Short Course on NGS

Next-generation sequencing technology is impacting almost all aspects of biomedical research. This technology generates an unprecedented wealth of data that demands novel analysis strategies. While IT infrastructure and bioinformatics developments are obviously required to enable sound information extraction, sophisticated statistical methodologies and algorithms are also essential for interpreting the data. In this regard, we are organizing a NHGRI funded four-day short course, calling statisticians, genetic epidemiologists, bioinformaticians, and genome biologists, to discuss the statistical challenges and opportunities in next-generation sequencing data analysis. We believe that this course will provide a venue for exchanging of cutting-edge information and ideas, and fostering collaborations among methodologists, analysts, and biomedical investigators.

Schedule of Events: Agenda

Mon 12/14/15 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
08:00 – 09:15 AM	Registration-Room 121 – Coffee, Tea, Juice, Associate Muffins, Fruit	Wanda C. Skipwith/Mary Ann Rice
09:15- 09:30 AM	Introductory Remarks	Hemant Tiwari, PhD – UAB
09:30 – 10:30 AM	High Performance DNA Sequencing	Shawn Levy, PhD – HudsonAlpha Institute of Biotechnology
10:30 – 10:45 AM	Discussion	Shawn Levy, PhD
10:45 – 11:00 AM	BREAK
11:00 – 12:00 PM	Next Generation Sequencing in Methylation Studies	Devin Absher, PhD – HudsonAlpha
12:00 – 12:15 PM	Discussion	Devin Absher, PhD
12:15 – 01:30 PM	LUNCH – You are free to try any of the local eating places in the area
01:30 – 02:30 PM	From Reads to Genotypes Variant Calling and Assembly	Degui Zhi, PhD – UAB
02:30 – 02:45 PM	Discussion	Degui Zhi, PhD
02:45 – 03:00 PM	BREAK
03:00 – 04:00 PM	StatGenLab, a Virtual Machine for Genetic Data Analysis	Jelai Wang – Wang Scientific Software Solutions, LLC
04:00- 05:00 PM	Software Demonstration & Hands-on Computing (R & Bioinformatics File Formats)	Xiangqin Cui, PhD – UAB

Tue 12/15/15 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
	Room 121 – Coffee, Tea, Juice, Associated Muffins, Fruit
09:30 – 10:30 AM	Functional Genomics	Dan Savic, PhD – HudsonAlpha
10:30 – 10:45 AM	Discussion	Dan Savic, PhD
10:45 – 11:00 AM	BREAK
11:00 – 12:00 PM	Predicting Causal Variation	Greg Cooper, PhD – HudsonAlpha
12:00 – 12:15 AM	Discussion	Greg Cooper, PhD
12:15 – 01:30 PM	LUNCH – You are free to try any of the local eating places in the area
01:30- 02:30 PM	Rare Variants Analysis	Michael Wu, PhD – Fred Hutchinson Cancer Research Center
02:30- 02:45 PM	Discussion	Michael Wu, PhD
02:45 – 03:00 PM	BREAK
03:00- 06:00 PM	Software Demonstration & Hands-on Computing (Exome & Whole Genome NGS)	Michael Wu, PhD; Degui Zhi, PhD
07:00- 09:00 PM	Dinner/Social @ The Edge of Chaos – 4th Floor, Lister Hill Library	Participants & Faculty

Wed 12/16/15 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
	Room 121 – Coffee, Tea, Juice, Associated Muffins, Fruit
09:30 – 10:30 AM	Transcriptome Analysis Using NGS	Xiangqin Cui, PhD – UAB
10:30 – 10:45 AM	Discussion	Xiangqin Cui, PhD
10:45 – 11:00 AM	BREAK
11:00 – 12:00 PM	Analysis of Whole-genome Bisulfite Sequencing Data	Karen Conneely, PhD – Emory University
12:00 – 12:15 AM	Discussion	Karen Conneely, PhD
12:15 – 01:30 PM	LUNCH BREAK
01:30 – 02:30 PM	Introduction to ChIP-Seq Data Analyses	Hao Wu, PhD – Emory University
02:30 – 02:45 PM	Discussion	Hao Wu, PhD
02:45 – 03:00 PM	BREAK
03:00- 06:00 PM	Software Demonstration & Hands-on Computing (ChiP-seq Software, BSmooth and DSS)	Hao Wu, PhD; Karen Conneely, PhD

Thu 12/17/15 – UAB in Birmingham, AL

Time	Topic	Speaker	Video
	Room 121 – Coffee, Tea, Juice, Associated Muffins, Fruit
09:30 – 10:30 AM	Cloud Computing	Jonas Almeida, PhD – Stony Brook University
10:30 – 10:45 AM	Discussion	Jonas Almeida, PhD
10:45 – 11:00 AM	BREAK
11:00 – 12:00 PM	Galaxy	David Crossman, PhD, UAB
12:00 – 12:15 PM	Discussion	David Crossman, PhD
12:15- 01:30 PM	LUNCH – You are free to try any of the local eating places in the area
01:30 – 02:45 PM	Hands-on with Galaxy	David Crossman, PhD
02:45 – 03:00 PM	BREAK
03:00 – 05:00 PM	Software Demonstration & Hands-on Computing (RNA-Seq)	Xiangqin Cui, PhD
05:00 PM	Adjourn