From sherlock from genome.stanford.edu Fri Aug 1 06:50:59 2008 From: sherlock from genome.stanford.edu (Gavin Sherlock) Date: Fri Aug 1 10:23:59 2008 Subject: [Arrays] MGED 11 : Additional tutorial on Analysis of Short Reads from High-Throughput Sequencing Message-ID: <2183E540-5860-4828-BCCC-8F1D6CBA3563@genome.stanford.edu> 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@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 ---------------------------------------------------------------------------------- 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@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@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@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