= 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 - Bibi / Jing * 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 == === 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 [[BR]] {{{ 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 || === 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 introduction / kick off (Morris Swertz) ||2311-608 GCC room || ||11:15 - 12:00 ||Lunch break || ||12:00 - 13:00 ||Literature discussion || 3226-314 ERIBA Auditorium || ||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.) ||ERIBA 3rd floor Auditorium (3226-314)|| ||10:00 - 10:15 ||Break || || ||10:15 - 11:00 ||Project introduction: ||2311-608 GCC room || ||11:00 - 11:15 ||Break || || ||11:15 - 12:00 ||Project introduction: ||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) ||TBA || ||10:15 - 10:30 ||Break || || ||10:30 - 11:15 ||GWAS (Lude) ||TBA || ||11:15 - 11:30 ||Break || || ||11:30 - 12:15 ||NGS (Morris) 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