24-26 April 2018

San Francisco, USA


Workshop A
Date: April 25, 2017 | Time: 9.00am – 12.00pm

09.00 - 12.00
Understanding Innate Resistance to Anti-PD-1 Therapy in Melanoma Through Transcriptomics
Workshop Leader: Dr. Jean-Noel Billaud, Senior Principal Scientist, QIAGEN Workshop Leader: Dr. Samuel Rulli, Global Product Manager, QIAGEN

Immunotherapy consisting of blocking immune checkpoints, such as PD-1, has shown promise in treating melanoma. However, innate and acquired resistance to anti-PD-1 therapy often results in recurrence after initial successful treatment leading to advanced metastatic melanoma.

This workshop will include in-depth coverage of the bioinformatics solutions from QIAGEN used to analyze and interpret whole transcriptome and targeted RNA-sequencing results from pre-treatment mRNAs of patients with advanced metastatic melanoma and with respect to their subsequent immunotherapy treatment outcomes. We will show how to optimize the transcriptome data and will provide highlights into the biological signatures that determine non-responder versus responder status using Ingenuity Pathway Analysis (IPA).


By attending this workshop you learn about and discuss the following:


  • Take a deep dive and understand how to optimize the analysis of RNA-sequencing results to get the most out of each RNAseq experiment.
  • Standardize RNA-sequencing data analysis using industry leading algorithms and statistical analysis.
  • Learn how multi-factorial analysis can be used to optimize the statistical analysis or RNA-sequencing results.
  • Analyze non-responder versus responder gene expression signatures to pinpoint significant genes associated with detection of metastasis in melanoma.
  • Identify significantly differentially expressed isoforms and their association to metastatic melanoma.
  • Generate novel regulatory networks as hypotheses suggesting drivers of the expression changes observed in the innate resistance to PD1 treatment in metastatic melanoma.
  • Learn experimental approaches for pathway and gene expression model verification using QIASeq Targeted RNA panels.
  • Follow how unique molecular indexes can be used to increase gene expression precision in targeted RNAseq.

Dr. Jean-Noel Billaud, Senior Principal Scientist, QIAGEN

jean Noel Billaud

Jean-Noel Billaud, Ph.D. is Principal Scientist at Qiagen Bioinformatics. He joined Ingenuity Systems (now QIAGEN) in 2008 as staff scientist for in silico research program in oncology and infectious diseases. Jean-Noel Billaud holds a Ph.D. in Blood Cell Biology from Paris VII, and has done his post-doctoral work at the Scripps Research Institute (San Diego, CA).

Dr. Samuel Rulli, Global Product Manager, QIAGEN


Samuel Rulli received his PhD in 2002 from Tulane University and did post-doctoral research at Johns Hopkins University and the National Cancer Institute in Frederick, MD. Trained as a molecular biologist, Dr. Rulli has worked on different assay detection technologies for gene expression and nucleic acid analysis. Currently he is a global product manager at QIAGEN specializing in RNAseq applications and technologies.

Workshop C
Date: April 25, 2017 | Time: 1.30 – 4.30pm

13.30 - 16.30
Detection, quantification, and visualization of splicing variations from RNA-Seq data
Workshop Leader: Yoseph Barash, Assistant Professor, Perelman School of Medicine University of Pennsylvania

In this workshop, we will review best practices for detecting, quantifying and visualizing gene splice variants and differential splicing from RNA-Seq.

We will cover different scenarios ranging from small datasets w/wo replicates to large heterogeneous datasets containing hundreds or thousands of samples from patients and controls. Most of the workshop will focus on the pipelines and algorithms we developed in our lab for these tasks (MAJIQ, MAJIQ-HET), with a comparison to other tools/pipelines such as MISO, rMATS, SUPPA, RSEM, CuffDiff.

Emphasis will be given to how you can evaluate these tools on your own data and best practices.

Yoseph Barash, Assistant Professor, Perelman School of Medicine University of Pennsylvania


Yoseph Barash is a computational biologist who works on predictive models to understand RNA biogenesis, its regulation, and its role in human disease. His lab develops machine learning algorithms that integrate genomic and genetic data, followed by wet lab experimental verifications. Yoseph did his Ph.D. in machine learning under Prof. Nir Friedman at the Hebrew University, and his postdoctoral work with Prof. Ben Blencowe and Prof. Brendan Frey at the University of Toronto, focusing on alternative splicing of genes. His dry and wet lab work involves three main themes that pose computational, engineering, and experimental challenges: Deriving new mechanistic insights into RNA biogenesis; Applying the predictive algorithms for RNA processing the lab develops to the study of human disease and phenotypic diversity; Developing software tools that allow the greater scientific community to employ the lab’s algorithms.


Workshop D
Date: April 25, 2017 | Time: 1.30 – 4.30pm

13.30 - 16.30
An Advanced Users Guide to the UCSC Genome Browser
Workshop Leader: Robert Kuhn, Associate Director, UC Santa Cruz Genome Browser

The UCSC Genome Browser is a widely used platform for access to genomic data provided by laboratories around the world. When combined with user-supplied data, it is possible to discern complicated relationships among datasets as disparate as gene predictions, gene expression, regulation, evolutionary conservation, and known variation at all scales from single-base to large copynumber variants.

The Advanced Guide to the Genome Browser will explore:

  • How to load and visualize RNA-Seq data into the Browser
  • Utilizing the Table Browser to extract and visualize peak locations from those data
  • How exon-only view enhances the view of RNA-Seq data by removing non-coding regions from the display
  • Exporting lists of genes or known variants from selected regions using several different Browser tools, including the Data Integrator


Robert Kuhn, Associate Director, UC Santa Cruz Genome Browser


Robert Kuhn received his PhD at the University of California,  Santa Barbara in Biochemistry and Molecular Biology, where he  studied the centromeres of yeast. Following a postdoctoral at  UC Berkeley/USDA Plant Gene Expression Center, he taught  biochemistry, molecular biology and genetics at UC Santa Cruz.  He joined the UCSC Genome Browser project in 2003, where he is   now  Associate Director.  The Genome Browser is a widely used  visualization tool giving access to the genomes of human and   more than one hundred other animals.  Dr. Kuhn’s responsibilities   include enabling researchers through teaching the Genome Browser   in workshops and seminars and  learning from them how to improve   the Browser, including identification and integration of useful   new datasets