Algorithmic Systems Biology Course (ASBCourse09) starting on 25/3/09: it is an internal course organized by CoSBi and open to our collaborators.

Seminars 2010

Speaker	Title	Date
Kathryn McKinley	Towards Parallel Scalable Virtual Machine Services	23-06-2010
Rocco De Nicola	Compositional modelling of concurrent systems and their quantitative evaluation	21-06-2010
Alfred Aho	Computational Thinking in Language Design	14-06-2010
Nitin Baliga	Predicting consequences of environmental change on biological systems	08-06-2010
Joost Pieter Katoen	Verifying Large --and Infinite-- Markov Chains	26-05-2010
Lone Leth Thomsen	Project-oriented and problem based learning (POPBL) in Computer Science at Aalborg University	11-05-2010
Bent Thomsen	Trends in Programming Technology	11-05-2010
Jurg Baehler	Dynamic Repertoire of the Fission Yeast Transcriptome Surveyed at Single-Nucleotide Resolution	04-05-2010
Caner Kazanci	Network Particle Tracking (NPT) for Ecological Network	27-04-2010
Stefano Pluchino	Noncoding RNAs and therapeutic plasticity of neural stem cells	30-03-2010
Tina W. Wey	Causes and consequences of social variation in yellow-bellied marmots	17-03-2010
George Kampis	Food webs form RNA: "fat phenotypes" in interaction	03-03-2010
Kim Guldstrand Larsen	Validation, Performance Analysis and Synthesis of Embedded Systems Kim G Larsen	16-02-2010
Lars Juhl Jensen	Just-in-time assembly: transcriptional and post-translational cell-cycle regulation of protein complexes	12-01-2010

