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[Computational-biology] OIST Summer School and Workshop: Quantitative Evolutionary and Comparative Genomics 2010

Jonathan Miller via comp-bio%40net.bio.net (by jnthnmllr from gmail.com)
Thu Jan 14 21:42:44 EST 2010

May 24-June 4, 2010. OIST covers accommodation and travel expenses for
all participants.

Confirmed Lecturers

    * Nadav Ahituv, UCSF: Functional characterization of
evolutionarily conserved non-coding sequences.
    * Peter Arndt, MPI Berlin: Dynamical models describing nucleotide
    * Gill Bejerano, Stanford: Ultra-conservation: the hip and the
    * Emmanouil Dermitzakis, Geneva: Population genomics of gene
    * Takashi Gojobori, National Institute of Genetics, Japan: Genomic
evolution of the neural system.
    * Ueli Grossniklaus, Zurich
    * Jotun Hein, Oxford
    * Nancy Moran, Arizona: Genome reduction in genomes of symbiotic
    * Erik van Nimwegen, Basel: General probabilistic methods for
prediction of regulatory sites using comparative genomic data.
    * Howard Ochman, Arizona: The simplicity and complexity of
bacterial genomes.
    * Anirvan Sengupta, Rutgers: Long-range interactions: enhancers
and insulators.
    * Gasper Tkacik, U. Penn: From statistical mechanics to
information theory: tools for understanding biophysical systems.
    * Byrappa Venkatesh, IMCB Singapore: Evolutionarily conserved non-
coding sequences in vertebrate genomes.
    * Ting Wu, Harvard Medical School: Ultra-conservation from the
standpoint of genome integrity: from copy-counting to meiotic gene

OIST Summer School and Workshop: Quantitative Evolutionary and
Comparative Genomics 2010

The theme of the 2010 Summer School is the phenomenon of strong (or
extreme) sequence conservation, which will be explored from a
quantitative and multidisciplinary perspective, and connections forged
with parts of biology outside of genomics.

Sequence conservation forms the basis of comparative genomics, has
already played a pivotal role in biology and medicine, and is likely
to become increasingly important in the eras of abundant sequence data
and the personalized genome. Ultra-conservation has led to a broad
appreciation of the need for a reevaluation of how the action of
selection is inferred from sequence comparison. It has raised basic
questions about the character of "neutral drift," calling for new
quantitative developments that may be facilitated by the cultures of
mathematics, physics, computer science, and engineering; however, this
pursuit - and the interpretation of genome sequence in general - ought
to be firmly grounded in its biological context.

With a multitude of whole-genome sequences now publicly available,
ultra-conservation is trivial to exhibit, but so far difficult to
explain. Therefore it represents an ideal topic for a combined Summer
School and Workshop, where the phenomenon can be appreciated by
participants of diverse backgrounds, who can then bring their own
perspectives to bear on the problem.

Broad Topic Categories:

    * Ultra-conservation: Theory & Experiment.
    * Ultra-conserved Elements (UCEs) within Populations.
    * Comparative, Evolutionary and Population Genomics.
    * Recombination and Genome Rearrangement.
    * Neutral and Adaptive Evolution: Proteins, RNA, Regulatory
Sequences, Genomes.
    * Experimental Evolution.

The format of the summer school consists of a three-hour presentation
in the morning, with coffee breaks, followed by an hour or two of
discussion in the afternoon. The summer school is aimed primarily at
introducing approximately forty students and post-docs with
quantitative backgrounds - not necessarily in biology - to the
splitting edge of contemporary comparative and evolutionary genomics
research. As such, tutorials will be offered to get participants with
less-developed quantitative skills or sparse biological background up
to speed insofar as possible; however, we hope that presentations will
be intense and self-contained.

We are looking for a set of students with a broad range of
backgrounds, experimentalist and theorist: for example, biology,
chemistry, computer science, ecology, engineering, evolution,
genomics, mathematics, medicine, or physics. The essential
prerequisite is an enthusiasm to overcome traditional boundaries of
your own field of specialization. A small number of researchers at
later stages of their careers may be invited to participate,
particularly if we believe they can contribute to mediating the
interdisciplinary dialog; such applicants should be certain to address
this explicitly in their applications.

Okinawa is a subtropical divers' paradise of diverse ecology and
distinctive beauty and cultural flavor.

OIST provides summer school students with accommodation at Seaside
House and financial support for their travel. Students will be
selected competitively based upon their completed Applications,
submitted by February 15, 2010 to qecg2010#oist.jp (replacing the "#"
by "@" of course).

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