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Integrative Data Analysis - Day 1


(Formerly Microarray Data Analysis)


12:30-1:30 pm Registration

Explore available next-generation screening platforms as presented by sequencing leaders. An unparalleled opportunity to compare and contrast these next-generation sequencing platforms to best suit your research needs.

2:00 Chairperson's Remarks
Kevin Davies, Ph.D., Editor-in-Chief, BioIT World

2:05   AppliedBiosystems 
The SOLiD System - Setting New Standards in Genomic Analysis
Michael Rhodes, Ph.D., Product Applications Senior Manager, Genetic Analysis, High Throughput Discovery, Applied Biosystems
The SOLiD™ System generates in excess of 6Gb of mate paired sequence data from a single run and recent throughput in the range of 12-17Gb has been demonstrated in Applied Biosystems R&D labs as well as customer sites. This enables the rapid sequencing of entire human genomes. As a result of this data availability, Applied Biosystems has sequenced a single Yoruban and analyzed the data for SNPs, insertions and deletions and structural variations. This presentation will review some of the challenges of analyzing such data sets. The advantages di base encoding will be discussed, especially in context of SNP calling. In addition, the use of Mate pairs and the latest tools for utilizing SOLiD™ System data will be presented.

2:35  Helicos Logo
True Single Molecule Sequencing™: The Continuing Path to the $1000 Genome

Patrice M. Milos, Ph.D., Vice President and Chief Scientific Officer, Helicos
The Heliscope™ Single Molecule Sequencer, an advanced technology platform capable of directly measuring single DNA molecules without the cost and complexity of amplification, provides the opportunity for high throughput genomic studies to address important biological questions. This presentation will provide an update on the platform as well as describe scientific applications that are being developed for the platform including recent studies on genomic sequencing, SNP detection, expression studies, and paired reads.

3:20  Refreshment Break, Poster and Exhibit Viewing

Length Really Matters: 400 Base Pair Sequencing Reads Using the 454 Genome Sequencer FLX
Jason Affourtit, Director of Advanced Technologies, Roche 454 Life Sciences
With over 250 publications, the Genome Sequencer FLX system has been demonstrated to support an increasing number of applications from whole genome shotgun sequencing to the detection of somatic mutations. Recent advancements in the technology allow for the generation of over 1 million sequencing reads that are between 400 to 500 base pairs in length, allowing for the displacement of traditional Sanger sequencing technologies. The addition of paired end sequencing with spacing of 20kb between the sequencing tags has enabled whole genome sequencing of complex genomes. Data will be presented showing the de novo assembly of Arabidopsis and drosophila. Additional examples of cDNA, metagenomics, and amplicon studies will be shown.

4:30  Illumina
Enabling Genome Biology with the Illumina Genome Analyzer
Gary P. Schroth, Ph.D., Senior Director, Applications R&D, Illumina Inc.
The Illumina Genome Analyzer is an ultrs-high throughput DNA sequencing platform that routinely generates billions of bases of very high quality sequence information from each short run. We will show examples of how the instrument is being used for a large variety of applications in genome biology including human genome sequencing, SNP discovery, gene expression analysis, protein-DNA interactions (ChIP-seq), genome-wide DNA methylation analysis, and small RNA discovery and profiling. We will discuss the development of software and analysis tools that can help users glean biological meaning from the massive amounts of data produced by the system.

5:00  Interactive Panel Discussion
Moderator, Kevin Davies, Ph.D., Editor-in-Chief, BioIT World

5:30 Close of Tech Expo /Short Course Registration

6:30-8:30 SHORT COURSES*

Short Course III *

How to do Successful Gene Expression Analysis Using Real-time PCR
Jo Vandesompele, Ph.D., Professor, Center for Medical Genetics, Ghent University Hospital and Co-founder of Biogazelle
Jan Hellemans, Ph.D., Center for Medical Genetics, Ghent University Hospital and Co-founder of Biogazelle
In this short course, all aspects of the real-time PCR work flow will be covered, including RNA quality control, assay design and validation, selection of stably expressed reference genes, experiment design and finally data analysis using state-of-the art strategies, methods, and quantification models.  A light dinner will be served during the short course.

Who Should Attend & Why:
Both the first time real-time PCR user and the seasoned experimenter that want to learn state-of-the-art strategies, algorithms and validated work flow for real-time PCR gene expression analysis.  You will learn how to import quality controls during the work flow, insights into state-of-the art normalization using multiple reference genes, error propagation, inter-run calibration, and an introduction in biostatistical analysis of gene expression.

Short Course IV *

Experiment Design & Statistical Analysis of Multi-Assay Genomic Study
Thomas J.  Downey, President, Partek, Inc.
In order to better understand the causes of differential gene expression, researchers are beginning to correlate chromosomal copy number, methylation, chromatin-immunoprecipitation, and SNPs with gene expression changes. This workshop addresses statistical considerations both at the study design phase and the data analysis phase of the study. Examples, including correlating chromosomal copy number with gene expression, will be given to illustrate the methods.   A light dinner will be served during the short course.

Who Should Attend & Why:
This short course is intended to help biologists and other medical researchers who are planning to conduct studies that include multiple assay types.

*Separate Registration Required

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