Seminars 2009

Speaker	Title	Date
Greg Morrisett	Verifying Systems Software	15-12-2009
Dirk Pattinson	Knowledge Representation in Coalgebraic Logics	03-11-2009
Gul Agha	Space,Time, Probability, and Energy: Understanding Concurrent Computation	27-10-2009
Giovanni Sena	Plant organ regeneration: measuring self-organization	23-10-2009
Kevin Burrage	The visible cell: spatial-temporal modelling of processes in the living cell	20-10-2009
Jasmin Fisher	The Executable Pathway to Biological Networks	13-10-2009
Aneil Mallavarapu	Little b a language for modular biological models	23-09-2009
Vito Quaranta	Heterogeneity of Cancer Cell Phenotypic Traits	15-09-2009
Alissa Weaver	Integration of Experimentation with Modeling	15-09-2009
René Thomas	Circular causality: the crucial roles of circuits in biology and nonlinear dynamics	08-09-2009
Carlos J. Melian	Making connections between systems biology and evolving ecological networks	28-07-2009
Hans Meinhardt	Models for pattern formation in the development of higher organisms	15-07-2009
Eors Szathmary	the origin of natural language	30-06-2009
Benjamin Pierce	Foundations for Bidirectional Programming	24-06-2009
Tony Hoare	Graphical models of program behaviour	23-06-2009
Tony Hoare	Unifying models of data flow	22-06-2009
Richard Goldstein	Piecing together the history of the 1918 Spanish Flu epidemic	09-06-2009
David Basanta	An integrated computational approach to study cancer evolutionary dynamics	19-05-2009
Carloyn Talcott	Symbolic Systems Biology: Using Formal Methods Tools to Model Biological Processes	14-05-2009
Hiroki R. Ueda	Systems Biology of Biological Time	12-05-2009
Michele Forlin	ASBCourse09: Evolutionary approaches to inference	07-05-2009
Corrado Priami	ASBCourse09: Concluding remarks	07-05-2009
Matteo Cavaliere Attila Csikasz-Nagy	ASBCourse09: Tissue formation and the hallmarks of cancer	06-05-2009
Joerg Stelling	ASBCourse09: Geometries and dynamics of cellular networks	05-05-2009
Orkun Soyer	ASBCourse09: Evolution of biological networks	05-05-2009
Orkun Soyer	ASBCourse09: Co-evolution of host networks with their parasites	05-05-2009
Radu Mardare	ASBCourse09: Logical specification of systems	30-04-2009
Paolo Ballarini	ASBCourse09: Model checking: Model checking	30-04-2009
Paola Lecca	ASBCourse09: Diffusion and space: Diffusion and space	30-04-2009
Ivan Mura	ASBCourse09: Statistical analysis of simulation output	29-04-2009
Ivan Mura	ASBCourse09: Filtering and Monitoring	29-04-2009
Davide Prandi	ASBCourse09: Static and dynamic representations, static analysis and causality	29-04-2009
Alida Palmisano	ASBCourse09: Hybrid methods	23-04-2009
Hiroyuki Kuwahara	ASBCourse09: Stochastic simulation	23-04-2009
Sean Sedwards	ASBCourse09: Fourier analysis	23-04-2009
Alessandro Romanel	ASBCourse09: Process algebra (BlenX)	22-04-2009
Paolo Ballarini	ASBCourse09: Narrative modeling framework	22-04-2009
Paola Lecca Alida Palmisano	ASBCourse09: Biochemical kinetics, inference and missing information	22-04-2009
Mark Girolami	Inference-Based Modelling Establishes the Role of BRaf in ERK Signalling	07-04-2009
Attila Csikasz-Nagy	ASBCourse09: Continuous modeling and analysis	03-04-2009
Ferenc Jordan	ASBCourse09: Network software	02-04-2009
Ivan Mura	ASBCourse09: Petri Nets	02-04-2009
Matteo Cavaliere Sean Sedwards	ASBCourse09: P-systems and Colonies	02-04-2009
Matteo Cavaliere	ASBCourse09: Graph rewriting and game theory	01-04-2009
Ferenc Jordan	ASBCourse09: Networks and network analysis	01-04-2009
Jose Garcia Manteiga	ASBCourse09: High-throughput tools	27-03-2009
Jose Garcia Manteiga	ASBCourse09: Experimental design	27-03-2009
Adaoha Ihekwaba	ASBCourse09: Role of modelling, a comprehensive example: NF – kB	27-03-2009
Tommaso Mazza	ASBCourse09: Standards	27-03-2009
Orkun Soyer	ASBCourse09: Regulation of motility in bacteria / chemotaxis	26-03-2009
Ferenc Jordan	ASBCourse09: Challenges coming from population and ecosystem dynamics	26-03-2009
Phuong Nguyen	ASBCourse09: In silico databases	26-03-2009
Ferenc Jordan Corrado Priami	ASBCourse09: Systems biology	25-03-2009
Judit Zamborszky	ASBCourse09: Challenges coming from molecular biology	25-03-2009
Walter Fontana	Programs as models: Rule-based representations of complex molecular networks of interaction	17-03-2009
Kohei Honda	Pi-calculus and Abstraction of Interactional Behaviour	17-02-2009

Seminars 2008

Speaker	Title	Date
David Fell	Genome-Scale Modelling of Metabolism	02-12-2008
Ferenc Jordan	Topology and function: the role of central nodes in networks	27-11-2008
Rafael Carazo Salas	Dynamics of microtubule organization in live cells	11-11-2008
Sydney Brenner	The Architecture of Biological Complexity	04-11-2008
Mike Hall	TOR signaling and control of cell and organism growth	29-10-2008
Francois Kepes	Epigenomics and morphodynamics	21-10-2008
Andras Horvàth	Parameter estimation of kinetic rates in stochastic reaction networks by the em method	14-10-2008
Michael Hucka	An Overview of Several Standardization Efforts for Computational Systems Biology	30-09-2008
Hidde de Jong	Qualitative Modeling and Simulation of Bacterial Regulatory Networks	24-09-2008
Michael Samoilov	Engineering Designs of Biological Networks: Facilitating Computational Inference and Analysis of Biological Systems with Biochemical and Biophysical Modeling	16-09-2008
Flemming Nielson	MT-LAB - Static Analysis and Model Checking	09-09-2008
Danyel Fisher	Recent Information Visualization Work from Microsoft Research	29-07-2008
Cristian Calude	Halting or Non-Halting: That is the Question	22-07-2008
Robin Milner	The space and stochastic motion of bigraphs (2)	17-06-2008
Robin Milner	The space and stochastic motion of bigraphs (1)	16-06-2008
Dan Gillespie	Stochastic Chemical Kinetics	29-05-2008
Alexander Kurz	Coalgebraic Logic and Pi-Calculus in Logical Form (2)	14-05-2008
Alexander Kurz	Coalgebraic Logic and Pi-Calculus in Logical Form (1)	13-05-2008
Ian Laurenzi	Fast and exact stochastic simulation of the hybridization of DNA to microarrays	06-05-2008
Frederick R. Cross	Quantitative tests of models of cell cycle control in budding yeast	15-04-2008
Christian I. Hong	A Mathematical Model of Neurospora crassa Circadian Rhythms Provides Insights To Molecular Mechanisms	01-04-2008
Irun Cohen	Working day on computational systems biology	14-03-2008
Shuki Bruck	Working day on computational systems biology	14-03-2008
Gianni Cesareni	Working day on computational systems biology	14-03-2008
Ana Martins	A systems biology study of the early dynamical response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide	11-03-2008
Andrei Paun	Discrete nondeterministic modeling of cellular pathways	04-03-2008
Muffy Calder	Verification challenges of cell signalling	19-02-2008
Gianluigi Zavattaro	On the Computational Power of Biochemistry	14-02-2008
Patrick Cousot	Abstract Interpretation and Application to Static Analysis of Critical Software	05-02-2008
Tamás Turányi	Analysis of a budding yeast cell cycle model using the shapes of local sensitivity functions	31-01-2008
Peter Csermely	Stability, creativity and evolution of cellular networks	29-01-2008
Martí Aldea	Sizing cells with a speedometer?	24-01-2008
Radhika Nagpal	Emergent Geometric Order: Cell Division in Proliferating Tissue Networks.	08-01-2008

