Bioinformatics and Genomics

2014 Annual Retreat

The retreat consisted of a one-and-a-half day meeting featuring a keynote speaker, faculty and student talks, data visualization workshop and poster presentations. In 2014, we were honored to host the leader in Computational Genomics, Dr. Peter J. Park as the keynote speaker.

Program

Friday, September 12, 2014

When

What

Where

3:50-4:00pm

4:00-4:05pm

Coffee

Opening remarks

4:05-5:45pm

Session 1

Dr. Kateryna Makova : "Maternal Age Effect and Severe Germline Bottleneck in the Inheritance of Human Mitochondrial DNA" **

Dr. Raquel Assis : "Functional evolution of duplicate genes in Drosophila and mammals"

Dr. Michael DeGiorgio : "A likelihood-based approach for detecting selective sweeps"
Dr. William Noid : "Deciphering the glycosylation code"

Berg Auditorium, 100 Life Sciences Building

5:45-5:50pm

Break

First floor, Life Sciences Building

5:50-7:00pm

Keynote Speaker

Dr. Peter J Park (Harvard University)

"Discovering somatic alterations in cancer genomes using whole-genome sequencing"

Berg Auditorium, 100 Life Sciences Building

7:00pm-

Dinner and poster session 1

Third floor bridge, Life Sciences Building

Saturday, September 13, 2014

When

What

Where

8:30am

9:00-10:30am

Coffee and breakfast

Session 2

Dr. Ed O'Brien : "Physical Bioinformatics: Transcriptome-wide codon translation rates in yeast have broad distributions and diverse origins"

Rohit Reja : "Transcription Factor Organization at Ribosomal Protein Genes"

Dr. Feng Yue : "Dynamic Enhancer Landscapes during Pancreatic differentiation of human ES cells"

Yin Tang : "Hidden RNA codes revealed from the plant in vivo RNA structurome"

Dr. Vasant Honavar :"Computational Prediction of Macromolecular Interfaces, Interactions, and Complexes"

Berg Auditorium, 100 Life Sciences Building

10:30-10:45am

Coffee break

First floor, Life Sciences Building

10:45-12:30pm

Session 3

Dr. Georgia Dunston : "Introducing a Biophysics Perspective on the Science of Human Genome Information Dynamics in Population Genomics" **

Arslan Zaidi : "The world face space: Modeling the effects of genetic ancestry on 3D facial shape"

Dr. Judie Ann Howrylak : "Integrative Genomics Approaches to Acute Respiratory Distress"

Jason Miller : "RIP-seq provides new insight on how RNA is regulated"

Dr. Dajiang J. Liu : "Unveiling the genetic architecture of lipids levels via large scale meta-analysis"

Berg Auditorium, 100 Life Sciences Building

12:30-2:00pm

Lunch and poster session 2

Third floor bridge, Life Sciences Building

2:00-3:20pm

Session 4 -- Visualization Workshop

Dr. Sarah Pendergrass, Dr. Stephen W. Schaeffer and Anastasia Lucas

Berg Auditorium, 100 Life Sciences Building

3:20-3:40pm

Coffee break

First floor, Life Sciences Building

3:40-5:00pm

Session 5 — Visualization Workshop

Dr. Sarah Pendergrass, Dr. Stephen W. Schaeffer and Anastasia Lucas

Berg Auditorium, 100 Life Sciences Building

5:00-5:05pm

Concluding remarks

Berg Auditorium, 100 Life Sciences Building

6:00pm-

Students' evening social

TBD

** - Special talks

Data Visualization Workshop

A two-session workshop offered in conjunction with the 2014 BG Retreat featured a demo on data visualization in R and Cytoscape, and hands-on exercises.

This workshop included a talk on data visualization topics including:

  • Examples of the power of data visualization
  • Best practices for visualizing data
  • Breaking out of tables
  • Recommended data visualization software  

 The talk was followed by hands-on tutorial:

  • Generating basic plots in the versatile software package ggplot2 in the statistical package R
  • Plotting genomic results across chromosomal ideograms using PhenoGram
  • Basic use of Cytoscape, a powerful tool for visualizing networks of connections between data