COSBI - seminars

Martiall Guillaud: In silico model-based platform for the study of preneoplastic epithelial growth: application to oral, cervical and lung cancer
23 November 2011
Matteo Cavaliere: Formation and Sustainability of Cooperative Communities
08 November 2011
Andre S. Ribeiro: Dynamics of Gene Expression in Escherichia Coli: models and measurements at the single event level
27 September 2011
Catherine Yule: The Impact of Disturbance on the Food Webs of Tropical Streams
11 July 2011
Michael Mueller: From nutrigenomics to nutritional systems biology of fatty acid sensing
28 June 2011
Vahid Shahrezaei: Rule based modelling and switch-like response in biochemical networks
06 June 2011
Yoshihiro Yamanishi: Predicting drug-target interaction networks from the integration of chemical, genomic and pharmacological spaces
12 May 2011

Of yeast and men: a comparative nutritional systems biology approach to understand robustness and evolvability of fatty acid metabolic networks

Marco Villani: Of yeast and men: a comparative nutritional systems biology approach to understand robustness and evolvability of fatty acid metabolic networks

07 April 2011

Duccio Cavaliere: S.cerevisiae as a model in nutritional systems biology
07 April 2011
Lucas Joppa: Niche structure and nestedness of mutualistic and antagonistic bipartite networks
15 March 2011
Larry Wall: That Goes Without Saying (or Does It)
17 February 2011
Herbert Wiklicky: Probabilistic Program Semantics and Analysis
26 October 2010
Susumu Goto: KEGG databases for pathway prediction
19 October 2010
David Galas: At the boundary between systems biology and human genetics
04 October 2010
Kathryn McKinley: Towards Parallel Scalable Virtual Machine Services
23 June 2010
Rocco De Nicola: Compositional modelling of concurrent systems and their quantitative evaluation
21 June 2010
Alfred Aho: Computational Thinking in Language Design
14 June 2010
Nitin Baliga: Predicting consequences of environmental change on biological systems
08 June 2010
Joost Pieter Katoen: Verifying Large --and Infinite-- Markov Chains
26 May 2010
Lone Leth Thomsen: Project-oriented and problem based learning (POPBL) in Computer Science at Aalborg University
11 May 2010
Bent Thomsen: Trends in Programming Technology
11 May 2010
Jurg Baehler: Dynamic Repertoire of the Fission Yeast Transcriptome Surveyed at Single-Nucleotide Resolution
04 May 2010
Caner Kazanci: Network Particle Tracking (NPT) for Ecological Network
27 April 2010
Stefano Pluchino: Noncoding RNAs and therapeutic plasticity of neural stem cells
30 March 2010
Tina W. Wey: Causes and consequences of social variation in yellow-bellied marmots
17 March 2010
George Kampis: Food webs form RNA: "fat phenotypes" in interaction
03 March 2010
Kim Guldstrand Larsen: Validation, Performance Analysis and Synthesis of Embedded Systems Kim G Larsen
16 February 2010
Lars Juhl Jensen: Literature mining and large-scale data integration
12 January 2010
Lars Juhl Jensen: Just-in-time assembly: transcriptional and post-translational cell-cycle regulation of protein complexes
12 January 2010
Greg Morrisett: Verifying Systems Software
15 December 2009
Dirk Pattinson: Knowledge Representation in Coalgebraic Logics
03 November 2009
Gul Agha: Space,Time, Probability, and Energy: Understanding Concurrent Computation
27 October 2009
Giovanni Sena: Plant organ regeneration: measuring self-organization
23 October 2009
Kevin Burrage: The visible cell: spatial-temporal modelling of processes in the living cell
20 October 2009
Jasmin Fisher: The Executable Pathway to Biological Networks
13 October 2009
Aneil Mallavarapu: Little b a language for modular biological models
23 September 2009
Vito Quaranta: Heterogeneity of Cancer Cell Phenotypic Traits
15 September 2009
Alissa Weaver: Integration of Experimentation with Modeling
15 September 2009
René Thomas: Circular causality: the crucial roles of circuits in biology and nonlinear dynamics
08 September 2009
