Highlights
Maximal aggregation of polynomial dynamical systems (PNAS'17)
Morphisms of Reaction Networks that Couple Structure to Function (BMC Systems Biology'14)
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Programmable chemical controllers made from DNA (Nature Nanotech'13)
The
Cell Cycle Switch Computes Approximate Majority (Scientific eports'12)
Programming Chemistry in DNA Addressable Bioreactors (Interface '14)
Two-Domain
DNA Strand Displacement (MSCS'13)
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Molecular Programming
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The goal of molecular
programming is the systematic manipulation of matter at
the molecular scale, for applications in engineering +
technology and biology + medicine.
Structural DNA/RNA nanotechnology currently provides the
only fabrication pipeline for truly programmable
molecular structures, in the form of static and dynamic
nucleic acid assemblies. But through it we can organize
also other forms of matter.
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Papers
Syntax-Guided
Optimal Synthesis for Chemical Reaction Networks
(CAV'17)
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)
Two-Domain
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)
Two-Domain
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
|
The semantics of programming
languages is based on states and state transitions,
through which one can study for example termination,
nodeterminism, and concurrency. Adding rates to
transitions induces quantitative meanings that can be
related to stochastic and continuous dynamical systems,
and to their realizations as molecular systems.
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Papers
Maximal aggregation of polynomial dynamical systems (PNAS'17)
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,
TCS'17)
Programming Discrete Distributions with Chemical Reaction
Networks (DNA22 '16, NaCo '17)
Approximation of Probabilistic Reachability for Chemical
Reaction Networks... (QEST'16)
Efficient Syntax-Driven 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 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)
Processes in Space (CiE'10, TCS 2012)
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 π-Calculus
(BioConcur '05)
A Correct Abstract Machine for the Stochastic pi-calculus (BioConcur '04)
Processes in Space (CiE'10)
Pi in the Sky: Spatial Process Algebra for Developmental Biology (MeCBIC'09)
Posters
Stochastic Analysis of Chemical Reaction Networks Using Linear
Noise Approximation (DNA21'15)
Tools
ERODE
- SMT-based Automatic Exact Reduction of Ordinary Differential
Equations (POPL '16 Artifact
Evaluated)
CRNReducer
- Automatic exact reduction of Chemical Reaction Networks (CONCUR '15) |
Cell Cycle Switch
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At the core of the
biochemical networks that regulates the cell
cycle there is a switch that triggers an
irreversible transition from one critical
stage of cell division to the next. Its
dynamical system behavior is fairly well
understood, and could be achieved by many
different networks. But in nature, from yeast
to us, we find a specific universal structure
of the network: what is special about this
structure, beyond its required function? To
answer this question we shift our perspective
from dynamical systems to computing systems.
We ask: what does the cell cycle switch
compute, and how does it compute it?
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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
|
Organisms employ a variety of
signalling systems to sense and react to their
environment. Among the most basic, commonly found in
bacteria, lower eukaryotes and plants, are the so-called
phosphorelays. These systems transfer sensor information
(typically from the cellular membrane) very economically
through a chain of chemical reactions.
Despite their widespread use and simple architecture, we
are still far from a full understanding of the
signal-processing capabilities of 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
|
Major Histocompatibility
Complex (MHC) class I molecules are a key component of
the innate immune system. They continuously select a
signature of the cell contents (fragments of any protein
present) and present it to the cell surface, where it
can be inspected by cytotoxic T lymphocytes that destroy
virus-infected and cancerous cells based on such
signature. In this mechanism there is a trade-off
between speed and accuracy of presentation: we study how
various molecular components contribute to optimizing
this process.
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Papers
A
Peptide Filtering Relation Quantifies MHC Class I Peptide
Optimization (PLoS Computational
Biology)
Projects
A
Stochastic π-Calculus 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
|
We use stochastic pi-calculus
to represent and then simulate interactions within
protein networks. The pi-calculus approach allows a
biological system to be programmed in a scalable manner,
by allowing models of individual proteins to be directly
composed to form subsystems, which can in turn be
composed together to form larger systems. This allows
new components to be added incrementally without having
to re-wire the existing model, which also improves the
usability of models. Furthermore, the modular structure
of the biological system and the pi-calculus model are
in direct correspondence.
