BioComputing

DNA Computing and Molecular Programming 17 (Springer) [@Springer]

Overview

Abstract Machines of Systems Biology (TCSB) [@Springer]

Artificial Biochemistry (Algorithmic Bioprocesses)

Can a Systems Biologist Fix a Tamagotchi? (Gilles Kahn Colloquium)

 Visualization in Process Algebra Models of Biological Systems (The Fourth Paradigm)

Foundations

Modular Markovian Logic (ICALP'11)

Stochastic Pi-Calculus Revisited

Continuous Markovian Logic (CLS'11)

The Measurable Space of Stochastic Processes (QEST'10)

Processes in Space (CiE'10)

Turing Universality of the Biochemical Ground Form (MSCS)

On the Computational Power of Biochemistry (AB'08)

Termination Problems in Chemical Kinetics (CONCUR'08)

On Process Rate Semantics (TCS)

A Process Algebra Master Equation (QEST'07)

From Processes to ODEs by Chemistry (IFIP TCS'08)

Bitonal Membrane Systems (TCS)

A Universality Result for a (Mem)Brane Calculus Based on Mate/Drip Operations (IJFCS) [@WorldScientific]

Formal Languages

Design and Analysis of DNA Strand Displacement Devices using Probabilistic Model Checking (J.R.S. Interface)

Reversibility in Massive Concurrent Systems (SACS)

Reversible Structures (CMSB '11)

Two-Domain DNA Strand Displacement Animations (MSCS)

Exploring DNA Strand-Displacement Computational Elements

Strand Algebras for DNA Computing (Natural Computing)

A Programming Language for Composable DNA Circuits (J.R.S.Interface)

An Intuitive Modelling Interface for Systems Biology (DCM '09)

A Correct Abstract Machine for the Stochastic Pi-calculus (BioConcur '04)

Efficient, Correct Simulation of Biological Processes in Stochastic Pi-calculus (CMSB'07)

A Graphical Representation for Biological Processes in Stochastic Pi-calculus (TCSB) [@Springer]

Where Membranes Meet Complexes (BioConcur '05)

Brane Calculi (ENTCS, CMSB'04)

BioAmbients: An Abstraction for Biological Compartments (TCS)

Bioware Languages (Computing Systems - A Tribute to Roger Needham)

Biological Modeling

Transcriptional Regulation is a Major Controller of Cell Cycle Transition Dynamics (PLoS ONE)

A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization (PLoS Computational Biology)

Response Dynamics of Phosphorelays Suggest Their Potential Utility in Cell Signaling (J.R.S. Interface)

Computational Modeling of the EGFR Network Elucidates Control Mechanisms Regulating Signal Dynamics (BMC Systems Biology) [@Biomedcentral]

A Compositional Approach to the Stochastic Dynamics of Gene Networks (TCSB) [@Springer]

Compositionality, Stochasticity and Cooperativity in Dynamic Models of Gene Regulation (HFSP Journal)

A Process Model of Rho GTP-binding Proteins (FBTC'07) (TCS)

A Process Model of Actin Polymerisation (FBTC'08) (ENTCS)

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Spatial Logics

Deciding Validity in a Spatial Logic for Trees (JFP) 

A Spatial Logic for Concurrency (Part II) (TCS) 

A Spatial Logic for Concurrency (Part I) (I&C) 

Ambient Logic (MSCS) 

Logical Properties of Name Restriction (TLCA'01)

Anytime, Anywhere (POPL'00)

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Semistructured Data

Greedy Regular Expression Matching (ICALP'04) 

Manipulating Trees with Hidden Labels (PlotkinVolume'06) 

A Spatial Logic for Querying Graphs (ICALP'02) 

A Query Language Based on the Ambient Logic (MSCS)

Describing Semistructured Data (SIGMOD Record)

Semistructured Computation (DBPL'99)

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Ambients

Types for the Ambient Calculus (I&C)

Mobility and Security (Chapter for Foundations of Secure Computation) (A summary of several  Ambients papers)

Abstractions for Mobile Computation (Chapter for Secure Internet Programming)

Equational Properties of Mobile Ambients (ETAPS'99, MSCS)

Mobile Ambients (ETAPS'98/TCSB'00)