Carlos J. Melian: Making connections between systems biology and evolving ecological networks
28 July 2009
Hans Meinhardt: Models for pattern formation in the development of higher organisms
15 July 2009
Eors Szathmary: the origin of natural language
30 June 2009
Benjamin Pierce: Foundations for Bidirectional Programming
24 June 2009
Tony Hoare: Graphical models of program behaviour
23 June 2009
Tony Hoare: Unifying models of data flow
22 June 2009
Richard Goldstein: Piecing together the history of the 1918 Spanish Flu epidemic
09 June 2009
David Basanta: An integrated computational approach to study cancer evolutionary dynamics
19 May 2009
Carloyn Talcott: Symbolic Systems Biology: Using Formal Methods Tools to Model Biological Processes
14 May 2009
Hiroki R. Ueda: Systems Biology of Biological Time
12 May 2009
Michele Forlin: Evolutionary approaches to inference
07 May 2009
Corrado Priami: Concluding remarks
07 May 2009
Matteo Cavaliere: Tissue formation and the hallmarks of cancer
06 May 2009
Joerg Stelling: Geometries and dynamics of cellular networks
05 May 2009
Orkun Soyer: Evolution of biological networks
05 May 2009
Orkun Soyer: Co-evolution of host networks with their parasites
05 May 2009
Radu Mardare: Logical specification of systems
30 April 2009
Paolo Ballarini: Model checking: Model checking
30 April 2009
Paola Lecca: Diffusion and space: Diffusion and space
30 April 2009
Ivan Mura: Statistical analysis of simulation output
29 April 2009
Ivan Mura: Filtering and Monitoring
29 April 2009
Davide Prandi: Static and dynamic representations, static analysis and causality
29 April 2009
Alida Palmisano: Hybrid methods
23 April 2009
Hiroyuki Kuwahara: Stochastic simulation
23 April 2009
Sean Sedwards: Fourier analysis
23 April 2009
Alessandro Romanel: Process algebra (BlenX)
22 April 2009
Paolo Ballarini: Narrative modeling framework
22 April 2009
Paola Lecca: Biochemical kinetics, inference and missing information
22 April 2009
Mark Girolami: Inference-Based Modelling Establishes the Role of BRaf in ERK Signalling
07 April 2009
Attila Csikasz-Nagy: Continuous modeling and analysis
03 April 2009
Ferenc Jordan: Network software
02 April 2009
Ivan Mura: Petri Nets
02 April 2009
Matteo Cavaliere: P-systems and Colonies
02 April 2009
Matteo Cavaliere: Graph rewriting and game theory
01 April 2009
Ferenc Jordan: Networks and network analysis
01 April 2009
Jose Garcia Manteiga: High-throughput tools
27 March 2009
Jose Garcia Manteiga: Experimental design
27 March 2009
Adaoha Ihekwaba: Role of modelling, a comprehensive example: NF–kB
27 March 2009
Tommaso Mazza: Standards
27 March 2009
Orkun Soyer: Regulation of motility in bacteria / chemotaxis
26 March 2009
Ferenc Jordan: Challenges coming from population and ecosystem dynamics
26 March 2009
Phuong Nguyen: In silico databases
26 March 2009
Ferenc Jordan: Systems biology
25 March 2009
Judit Zamborszky: Challenges coming from molecular biology
25 March 2009
Walter Fontana: Programs as models: Rule-based representations of complex molecular networks of interaction
17 March 2009
Kohei Honda: Pi-calculus and Abstraction of Interactional Behaviour
17 February 2009
David Fell: Genome-Scale Modelling of Metabolism
02 December 2008
Ferenc Jordan: Topology and function: the role of central nodes in networks
27 November 2008
Rafael Carazo-Salas: Dynamics of microtubule organization in live cells
11 November 2008
Sydney Brenner: The Architecture of Biological Complexity
04 November 2008
Mike Hall: TOR signaling and control of cell and organism growth
29 October 2008
Francois Kepes: Epigenomics and morphodynamics
21 October 2008
Andras Horvàth: Parameter estimation of kinetic rates in stochastic reaction networks by the em method
14 October 2008
Michael Hucka: An Overview of Several Standardization Efforts for Computational Systems Biology
30 September 2008
Hidde de Jong: Qualitative Modeling and Simulation of Bacterial Regulatory Networks
24 September 2008