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Papers
Computational
Modeling of the EGFR Network Elucidates Control Mechanisms
Regulating Signal Dynamics (BMC
Systems Biology)
A
Process Model of Rho GTP-binding 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 Pi-Calculus (Imperial
College London 2005) |
Systems Biology
|
An abstract machine is a
fictional information-processing device that can, in
principle, have a number of different physical
realizations (mechanical, electronic, biological, or
software). Biochemical toolkits in cellular biology
(nucleotides, amino acids, and phospholipids) can be
seen as abstract machines with appropriate sets of
states and operations, corresponding respectively to
genes, proteins, and membranes. To understand the
functioning of a cell, one must understand (at least)
how the various machines interact. This involves
considerable difficulties in modeling and simulations
because of the drastic differences in the "programming
model" of each machine, and in the time and size scales
involved.
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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)
A Compositional Approach to the Stochastic Dynamics of Gene Networks (TCSB)
Compositionality, Stochasticity and Cooperativity in Dynamic Models of Gene Regulation (HFSP ournal)
Lectures
Artificial Biochemistry - Graduate Course (Trento, May 22-26 '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)
A Compositional Approach to the Stochastic Dynamics of Gene Networks (Concur '05)
Links
Adrian Thompson: Evolution of circuits in hardware (archive)
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Continuous Markov Processes
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We introduce stochastic
extensions of process algebras endowed with structural
operational semantics expressed in terms of measure
theory. The set of processes is organised as a
measurable space by the sigma-algebra generated by
structural congruence. The structural operational
semantics associates to each process a set of measures
over the space of processes. The measures encode the
rates of the transitions from a process (state of a
system) to a measurable set of processes. We prove that
stochastic bisimulation is a congruence that extends
structural congruence. In addition to an elegant
operational semantics, our approach provides a canonic
way to define metrics on processes that measure how
similar two processes are in terms of behaviour.
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Papers on
Logic
Continuous
Markovian Logic Axiomatization and Quantified Metatheory (LMCS'12)
Modular
Markovian Logic (ICALP'11)
Continuous
Markovian Logic (CLS'11)
Papers on
Algebra
Stochastic Pi-Calculus Revisited (ICTAC'13)
The
Measurable Space of Stochastic Processes (QEST'10,
Fundamenta Informaticae)
Talks
Stochastic Pi-Calculus Revisited (ICTAC'13)
Continuous Markovian Logic (CSL'11)
Modular Markovian Logic (ICALP'11)
The Measurable Space of Stochastic Processes (QEST'10)
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Membrane Computing
|
The basic physical operations
on membranes are local fusion (two patches merging) and
local fission (one patch splitting in two). When seen at
the global scale of whole membranes, these local
operations induce four transformations: in addition to
the obvious splitting (Mito) and merging (Mate) of
membranes, there are also operation, quite common in
reality, that cause a membrane to eat (Endo) or spit
(Exo) another subsystem. Although this is an unusual
computational model, the membrane operations supports
the execution of real algorithms, some of which occur in
nature. Some sets of operations are Turing-complete, and
can encode the other membrane operations.
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Papers on
Brane Calculi
Programming Chemistry in DNA Addressable Bioreactors (Interface '14)
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
BioAmbients:
An Abstraction for Biological Compartments
(TCS)
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)
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Natural Computability
|
We investigate the question of
whether basic chemical kinetics (kinetics of unar yand
binary chemical reactions), formulated as a process
algebra, is capable of general computation. In
particular, we investigate nondeterministic and
probabilistic termination problems. The answers to those
problems reveal a surprisingly rich picture of what is
decidable and undecidable in basic chemistry.
We introduce an algebra for massive concurrent systems,
called reversible structures, where terms retain bits of
causal dependencies that allow one to reverse
computation histories. These bits permit to trace
effects of interactions, but not to the point of being
able to identify the precise molecule that caused an
effect. The algebra and the causal hints match a
particular form of DNA computation.
|
Papers on
Termination
Turing Universality of the Biochemical Ground Form (MSCS)
On the Computational Power of Biochemistry (AB'08)
Termination Problems in Chemical Kinetics (CONCUR'08)
Papers on
Reversibility
Reversibility
in Massive Concurrent Systems (SACS)
Reversible
Structures (CMSB '11)
Talks
Termination Problems in Chemical Kinetics (CONCUR'08)
On The Computational Power of Biochemistry (AB'08)
Reversible Structures (CMSB'11) |
University of Oxford Computer Science
| Automated Verification Group
Microsoft Research Cambridge
| Biological Computation Group
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