26th IEEE International Real-Time Systems Symposium (RTSS 2005), IEEE Press (2005). • M. Agrawal and P.S. Thiagarajan: The Discrete Time Behavior of Lazy Linear Hybrid Automata. Proc. of 8th International Workshop on Hybrid Systems: Computation and Control (HSCC 2005), Springer Lecture Notes in Computer Science 3414 (2005) • P. Madhusudan, P S Thiagarajan and S Yang: The MSO Theory of Connectedly Communicating Processes. Proc. of Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2005), Springer Lecture Notes in Computer Science 3821 (2005). • K.D. Nguyen, Z Sun, P S Thiagarajan and W F Wong: Model-driven SOC Design via Executable UML to SystemC. Proc. 25th IEEE International Real-time Systems Symposium (RTSS 2004), IEEE Press (2004) • A. Roychoudhury, P S Thiagarajan, T.A. Tran and V Zvereva: Automatic Generation of Protocol Converters from Scenario-based Specifica14

tions. Proc. Of 25th IEEE International Real-time Systems Symposium (RTSS 2004), IEEE Press (2004). • L. Feng, W M Wonham and P S Thiagarajan: Designing Communicating Transaction Processes by Supervisory Control Theory. the 42nd Allerton Conference on Communication, Control and Computing (2004) • P. Krcal, L. Mokrushin, P.S. Thiagarajan and W Yi: Timed vs. TimeTriggered Automata. Proc. of the 15th International Conference on Concurrency Theory (CONCUR’04), Springer Lecture Notes in Computer Science 3170 (2004) • M. Agrawal and P.S. Thiagarajan: Lazy Rectangular Hybrid Automata. Proc. of 7th International Workshop on Hybrid Systems: Computation and Control (HSCC 2004), Springer Lecture Notes in Computer Science 2993 (2004) • A. Roychoudhury and P.S. Thiagarajan: Communicating Transaction Processes. Proc. of the 3rd IEEE International Conference on Application of Concurrency in System Design (ACSD’03), IEEE Press (2003) • A. Roychoudhury and P.S. Thiagarajan: An Executable Specification Language based on Message Sequence Charts. Proc. of Formal Methods at the Crossroads: From Panacea to Foundational Support, Springer-Verlag, LNCS 2757 (2003). • M. Mukund, K Narayan Kumar and P.S. Thiagarajan: Netcharts: Bridging the gap between HMSCs and executable specifications. Proc. of the 14th International Conference on Concurrency Theory (CONCUR’03), Springer Lecture Notes in Computer Science 2761, SpringerVerlag, (2003). • P. Madhusudan and P.S. Thiagarajan: Effective Strategies for Asynchronous Distributed Control. Proc. of the 13th International Conference on Concurrency Theory (CONCUR 2002), Springer Lecture Notes in Computer Science 2421 (2002).

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• P.S. Thiagarajan: Regular Event Structures and Finite Petri Nets: A Conjecture. Formal and Natural Computing, Lecture Notes in Computer Science, 2300, Springer-Verlag (2002) • M. Nielsen and P.S. Thiagarajan. Regular Event Structures and Finite Petri Nets: The Conflict-free Case. Proc. of the 23rd International Conference on the Applications and Theory of Petri Nets (ICATPN 2002), Springer Lecture Notes in Computer Science 2360 (2002) • P.S. Thiagarajan. Regular Event Structures and Finite Petri Nets: A Conjecture. Formal and Natural Computing: Essays Dedicated to Grzegorz Rozenberg, Springer Lecture Notes in Computer Science 2300 (2002) • P. Madhusudan and P.S. Thiagarajan. Distributed Controller Synthesis for Local Specifications. Proceedings of the 28th International Conference on Automata, Languages and Programming (ICALP’01), Springer Lecture Notes in Computer Science 2076 (2001) • P. Madhusudan, O. Kupferman, P.S. Thiagarajan and Moshe Y. Vardi : Open Systems in Reactive Environments : Control and Synthesis. Proceedings of CONCUR’00, Penn State University, PA, U.S.A., Springer Lecture Notes in Computer Science 1877 (2000). • J. G. Henriksen, M. Mukund, K. Narayan Kumar and P.S. Thiagarajan. On Message Sequence Graphs and Finitely Generated Regular MSC Languages. Proceedings of the 27th International Conference on Automat, Languages and Programming (ICALP’00) , Springer Lecture Notes in Computer Science 1853 (2000). • J. G. Henriksen, M. Mukund, K. Narayan Kumar and P.S. Thiagarajan. Regular Collections of Message Sequence Charts. Proceedings of the 25th International Conference on the Mathematical Foundations of Computer Science(MFCS’00), Springer Lecture Notes in Computer Science 1893 (2000). • I. Castellani, M.Mukund and P.S. Thiagarajan : Synthesizing Distributed Transition Systems from Global Specifications. Proceedings

