************************************************************** FIFTH INTERNATIONAL SCHOOL ON BIOLOGY, COMPUTATION AND INFORMATION (BCI 2008)
************************************************************** September 8-12, 2008, Trieste, Italy ************************************************************** CALL FOR PARTICIPATION ************************************************************** The School of Biology, Computation, and Information (BCI), reaching this year its fifth edition, 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 centered on (Re)Sequencing and Annotating Genomes, touching a field in which new technologies and old problems meet in a context calling for an even higher level of interaction among the three different disciplines at the core of the School. The three distinguished speakers for this year's edition are Michele Morgante (Biology), Alberto Apostolico (Computer Science), and Laxmi Parida (Mathematics) and the school will take place during the second week of September (September 8-12, 2008). During the school, on Tuesday September 9th, a one-day workshop will take place. It will be titled "New Sequencing Technologies". Excellence lecturers and technological representatives will be invited and the participants to the School may submit an abstract leading to a twenty-minute presentation during the workshop. Abstracts will be sent to and selected/judged by the Scientific Committee. ************************************************************** COURSES Main topic: (Re)Sequencing and Annotation of Genomes ------------------------------------------------------------- Area: Mathematics Lecturer: Prof. Laxmi Parida, IBM Watson Research Center (Yorktown, USA) and Courant Institute of Mathematical Sciences, New York University, USA Prof. Laxmi Parida's research is focussed in the area of computational biology, bioinformatics, and design and analysis of algorithms. One of the threads of her recent work has been in combinatorics and statistics of patterns in bioinformatics and another in recombination patterns for phylogeography in the ongoing Genographic Project. Abstract: We will begin the course with a discussion on comparative genomics via gene clusters: combinatorics, algorithmics and statistics of gene clusters with applications in phylogeny and proximity analysis. Continuing the theme, we will look at the underlying mathematical ideas in the network motif software "Motivo". I will conclude with a brief discussion on phylogeography algorithmics. ------------------------------------------------------------- Area: Computer Science Lecturer: Prof. Alberto Apostolico, College of Computing, Georgia Institute of Technology and Centro Interdisciplinare ''Beniamino Segre'', Accademia Nazionale dei Lincei Professor Apostolico's research interests are in the areas of algorithmic analysis and design and applications. His recent work deals with algorithms and data structures for combinatorial pattern matching and discovery problems as arising in biomolecular sequence analysis and other application areas. Abstract: The problem of characterizing and detecting surprisingly recurrent sequence patterns such as substrings or motifs and related associations or rules is pursued ubiquitously in order to compress data, unveil structure, infer succinct descriptions, extract and classify features, etc. In Molecular Biology, some such patterns are variously implicated in facets of biological structure and function. Because of that, Pattern Discovery constitutes one of the most battered, flourishing and arguably useful applications of Computational Molecular Biology. The very notion of a pattern still embodies subtleties and ambiguities, as do related concepts such as class and structure. The discovery, particularly on a massive scale, of surprising patterns and correlations there of poses interesting methodological and algorithmic problems. Often, the tables and descriptors at the outset often grow faster and bigger than the phenomena they are meant to encapsulate, which generates daunting computational burdens, and gives rise to a throughput that seems impossible to visualize and digest. While part of these problems are endemic, another part seems rooted in the characterizations traditionally offered for the notion of a motif or association pattern, that are typically based either on syntax or on statistics alone. This short lecture series reviews such classical notions as well as alternate ones based on constraints of pattern saturation and monotonicity of scores that tightly combine syntactic and statistical specifications, and shows how they afford some parsimony in the generation and testing of surprising patterns. ------------------------------------------------------------- Area: Biology Lecturer: Prof. Michele Morgante University of Udine, Italy. Institute for Applied Genomics, Udine, Italy. Professor Morgante's research is focused on genetic and physical mapping of plant genomes, genome sequencing and resequencing, transposable elements and plant genome evolution, plant genome organization, and population