Current  Past  Me  Papers  Talks  Artifacts  Extra  HotPage 
HighlightsSymbolic Computation of Differential Equivalences (POPL'16)Morphisms of Reaction Networks that Couple Structure to Function (BMC Systems Biology'14) 
Programmable chemical controllers made from DNA (Nature Nanotech'13)
The Cell Cycle Switch Computes Approximate Majority (Scientific Reports'12) Programming Chemistry in DNA Addressable Bioreactors (Interface '14) TwoDomain DNA Strand Displacement (MSCS'13) 

Molecular Programming
Papers
Chemical Reaction Network Designs for Asynchronous Logic Circuits (DNA22 '16, NaCo '17)
The Formal Language and Design Principles of Autonomous DNA Walker Circuits (ACS Synthetic Biology'16) Automated Design and Verification of Localized DNA Computation Circuits (DNA21 '15) Programmable chemical controllers made from DNA (Nature Nanotech '13) TwoDomain DNA Strand Displacement (MSCS'13) Abstractions for DNA circuit design (J.R.S. Interface '12) Design and Analysis of DNA Strand Displacement Devices using Probabilistic Model Checking (J.R.S. Interface '12) Strand Algebras for DNA Computing (Natural Computing '11) A Programming Language for Composable DNA Circuits (J.R.S.Interface '09) Edited Proceedings
DNA 17
Talks
Telling Molecules What To Do (Lisbon Distinguished Lecture)
Molecular Programming (ECOOP'14) Computing with Molecules (DCM'12) TwoDomain DNA Strand Displacement (DCM'10) Strand Algebras for DNA Computing (DNA '09) Tools
DSD  DNA Strand Displacement Simulator ( J.R.S. Interface '13)
Gener  DNA Strand Displacement Reductions ( Bioinformatics '15) Links
Correctness of DNA encodings of chemical reaction networks
DNA Computing and Molecular Programming Conferences NYU • Caltech • UW • Duke • Oxford • Aarhus • Microsoft Outreach
Inner Life of A Cell  Movie
Powering the Cell: Mitochondria  Movie DNA Strand Displacement  Movies Nanocrafter  Game EteRNA  Game 
Molecular Semantics
Papers
Reachability Computation for Switching Diffusions (HSCC'17)
ERODE: A Tool for the Evaluation and Reduction of Ordinary Differential Equations (TACAS'17) Syntactic Markovian Bisimulation for Chemical Reaction Networks A Stochastic Hybrid Approximation for Chemical Kinetics Based on the Linear Noise Approximation (CMSB'15, BioSystems'16) Comparing Chemical Reaction Networks: A Categorical and Algorithmic Perspective (LICS'16) Programming Discrete Distributions with Chemical Reaction Networks (DNA22 '16, NaCo '17) Approximation of Probabilistic Reachability for Chemical Reaction Networks... (QEST'16) Efficient SyntaxDriven Lumping of Differential Equations (TACAS'16) Symbolic Computation of Differential Equivalences (POPL'16) Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation (CMSB'15) Forward and Backward Bisimulations for Chemical Reaction Networks (CONCUR'15) Morphisms of Reaction Networks that Couple Structure to Function (BMC Systems Biology'14) On Process Rate Semantics (TCS'08) A Process Algebra Master Equation (QEST'07) From Processes to ODEs by Chemistry (IFIP TCS'08) A Correct Abstract Machine for the Stochastic Picalculus (BioConcur'04) Efficient, Correct Simulation of Biological Processes in Stochastic Picalculus (CMSB'07) A Graphical Representation for Biological Processes in Stochastic Picalculus (TCSB) Lectures
On Process Rate Semantics (Warsaw Lectures Extract, March'09)
Molecules as Automata  Open Lectures (Warsaw, March&May'09) Molecules as Automata  Summer School on Natural Computation (BNC'08) Process Rate Semantics  Computational and Systems Biology Course (Trento 2008) Talks
Morphisms of Reaction Networks (CMSB'16)
Molecules as Automata (DNA'08, ECS'09) From Processes to ODEs by Chemistry (TCS'08) On Process Rate Semantics (MFPS'08) A Graphical Representation for Stochastic πCalculus (BioConcur '05) A Correct Abstract Machine for the Stochastic picalculus (BioConcur '04) Posters
Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation
(DNA21'15)
Tools
ERODE  SMTbased Automatic Exact Reduction of Ordinary Differential Equations (POPL '16 Artifact Evaluated)
CRNReducer  Automatic exact reduction of Chemical Reaction Networks (CONCUR '15) 