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of the 19th International Conference on Foundations of Software Technology and Theoretical Computer Science(FST & TCS’99), Springer Lecture Notes in Computer Science 1738 (1999) • D. D’Souza and P.S. Thiagarajan : Product Interval Automata ; A Subclass of Timed Automata. Proceedings of the 19th International Conference on Foundations of Software Technology and Theoretical Computer Science (FST & TCS’99), Springer Lecture Notes in Computer Science 1738 (1999). • M.Madhusudan and P.S. Thiagarajan : Controllers for Discrete Event Systems via Morphisms, Proceedings of CONCUR’98, Nice, France, Springer Lecture Notes in Computer Science 1466 (1998). • J.G. Henriksen and P.S. Thiagarajan : Distributed Versions of Linear Time Temporal Logic, Lectures on Petri Nets : Basic Models, Springer Lecture Notes in Computer Science 1491 (1998) • J.G. Henriksen and P.S. Thiagarajan: A Product Version of Dynamic Linear Time Temporal Logic, (Invited paper)Proceedings of CONCUR’97, Springer Lecture Notes in Computer Science 1243 (1997) • P.S. Thiagarajan, I. Walukiewicz: An Expressively Complete Linear Time Temporal Logic for Mazurkiewicz Traces, Proceedings of the 12th IEEE Symposium on Logic in Computer Science(LICS’97) , Warsaw, Poland, IEEE Computer Press (1997). • M. Mukund, P.S. Thiagarajan: Linear Time Temporal Logics over Mazurkiewicz Traces, (Invited Paper) Proceedings of the 21st International Symposium on the Mathematical Foundations of Computer Science (MFCS’96), Cracow,Poland, Springer Lecture Notes In Computer Science 1113. Also appears in the DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Volume 29 (1997) • P.S. Thiagarajan: A Trace Consistent Subset of PTL, Proceedings of CONCUR’95, Philadelphia, U.S.A., Springer Lecture Notes in Computer Science 962 (1995).

