Genetics, Bioinformatics and Systems Biology Colloquium
Thursdays, 12:00 pm – 1:00 pm
UC San Diego, Powell-Focht Bioengineering Hall, Fung Auditorium
Complete schedule here

9/28/12 NextGen Gene Expression Analysis

NextGen Gene Expression Analysis Symposium and Workshop

Friday, September 28th, 2012 – 9:00AM-4:00PM

Salk Institute, Frederic de Hoffmann Auditorium

This event will bring together researchers from local academic institutes and industry that are interested in emerging experimental techniques and analysis strategies for studying gene expression. Advances in sequencing methodology have enhanced our ability to detect both different types of RNA and their dynamics, the effects of DNA mutation, chromatin states, and even the 3D organization of the genome, fundamentally changing our understanding of transcriptional regulation and the role of RNA in the cell. Presentations by local researchers will show how innovative approaches to RNA profiling by next Generation Sequencing methods (and many other techniques) have advanced their research across a wide range of complex biological questions. An interactive workshop will follow to introduce attendees to command-line tools and strategies for conducting their own next-gen sequencing analysis.  ***Participation is FREE.  Please register below.***Speakers:

Dr. Han Cho (Evans Lab, Salk)

Dr. Fulai Jin (Ren Lab, UCSD)

“Genome-wide investigation of DNA topological structure associated with cis-regulatory elements”

Dr. Sven Heinz (Glass Lab, UCSD)

“Enhancer RNA transcription initiation at base-pair resolution”

Dr. Fernando Lopez Diaz (Emerson Lab, Salk)

Dr. Erin Smith (Frazer Lab, UCSD)

“Genomic Analysis of Serial Chronic Lymphocytic Leukemia Samples to Identify Genetic and Epigenetic Changes during Disease Progression”

Melissa Wilbert (Yeo Lab, UCSD)

“LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor Abundance”

***Workshop Organizer: Dr. Chris Benner***

This interactive workshop will provide an introduction to next-gen sequencing analysis using command-line tools with the goal of educating researchers about RNA-Seq/ChIP-Seq methodology and analysis strategies.  This session will be appropriate for anyone interested in performing his/her own genomics analysis.

Topics covered will include:

1. Experimental Design for RNA/ChIP-Seq

2. Introduction to the computing environment of a modern genomics lab: computer hardware, software, and other resources

3. Popular tools for processing RNA/ChIP-Seq experiments and their use (mapping, visualization, gene expression, etc.)

4. Clever ways to use standard tools to analyze data in novel ways

Throughout this workshop, we will interactively analyze a small data to demonstrate analysis in action. Those with laptops will be encouraged to follow along.


  • 8:30 –  9:00AM – Registration/Light Refreshments
  • 9:00 – 9:10AM – Welcome Remarks
  • 9:10 – 10:30AM – Session I
  • 10:30 – 10:45AM – Break
  • 10:45AM – 12:00PM – Session II
  • 12:00PM – Lunch provided to first 100 registered attendees
  • 1:15 – 2:30 PM – Session III
  • 2:30 – 4PM – Workshop


Click here to register online

Deadline to register is September 22, 2012. Free lunch to first 100 registered attendees.

With many thanks for the support from: