Probabilistic Methods for the Analysis of Next Generation Sequencing Data
Probabilistic Methods for the Analysis of Next Generation Sequencing Data
General info
- Introductory meeting: Nov 7, 2014, time 13:00-15:00, room 001 cluster building E1.7
- Block seminar: 5-6 March 2015, 9:00 till 16:00, room 001 cluster building E1.7 . Reports have to be handed in until latest 27t of February (midnight).
- You get 7 credit points
- Master students are eligible
- Limit of 12 participants
- Required to follow the seminar: Basic knowledge of genetics
- Recommended lectures: Bioinformatics 1-3, The Elements of Statistical Learning I or Machine Learning
- Registration: Please send an email to mschulz at mpi-inf.mpg.de (topic: Seminar Probabilistic Methods for Analysis of Next Generation Sequencing Data)
- Teaching assistant: Fatemeh Behjati
Course overview
Next Generation Sequencing (NGS) methods have revolutionized genetics. Applications of these technologies to e.g. genome or transcriptome sequencing create computationally challenging analysis problems. This seminar covers recent literature about new algorithmic and statistical developments that apply probabilistic methods to the analysis of NGS data. There will be a particular focus on the analysis of epigenetics and RNA sequencing data.
Every student will give a 45 minute presentation on the assigned topic and will also hand in a report of 10-12 pages.
Details introductory meeting
Participants that have registerd to the seminar need to attent the introductory meeting, where the topics are assigned and general rules of the seminar are explained.Course material
Topics are available here: password protected area.
Talk schedules
Below you find the schedule of the seminar talks with title and link to abstract. Talks are intended to last not more than 45 minutes with 15 minutes discussion afterwards.
Students can bring their own laptop or send the slides in ppt or pdf format one day before their presentation to mschulz@mmci.uni-saarland.de and use a Mac Airbook for presentation. A pointer will be available.
Information about how to make a good presentation can be found here.
| Topic / Time | Title | link to paper |
|---|---|---|
| ChIP-seq and RNA-seq | Thursday 5th March | |
| 10:00-10:45 | The next generation of transcription factor binding site prediction | link |
| 11:00-11:45 | Bayesian Transcriptome Assembly | link |
| 12:00-13:00 | Lunch Break | |
| 13:00-13:45 | Corset: enabling differential gene expression analysis for de novo assembled transcriptomes | link |
| 14:00-14:45 | Modeling mutual exclusivity of cancer mutations | link |
| 15:00-15:45 | Bridging the gap between transcriptome and proteome measurements identifies post-translationally regulated genes | link |
| Epigenetics | Friday 6th March | |
| 10:00-10:45 | Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of CpG Islands | link |
| 11:00-11:45 | Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods | link |
| 12:00-13:00 | Lunch Break | |
| 13:00-13:45 | RFECS: a random-forest based algorithm for enhancer identification from chromatin state | link | 14:00-14:45 | Comparative annotation of functional regions in the human genome using epigenomic data | link |