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• P.S. Thiagarajan: A Trace Based Extension of Linear Time Temporal Logic, Proceedings of the 9th IEEE Symposium on Logic in Computer Science(LICS’94), Paris, France, IEEE Computer Press (1994). • K. Lodaya, R. Ramanujam and P.S. Thiagarajan.: Decidability of a Partial Order Based Temporal Logic, Proceedings of the 20th International Colloquium on Automata, Languages and Programming(ICALP’93), Lund, Sweden, Springer Lecture Notes in Computer Science 700 (1993). • P.W. Hoogers, H.C.M. Kleijn and P.S. Thiagarajan: Local Event Structures and Petri Nets, Proceedings of CONCUR’93, Springer Lecture Notes in Computer Science 715 (1993). • P.W. Hoogers, H.C.M. Kleijn and P.S. Thiagarajan.: A Trace Semantics for Petri Nets, Proceedings of the 19th International Colloquium on Automata, Languages and Programming(ICALP’92), Vienna, Springer Lecture Notes in Computer Science, 623 (1992). • M. Mukund and P.S. Thiagarajan.: A Logical Characterization of Well Branching Event Structures, Theoretical Computer Science 96 (1992). • K. Lodaya, R. Ramanujam and P.S. Thiagarajan: A logic for Distributed Transitions Systems (Invited Paper), Proceedings of the REX School/ Workshop on Linear Time, Branching Time and Partial Order in Logics and Models of Concurrency, Noordwijkehout, Springer Lecture Notes in Computer Science 354 (1988). • K. Lodaya and P.S. Thiagarajan.: A Modal Logic for a Subclass of event Structures, Proceedings of the 14th International Colloquium on Automata, Languages and Programming(ICALP’87) , Karlsruhe, Springer Lecture Notes in Computer Science 267 (1987). • P.S. Thiagarajan.: Some Behavioral Aspects of Net Theory (Invited Paper), Proceedings of the 15th International Colloquium on Automata, Languages and Programming(ICALP’88), Tampere, Springer Lecture Notes in Computer Science 317 (1988). • G. Rozenberg G and P.S. Thiagarajan.: Petri Nets: Basic Notions, Structure and Behavior (Invited Paper), Proceedings of the Advanced 18

Course on Current Trends in Concurrency, Springer Lecture Notes in Computer Science 267 (1987). • P.S. Thiagarajan: Elementary Net Systems (Invited Paper), Proceedings of the Advanced Course on Net Theory and Applications, Springer Lecture Notes in Computer Science 254 (1986). • M. Nielsen, P.S. Thiagarajan.: Degrees of Non-Determinism and Concurrency - A Petri Net View (Invited Paper), Fourth Conference on Foundations of Software Technology and Theoretical Computer Science, Springer Lecture Notes in Computer Science 181 (1984). • H.J. Genrich and P.S. Thiagarajan.: Well-Formed Flow Charts for Concurrent Programming, Proceedings of the IFIP Working Group Conference on Formal Descriptions of Programming Concepts, North-Holland Publishing Company (1983). • C. Fernandez and P.S. Thiagarajan.: Some Properties of D-Continuous Causal Nets, Proceedings of the 9th International Colloquium on Automata, Languages and Programming(ICALP’82), Springer Lectures Notes in Computer Science 140 (1982). • H.J. Genrich and P.S. Thiagarajan.: The Synthesis of Well Behaved Bipolar Synchronization Schemes, Proceedings of the 7th International Colloquium on Automata, Languages and Programming(ICALP’80), Noordwijkehout, Springer Lecture Notes in Computer Science 86 (1980). • H.J. Genrich, K. Lautenbach and P.S. Thiagarajan.: Substitution Systems -A Family of System Models based on Concurrency (Invited Paper), Proceedings of the 9th Symposium on the Mathematical Foundations of Computer Science, Springer Lecture Notes in Computer Science 88 (1980). • H.J. Genrich , K. Lautenbach and P.S. Thiagarajan.: Elements of General Net Theory (Invited Paper), Proceedings of the Advanced Course on General Net Theory of Processes and Systems, Springer Lecture Notes in Computer Science 84 (1980). • J. Robert Jump, P. S. Thiagarajan: On the Equivalence of Asynchronous Control Structures. Proc. of 13th Annual Symposium on 19

