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Organisers
Gustavo Stolovitzky, IBM Research, USA
Raul Rabadan, Columbia University, USA
Pascal Kahlem, European Bioinformatics Institute, UK
Roderic Guigo, Centre for Genomic Regulation, Barcelona, Spain
Luis Serrano, Centre for Genomic Regulation, Barcelona, Spain
Introduction
Parallel advances in two insofar relatively disconnected areas of science are boosting our understanding of biological systems. On the one hand, systems biology, with its promise of integration of high-throughput biological data and its emphasis on quantitative modeling and simulation, is providing a global perspective of biological systems that goes beyond the classical reductionist approach that has dominated the field until recently. On the other hand, new sequencing technologies are developing at an enormous speed, and provide whole genome data that revealed previously unexplored genomic features such as functional intergenic regions, copy number variations and other genomic differences between members of the same species.
The new sequencing technologies are allowing to measure and quantify,
with unprecedented detail, functional features of the cellular realm that were
previously reserved for micro-array technologies. With increasing frequency,
we are starting to see studies that quantify transcriptomics by literally
counting the number of mRNA of a given sequence. In like manner,
technologies that were at the leading edge of systems biology studies such
as ChIP-on-chip, are yielding to ChIP-seq, which is revolutionising our
understanding of transcription factor-DNA binding. Previously hard to detect
effects of alternative splicing and epigenomics are also being enabled by
sequencing technologies. In applications such as cancer research, the ability
to detect the complement of translocations, aneuploidy and other genomic
aberrations will allow us to have a much more detailed appreciation of the
impact to the genome reorganisation in all cancers, and will, probably, allow
us to treat each cancer in the context of the specific patient. Promise in
areas such as Genome Wide Association Studies (GWAS) to stratify
populations according to disease risks, adverse side effects under treatment
and theragnostic applications enabled by novel sequencing technologies
will likely benefit from putting them in the context of analysis of their
pathways, the realm of systems biology. to get a more quantitative grasp on
the qualitative nature of those associations.
The above mentioned applications are a few of the potentially revolutionising
byproducts of the truly innovative efforts to sequence DNA fast and cheap.
The possibility to achieve the goal of sequencing a human genome at a
price of €1000 and in 1 day has triggered a veritable race towards achieving
these milestones. Those milestones will put sequencing at the price and
time scales that will make sequencing individual genomes for medical tests
a reality. This race, fueled in part by awards such as those promised by the J. Craig Venter Foundation (€500,000 for the achievement of a €1K
genome) and the X-prize foundation (US€10 million prize to the first team to
sequence 100 human genomes in 10 days at less than
US€10,000/genome), have had an enormous influence in the advancement
of new sequencing technologies. The history of modern DNA sequencing
can be traced back to the pioneering work of Maxan and Gilbert, who in
1977 proposed their chemical sequencing method), and Sanger, Nicklen
and Coulson, who in the same year proposed the chain terminating
inhibitors. (Gilbert and Sanger shared the 1980 Nobel Prize in Chemistry for
these achievements.) The progress in the last 30 or so years has been truly
remarkable, allowing the price of DNA sequencing to go from €10 per
finished base-pair in 1990 to €10-6 per finished base pair in 2009, a rate
equivalent to halfing the price per finished base every 10 months. What
allowed this incredible accomplishment is the ingenuity of the novel
sequencing techniques. Improving over traditional chain-termination
sequencing innovations included the use fluorescent tags instead of autoradiographic
tags, through sequencing by hybridisation and sequencing by
synthesis, to what promises to be the simplest method for sequencing (in
that it will need no sample preparation or optics for detection): nanopore
sequencing.
In this meeting, we will gather an inter-disciplinary group of scientists with roots in these two disciplines: systems biology and new generation sequencing, with the aim to create a forum to discuss new ideas and explore what lies in overlap between these two growing fields. If these two fields have evolved almost on parallel paths, we believe that a forum to enable the cross-fertilisation of both fields will create a much needed synergy between these two disciplines.
Stan Leibler, Rockefeller University
Saeed Tavazoie, Princeton University
Andrea Califano, Columbia University
Luis Serrano, CRG
Bud Mishra (New York University)
Christian Haudenschield (Director of Sequencing Technologies,Illumina)
Joe Beechem (Life Technolgies)
Michael Egholm, 454 Life Sciences Corporation
Ihor Lemishka, Mount Sinai School of Medicine
Carlos Cordon-Cardo, Columbia University
Henk Stunnenberg, Nijmegen Center for Molecular Sciences, The Netherlands
Jeffrey Schloss, NIH
Eric Schadt (PacBio and Sage)
Arnold Levine, Institute for Advanced Study, Princeton
Stan Leibler, Rockefeller University and Institute for Advanced Study, Princeton
Saeed Tavazoie, Princeton University
Andrea Califano, Columbia University
Luis Serrano, CRG
Jeffrey Schloss, NIH
Bud Mishra, New York University
Christian Haudenschield, Sequencing Technologies, Illumina
Joe Beechem, Life Technolgies
Arnold Levine, Institute for Advanced Study, Princeton
Ihor Lemishka, Mount Sinai School of Medicine
Carlos Cordon-Cardo, Columbia University
Henk Stunnenberg, Nijmegen Center for Molecular Sciences, The Netherlands
Eric Schadt, Chief Scientific Officer, Pacific Biosciences
Michael Egholm, 454 Life Sciences Corporation
Ioannis Xenarios, Swiss Institute of Bioinformatics
The conference will take place at the Centre for Genomics Regulation (CRG), Barcelona Biomedical Research Park (PRBB), C/ Dr. Aiguader, 88, 08003 Barcelona
Registration
Registration is now closed .