Wikipedia Entry

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Programming

Modern Concurrency Abstractions for C# (TOPLAS)

Service Combinators for Web Computing (DSL'97, TSE)

A Language with Distributed Scope (POPL'95, Computing Systems)

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Types and Semantics

Classical Cut Elimination in the Pi-Calculus

From X to Pi: Representing Classical Sequent Calculus in Pi-calculus (CL&C'08)

Secrecy and Group Creation (I&C'05 - Concur'00)

Type Systems (Chapter for the CRC Handbook of Computer Science ad Engineering, 2nd Edition)

Program Fragments, Linking, and Modularization (POPL'97)

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Objects

Comparing Object Encodings (TACS'97, I&C)

On Binary Methods (TAPOS)

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 On Switches and Oscillators 

 Speaking the Language of Molecules (CDE Distinguished Lacture, U.Washington)

 The Measurable Space of Stochastic Processes  (QEST'10)

 Two-Domain DNA Strand Displacement (DCM'10)

 Molecular Programming (SimuTools'10 Keynote)

 Molecular Programming - Tutorial (Microosft Research Cambridge)

 Pi in the Sky: Spatial Process Algebra for Developmental Biology (MeCBIC'09)

Molecules as Automata - Open Lectures for PhD Students in Computer Science (Warsaw, March&May'09)

 Strand Algebras for DNA Computing (DNA Computing '09)

Molecules as Automata - International Summer School on Natural Computing  (BNC'08)

 Termination Problems in Chemical Kinetics (CONCUR'08)

 On The Computational Power of Biochemistry (AB'08)

 Process Rate Semantics (Trento Minicourse)

 Living Software (L'INRIA a Quarante Ans)

 From Processes to ODEs by Chemistry (TCS'08)

 Molecules as Automata (DNA Computing '08)

 An Accidental Simula User (2007 Dahl-Nygaard Senior Prize)

 On Process Rate Semantics (MFPS'08 Invited)

 Artificial Biochemistry

 Can a Systems Biologist Fix a Tamagotchi?

 Artificial Biochemistry - Graduate Course (University of Trento, May 22-26 '06)

 Abstract Machines of Systems Biology

 Biological Networks in Stochastic Pi-Calculus

 Bitonal Membrane Systems  (MeCBIC'06)

 Biological Systems as Reactive Systems (ECCS'05)

 A Compositional Approach to the Stochastic Dynamics of Gene Networks (Concur '05)

 A Graphical Representation for Stochastic π-Calculus (BioConcur '05)

 Languages and Notations for Systems Biology

 Membrane Interactions

 A Correct Abstract Machine for the Stochastic pi-calculus (BioConcur '04)

 Transitions in Programming Models (ICSE'05 Keynote Talk)

Membrane Interactions   (CSSB School Rovereto, April'04)

 Languages for Molecular Cell Biology

Mobility and Spatial Logics   (Bertinoro School '05)

 Manipulating Trees with Hidden Labels  (FOSSACS'03)

 Spatial Logics for Distributed Systems  (FWAN'02, Strachey Lecture '02)

Computation on Wide Area Networks   (Lipari School '01)

A Query Language Based on the Ambient Logic  (Concoord Workshop Invited Talk, July '01)

Globality (ETAPS'01 Invited Talk)

Wide Area Computation (Valladolid, Nov '00. Tokyo, Aug'00)

Global Computing (Edinburgh, Sep '00)

Logics for Mobility (Cambidge, Nov '00. Lausanne, Oct '00, Tokyo, Aug '00)

Secrecy and Group Creation (MFCSIT'00 Cork)

Semistructured Computation (DBPL'99 Invited Talk)

Mobility and Security (Marktoberdorf'99 Lectures)

Anytime, Anywhere (POPL'00)

Abstractions for Mobile Computation (FMOODS'97 Tutorial "Foundations for Wide Area Systems")

Everything is an Object (ECOOP'97 WS on Prototype-based languages Keynote Talk)

Objects, Classes, Abstractions (FOOL'97 Invited Talk)

Program Fragments, Linking, and Modularization (POPL'97 Talk)

A Theory of Objects (LICS'97 Invited Talk, ECOOP'97 Tutorial)

Class-based vs Object-based Languages (PLDI'96 Tutorial)

Distributed Mobile Computation in Obliq