Foundations of Computer Science (FOCS’72), IEEE Computer Society, (1972) INVITED TALKS AT INTERNATIONAL CONFERENCES AND WORKSHOPS: • 24th Genome Informatics Workshop (GIW’2013), Singapore, 2013. • 15th International Conference on Formal Engineering Methods (ICFEM’2013), Queenstown, New Zealand, 2013. • 10th International Symposium on Automated Technology for Verification and Analysis (ATVA2012), Trivandrum, India, 2012. • CMACS workshop on Systems Biology and Formal methods(SBFM’12), New York, USA, March 2012. • 4th International conference on Computational and Systems biology (ICCSB2012), Shanghai, China, October, 2012. • ”Towards Systems Biology” workshop, VERIMAG, Grenoble, France, April, 2011 • Automata, Concurrency and Timed Systems (ACTS) II, Chennai Mathematical Institute, January, 2010. • Bio-Computation workshop, Asia University, Taichung, Taiwan, November, 2010 • International Conference on Algebraic and Numerical Biology, Hagenberg, Austria, July, 2010 • Dagstuhl Seminar on “Formal methods in Molecular Biology”, Schloss dagstuhl, Germany, February, 2009 • Microsoft Research India, Theory Day, Bangelore, India, December, 2008 • The 16th Nordic Workshop on Programming Theory (NWPT 2004), Uppsala, Sweden, October, 2004. 20

• Workshop on Discrete Event Systems Control, Eindhoven, The Netherlands, June, 2003. • 3rd International Conference on Applications of Concurrency to System Design” (ACSD) , Guimaeres, Portugal, June 2003. • Twenty-third International Conference on Applications and Theory of Petri Nets (ICATPN’2002), Adelaide, Australia 2002. • Conference on Current Practice and Future Challenges in Computer Science, New Building Inaugural Conference, Indian Institute of Technology, Kanpur, January, 2002. • Formal Methods at the Crossroads: From Panacea to Foundational Support, 10th Anniversary Colloquium of UNU/IIST, Lisbon, Portugal (2002) • Fifth International Workshop on Expressiveness in Concurrency (EXPRESS’98), Nice, France (1998). • Eighth International Conference on Concurrency Theory (CONCUR’97), Warsaw, Poland (1997). • Twenty-first International Symposium on the Mathematical Foundations of Computer Science (MFCS’96), Cracow, Poland (1996). • Fifteenth International Colloquium on Automata, Languages and Programming (ICALP’88), Tampere, Finland (1988). • REX School/Workshop on Linear Time,Branching Time and Partial Order in Logics and Models for Concurrency, Noordwijkerhout, The Netherlands (1988). • Eighth International Conference on Application and Theory of Petri Nets(ICATPN’87), Zaragoza, Spain (1987). • Fourth International Conference on Foundations of Software Technology and Theoretical Computer Science (FST & TCS), Bangalore, India (1984).

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INVITED LECTURE SERIES • Pre-conference tutorial lectures at the International Conference on the Applications and Theory of Petri Nets (ICATPN 2005), Miami, Florida, USA, June, 2005. • Lecture Series at the Fourth Advanced Course on Net Theory and Applications, Eichstaett, Germany, 2003. • A course of lectures on “Scenario-based Methods for System Design”, Department of Software, Politecnica de Catalunia, Barcelona, Spain, May, 2003 . • A course of lectures on “Temporal Logics” at the Ecole Normale Superioure de Cachan, Paris, France to undergraduate students (1997). • Lecture Series at the Advanced Tutorials on ”Logics of Concurrency ” as a part of the 18th International Conference on the Applications and Theory of Petri Nets, Toulouse, France (1997). • Lecture Series at the Third Advanced Course on Net Theory and Applications, Dagstuhl, Germany (1996). • Lecture series at the Summer School on Logical Methods in Concurrency. Aarhus, Denmark (1993). • Lecture Series at the Advanced School on the Algebraic, Logical and Categorical Foundations of Concurrency. Gargnano del Garda, Italy (1991). • Lecture Series at the Advanced Course on Current Trends in Concurrency. Noordwijkehout, The Netherlands (1987). • Lecture Series at the Second Advanced Course on Net Theory and Applications. Bad Honnef, West Germany (1985). • Lecture series at the First Advanced Course on General Net Theory of Processes and Systems. Hamburg, West Germany (1979).