genetics of plants. He is currently the director of IGA, a research center in Udine that has recently sequenced the grape genome. He is also member of the prestigious "Accademia dei Lincei". Abstract: "New DNA sequencing technologies and their applications in biology" The DNA sequencing field is going through a phase of dramatic changes. The traditional Sanger DNA sequencing method is being abandoned in favor of new technologies that dramatically increase the output in terms of sequenced bases per workday and reduce their costs by several orders of magnitude. Such improvements come at the expense of sequence length and require the adoption of new hardware and software for the data analysis. These technologies hold the promise of revolutionizing biological research. We will describe the basic principles underlying the most commonly used new sequencing technologies and discuss how they can be applied to a variety of problems in biological research, even in areas where DNA sequencing was previously not utilized. ************************************************************** WORKSHOP "New Sequencing Technologies" The recent advances in sequencing technology are leading to new challenges in biology, computer science, and mathematics. The workshop aims at discussing the advantages and the problems of these new technologies. ------------------------------------------------------------- Invited speakers Mike Brudno, Toronto University, Canada. "Discovering Genomic Variation with Next Generation Sequencing Technologies" Stefano Gustincich, ISAS, Trieste, Italy. "Functional Genomics of the Brain" Heinz Himmelbauer, Max Planck Institute for Molecular Genetics, Germany. "Massively parallel sequencing: Promises, prospects and pitfalls" Alberto Policriti, IGA, Udine, Italy. "Experiences in placing short sequences" Claudio Altafini, ISAS, Trieste, Italy. "Modeling the genome-wide transient response to stimuli in yeast: adaptation through integral feedback" ************************************************************** REGISTRATION Early registration deadline: 15 June 2008. Late registration deadline: 15 August 2008. We can provide accommodation in Hotels located in the city center at a discounted rate, please visit the School website for booking details. For persons accompanying the School participants, please, contact the organizing committee. Early registration fee: EUR 200. Late registration fee: EUR 250. The registration fee covers participation to all lectures and to the workshop, course texts and general course material, coffee breaks, mid-day lunches, and transport to the conference venue. ************************************************************** LOCATION This school will be held at CBM, the company appointed for the coordination of the Friuli Venezia Giulia Technology District of Molecular Biomedicine. CBM operates around Area Science Park in Basovizza, within a picturesque woody landscape just a few miles from Trieste city centre. ************************************************************** WEBSITE AND CONTACT For all additional information, please visit the website: http://bci2008.cbm.fvg.it You can also contact the school organizers. ********************************************************************************* SPONSORS - CBM (Cluster in Biomedicine), Area Science Park, Trieste. - Department of Mathematics and Computer Science, University of Trieste. - IGA (Institute for Applied Genomics), Scientific Research Park, Udine. - Department of Mathematics and Computer Science, University of Udine. - National Group of Scientific Computation of the National Institute of High Mathematics. ********************************************************************************* ORGANIZING COMMITTEE - Alberto Policriti, University of Udine (school director) - Luca Bortolussi, University of Trieste (school co-director) - Elia Stupka, CBM, Trieste (school co-director) - Alberto Casagrande, IGA, Udine - Cristian Del Fabbro, IGA, Udine - Margherita Francescatto, University of Trieste - Cristina Leonesi, CBM, Trieste - Simone Scalabrin, IGA, Udine - Andrea Sgarro, University of Trieste - Nicola Vitacolonna, University of Udine ********************************************************************************* SCIENTIFIC COMMITTEE - Alberto Apostolico, Georgia Institute of Technology - Luca Bortolussi, University of Trieste - Michael Brudno, University of Toronto - Alberto Casagrande, IGA, Udine - Francesco Fabris, University of Trieste - Michele Morgante, University of Udine - Eugenio Omodeo, University of Trieste - Laxmi Parida, IBM Watson Research Center - Carla Piazza, University of Udine - Alberto Policriti, University of Udine - Simone Scalabrin, IGA, Udine - Andrea Sgarro, University of Trieste - Elia Stupka, CBM, Trieste - Nicola Vitacolonna, University of Udine ********************************************************************************* _________________________________________________________________________________ mozart-users mailing list [email protected] http://www.mozart-oz.org/mailman/listinfo/mozart-users