Engineering Designs of Biological Networks: Facilitating Computational Inference and Analysis of Biological Systems with Biochemical and Biophysical Modeling

Michael Samoilov: Engineering Designs of Biological Networks: Facilitating Computational Inference and Analysis of Biological Systems with Biochemical and Biophysical Modeling

16 September 2008

Flemming Nielson: MT-LAB - Static Analysis and Model Checking
09 September 2008
Danyel Fisher: Recent Information Visualization Work from Microsoft Research
29 July 2008
Cristian Calude: Halting or Non-Halting: That is the Question
22 July 2008
Robin Milner: The space and stochastic motion of bigraphs (2)
17 June 2008
Robin Milner: The space and stochastic motion of bigraphs (1)
16 June 2008
Dan Gillespie: Stochastic Chemical Kinetics
29 May 2008
Alexander Kurz: Coalgebraic Logic and Pi-Calculus in Logical Form (2)
14 May 2008
Alexander Kurz: Coalgebraic Logic and Pi-Calculus in Logical Form (1)
13 May 2008
Ian Laurenzi: Fast and exact stochastic simulation of the hybridization of DNA to microarrays
06 May 2008
Frederick R. Cross: Quantitative tests of models of cell cycle control in budding yeast
15 April 2008
Christian I. Hong: A Mathematical Model of Neurospora crassa Circadian Rhythms Provides Insights To Molecular Mechanisms
01 April 2008
Irun Cohen: Working day on computational systems biology
14 March 2008
Shuki Bruck: Working day on computational systems biology
14 March 2008
Gianni Cesareni: Working day on computational systems biology
14 March 2008
Ana Martins: A systems biology study of the early dynamical response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide
11 March 2008
Andrei Paun: Discrete nondeterministic modeling of cellular pathways
04 March 2008
Muffy Calder: Verification challenges of cell signalling
19 February 2008
Gianluigi Zavattaro: On the Computational Power of Biochemistry
14 February 2008
Patrick Cousot: Abstract Interpretation and Application to Static Analysis of Critical Software
05 February 2008
Albert Goldbeter: Modeling the circadian clock: From molecular mechanism to physiological disorders
03 February 2008
Jacky L. Snoep: MCA as a tool for the analysis of Silicon Cell models
01 February 2008
Tamás Turányi: Analysis of a budding yeast cell cycle model using the shapes of local sensitivity functions
31 January 2008
Peter Csermely: Stability, creativity and evolution of cellular networks
29 January 2008
Martí Aldea: Sizing cells with a speedometer?
24 January 2008
Sven Panke: Synthetic biology
23 January 2008
Corrado Priami: A computational modelling framework for the dynamics of biosystems
13 January 2008
Attila Becskei: Readout of concentration- and chromosomal gradients by combinatorial promoter constructs
09 January 2008
Radhika Nagpal: Emergent Geometric Order: Cell Division in Proliferating Tissue Networks.
08 January 2008
Guy Shinar: Input-output robustness in simple bacterial signaling systems
06 January 2008
Luca Cardelli: Process Rate Semantics
03 January 2008
Jorge Carneiro: Regulation robustness in the immune system
27 November 2007
Andrea Musacchio: Protein networks that control the process of microtubule-kinetochore attachment during cell division
20 November 2007
Andrea Ciliberto: An autocatalytic circuit is required for an efficient sequestration of Cdc20 by Mad2
20 November 2007
Pedro Mendes: Adventures in Reverse Engineering of Biochemical Networks
16 November 2007
Radu Mardare: Robustness: from randomness to logical deduction
15 November 2007
Jason Zwolak: "PET: A Tool for Estimating Rate Constants in Models of Molecular Networks"
13 November 2007
Orkun Soyer: Using evolutionary approaches to study signaling pathways
28 October 2007
Csaba Pal: Evolution of biological networks in microbes
25 October 2007
John J. Tyson: Regulation of the Eukaryotic Cell Cycle: From Molecular Networks to Cell Physiology
23 October 2007
Marek Kwiatkowski: A process algebraic approach to robustness and evolvability of biochemical pathways.
16 October 2007