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PROGRAMME COMMITTEES: • 2nd Symposium on Complex Biodynamics and Networks (cBio 2015), Tsuruoka, Japan (2015) • 18th International Symposium on Hybrid Systems: Computation and Control, Seattle (HSCC’2015), USA (2015) • 13th International Conference on Computational Methods in Systems Biology, Nantes, France (2015) • 3rd International Workshop on Hybrid systems and Biology (HSB’14), Vienna, Austria (2014) • 29th Annual ACM/IEEE Symposium on Logic in Computer Science (LICS’2014), Vienna, Austria (2014) • 12th International Conference on Formal Modeling and Analysis of Timed Systems (FORMATS’2014), Rennes, France (2014) • 24th Genomic Informatics Workshop (GIW 2014), Singapore (2014) • 24th International Conference on Concurrency Theory (CONCUR2013), Buenos Aires, Argentina (2013) • International Conference on Intelligent Biology and Medicine (ICIBM’2013), Nashville, USA (2013) • 11th International Conference on Computational Methods in Systems Biology, Vienna, Austria (2013) • 37th International Symposium on Mathematical Foundations of Computer Science (MFCS2012), Bratislava, Slovakia (2012) • 10th International Conference on Formal Modeling and Analysis of Timed Systems (FORMATS2012), Warwick, UK (2012) • 10th International Conference on Computational Methods in Systems Biology, London, UK (2012) • 3rd International Workshop on Biological Processes and Petri Nets, Hamburg, Germany (2012) 23

• 2nd International Workshop on Biological Processes and Petri Nets, Newcastle upon Tyne, UK (2011) • 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Chicago, USA (2011) • 5th International Conference on Bio-inspired Models of Network, Information and Computing Systems (Bionets2010), Boston, USA (2010) • 8th International Conference on Formal Modeling and Analysis of Timed Systems (FORMATS 2010), IST, Austria (2010) • 21st International Conference on Concurrency Theory (CONCUR’10), Paris, France, (2010) • 5th International ICST Conference on Bio-Inspired Models of Network, Information and Computing Systems (Bionetics 2010), Boston, USA (2010) • 13th International Workshop on Hybrid systems: Computation and Control (HSCC 2010), KTH, Sweden (2010) • 8th International Conference on Applications of Concurrency to Systems Design (ACSD2008), Xi”an, China (2008) • 6th International Conference on Formal Modeling and Analysis of Timed Systems (FORMATS 2008), Saint-Malo, France (2008) • 6th International Symposium on Automated Technology for Verification and Analysis (ATVA 2008), Seoul, South Korea (2008) • 5th IFIP International Conference on Theoretical Computer Science (TCS 2008), Milan, Italy (2008) • 7th ACM & IEEE Conference on Embedded Software (EMSOFT 2007), Salzburg, Austria (2007) • 6th IFIP Working Conference on Distributed and Parallel Embedded Systems (DIPES 2008), Milan, Italy (2008)

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• 6th ACM-IEEE International Conference on Formal Methods and Models for Codesign (MEMOCODE 2008), Anaheim, California, USA (2008) • 29th IEEE real Times Symposium (RTSS 2008), Barcelona, Spain (2008) • 5th ACM-IEEE Conference on Formal Methods and Models for Codesign (MEMOCODE 2007), Nice, France, USA, (2007) • 5th International Conference on Formal Modeling and Analysis of Timed Systems (FORMATS 2007), Salzburg, Austria (2007) (Co-Chair) • 10th International Conference on Foundations of Software Science and Computation Structures (FoSSaCS 2007), Braga, Portugal (2007) • 17th International Conference on Concurrency Theory (CONCUR’06), Bonn, Germany, (2006) • 6th Annual Conference on Embedded Software (EMSOFT 2006), Seoul, South Korea (2006) • 14th Formal methods Conference (FM 2006), Hamilton, Canada (2006) • 9th International Workshop on Hybrid systems: Computation and Control (HSCC 2006), UC Santa Barbara, USA (2006) • (PC Co-Chair) 27th International Conference on Applications and Theory of Petri Nets and other Models of Concurrency (ATPN 06), Turku, Finland (2006) • (PC Co-Chair) 5th IFIP Working Conference on Distributed and Parallel Embedded Systems (IFIP-DIPES 2006), Braga, Portugal (2006). • 4th ACM-IEEE International Conference on Formal Methods and Models for Co-Design (MEMOCODE 2006), Napa, California, USA (2006). • 5th International Conference on Application of Concurrency to System Design (ACSD’05), St. Malo, France (2005). • International Conference on Formal Modelling and Analysis of Timed Systems (FORMATS 05), Uppsala, Sweden (2005) 25

