For all additional information, please visit the website:http://bci2013.units.it/
CALL FOR PARTICIPATION
The School of Biology, Computation, and Information (BCI), reaching this year its eighth edition, as a joint event with the third FVG summer school on bioinformatics, aims at bringing together teachers and students in Biology, Mathematics, and Computer Science.
The main goal of the School is to give an updated overview of interdisciplinary techniques and problems cross-bordering the three fields.
This year's edition will be dedicated to the study of cancer bioinformatics, with emphasis on genetic and protein interaction networks involved and on multi-scale modeling of cancer tissues.
The topics of the school will cover such issues as production and analysis of experimental data and construction and validation of mathematical and computational models.
The three distinguished speakers for this year's edition are Francesca Ciccarelli (Biology), Pietro Liò (Computer Science), and Luigi Preziosi (Mathematics) and the school will take place during the second week of September (September 09-13, 2013).
A workshop will take place during the last day of the summer school,while poster session will be organized throughout the conference.
COURSES
Main topic: cancer modelling
Area: Mathematics
Lecturer: Prof. Luigi Preziosi,Politecnico di Torino, Italy.
Bio: Luigi Preziosi is full professor of Mathematical Physics at the Politecnico di Torino, where he is also head of the School of Mathematical Engineering. He got a Master degree in Mathematics cum laude at the University of Naples, a Ph.D. in Mechanics with minor in Mathematics at the University of Minnesota and a Ph. D. in Mathematics at the University of Naples.
He is author of more than 100 publications in the international literature in several fields of Applied Mathematics, such as dynamics of immiscible fluid and viscoelasticity, kinetic models in gas and population dynamics, cancer modelling, biomechanics of living tissues, and deformable porous media applied to bio-mathematics, composite materials manufacturing processes, and soil mechanics.
Abstract: Multiscale Developments of Cellular Potts Models and Individual Cell-based Models in Cancer Modelling.
All biological phenomena emerge from an intricate interconnection of multiple processes occurring at different levels of organization: namely, at the molecular, the cellular and the tissue level. These natural levels can approximately be connected to a microscopic, mesoscopic, and macroscopic scale, respectively. The microscopic scale refers to those processes that
occur at the subcellular level, such as DNA synthesis and duplication, genedynamics, activation of receptors, transduction of chemical signals and diffusion of ions. The mesoscopic scale, on the other hand, can refer to cell-level phenomena, such as adhesive interactions between cells or between cells and ECM components, cell duplication and death and cell motion.
The macroscopic scale finally corresponds to those processes that are typical of multicellular behavior, such as population dynamics, tissue mechanics and organ growth and development.
One of the most widespread hybrid approaches, that is particularly suitable for cancer modelling and other biological problems, is the Cellular Potts Model, a stochastic Monte Carlo method based on energy minimization principles.
The scope of the series of lectures is to present some innovative multiscale extensions of the Cellular Potts models and of Individual Cell-based models.
In particular, we focus on ways to integrate and interface the standard method with detailed descriptions of microscopic dynamics located not only in the external space but also within the simulated elements. We aim therefore to introduce some nested characteristics in the basic hybrid environment, that realistically reproduce the multiscale organization typical of biological development, where the individual behavior is driven by the constant interplay between different levels of description.
Area: Computer Science
Lecturer: Dr. Pietro Liò, University of Cambridge, UK.
Bio: Dr. Pietro Liò research activities focus in several areas of computational medicine and biology. He is Senior Lecturer in the Computer Laboratory which is the department of Computer Science of the University of Cambridge where he supervises a group of four PhD students and one postdoc. He teaches Bioinformatics algorithms (undergraduates) at the Computer Laboratory and Model and Methods in Genomics at the MPhil in Computational Biology, Dept. of Mathematics and Applied Physics. He is affiliated staff of the Systems Biology tripos. Dr. Liò holds a PhD in Complex Systems and Non Linear Dynamics (School of Informatics, dept of Engineering of the University of Firenze, Italy) and a PhD in Genetics (University of Pavia, Italy).
Abstract: Medicine is moving from reacting to a disease to a proactive P4 medicine: personalized, predictive, preventive and participatory medicine. A difficult step is to bridge the actual distance between biomedical research and clinical practice. I would like to focus on the challenges in data analysis and modeling in cancer bioinformatics. In particular I would like to discuss the following issues:
Multi omics (1 lecture)
Expensive and complex data are gathered and analysed in a rather simple way that completely misses the opportunity to uncover combinations of predictive and meaningful profiles among the omics data. Novel methodological frameworks, beyond single datasets, should integrate multilevel omics data to bring biological understanding to the next level. "Super-Meta" methods combining multilevel data across populations need to be developed. Omics may include HI-C, epigenetic, gene expression and sequence data; they are not independent each other. I will provide details of the algorithms and the software
Multi scale modeling (1 lecture)
A disease manifests first as a dysfunction at the cell level and is then translated at the tissue level due to a change in the cell response. Here I am considering tgb-beta as a coupling factors for modeling breast cancer at different scales (from molecules to tissues).
Multi morbidities (1 lecture)
Comorbidity addresses the occurrence of different medical conditions or diseases, usually complex and often chronic ones, in the same patient.
I am addressing bone diseases as a secondary effect of several types of cancers.
Multi objective optimisation (1 lecture)
If there is time I will show use multi objective optimisation to investigate how energetic factors enters the tissue dynamics.
Area: Biology
Lecturer:Dr. Francesca Ciccarelli, IEO-IFOM Milano, Italy.
Bio: Francesca Ciccarelli is group leader at the European Institute of Oncology (IEO) in Milan. She earned a PhD in Natural Science at the University of Heidelberg. Her expertise is in computational biology and her research focuses on applying computational methods to study cancer genetics and to model tumor evolution. She is also the scientific coordinator of the PhD program in computational biology at the European School of Molecular Medicine (SEMM) in Milan.
Abstract: In this series of lectures I will discuss the recent advances in on our understanding of cancer genetics and evolution. I will start by reviewing the accumulating evidence of cancer heterogeneity in terms of acquired genetic mutations and genomic rearrangements. I will then describe the impact of these novel results on our modeling of cancer networks. In the last lectures, I will focus on the current attempts of using large-scale genomics data for rebuilding tumor evolution and how this is changing also anti-cancer therapeutic approaches.
WORKSHOP
A workshop, will take place during the last day of the summer school, with title "Cancer Bioinformatics".
Invited speakers for the workshop are:
Marco Antoniotti (University of Milano Bicocca)
Silvio Bicciato (University of Modena-Reggio Emilia) ?
Barbara Di Camillo (University of Padova)
Bud Mishra (NYU) ?
Francesca De Michelis ?
REGISTRATION
Registration deadline: 31 August.
To apply use the online registration form available at school's website
Acceptance of more participants will be evaluated by the organizers.
Registration fee: EUR 100 (#)
The registration fee covers participation at all lectures, course materials, coffee break, and lunches.
Accommodation is not included. Please contact the organization or visit the web site for additional information.
(#) The registration is free for students and staff of the University of Udine, University of Trieste, SISSA, and other FVG research institutions.
LOCATION
The school will take place in Trieste, Friuli Venezia Giulia, Italy.
Lessons will be held at the University Campus, H3 Building, Piazzale Europa 1, 34127, Trieste.
The congress center is 15 minutes by bus from the train station (line 17/).
SPONSORS
- Regione Autonoma del Friuli Venezia Giulia
- University of Trieste.
- University of Udine.
- SISSA, Trieste.
ORGANIZING AND SCIENTIFIC COMMITTEE
- Luca Bortolussi, University of Trieste (school co-director)
- Alberto Policriti, University of Udine (school co-director)
- Claudio Altafini, SISSA, Trieste (school co-director)
- Alberto Casagrande, University of Trieste