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 (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 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