Dear Colleagues,
Apologies if you receive this more than once (and sorry for the second
email in a week).
We are pleased to announce the addition of a new tutorial/workshop,
run by Martin Morgan from the FHCRC in Seattle, that will take place
at MGED 11 on September 4th:
Analysis of Short Reads from High-Throughput Sequencing using R and
Bioconductor
DESCRIPTION: Short reads are DNA sequences derived from ultra-high
throughput sequencing technologies. Data can consist of millions of
reads, ranging from 10's to 100's of nucleotides each. This hands-on
presentation and workshop introduces BioConductor tools for initial
exploration of short read data. Participants will learn how to import
and manipulate reads, visualize and assess read quality, work with
genome-sized sequences, and perform fast matching or flexible
alignment. Available tools provide effective ways to explore short
read data, and form the foundation for creative methodologies for
downstream statistical analysis.
Participants excited by next-generation sequencing technologies and
eager to engage R's scripting language will get the most out of this
workshop if they come with a laptop with the 'development' version of
R and software installed by the commands "source('http://bioconductor.org/biocLite.R')
; biocLite('ShortRead')".
If you have already registered for MGED 11, you can enroll in this
tutorial/workshop by sending an email to mged11 from fbk.eu
Please put into the Subject line: "Registration to Short Reads
Tutorial"; and provide your Name, Surname, and affiliation.
For payment: we will send a reply document with details for a bank
transfer before Aug 29 2008, or by credit card or cash on site in Riva
del Garda.
If you have yet to register for the conference, you can sign up for
the workshop during the registration process.
Acceptance into the workshop is on a first come, first served basis.
Finally, a reminder that the abstract submission deadline is next
Tuesday, August 5th. Registration will stay open until the meeting
begins.
More information about the meeting is available at http://www.mgedmeeting.org/
We look forward to seeing you all in Trentino,
Sincerely,
The Microarray and Gene Expression Data (MGED) Society
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MGED 11 Program
Sunday 31st Aug.
15:00 - Registration and Exhibit Area are open
Monday 1st Sept.
07:30 Registration opens
08:30- 09:00 Welcome, Introduction and organization details: Chris
Stoeckert, Cesare Furlanello
ENCODE Session
09:00-10:00 Keynote Lecture: Piero Carninci
10:00-10:45 Plenary Lecture: Barbara Wold
10:45-11:15 Break
11:15-12:00 Plenary Lecture: Shirley Liu
12:00-12:15 Geoffrey Faulkner
Short sequence tags reveal global transcription of repetitive elements
in mammalian genomes
12:15-12:30 Alessandro Coppe
Motif Discovery In Promoters Of Genes Co-Expressed And Co-Localized In
Myelopoiesis By A Novel Computational Framework
12:30-14:00 Lunch (Palameeting)
PARALLEL EVENT in President Room (floor1):
talk-and-lunch sponsored by TECAN
"Microarray experiment quality: on direct route to reliable data"
(register at mged11 from fbk.eu)
Wine and Yeast Genomics Session
14:00-14:45 Plenary Talk: Claudio Moser
14:45-15:00 Dan Riordan
Uncovering RNA Regulatory Information in the Yeast Genome
15:00-15:15 Gavin Sherlock
Molecular Characterization of Clonal Interference during Adaptive
Evolution in Asexual Populations of Saccharomyces cerevisiae
15:30-16:00 Break
16:00-16:45 Plenary Talk: Duccio Cavalieri
16:45-17:45 Keynote Talk: Grant Cramer
18:00-20:00 Welcome cocktail
Tuesday 2nd Sept.
Human Disease Session
09:00-10:00 Keynote Lecture: Joe Gray
10:00-10:45 Plenary Lecture: Mike Bittner
10:45-11:00 Break
11:00-11:45 Plenary Lecture: Nigel Carter
11:45-12:00 Adam Butler
Mining Affymetrix SNP6.0 Copy Number Data In Human Cancer
12.00-12.15 Alistair Chalk
An integrated transcriptome analysis approach to characterise adult
neural stem cells and study complex disease
12.15-12.30 Silvio Bicciato
A Computational Procedure To Identify Significant Overlap Of
Differentially Expressed And Genomic Imbalanced Regions In Cancer
Datasets
12:30-14:00 Lunch
PARALLEL EVENT:
talk-and-lunch sponsored by Molecular Stamping (register at mged11 from fbk.eu
)
Quality and Standards in Action
14:00-14:15 Introduction and update on MGED Standards: Chris
Stoeckert
14:15-14:30 MAGE-TAB Tools: Helen Parkinson/Tim Rayner
14:30-14:45 ISA-TAB and integrative standards: Susanna-Assunta
Sansone/Philippe Rocca-Serra
14:45-15:30 Semantic Web and Gene Expression: Alan Ruttenberg
15:30-16:00 Break
16:00-18:00 Poster Session I
19:00-21:00 Conference Dinner
Wednesday 3rd Sept.
Learning from Microarray Data
09:00-10:00 Keynote Lecture: Naama Barkai
10:00-10:45 Plenary Talk: Atul Butte
10:45-11:00 Break
11:00-11:45 Plenary Talk: Rainer Spang
11:45-12:00 Misha Kapushesky
A cross-study and platform meta-analysis of condition-specificity of
gene expression in 20,000+ assays in ArrayExpress
12:00-12:15 Peter Murakami
Evaluation of Metrics for the Assessment of Microarray Data Quality
12:15-12:30 Paul Boutros
Systematic evaluation of the microarray analysis pipeline
12:30-14:00 Lunch
PARALLEL EVENT:
talk-and-lunch sponsored by INTEGROMICS
"Microarray Gene Expression Data Analysis: Avoiding Pitfalls"
(register at mged11 from fbk.eu)
Functional Genomics and Systems Biology
14:00-15:00 Keynote Lecture : Stephen Oliver
15:00-15:45 Break
15:45-16:00 Josselin Noirel
Network-based integration of transcriptomic and proteomic data
16:00-16:15 Christine Wells
Diversification of inflammatory outcomes in human macrophages via
alternate transcription in the Toll-like Receptor signalling
16:15-17:00 Keynote Lecture: Ewan Birney
17:00-19:00 Poster Session II
20.45 Public Science Conference
Thursday 4th Sept.
Workshops
8:00 - 11:00 Morning Parallel Sessions
• Data Analysis Tutorial: John Quackenbush and Roger Bumgarner
• Tutorial on using Bioconductor for Array Quality Assessment:
Audrey Kauffmann and Wolfgang Huber
11:00 - 14:30 Mid Morning Parallel Sessions
• Gene Pattern tutorial: Ted Liefeld
• Analysis of Short Reads from High-Throughput Sequencing using R
and Bioconductor: M. Morgan
15:00 - 18:00 Afternoon Parallel Sessions
• Using ArrayExpress Tutorial: Gabriella Rustici and Misha
Kapushesky
• EMERALD Workshop on Array Quality Assessment Methods:
Marc Salit and Wolfgang Huber