Cell Cycle Switch
Papers
Efficient Switches in Biology and Computer Science (PLOS Computational Biology'17)
Noise Reduction in Complex Biological Switches (Scientific Reports'16) The Cell Cycle Switch Computes Approximate Majority (Scientific Reports'12) Transcriptional Regulation is a Major Controller of Cell Cycle Transition Dynamics (PLoS ONE) Talks
The Cell Cycle Switch Computes Approximate Majority Robert Stewart Distinguished Lecture (Iowa State 2014)
Posters
Evolution of Simple Systems to Complex Behaviours (King's College PhD Symposium'16)
Analyzing Efficiency of Biological Switches (SSBSS'15) Evolution of Biological Switches (King's College PhD Symposium'15) 
Phosphorelays
Papers
Unlimited multistability and Boolean logic in microbial signaling
(J.R.S. Interface)
Phosphorelays provide tunable signal processing capabilities for the cell (PLOS CompBio) Response Dynamics of Phosphorelays Suggest Their Potential Utility in Cell Signaling (J.R.S. Interface) 

Immune System
Papers
A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization
(PLoS Computational Biology)
Projects
A Stochastic πCalculus Models of MHC Class I Antigen Presentation
(Computational Biology MPhil Project)
Links
Selector function of MHC I molecules is determined by protein plasticity
Computational Modeling of Immune System Processes 
Biological Network Modeling
Papers
Computational Modeling of the EGFR Network Elucidates Control Mechanisms Regulating Signal Dynamics
(BMC Systems Biology)
A Process Model of Rho GTPbinding Proteins (FBTC'07) (TCS) A Process Model of Actin Polymerisation (FBTC'08) (ENTCS) Lectures
Biochemical Systems as Reactive Systems  Bioinformatics Master Course (Cabridge '16)
Talks
Biological Networks in Stochastic PiCalculus (Imperial College London 2005)


Systems Biology
Papers
Lineage Grammars: Describing, Simulating and Analyzing Population Dynamics.
(BMC Bioinformatics'14)
An Intuitive Modelling Interface for Systems Biology (DCM'09) (IJSI'13) Abstract Machines of Systems Biology (TCSB) 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) Lectures
Artificial Biochemistry  Graduate Course (Trento, May 2226 '06)
Talks
Speaking the Language of Molecules (CDE Distinguished Lacture, U.Washington)
Living Software (L'INRIA a Quarante Ans) Artificial Biochemistry (Longo Symposium 2007) Can a Systems Biologist Fix a Tamagotchi? (Kahn Colloquium 2007) Abstract Machines of Systems Biology (Dagstuhl 2006) Languages and Notations for Systems Biology (UPP'04 Invited Talk) Links
Adrian Thompson: Evolution of circuits in hardware (archive)

Continuous Markov Processes
Papers on
Continuous Markovian Logic Axiomatization and Quantified Metatheory
(LMCS'12)
Logic Modular Markovian Logic (ICALP'11) Continuous Markovian Logic (CLS'11) Papers on
Stochastic PiCalculus Revisited (ICTAC'13)
Algebra The Measurable Space of Stochastic Processes (QEST'10, Fundamenta Informaticae) Talks
Stochastic PiCalculus Revisited (ICTAC'13)
Continuous Markovian Logic (CSL'11) Modular Markovian Logic (ICALP'11) The Measurable Space of Stochastic Processes (QEST'10) 

Membrane Computing
Papers on
Programming Chemistry in DNA Addressable Bioreactors (Interface '14)
Brane Calculi Brane Calculi (ENTCS, CMSB'04) Bitonal Membrane Systems (TCS) Where Membranes Meet Complexes (BioConcur '05) A Universality Result for a (Mem)Brane Calculus Based on Mate/Drip Operations (IJFCS) Papers on
BioAmbients: An Abstraction for Biological Compartments
(TCS)
BioAmbients Bioware Languages (Computing Systems  A Tribute to Roger Needham) Lectures
Membrane Interactions (CSSB School Rovereto, April'04)
Talks
Bitonal Membrane Systems (MeCBIC'06)
WhereMembranesMeetComplexes (BioConcur'05) Biological Systems as Reactive Systems (ECCS'05) 
Natural Computability
Papers on
Turing Universality of the Biochemical Ground Form
(MSCS)
Termination On the Computational Power of Biochemistry (AB'08) Termination Problems in Chemical Kinetics (CONCUR'08) Papers on
Reversibility in Massive Concurrent Systems
(SACS)
Reversibility Reversible Structures (CMSB '11) Talks
Termination Problems in Chemical Kinetics (CONCUR'08)
On The Computational Power of Biochemistry (AB'08) Reversible Structures (CMSB'11) 

Stochastic Gene Networks
Papers
A Compositional Approach to the Stochastic Dynamics of Gene Networks
(TCSB)
Compositionality, Stochasticity and Cooperativity in Dynamic Models of Gene Regulation (HFSP Journal) Talks
A Compositional Approach to the Stochastic Dynamics of Gene Networks (Concur '05)

Geometric Process Algebra
Papers
Processes in Space
(CiE'10, TCS 2012)
Talks
Processes in Space(CiE'10)
Pi in the Sky: Spatial Process Algebra for Developmental Biology (MeCBIC'09) 

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