Seminars 2007

Speaker	Title	Date
Jorge Carneiro	Regulation robustness in the immune system	27-11-2007
Andrea Musacchio	Protein networks that control the process of microtubule-kinetochore attachment during cell division	20-11-2007
Andrea Ciliberto	An autocatalytic circuit is required for an efficient sequestration of Cdc20 by Mad2	20-11-2007
Pedro Mendes	Adventures in Reverse Engineering of Biochemical Networks	16-11-2007
Radu Mardare	Robustness: from randomness to logical deduction	15-11-2007
Jason Zwolak	"PET: A Tool for Estimating Rate Constants in Models of Molecular Networks"	13-11-2007
John J. Tyson	Regulation of the Eukaryotic Cell Cycle: From Molecular Networks to Cell Physiology	23-10-2007
Marek Kwiatkowski	A process algebraic approach to robustness and evolvability of biochemical pathways.	16-10-2007
Marvin Cassman	Modularity and robustness in mechanistic modeling	08-10-2007
Leroy Hood	Systems Biology and Systems Medicine	08-10-2007
Manuel Peitsch	How can Systems Biology impact Pharmaceutical Research?	08-10-2007
Judy Armitage	Systems Biology in Oxford: Microbial Sensory Networks and Cautionary Tales	08-10-2007
Richard R. Neubig	Simplicity and complexity in G protein signaling	11-09-2007
David Liberles	Gene duplication and functional evolution	04-09-2007
Vanna Micheli	Purine metabolism of human erythrocyte as a model of study.	10-07-2007
Sailesh Chutani	Rethinking the role of ICT in Healthcare	05-07-2007
Ehud Keinan	Bio-Molecular Computing Devices	22-06-2007
Hisao Moriya	Upper limit dosage of genes involved in cell division cycle in S. pombe.	13-06-2007
Alberto Policriti	Stochastic Biological Modeling and Differential Equations	15-05-2007
Yuri Gurevich	The Abstract State Machine Approach	08-05-2007
Melvin Cohn	Default model of the decision process of the immune system	18-04-2007
Dennis Bray	Computer-based Analysis of Bacterial Chemotaxis	12-04-2007
Judy Armitage	Modelling the E.coli chemosensory pathway: strengths and weaknesses	22-03-2007
Ivan Mura	Stochastic Petri Net languages and tools for modeling and analyzing complex systems	13-03-2007
Csaba Pal	Evolution of metabolic networks	06-03-2007
Luca Cardelli	Artificial Biochemistry	21-02-2007
Andrea Becchetti	Modulation of the cerebral cortex by the ascending cholinergic system: physiology, pathology and theoretical problems.	20-02-2007
Marcel Salathé	Sex - the queen of puzzles in evolutionary biology	15-02-2007
Guido Sanguinetti	Bayesian inference in systems biology and bioinformatics: some examples.	13-02-2007
Vladimiro Sassone	Semantic barbs: what's in an observation?	06-02-2007
Gianfranco Balbo	Stochastic Petri Nets in practice	30-01-2007
Rich Williams	Structure and Dynamics of Complex Food Webs	16-01-2007