• International Conference on Embedded Software and Systems (ICESS 05), Xian, PRC (2005) • International Colloquium on Theoretical Aspects of Computing (ICTACS 05), Hanoi, Vietnam (2005) • 26th International Conference on Applications and Theory of Petri Nets and other Models of Concurrency (ATPN 05), Miami, Florida, USA (2005) • Workshop on “Games in Design and Verification” (Co-located with 16th International Conference on Computer Aided Verification ; CAV 2004), Boston, USA (2004). • 15th International Conference on Concurrency Theory (CONCUR’04), London, UK, (2004). • 25th International Conference on the Applications and Theory of Petri Nets, Bologna, Italy. (2004). • 4th International Conference on Application of Concurrency to System Design (ACSD’04), Hamilton, Canada (2004). • (Conference Co-Chair) 5th International Conference on Formal Engineering Methods (ICFEM’03), Singapore (2003). • 24th International Conference on Applications and Theory of Petri Nets, Eindhoven, The Netherlands (2003) • FOSSACS(Foundations of Software Science and Computation Structures) 2003, Warsaw, Poland (2003) • Third Workshop on ”Verification of Infinite-State Systems” (Co-located with CONCUR’2002), Bruno, Czech Republic (2002). • Workshop on ”Models for Time-Critical Systems” (co-located with CONCUR’2002), Bruno, Czech Republic (2002). • Third IFIP International Conference on Theoretical Computer Science, (TCS’2002), Montreal, Canada (2002). 26

• IFIP-WG2.3/UNU-IIST School on ”Formal Software Engineering”, Pune, India (2002) • Workshop on ”Reasoning about Parameterized and Infinite State Systems”, Chennai, India (2001). • First IFIP International Conference on Theoretical Computer Science(TCS’2000), Sendai, Japan (2000) • 21th International Conference on the Applications and Theory of Petri Nets, Aarhus, Denmark (2000). • (PC Co-Chair) 5th Asian Computing Science Conference (ASIAN’99), Phuket, Thailand (1999). • 20th International Conference on the Applications and Theory of Petri Nets, Williamsburg, U.S.A.(1999) • 10th International Conference on Concurrency Theory (CONCUR’99), Eindhoven (1999) • 4th Asian Computing Science Conference (ASIAN’98), Manila (1998). • 19th International Conference on Applications and Theory of Petri Nets, Lisbon, Portugal(1998) • 24th International Colloquium on Automata, Languages and Programming (ICALP’97), Bologna, Italy (1997) • 16th International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS’96), Pune, India (1996). • (PC Chair) 15th International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS’95), Bangalore, India (1995). • 5th International Conference on Concurrency Theory (CONCUR’94), Uppsala, Sweden (1994). • (PC Chair) 14th International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS’94), Madras, India (1994). 27

• 4th International Conference on Concurrency Theory (CONCUR’93), Hildesheim, Germany (1993) • 13th International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS’93), Bombay, India (1993). • 12th International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS’88), New Delhi, India (1992). • 10th International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS’88), Bangalore, India (1990). • 9th International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS’89), Bangalore, India (1989). • 8th International Conference on Foundations of Software Technology and Theoretical Computer Science (FST&TCS’88), Pune, India (1988).

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