Advances in numerical and analytic approaches for the study of non-spatial stochastic dynamical systems in molecular biology

Workshop theme

This workshop focuses on numerical methods and mathematical analysis for non-spatial stochastic dynamical models that arise in molecular biology. New experimental techniques at a molecular level boosted the interest for such models in recent years, for example for gene regulatory networks, biochemical signaling and transduction cascades, molecular motors, and morphogenesis. The workshop brings together computational, mathematical, and experimental scientists, with attention falling on both current research and promising avenues for future research. It reports on the exciting synergistic interplay between advanced experimental, computational, and mathematical techniques that together provide a deeper understanding of the biological system.

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Timetable

Monday 4th April 2016
09:00 to 09:20	Registration	Room 1
09:20 to 09:30	Welcome from Christie Marr (INI Deputy Director)	Room 1
09:30 to 10:15	Thomas Kurtz University of Wisconsin-Madison Approximations for Markov chain models	Room 1
10:15 to 11:00	James Faeder University of Pittsburgh Towards large scale models of biochemical networks	Room 1
11:00 to 11:30	Morning Coffee	No Room Required
11:30 to 12:15	Simon Cotter University of Manchester A constrained approach to the simulation and analysis of stochastic multiscale chemical kinetics	Room 1
12:15 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 14:45	Raul Fidel Tempone King Abdullah University of Science and Technology (KAUST) Efficient Simulation and Inference for Stochastic Reaction Networks	Room 1
14:45 to 15:30	Erkki Somersalo Case Western Reserve University tba	Room 1
15:30 to 16:00	Afternoon Tea	No Room Required
16:00 to 16:45	Poster pitches	No Room Required
16:45 to 18:00	Welcome Wine Reception and Poster Session	No Room Required

Tuesday 5th April 2016
09:00 to 09:45	Rosalind Allen University of Edinburgh Inherent variability in the kinetics of amyloid fibril formation	Room 1
09:45 to 10:30	Muruhan Rathinam University of Maryland, Baltimore County Analysis of Monte Carlo estimators for parametric sensitivities in stochastic chemical kinetics	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:45	David Doty University of California, Davis "No We Can't": Impossibility of efficient leader election by chemical reactions	Room 1
11:45 to 12:30	Jay Newby First-passage time to clear the way for receptor-ligand binding in a crowded environment	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 14:45	John Albeck University of California, Davis Linking dynamic signaling events within the same cell	Room 1
14:45 to 15:30	Aleksandra Walczak ENS - Paris tba	Room 1
15:30 to 16:00	Afternoon Tea	No Room Required
16:00 to 16:45	Vahid Shahrezaei Inference of size dependence of transcription parameters from single cell data using multi-scale models of gene expression	Room 1

Wednesday 6th April 2016
09:00 to 09:45	Omer Dushek Cellular signalling in T cells is captured by a tractable modular phenotypic model	Room 1
09:45 to 10:30	Eric Deeds University of Kansas tba	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:45	Carlos Lopez Vanderbilt University Intracellular signaling processes and cell decisions using stochastic algorithms	Room 1
11:45 to 12:30	Tomas Vejchodsky Tensor methods for higher-dimensional Fokker-Planck equation	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
13:30 to 17:00	Free Afternoon	No Room Required

Thursday 7th April 2016
09:00 to 09:45	Pieter Rein ten Wolde Fundamental limits to transcriptional regulatory control	Room 1
09:45 to 10:30	Andrew Duncan Hybrid modelling of stochastic chemical kinetics	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:45	Kevin Burrage Queensland University of Technology Sampling Methods for Exploring Between Subject Variability in Cardiac Electrophysiology Experiments	Room 1
11:45 to 12:30	Vikram Sunkara Freie Universität Berlin; Konrad-Zuse-Zentrum für Informationstechnik Berlin Insights into the dynamics of Hybrid Methods through a range of biological examples. A hands on approach	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 14:45	Carmen Molina-Paris University of Leeds A stochastic story of two receptors and two ligands	Room 1
14:45 to 15:30	Ankit Gupta ETH Zürich Stability properties of stochastic biomolecular reaction networks: Analysis and Applications	Room 1
15:30 to 16:00	Afternoon Tea	No Room Required
16:00 to 16:45	Mustafa Khammash ETH Zürich Subtle is the noise, but malicious it is not: dynamic exploits of intracellular noise	Room 1
19:30 to 22:00	Formal Dinner at Christ's College	No Room Required

Friday 8th April 2016
09:00 to 09:45	Yiannis Kaznessis Closure Scheme for Chemical Master Equations - Is the Gibbs entropy maximum for stochastic reaction networks at steady state?	Room 1
09:45 to 10:30	Darren Wilkinson Newcastle University Scalable algorithms for Markov process parameter inference	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:45	Christian Ray University of Kansas Lineage as a conception of space in compartmental stochastic processes across cellular populations	Room 1
11:45 to 12:30	Ramon Grima University of Edinburgh The system-size expansion of the chemical master equation: developments in the past 5 years	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required

