Computational Molecular Biology Research

Course Overview

This research course demonstrates the in silico data analysis used for genetics research at the RUG and UMCG. The emphasis of the research topics is on finding better methods for the analysis of high throughput data generated using technologies like Next Generation Sequencing (both DNA and RNA), Gene expression arrays, Genome wide association studies (GWAS), etc.

In the first week the research topics will be introduced and a minimal introduction for scripting in Bash and R will be provided. At the beginning of the second week the students will choose a research project to work on under supervision of a PhD-student or Postdoc.

Projects

Increasing diagnostic yield of fast whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (NICU)

1A. Improved variant calling for CNVs? - Pieter / Freerk
1B. Improved variant calling for large insertions? - Pieter / Freerk
1C. Improved variant calling for sex chromosomes? - Pieter / Freerk
1D. Improved variant calling for MtDNA? - Pieter / Freerk
1E. Improved variant calling of medium sized !InDels? - Pieter / Freerk

2. Improved variant interpretation by combining gene networks with phenotype networks - Juha / Joeri

Transcriptome analysis to elucidate human fatty liver disease development

3. Improving Ribo-zero RNA seq data analysis to detect non-coding RNAs in addition to coding RNAs - Bibi / Jing
   

Interaction of microbe and host genomes in IBD

4. Microbiome anaylses - Floris / Arnau / Marc Jan
   

===Non-invasive early detection of (pre-)diabetes using Advanced Glycemic Endproduct detection ===

5. Optimizing decision trees to differentiate between healthy and diseased using parameter optimisation - Martijn / Patrick
   

Towards better treatment of cancer patients: Identifying new tumor (sub) types

6. By re-analysing DNA aberrations in 16,000 tumor samples - Lude

Course Schedule

Venue

Course will be organized at or near the UMCG Genetics department, which is located on the 5th floor of the European Research Institute for the Biology of Aging - ERIBA building plus the complete 5th and partial 6th floor of the adjacent Dentistry building. The address for both buildings is

Antonius Deusinglaan 1
9713 AV Groningen

Building	Room	Name
3226	302	ERIBA building, meeting room, 3rd floor, in the corner and next to auditorium
3226	314	ERIBA building, auditorium, 3rd floor
3211	608	Dentistry building, GCC room, 6th floor, at the end of the corridor
3211	flex desks	Dentistry building, 5th floor
3226	flex desks	ERIBA building, 5th floor

Regular events

Day	Time	What	Where
Mondays	09:15 - 10:30	Research meeting (Wijmenga/Weersma/Franke groups)	3226-302 ERIBA meeting room
Mondays	12:00 - 13:00	Literature discussion	3226-302 ERIBA meeting room
Tuesdays	08:45 - 10:00	Research meeting (Entire genetics dept.)	3226-314 ERIBA Auditorium

Week 1

Monday 02-02-2015

When	What	Where
09:15 - 10:30	Research meeting (Wijmenga/Weersma/Franke groups)	3226-302 ERIBA meeting room
10:30 - 10:45	Break
10:45 - 11:15	Course kick off (Morris Swertz)	2311-608 GCC room
11:15 - 12:00	Lunch break
12:00 - 13:00	Literature discussion	3226-302 ERIBA meeting room
13:00 - 13:15	Break
13:15 - 14:15	Project introduction: 5GpM - whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (NICU) (?)	2311-608 GCC room
14:15 - 14:45	Break
14:45 - 15:45	Project introduction: Improved variant calling (Freerk van Dijk)	2311-608 GCC room
15:45 - 16:00	Break
16:00 - 16:45	Project introduction: Improved variant interpretation (Juha Karjalainen)	2311-608 GCC room

Tuesday 03-02-2015

When	What	Where
08:45 - 10:00	Research meeting (Entire genetics dept.)	3226-314 ERIBA Auditorium
10:00 - 10:15	Break
10:15 - 11:00	Project introduction: Transcriptome analysis to elucidate human fatty liver disease development (Biljana Atanasovska)	2311-608 GCC room
11:00 - 11:15	Break
11:15 - 12:00	Project introduction: Non-invasive early detection of (pre-)diabetes (Anries Smit & Martijn Dijkstra)	2311-608 GCC room
12:00 - 13:00	Lunch break
13:00 - 13:45	Project introduction: Microbiome anaylses (Floris Imhann)	2311-608 GCC room
13:45 - 14:00	Break
14:00 - 14:45	Project introduction: ? (?)	2311-608 GCC room
14:45 - 15:00	Break
15:00 - 16:00	Discuss options, ask questions and choose project	2311-608 GCC room

Wednesday 04-02-2015

When	What	Where
09:30 - 10:15	Experimental Design (Lude)	2311-608 GCC room
10:15 - 10:30	Break
10:30 - 11:15	GWAS (Lude)	2311-608 GCC room
11:15 - 11:30	Break
11:30 - 12:15	NGS (Morris)	2311-608 GCC room
12:15 - 13:00	Lunch break
13:00 - 13:45	R and bash scripting intro (Martijn Dijkstra)	2311-608 GCC room
13:45 - 14:00	Break
14:00 - 17:00	R and bash scripting tutorials	2311-608 GCC room

17:00 Preferences for project mailed to course coordinator

Thursday 05-02-2015

When	What	Where
09:30 - 10:15	Gene Expression (Lude)	2311-608 GCC room
10:15 - 10:30	Break
10:30 - 11:15	Integrating Datasets (Lude)	2311-608 GCC room
11:15 - 11:30	Break
11:30 - 12:15	Data visualization (Lude)	2311-608 GCC room
12:15 - 13:00	Lunch break
13:00 - 13:45	R and bash scripting intro (Martijn Dijkstra)	2311-608 GCC room
13:45 - 14:00	Break
14:00 - 17:00	R and bash scripting tutorials	2311-608 GCC room

Friday 06-02-2015

When	What	Where
19:30 - 10:15	R and bash scripting intro (...)	2311-608 GCC room
10:15 - 10:30	Break
10:30 - 12:15	R and bash scripting tutorials	2311-608 GCC room
12:15 - 13:00	Lunch break
13:00 - .....	Getting familiar with your project: search literature and read more.	2311-608 GCC room
..... - 17:00	Designing experiment / writing (validation) plan	2311-608 GCC room

Weeks 2-5

Monday 09-02-2015

When	What	Where
all day except for regular meetings	Finish experimental design / (validation) plan	2311-608 GCC room
16:00 - 17:00	Discuss final version of design / plan with supervisor and have it approved by the end of the day	2311-608 GCC room

• Regular meetings
• Execute your experiment / plan

Week 6

• Regular meetings
• Write report and prepare presentation.

Thursday 12-03-2015

When	What	Where
13:00 - 13:30	Presentation project 1	T.B.A.
13:30 - 14:00	Presentation project 2	T.B.A.
14:00 - 14:15	Break
14:15 - 14:45	Presentation project 3	T.B.A.
14:45 - 15:15	Presentation project 4	T.B.A.
15:15 - 15:30	Break
15:30 - 16:00	Presentation project 5	T.B.A.
16:00 - 16:30	Presentation project 6	T.B.A.
16:30 - 17:00	Wrap up (Morris Swertz)	T.B.A.

Friday 13-03-2015

When	What	Where
17:00	Report submission deadline	Your project supervisor's email inbox

Rating: 50% Practical work 30% Report 20% Presentation