ISMB 2008 ISCB





















ISMB/ECCB 2009 Keynotes

Trey Ideker, PhD
ISCB Overton Prize
Associate Professor
Department of Bioengineering
UC San Diego, La Jolla, California, USA
Trey Ideker
Presentation Title: New Challenges and Opportunities in Network Biology
Date: Tuesday, June 30
Time: 4:45 p.m.
Room: Victoria Room




ISMB/ECCB 2009 Blog
Keynote: Trey Ideker - New Challenges and Opportunities in Network Biology
Trey Ideker has an impressed career. He obtained his PhD in 2001, now at UCSD - Diego M. Riaño-Pachón
The curse of systems biology: you will be a jack of all trades, rather than a master of one. - Allyson Lister
How does one automatically model systems and pathways from a variety of data - Oliver Hofmann
Ideker et al.: Ann Rev Genomics Hum Genetics 2001 - his PhD work (Systems Biology: A new approach to decoding life. - Allyson Lister
Given basic knowledge of a pathway measure the global response to systematic perturbations, compare predictions and observations and determine the goodness of fit, revise and repeat - Oliver Hofmann
Ideker (Sciene 2001), GAL metabolic flow as an example - Oliver Hofmann
Use systematic interaction data (Protein-DNA, PPI, biochemical reactions) to zoom out from a well-understood small pathway to a more global view - Oliver Hofmann
The final figure of that Science manuscript, he feels, launched his career. - Allyson Lister
Change to the 'modern area'. Querying large biological networks for active modules, colouring graphs with expression states, enzyme activity, any kind of activity. Automatically extract subnetworks / modules from the global 'hairball' - Oliver Hofmann
Interaction Database Dump, aka "Hairballs", which aren't good for a whole lot. - Allyson Lister
...more...

Webb Miller
ISCB Senior Scientist Accomplishment Award
Pennsylvania State University
University Park, PA, USA
Webb Miller
Presentation Title: Bioinformatics Methods to Study Species Extinctions
Date: Thursday, July 2
Time: 2:00 p.m.
Room: Victoria Room




ISMB/ECCB 2009 Blog
Keynote: Webb Miller - Bioinformatics Methods to Study Species Extinctions
10 Steps to Success in Bioinformatics - sebi
has been 40 yrs in computers, 20 yrs in bioinformatics: but doesn't have enough money to retire (tongue-in-cheek) - Michael Kuhn
Step 1: Become a biologist. - sebi
Extinction: How to save endangered species - Peter Menzel
which species are in trouble? - Venkata P. Satagopam
(out of batteries, not sure the iPhone is adequate for this. So far a great intro :) ) - Oliver Hofmann
...more...

Pierre-Henri Gouyon
Muséum National d’Histoire Naturelle
Equipe Botanique
MNHN/CNRS Origine, Structure et Evolution de la Biodiversité
Paris, France
Pierre-Henri Gouyon
Presentation Title: Information and Biology
Date: Monday, June 29
Time: 9:00 a.m.
Room: Victoria Room




ISMB/ECCB 2009 Blog
Keynote: Pierre-Henri Gouyon - Information and Biology
intro by Gene Myers: 2 PhDs, 1 Master in Philosophy (after the PhDs) - Michael Kuhn
Dr. Gouyon, PhD in Genetics and Evolution and master in Phylosophy - Diego M. Riaño-Pachón
Biodiversity is at the same time a treasure and a danger - Allyson Lister
biology is a young science, even compared to physics - Michael Kuhn
What is biodiversity? Long standing question in biology - Diego M. Riaño-Pachón
1605: leaves fall from a tree and become fish / birds - Michael Kuhn
Many good scientists have had problems with society, but it is not sufficient to have problems with society to be a good scientist. :) - Allyson Lister
not much progress in bio during 17th century - Michael Kuhn
Biodiversity from Linnaeus' POV: "eternal law of reproduction and nultiplication within the limits of their proper types". - Allyson Lister
...more...

Daphne Koller
Department of Computer Science, Stanford University
Stanford, USA
Daphne Koller
Presentation Title: Individual Genetic Variation: From Networks to Mechanisms
Date: Tuesday, June 30
Time: 9:00 a.m.
Room: Victoria Room




ISMB/ECCB 2009 Blog
Keynote: Daphne Koller - Individual Genetic Variation: From Networks to Mechanisms
aka Understanding Gene Regulation: From Networks to Mechanisms - Allyson Lister
(as some results only arrived last night) - Oliver Hofmann
There are many mechs (chromatin modification, rna degradation) that modify gene regulation - Allyson Lister
use 'omics' data to understand and infer GRNs - Diego M. Riaño-Pachón
mRNA level of regulator an (imprecise) indicator of regulator activity - Oliver Hofmann
So you can model RNA level of a gene as a variable in a model - Allyson Lister
The expression of a target genes can often be predicted by the expression of its regulators - Diego M. Riaño-Pachón
Regulators: transcription factors, signal transduction, chromatin remodeling . . . - Diego M. Riaño-Pachón
Broad view of a regulator gene: TFs, signal transduction proteins, RNA processing factors, anything that *might* play a direct or indirect role in gene regulation - Oliver Hofmann
Second assumption: co-regulated genes have similar regulatory mechanisms, group genes into modules and predict expression profile for the entire module - Oliver Hofmann
...more...

