September 28, 2005

18:00/19:30 - Auditorium
K1: Prespectives in Bioinformatics (Sponsored by: Fundación BBVA)
A view of the future of bionformatics from those that have been there since the beginning
Area chair: Alfonso Valencia

KS-1: Is Biology too fast for Bioinformatics?
Jean-Michel Cleverie

Biology is full of surprises, and the past months have had their share of unexpected discoveries, some of them refuting what we thought were well established dogmas. In the meantime, bioinformatics is devoting most of its energy into ancillary tasks, perfecting 20-year old algorithms or focusing on topic of little scientific significance. On the other end of the spectrum, traditional bioinformatics is prematurely evolving into trendy "systemics", while the above experimental results amply demonstrate that we still don't know half of the parts, functions and relationships constituting the biological systems the modeling of which is attempted. Following an overview of my personal choice of recent biological breakthroughs, I'd like to encourage the young bioinformaticist in the audience to better follow the fast evolutionary pace of Biology, and try to turn Bioinformatics into an efficient discovery approach rather than comforting it as an after-the-fact biological information management system (ABIMS) or wasting their time on "holistic" research directions that are nothing more than computer assisted sophisticated hand-waving (CASH), a 21st century remake of the Von Bertalanffy imposture.

KS-2: A Tale of Two Domains: With apologies to Dickens
Temple F. Smith, Ph.D.

The need to associate both biochemical function and cellular roles to protein domains, rather than the individual proteins, has been recognized for a number of years. However, the ability to identify functional and/or evolutionary domains in proteins from the many full genomic sequence projects is still somewhat problematic. The problem is compounded by the large number of proteins and domains with no obvious currently recognized homologues. In research on these and related problems, our group has developed a number of tools and discovered some interesting examples of domain functions and deep evolutionary histories. Two cases will be discussed demonstrating both the utility of various bioinformatics approaches and the importance of very large-scale data integration.


September 30, 2005

9:00/10:45 - Auditorium
K2: How complete is Knowledge of genome sequence (Sponsored by: Fundación Ramón Areces)
How far are we in identifying all functional elements in human DNA
Area chair: Roderic Guigó

KS-3: A glass half full: What we know and what we don't know about big genomes
Ewan Birney

The genome of an organism is a unique resource. It encodes all the information to make each cell type, tissue and organ of a large organism. Understanding this information requires both insights from specific pieces of molecular biology, large scale functional genomics experiments and computational work. A sensible question to ask is how much do we understand in large genomes. I will attempt to answer this question with reference to the human, mouse and other vertebrate genomes, with some surprising results about the extent of our knowledge.

KS-4: Functional RNA transcripts: Lessons learned and forgotten
Tom Gingeras

The current status of the functional annotations associated with the most genomes is in an unfinished state. The majority of current genome annotations and the databases that underlie them is heavily protein-coding-gene centric. This focus on protein coding transcript intrinsically influences current perceptions of how a genome is organized and regulated. This view of a genome also has an underlying supposition that transcripts with very little coding potential are not biologically important. However, recent experiments analyzing the sites of transcription across large sections of many genomes point to the ubiquitous presence of transcripts with little protein-coding potential and their shared characteristics compared with protein coding transcripts. These shared characteristics argue that such transcripts are biologically important and remind us that RNA itself is an important functional agent in living cells.


October 1, 2005

9:00/10:45 - Auditorium
K3: The future of Systems Biology (Sponsored by: Merk & Co)
Area chair: Søren Brunak

KS-5: From Genome Sequence to Function
Richard Durbin


KS-6: Biological Networks: Information and Prediction
Chris Sander

Community efforts to organize information in biomolecular networks and the advantages of integrating theory, computation and experiment for the purpose of predicting the effects of perturbations in a biological system.



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