Seminars 2006

Speaker	Title	Date
Stefano Monti	Molecular Cancer Classification: from Integrative Data Analysis to Therapeutics	07-12-2006
Adam Wasserstrom	Reconstructing Cell Lineage Trees - The Brighter Side of Mutations	30-11-2006
Attila Csikasz-Nagy	Models of eukaryotic cell cycle regulation	22-11-2006
Wolfgang Marwan	Reconstructing the Network Controling Commitment to Cell Differentiation in the Eukaryote Physarum polycephalum	16-11-2006
Herbert Sauro	An Overview of Research Efforts: Standardization and Modularity	14-11-2006
Grzegorz Rozenberg	Gene Assembly in Ciliates - a Splendid Example of Natural Computing	09-11-2006
Ruth Baker	Mathematical modelling in developmental biology	07-11-2006
Gheorghe Păun	Membrane Computing: Power, Efficiency, Applications (Introduction and Some Recent Results)	26-10-2006
Mihai Ionescu	Spiking Neural P Systems: Results and New Model	05-10-2006
Enrico Blanzieri	Detecting Uncertainty in Microarray Data Labeling by Data Perturbation	28-09-2006
John Heath	Computational reasoning about biological signalling pathways	21-09-2006
George Cowan	Modeling and Prediction in Early Stage Drug Discovery	14-09-2006
Pietro Liò	A topological analysis of a network of periodic genes in S. pombe cell cycle	06-07-2006
Francesco Amato	Reconstruction of Biological Interaction Networks: A Linear Matrix Inequalities Approach	05-07-2006
Diego Di Bernardo	Reverse engineering of genetic networks and its applications to biology and drug discovery	22-06-2006
Forbes Dewey	An Integrated Software Architecture to Support Modern Experimental Biology	21-06-2006
Forbes Dewey	Distributed Computing of Complex Collections of Biological Pathways	20-06-2006
Holger Hoos	An High-Performance Heuristic Approach for Finding Maximum Cliques in Graphs with Applications to Analysing Market Data and Biological Systems	19-06-2006
Marta Kwiatkowska	Probabilistic model checking of biological processes	16-06-2006
Giovanni Sebastiani	Bayesian Analysis of Signals and Images with Applications to Medicine and Biology	08-06-2006
Luca Cardelli	Artificial Biochemistry	22-05-2006
Dominique Chu	Understanding "Orientational Control" of phase variation in the E.coli fim system.	18-05-2006
Henry Adorna	Modeling the Receptor-Mediated Pathway of Apoptosis Using Hybrid Petri Nets	11-05-2006
Natasha Jonoska	Computing by DNA Graph Self-Assembly	08-05-2006
Celine Kuttler	Simulation of bacterial transcription and translation in the pi calculus.	04-05-2006
Jane Hillston	Process algebra abstractions of biochemical pathways	30-03-2006
Corrado Priami	Process calculi for biology	23-03-2006
Nadia Busi	Expressiveness issues in Brane Calculi	16-03-2006
Ralf Blossey	A compositional approach to the stochastic dynamics of gene networks	23-02-2006
Andrew Phillips	Simulating Biological Systems in the Stochastic Pi-calculus	23-02-2006
Charles Auffray	Systems Biology: a Research Strategy to Tackle Biological Complexity in Medicine.	21-02-2006
Jaroslaw Wisniewski	On phylogenetic trees from algebraic geometer's point of view	16-02-2006
Ela Hunt	Moving data integration and visualisation support into the database engine	02-02-2006
Pierpaolo Degano	VICE: a virtual cell	01-02-2006
Gordon Plotkin	A Calculus for Biochemical Systems	26-01-2006
Sean Sedwards	An Introduction to Chaos and Chaotic Spiking Neurons	19-01-2006
Matteo Cavaliere	Membrane Systems with Marked Membranes	12-01-2006