Computational Molecular Biology Research

Course Overview

Projects

• Increasing diagnostic yield of fast whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (NICU):
  1. Improved variant calling of CNVs or large insertions or sex chromosome specific variants (choose one) - Pieter / Freerk
  2. Improved variant calling of medium sized InDels - Pieter / Freerk
  3. Improved variant interpretation by combining gene networks with phenotype networks - Juha / Joeri

• Transcriptome analysis to elucidate human fatty liver disease development:
  4. Improving Ribo-zero RNA seq data analysis to detect non-coding RNAs in addition to coding RNAs - Jing / Bibi

• Interaction of microbe and host genomes in IBD???:
  5. Microbiome anaylses - Floris / Arnau? / Marc Jan?

• Non-invasive early detection of (pre-)diabetes using Advanced Glycemic Endproduct detection:
  6. Optimizing decision trees to differentiate between healthy and diseased using parameter optimisation - Martijn

• Towards better treatment of cancer patients: Identifying new tumor (sub) types:
  7. By re-analysing DNA aberrations in 16,000 tumor samples - Lude?

Course Schedule

Week 1

Monday 02-02-2015

When	What	Where
09:15 - 10:30	Research meeting (Wijmenga/Weersma/Franke groups)	ERIBA 3rd floor corner room next to Auditorium
10:30 - 10:45	Break
10:45 - 11:15	Course introduction / kick off	TBA
11:15 - 12:00	Lunch break
12:00 - 13:00	Literature discussion	ERIBA 3rd floor corner room next to Auditorium
13:00 - 13:15	Break
13:15 - 14:15	Lecture project 1	TBA
14:15 - 14:45	Break
14:45 - 15:45	Lecture project 2	TBA
15:45 - 16:00	Break
16:00 - 16:45	Lecture project 3	TBA

Tuesday 03-02-2015

When	What	Where
08:45 - 10:00	Research meeting (Entire genetics dept.)	ERIBA 3rd floor Auditorium
10:00 - 10:15	Break
10:15 - 11:00	Lecture project 4	TBA
11:00 - 11:15	Break
11:15 - 12:00	Lecture project 5	TBA
12:00 - 13:00	Lunch break
13:00 - 13:45	Lecture project 6	TBA
13:45 - 14:00	Break
14:00 - 14:45	Lecture project 7	TBA
14:45 - 15:00	Break
15:00 - 16:00	Discuss options, ask questions and choose project	TBA

Wednesday 04-02-2015

When	What	Where
09:30 - 10:15	Experimental Design (Lude)	TBA
10:15 - 10:30	Break
10:30 - 11:15	GWAS (Lude)	TBA
11:15 - 11:30	Break
11:30 - 12:15	NGS (Morris)	TBA

Afternoon:

• Getting familiar with the topic: search literature and read read read.

Thursday 05-02-2015

When	What	Where
09:30 - 10:15	Gene Expression (Lude)	TBA
10:15 - 10:30	Break
10:30 - 11:15	Integrating Datasets (Lude)	TBA
11:15 - 11:30	Break
11:30 - 12:15	Data visualization (Lude)	TBA

Afternoon:

• Getting familiar with the topic: search literature and read more.
• Learning to script depending on project either R or Bash or...

/ Friday 06-02-2015 /

• Getting familiar with the topic: search literature and read more.
• Learning to script depending on project either R or Bash or...
• Start designing experiment / writing (validation) plan

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Week 2-5

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/ Monday 09-02-2015 /

• Regular meetings
• Finish experimental design / (validation) plan. Discuss design with supervisor and have approved experimental design ready by the end of the day.

/ Regular events /

Mondays 09:15 - 10:30 Research meeting (Wijmenga/Weersma/Franke? groups) @ ERIBA 3rd floor corner room next to Auditorium. Mondays 12:00 - 13:00 Literature discussion @ ERIBA 3rd floor corner room next to Auditorium. Tuesdays 08:45 - 10:00 Research meeting (Entire genetics dept.) @ ERIBA 3rd floor Auditorium. Other 09:00 - 17:00 Perform experiments and continue to learn scripting.

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Week 6

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Mondays 09:15 - 10:30 Research meeting (Wijmenga/Weersma/Franke? groups) @ ERIBA 3rd floor corner room next to Auditorium. Mondays 12:00 - 13:00 Literature discussion @ ERIBA 3rd floor corner room next to Auditorium. Tuesdays 08:45 - 10:00 Research meeting (Entire genetics dept.) @ ERIBA 3rd floor Auditorium.

Full days: Write report and prepare presentation.

/ Thursday 12-03-2015 /

13:00 - 13:30 Presentation project 1 13:30 - 14:00 Presentation project 2 14:00 - 14:15 Break 14:15 - 14:45 Presentation project 3 14:45 - 15:15 Presentation project 4 15:15 - 15:30 Break 15:30 - 16:00 Presentation project 5 16:00 - 16:30 Presentation project 6 16:30 - 17:00 Wrap up by Morris

/ Friday 13-03-2015 /

17:00 Report submission deadline