ISMB 2009 Special Interest Group on Short Read Sequencing Schedule

8:40-10:15am:    Session 1: Welcome, SNP Discovery & Cancer Genomics

• VARiD: Variation Detection in Color-Space and Letter-Space  – Adrian V. Dalca and Michael Brudno

• Evaluation of a Bayesian mixture model for detection of single nucleotide variants in ovarian cancer transcriptomes by next generation sequencing – Sohrab P. Shah, Rodrigo Goya, Mark G.F. Sun, Gavin Ha, Ryan Morin, Kim Wiegand, Kevin Murphy, Sam Aparicio, David Huntsman

• Detecting Polymorphisms in Cancer Tumour/Normal Pairs – Dirk Evers

• ISOLATE: A computational strategy for identifying the primary origin of cancers using high throughput sequencing – Gerald Quon and Quaid Morris

10:15-10:45am:                             Coffee break

10:45am-12:30pm:    Session 2: Variation Discovery

• Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads – Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler and Zemin Ning

• Next-generation algorithms: detection of SNPs, InDels, and Copy Number Variation in massively parallel short-read oligonucleotide ligation sequencing – Fiona C.L. Hyland, Rajesh Gottimukkala, Ryan Koehler, Susan Tang, Eric Tsung, Heather Peckham, Kevin McKernan, Francisco De La Vega.

• Detecting Copy Number Variation with Mated Short Reads – Paul Medvedev, Marc Fiume, Tim Smith, Adrian Dalca, Seunghak Lee, Michael Brudno

• A method for detecting small scale human microsatellite length- polymorphism using Solexa/Illumina paired-end sequencing data – Weldon Whitener, Avril Coghlan, Li Heng, Richard Durbin

• MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions – Seunghak Lee, Fereydoun Hormozdiari, Can Alkan, Michael Brudno.

12:30-1:45pm:                             Lunch

1:45-3:30pm:    Session 3: RNA Sequencing (5 talks)

• TopHat: discovering splice junctions with RNA-Seq – Cole Trapnell, Lior Pachter and Steven L. Salzberg

• Quantitative Detection of Alternative Transcripts with RNA-Seq Data – Regina Bohnert, Jonas Behr, and Gunnar Rätsch

• MapSplice:  Map RNA-seq Short Reads for Splice Junction Discovery – Jinze Liu, Kai Wang, Zheng Zeng, Stephen J. Coleman, James N. MacLeod , Jan Prins

• De novo Transcriptome Assembly with ABySS – İnanç Birol, Shaun D Jackman, Cydney Nielsen, Jenny Q Qian, Richard Varhol, Greg Stazyk, Ryan D Morin, Yongjun Zhao, Martin Hirst, Jacqueline E Schein, Doug E Horsman, Joseph M Connors, Randy D Gascoyne, Marco A Marra and Steven JM Jones

• Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data – Chol-Hee Jung, Martin A. Hansen, Igor V. Makunin, Darren Korbie and John S. Mattick

3:30-4:00pm:                             Coffee break

4:00pm-6:15pm:    Session 4  Metagenomics, Assembly, Statistics & Keynote

• Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly – Bas E. Dutilh, Martijn A. Huynen and Marc Strous

• LOCAS: A new low coverage assembler for short reads – Juliane D. Klein, Stephan Ossowski, Korbinian Schneeberger, Detlef Weigel and Daniel H. Huson

• Poisson Model of Significance for Short Reads Concentrations – Adam Kowalczyk, Thomas Conway, Bryan Beresford-Smith, Sibgat Choudhury, Saraswati Sukumar, Kornelia Polyak and Izhak Haviv

• Design of Association Studies with Pooled Next-Generation Sequencing Data – Su Yeon Kim, Yingrui Li, Yiran Guo, Ruiqiang Li, Torben Hansen, Oluf Pedersen, Jun Wang, and Rasmus Nielsen

Keynote: Edwin Cuppen

Biologically Relevant Advantages and Limitations of Short Read Sequencing Data