= Computational Molecular Biology Research =

[[TOC()]]

== Course Overview ==

== Projects ==

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

* Transcriptome analysis to elucidate human fatty liver disease development:
 D. 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???:
 E. Microbiome anaylses - Floris / Arnau? / Marc Jan?

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

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

===================================================================================================
 Week 2-5
===================================================================================================

///// 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.

===================================================================================================
 Week 6
===================================================================================================

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