[Arrays] MGED 11 : Additional tutorial on Analysis of Short Reads from High-Throughput Sequencing

Gavin Sherlock via arrays%40net.bio.net (by sherlock from genome.stanford.edu)
Fri Aug 1 06:50:59 EST 2008

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  

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  

More information about the meeting is available at http://www.mgedmeeting.org/

We look forward to seeing you all in Trentino,


The Microarray and Gene Expression Data (MGED) Society

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  

12:30-14:00 Lunch

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  
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

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.

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  
    • EMERALD Workshop on Array Quality Assessment Methods:
      Marc Salit and Wolfgang Huber

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