Bioinformatics and Genomics

2015 Annual Retreat

The 2015 Bioinformatics and Genomics retreat was held August 28th and 29th.  The one and a half day retreat featured Dr. Eric Schadt, Director of Icahn Institute for Genomics and Multiscale Biology at Mount Sinai Hospital, New York, as the keynote speaker. A wide range of faculty and student talks and a workshop session was held on the 29th.

Itinerary

Friday, August 28, 2015

When

What

Where

4:50-5:00pm

Registration

Opening remarks

Lobby Life Science Building

5:00-6:20pm

Session 1

Dr. Dan Kifer : "The voter turnout paradox and the availability of biomedical data"

Dr. Kamesh Madduri : "The SPRITE pipeline for genomic variant calling"

Dr. Christina Grozinger : "Sociogenomics of cooperation and conflict in social insect societies"

Dr. Phil Bevilaqua : "Genome-wide profiling of RNA structure"

Berg Auditorium, 100 Life Sciences Building

6:20-6:30pm

Break

First floor, Life Sciences Building

6:30-7:30pm

Keynote Speaker

Dr. Eric Schadt (Mount Sinai, New York)

"Linking patient acquired data with molecular and electronic medical record data to construct predictive models of disease"

Berg Auditorium, 100 Life Sciences Building

7:30pm-

Dinner and poster session 1

Third floor bridge, Life Sciences Building

Saturday, August 29, 2015

When

What

Where

8:30am

8:45-10:10am

Continental Breakfast

Session 2

Dr. Yu Zhang : "New IDEAS for joint genome segmentation across many cell types"

Yafei Lyu : "A semi-parametric statistical model for integrating gene expression profiles across different platforms"

Dr. Le Bao : "Assigning viruses from sequence count data via a mixture model"

Zach Fuller : "The genomic consequences and molecular evolution of segregation distortion in Drosophila pseudoobscura"

Monika Cechova Michalovova: "Comparative Analysis of the Y Chromosome Genomes from Great Apes"

Lobby Life Science Building

Berg Auditorium, 100 Life Sciences Building

10:10-10:30am

Coffee break

First floor, Life Sciences Building

10:30-11:45am

Precision Medicine Session

Dr. Jim Broach : "Genomics of Amyotrophic Lateral Sclerosis: identification of the missing heritability"

Lucilla Pizzo : "The 16p12.1 deletion as a paradigm for understanding the complex genetics of intellectual disability disorders"

Dr. Darrin Bann: "Genomic studies of familial and sporadic thyroid cancers"

Dr. Sinisa Dovat : "Epigenetic regulation of gene expression by Ikaros and Casein Kinase II in leukemia"

Berg Auditorium, 100 Life Sciences Building

11:45-12:30pm

Special invited talk

Dr. Marylyn Ritchie : "Electronic health records and genomics - a dynamic duo for precision medicine"

Berg Auditorium, 100 Life Sciences Building

12:30-2:00pm

Lunch and poster session 2

Third floor bridge, Life Sciences Building

2:00-5:00pm

Session 2

Data Visualization Workshop

Berg Auditorium, 100 Life Sciences Building

5:00-5:05pm

Concluding remarks

Berg Auditorium, 100 Life Sciences Building

6:00pm-

Students' evening social

TBD

Data Visualization Workshop

Visualizing genomic datasets using IGV genome browser

This workshop introduced easy ways to visualize different types of NGS datasets using IGV (Integrative Genomics Viewer), a popular tool to visualize genomics datasets. The first part of the workshop aims familiarized participants with different options and the user interface of IGV. The second part of the workshop focused on three hands-on data centric modules emphasizing the importance of data exploration through genomic browsers. 

The workshop began with an introduction to the Integrative Genomics Viewer (IGV) browser including:

  • Pre-processing your data for visualization.
  • Loading references and gene annotations.
  • Sharing your session with your collaborators.

After the introductory talk three data centric modules were explored:

  • Transcriptome visualization and exploration.
  • Genome missassemblies
  • SNPs discovery and genome rearrangements.