Joint Third FVG International Summer School on Bioinformatics
Eighth International Summer School on
Biology, Computation and Information
BCI 2013
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September 09-13, 2013, Trieste, Italy
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CALL FOR PARTICIPATION
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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.
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COURSES
Main topic: cancer modelling
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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, gene
dynamics, 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.
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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.
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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.
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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 ?
*
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REGISTRATION
Registration deadline: 31 August.
To apply use the online registration form available
at school's website
http://bci2013.units.it/
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.
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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/).
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WEBSITE AND CONTACT
For all additional information, please visit the website:
http://bci2013.units.it/
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SPONSORS
- Regione Autonoma del Friuli Venezia Giulia
- University of Trieste.
- University of Udine.
- SISSA, Trieste.
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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