Stochastic dynamical systems in biology: numerical methods and applications

Advances in numerical and analytic approaches for the study of non-spatial stochastic dynamical systems in molecular biology

Organisers

David Anderson
Radek Erban
Samuel Isaacson
Carlos Lopez Vanderbilt University
Jürgen Reingruber CNRS - Ecole Normale Superieure Paris
Konstantinos Zygalakis

Speakers

John Albeck University of California, Davis
Rosalind Allen University of Edinburgh
Kevin Burrage Queensland University of Technology
Simon Cotter University of Manchester
Eric Deeds University of Kansas
David Doty University of California, Davis
Andrew Duncan
Omer Dushek
James Faeder University of Pittsburgh
Ramon Grima University of Edinburgh
Ankit Gupta ETH Zürich
Yiannis Kaznessis
Mustafa Khammash ETH Zürich
Thomas Kurtz University of Wisconsin-Madison
Carlos Lopez Vanderbilt University
Carmen Molina-Paris University of Leeds
Jay Newby
Muruhan Rathinam University of Maryland, Baltimore County
Christian Ray University of Kansas
Vahid Shahrezaei
Erkki Somersalo Case Western Reserve University
Vikram Sunkara Freie Universität Berlin; Konrad-Zuse-Zentrum für Informationstechnik Berlin
Raul Fidel Tempone King Abdullah University of Science and Technology (KAUST)
Pieter Rein ten Wolde
Tomas Vejchodsky
Aleksandra Walczak ENS - Paris
Darren Wilkinson Newcastle University

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Participants

Assyr Abdulle
Rosalind Allen University of Edinburgh
David Anderson University of Wisconsin-Madison
Steve Andrews Fred Hutchinson Cancer Research Centre
Sandro Azaele
Chiheb Ben Hammouda King Abdullah University of Science and Technology (KAUST)
Pamela Burrage Queensland University of Technology
Kevin Burrage Queensland University of Technology
Daniele Cappelletti Københavns Universitet (University of Copenhagen)
Jérôme Cartailler École Normale Supérieure
Dominique Chu University of Kent
Edward Codling
Simon Cotter University of Manchester
Ulrich Dobramysl University of Cambridge
David Doty University of California, Davis
Andrew Duncan
Omer Dushek
Richard Dybowski University of Cambridge
German A. Enciso
Radek Erban University of Oxford
James Faeder University of Pittsburgh
Raymond Goldstein University of Cambridge
Ramon Grima University of Edinburgh
Claire Guerrier CNRS - Ecole Normale Superieure Paris; CREST and Université Paris 6
Ankit Gupta ETH Zürich
Mads Christian Hansen University of Copenhagen
David Holcman CNRS - Ecole Normale Superieure Paris
Nick Jones Imperial College London
Yiannis Kaznessis
Jinsu Kim University of Wisconsin-Madison
Peter Roland Kramer Rensselaer Polytechnic Institute
Thomas Kurtz University of Wisconsin-Madison
Rachel Kuske University of British Columbia
André Leier
Ben Leimkuhler University of Edinburgh
Christopher Lester University of Oxford
Tiejun Li Peking University
Shuohao Liao University of Oxford
Karen Lipkow University of Cambridge
Alexander Lubbock Vanderbilt University
Per Lötstedt
Tatiana T Marquez Lago
Carmen Molina-Paris University of Leeds
Bence Mélykúti Albert-Ludwigs-Universität Freiburg
Olga Nev University of Warwick
Jay Newby
Marco Nobile Università degli Studi di Milano - Bicocca
James Norris University of Cambridge
Abhishek Pal Majumder Københavns Universitet (University of Copenhagen)
Federico Paoletti University of Oxford
James Pino Vanderbilt University
Tomislav Plesa University of Oxford
Muruhan Rathinam University of Maryland, Baltimore County
Christian Ray University of Kansas
Jürgen Reingruber CNRS - Ecole Normale Superieure Paris
Sten Rüdiger
David Schnoerr University of Edinburgh
Vahid Shahrezaei
Erkki Somersalo Case Western Reserve University
Michael Stich Aston University
Vikram Sunkara Freie Universität Berlin; Konrad-Zuse-Zentrum für Informationstechnik Berlin
Raul Fidel Tempone King Abdullah University of Science and Technology (KAUST)
Pieter Rein ten Wolde
Philipp Thomas Imperial College London
Tomas Vejchodsky
Pedro Andres Vilanova King Abdullah University of Science and Technology (KAUST)
Artur Wachtel Université du Luxembourg
Aleksandra Walczak ENS - Paris
Jonathan Wattis
Darren Wilkinson Newcastle University
Chaojie Yuan University of Wisconsin-Madison
Romain Yvinec INRA - Institut National de la Recherche Agronomique
Ying Zhang Boston University
Konstantinos Zygalakis University of Southampton