Dr. Thomas Lengauer
Max-Planck Institute for Informatics
Saarbrücken, Germany
Thomas Lengauer
Presentation Title: Chasing the AIDS Virus
Date: Wednesday, July 1
Time: 4:45 p.m.
Room: Victoria Room




ISMB/ECCB 2009 Blog
Keynote: Thomas Lengauer - Chasing the AIDS Virus
Background in mathematics and Computer Science - Allyson Lister
protein bioinformatics, computational drug screening and design - Ruchira S. Datta
previously full prof at U. Paderborn - Ruchira S. Datta
on steering board of ECCB since its founding - Ruchira S. Datta
an exciting story, downstream of the bulk of computational biology in the medical field - Ruchira S. Datta
process flow usually ends with finding and optimizing potential drug targets - Ruchira S. Datta
Start when the drugs are available on the marketplace and they support personalized medicine, and which drugs to give to AIDS patients. - Allyson Lister
Personalized medicine, they start when the drugs are in the market place - Diego M. Riaño-Pachón
in this case, support difficult decision of a doctor: what drug to give to the AIDS patient - Ruchira S. Datta
33m HIV infected patients in 2007 - Peter Menzel
...more...

Eugenia María del Pino Veintimilla
Pontifical Catholic University of Ecuador (PUCE)
Quito, Ecuador
Eugenia María del Pino Veintimilla
Presentation Title: The comparative analysis reveals independence of developmental processes during early development in frogs
Date: Wednesday, July 1
Time: 9:00 a.m.
Room: Victoria Room




ISMB/ECCB 2009 Blog
Keynote: Eugenia del Pino - The comparative analysis reveals independence of developmental processes during early development in frogs
Has studied "marsupial" frogs, found in the gardens of her university. - Allyson Lister
Brief description of Ecuador, and the Galápagos islands - Diego M. Riaño-Pachón
And, there are no native frogs in the Galapagos. - Allyson Lister
Most of frog diversity is in Brasil, Colombia and Ecuador - Diego M. Riaño-Pachón
Why not just studying Xenopus laevis? To discover developmental differences and for training of local researchers - Diego M. Riaño-Pachón
X. laevis comes from S. Africa as the early development of this frog is better known than that of humans. - Allyson Lister
Beautiful pictures of foam-nesting frog embryos - Diego M. Riaño-Pachón
embryos are white for camoflage in the foam-nest frog - Allyson Lister
Dendrobatid frogs include the poison arrow frogs, though they don't study the poisonous ones. - Allyson Lister
The males find an appropriate nest spot, then call the females. Males care for the embryos for 20 days. - Allyson Lister
...more...

Tomaso A. Poggio
Massachusetts Institute of Technology
Cambridge, USA
Tomaso A. Poggio
Presentation Title: Computational Neuroscience: Models of the Visual System
Date: Monday, June 29
Time: 4:45 p.m.
Room: Victoria Room




ISMB/ECCB 2009 Blog
Keynote: Tomaso Poggio - Computational Neuroscience: Models of the Visual System
Not a talk about bioinformatics but computational neuroscience - Roland Krause
Learning in supervised and non-supervised settings to understand the processes in the brain. - Roland Krause
Just now computational neuroscience can feed back into more classical disciplines. - Roland Krause
15 years ago, machine learning techniques were developed for face recognition. Now present in many consumer digital cameras. - Roland Krause
Now, detection of pedestrians with Daimler and the future will be detecting people in cars. - Roland Krause
No brain research involved so far, only engineering. - Roland Krause
Basics on learning theory, the mathematics of learning: Poggio & Smale, 2003 - Diego M. Riaño-Pachón
[...] How the ventral stream works. - Roland Krause
Build quantitative models, only modeling feed forward connections. - Roland Krause
A good place to start because we can quickly recognize e.g. animals in pictures, no time for real feedback[?]. - Roland Krause
...more...

Mathias Uhlen
Royal Institute of Technology (KTH)
Stockholm, Sweden
Mathias Uhlen
Presentation Title: A global view on protein expression based on the Human Protein Atlas
Date: Thursday, July 2
Time: 9:00 a.m.
Room: Victoria Room




ISMB/ECCB 2009 Blog
Keynote: Mathias Uhlen - A global view on protein expression based on the Human Protein Atlas
Introduction: Works a lot on affinity reagents. Invented and developed pyrosequencing technology (http://en.wikipedia.org/wiki/Pyrosequencing) now used in 454 - Allyson Lister
Out line of the talk - 1. systematic biology -introduction, 2. HPR project 3. The Human protein Atlas - Venkata P. Satagopam
18th century - biologist. 19th - chemist (1/3 of elements discovered in Sweden in this century). 20th - physicists and at the end, computer scientist. He'd now like to say that the 21st century is the century of medicine. - Allyson Lister
HPR one of the largest projects in Sweden wrt funding, about 100 million euro so far - Oliver Hofmann
An impressive log-scale plot of number of bases sequenced since 1965. - Allyson Lister
developer of sequencing by synthesis via pyrosequencing in late 90s -- basis of 454 technology - Andrew Su
Personalized genomics ... 454 technology developed in our lab - Venkata P. Satagopam
Bioinformatics is the key in the new era of genomics. - Allyson Lister
95% of drugs (still) aimed at proteins - Oliver Hofmann
(Personal opinion: I like how it's not the "post-genomic era", but a new era of genomics :) ) - Allyson Lister
...more...




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