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.

Rating

Students will be rated as follows:

• 50% Practical work
• 30% Report
• 20% Presentation

Projects

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

1. Improved variant calling for CNVs - Pieter / Freerk
2. Improved variant calling for large insertions - Pieter / Freerk
3. Improved variant calling for sex chromosomes - Pieter / Freerk
4. Improved variant calling for MtDNA - Pieter / Freerk
5. Improved variant calling of medium sized InDels - Pieter / Freerk
6. Improved variant interpretation by combining gene networks with phenotype networks - Juha / Joeri

Transcriptome analysis to elucidate human fatty liver disease development

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

Changes in the gut microbiome

8. Analyzing Whole Genome Shotgun data - Floris / Arnau / Marc Jan

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

9. Optimizing decision trees to differentiate between healthy and diseased using parameter optimization - Martijn / Patrick / Andries / Bernadette

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	10:45 - 11:00	Course SCRUM in weeks 2-6	3211-608 GCC 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
Tuesdays	10:15 - 10:30	Course SCRUM in weeks 2-6	3211-608 GCC room
Wednesdays	09:30 - 09:45	Course SCRUM in weeks 2-6	3211-608 GCC room
Thursdays	09:30 - 09:45	Course SCRUM in weeks 2-6	3211-608 GCC room
Fridays	09:30 - 09:45	Course SCRUM in weeks 2-6	3211-608 GCC room

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 - 11:00	Course kick off (Morris Swertz)	3211-608 GCC room
11:00 - 12:00	Lecture: Next Generation Sequencing (Morris Swertz)	3211-608 GCC room
12:00 - 13:00	Lunch break
13:00 - 13:45	Project introduction: Whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (Cleo van Diemen)	3211-608 GCC room
13:45 - 14:00	Break
14:00 - 14:45	Project introduction: Improved variant calling (Freerk van Dijk)	3211-608 GCC room
14:45 - 15:00	Break
15:00 - 15:45	Project introduction: Improved variant interpretation (Juha Karjalainen)	3211-608 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)	3211-608 GCC room
11:00 - 11:15	Break
11:15 - 12:00	Project introduction: Non-invasive early detection of (pre-)diabetes (Andries Smit & Martijn Dijkstra)	3211-608 GCC room
12:00 - 13:00	Lunch break
13:00 - 13:45	R scripting intro (Martijn Dijkstra)	3211-608 GCC room
13:45 - 14:00	Break
14:00 - 17:00	R tutorials	3211-608 GCC room

Wednesday 04-02-2015

When	What	Where
09:30 - 10:15	Lecture: Experimental Design (Lude Franke)	3211-608 GCC room
10:15 - 10:30	Break
10:30 - 11:15	Lecture: GWAS (Lude Franke)	3211-608 GCC room
11:15 - 11:30	Break
11:30 - 12:15	Project introduction: Microbiome anaylses (Floris Imhann)	3211-608 GCC room
12:15 - 13:00	Lunch break
13:00 - 13:45	R scripting intro (Martijn Dijkstra)	3211-608 GCC room
13:45 - 14:00	Break
14:00 - 17:00	R scripting tutorials	3211-608 GCC room
18:00	Deadline: Preferences for project mailed to course coordinator Morris Swertz

Thursday 05-02-2015

When	What	Where
09:30 - 10:15	Lecture: Gene Expression (Lude Franke)	3211-608 GCC room
10:15 - 10:30	Break
10:30 - 11:15	Lecture: Integrating Datasets (Lude Franke)	3211-608 GCC room
11:15 - 11:30	Break
11:30 - 12:15	Lecture: Data visualization (Lude Franke)	3211-608 GCC room
12:15 - 13:00	Lunch break
13:00 - 13:45	Bash scripting intro (Lennart Johansson)	3211-608 GCC room
13:45 - 14:00	Break
14:00 - 17:00	Bash scripting tutorials	3211-608 GCC room

Friday 06-02-2015

When	What	Where
09:30 - 10:15	Bash scripting intro (Lennart Johansson)	3211-608 GCC room
10:15 - 10:30	Break
10:30 - 12:15	Bash scripting tutorials	3211-608 GCC room
12:15 - 13:00	Lunch break
13:00 - 17:00	Getting familiar with your project: search literature Start designing experiment / writing (validation) plan	3211-608 GCC room

Weeks 2-5

Monday 09-02-2015

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 - 12:00	Finish experimental design / (validation) plan	3211-608 GCC room
12:00 - 13:00	Literature discussion	3226-302 ERIBA meeting room
12:00 - 17:00	Finish experimental design / (validation) plan	3211-608 GCC room
17:00	Deadline: have experimental design / (validation) plan approved by your supervisors	3211-608 GCC room

From Tuesday 10-02-2015 onwards

• 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 Improving Ribo-zero RNA seq data analysis to detect non-coding RNAs in addition to coding RNAs (Selle)	3211-S42A
13:30 - 14:00	Presentation Improved variant calling for large insertions (Glenn)	3211-S42A
14:00 - 14:15	Break
14:15 - 14:45	Presentation Optimizing decision trees to differentiate between healthy and diseased using parameter optimization (Sandra)	3211-S42A
14:45 - 15:15	Presentation Improved variant calling for MtDNA (Falke)	3211-S42A
15:15 - 15:30	Break
15:30 - 16:00	Presentation Improved variant interpretation by combining gene networks with phenotype networks (Tessa)	3211-S42A
16:00 - 16:30	Presentation Analyzing Whole Genome Shotgun Microbiomome data (Rogier)	3211-S42A
16:30 - 17:00	Wrap up (Morris Swertz)	3211-S42A

Friday 13-03-2015

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

Contact

Morris Swertz	coordinator	m.a.swertz AT rug DOT nl
Pieter Neerincx	daily supervision	pieter.neerincx AT gmail DOT com
Martijn Dijkstra	daily supervision	m.dijkstra.work AT gmail DOT com
Elisa Hoekstra	daily supervision	e.j.hoekstra AT umcg DOT nl