Marvin Cassman: Modularity and robustness in mechanistic modeling
08 October 2007
Leroy Hood: Systems Biology and Systems Medicine
08 October 2007
Manuel Peitsch: How can Systems Biology impact Pharmaceutical Research?
08 October 2007
Judy Armitage: Systems Biology in Oxford: Microbial Sensory Networks and Cautionary Tales
08 October 2007
Richard R. Neubig: Simplicity and complexity in G protein signaling
11 September 2007
David Liberles: Gene duplication and functional evolution
04 September 2007
Vanna Micheli: Purine metabolism of human erythrocyte as a model of study.
10 July 2007
Sailesh Chutani: Rethinking the role of ICT in Healthcare
05 July 2007
Ehud Keinan: Bio-Molecular Computing Devices
22 June 2007
Hisao Moriya: Upper limit dosage of genes involved in cell division cycle in S. pombe.
13 June 2007
Alberto Policriti: Stochastic Biological Modeling and Differential Equations
15 May 2007
Yuri Gurevich: The Abstract State Machine Approach
08 May 2007
Melvin Cohn: Default model of the decision process of the immune system
18 April 2007
Dennis Bray: Computer-based Analysis of Bacterial Chemotaxis
12 April 2007
Judy Armitage: Modelling the E.coli chemosensory pathway: strengths and weaknesses
22 March 2007
Ivan Mura: Stochastic Petri Net languages and tools for modeling and analyzing complex systems
13 March 2007
Csaba Pal: Evolution of metabolic networks
06 March 2007
Luca Cardelli: Artificial Biochemistry
21 February 2007
Andrea Becchetti: Modulation of the cerebral cortex by the ascending cholinergic system: physiology, pathology and theoretical problems.
20 February 2007
Marcel Salathé: Sex - the queen of puzzles in evolutionary biology
15 February 2007
Guido Sanguinetti: Bayesian inference in systems biology and bioinformatics: some examples.
13 February 2007
Vladimiro Sassone: Semantic barbs: what's in an observation?
06 February 2007
Gianfranco Balbo: Stochastic Petri Nets in practice
30 January 2007
Rich Williams: Structure and Dynamics of Complex Food Webs
16 January 2007
Stefano Monti: Molecular Cancer Classification: from Integrative Data Analysis to Therapeutics
07 December 2006
Adam Wasserstrom: Reconstructing Cell Lineage Trees - The Brighter Side of Mutations
30 November 2006
Attila Csikasz-Nagy: Models of eukaryotic cell cycle regulation
22 November 2006
Wolfgang Marwan: Reconstructing the Network Controling Commitment to Cell Differentiation in the Eukaryote Physarum polycephalum
16 November 2006
Herbert Sauro: An Overview of Research Efforts: Standardization and Modularity
14 November 2006
Grzegorz Rozenberg: Gene Assembly in Ciliates - a Splendid Example of Natural Computing
09 November 2006
Ruth Baker: Mathematical modelling in developmental biology
07 November 2006
Gheorghe Păun: Membrane Computing: Power, Efficiency, Applications (Introduction and Some Recent Results)
26 October 2006
Mihai Ionescu: Spiking Neural P Systems: Results and New Model
05 October 2006
Enrico Blanzieri: Detecting Uncertainty in Microarray Data Labeling by Data Perturbation
28 September 2006
John Heath: Computational reasoning about biological signalling pathways
21 September 2006
George Cowan: Modeling and Prediction in Early Stage Drug Discovery
14 September 2006
Pietro Liò: A topological analysis of a network of periodic genes in S. pombe cell cycle
06 July 2006
Francesco Amato: Reconstruction of Biological Interaction Networks: A Linear Matrix Inequalities Approach
05 July 2006
Diego Di Bernardo: Reverse engineering of genetic networks and its applications to biology and drug discovery
22 June 2006
Forbes Dewey: An Integrated Software Architecture to Support Modern Experimental Biology
21 June 2006
Forbes Dewey: Distributed Computing of Complex Collections of Biological Pathways
20 June 2006

An High-Performance Heuristic Approach for Finding Maximum Cliques in Graphs with Applications to Analysing Market Data and Biological Systems

Holger Hoos: An High-Performance Heuristic Approach for Finding Maximum Cliques in Graphs with Applications to Analysing Market Data and Biological Systems

19 June 2006

Marta Kwiatkowska: Probabilistic model checking of biological processes
16 June 2006
Giovanni Sebastiani: Bayesian Analysis of Signals and Images with Applications to Medicine and Biology
08 June 2006
Luca Cardelli: Artificial Biochemistry
22 May 2006
Dominique Chu: Understanding "Orientational Control" of phase variation in the E.coli fim system.
18 May 2006
Henry Adorna: Modeling the Receptor-Mediated Pathway of Apoptosis Using Hybrid Petri Nets
11 May 2006
Natasha Jonoska: Computing by DNA Graph Self-Assembly
08 May 2006
Celine Kuttler: Simulation of bacterial transcription and translation in the pi calculus.
04 May 2006
Jane Hillston: Process algebra abstractions of biochemical pathways
30 March 2006
Corrado Priami: Process calculi for biology
23 March 2006
Nadia Busi: Expressiveness issues in Brane Calculi
16 March 2006
Ralf Blossey: A compositional approach to the stochastic dynamics of gene networks
23 February 2006
Andrew Phillips: Simulating Biological Systems in the Stochastic Pi-calculus
23 February 2006
Charles Auffray: Systems Biology: a Research Strategy to Tackle Biological Complexity in Medicine.
21 February 2006
Jaroslaw Wisniewski: On phylogenetic trees from algebraic geometer's point of view
16 February 2006
Ela Hunt: Moving data integration and visualisation support into the database engine
02 February 2006
Pierpaolo Degano: VICE: a virtual cell
01 February 2006
Gordon Plotkin: A Calculus for Biochemical Systems
26 January 2006
Sean Sedwards: An Introduction to Chaos and Chaotic Spiking Neurons
19 January 2006
Matteo Cavaliere: Membrane Systems with Marked Membranes
12 January 2006
Alessandro Quattrone: Challenges coming from cell biology
25 March 1984
Orkun Soyer: What can we learn from studying the evolution of signaling pathways?
Luca Cardelli: Artificial Biochemistry
David Harel: Playing with Biology in silico
Eric Werner: Net Based Pharmacodynamics May Change the Pharmaceutical Industry
R. A. Goldstein: Emergent Robustness in Prebiotic Autocatalytic Chemical Networks
Fausto Giunchiglia: Companies, Universities, users and funding agencies: How can we talk?
Fausto Giunchiglia: Short CV, May 17, 2006
Daniel Figeys: Proteomics and Systems Biology
Darren Green: Maximising the utility of predictive science by embracing modern computer science
David Harel: Towards an Odor Communication and Synthesis System
Heikki Salmi: EU strategies on industries
Luciano Milanesi: New challenges of using the high performance computing and GRID technology for Bioinformatics applications in life science.
Carlo Mango: The support to the scientific research and the valorization of the research results: the experience of Cariplo Foundation
Luca Cardelli: Artificial Biochemistry
Raffaele Menolascino: Advanced user interfaces and autonomics concepts applied to future wireless systems
Patrick van Hove: Reinventing ICT by bringing converging sciences into information technology.
Andrew Herbert: Converging Sciences and Microsoft
Colin Hill: Addressing two mission-critical problems in drug development with data driven computation
Michael Foster: Computational Discovery
Carlo Mango: Abstract
Manuel Peitsch: Systems Biology in Pharmaceutical Research: integrating Mathematical and Experimental Approaches to Study Cell Signalling
Giampietro Tecchiolli: Pervasive Computing and Human factors
Steven Wiley: Handling Complex Datasets to Enable Systems Biology
Jacques Demongeot: A complexity view on the RNA world
Anthony Finkelstein: Model Management & Orchestration: software engineering challenges of systems biology
Gabor Balazsi: Biomolecular interaction networks
Victor Sourjik: Quantitative analysis of chemotaxis network in bacteria
Matteo Cavaliere: Natural Computing
Attila Csikasz-Nagy: Dynamics of cell cycle regulatory networks
Stefan Bornholdt: Boolean networks as toy models for biological regulation: Prospects and limitations.

"I have enjoyed meeting the bright and energetic people on the staff of COSBI, who are engaged in this exciting and ambitious program"

Dan Gillespie