Advanced Topics in Next Generation Sequencing Analysis

Advanced Topics in Next Generation Sequencing Analysis

General info

  • Introductory meeting: Oct 15, 2013, time 14:00-16:00 , room 001 cluster building E1.7
  • Block seminar: March 19th - March 20st, 2014, 9:00 till 16:00, room 008 cluster building E1.7. Reports have to be handed in until the 12th of March 2014.
  • You get 7 credit points
  • Master students are eligible
  • Limit of 15 participants
  • Required to follow the seminar: Basic knowledge of genetics
  • Recommended lectures: Bioinformatics 1-3, The Elements of Statistical Learning I or Machine Learning
  • This seminar can serve as an in-depth follow-up to the lecture Bioinformatics for Next Generation Sequencing
  • Registration: Please send an email to mschulz at (topic: seminar Advanced Topics in Next Generation Sequencing Analysis)

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 for different problems in the analysis of NGS data. Some of the topics covered will be algorithms for de novo assembly, detection of differential expression and human genomic variations,sequencing error correction. Every student will give a 45 minute presentation on the assigned topic and will also hand in a report of 10 - 12 pages.

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 Abstract
DNA sequencing / RNA-sequencing Wednesday 19th March
9:00-9:45 PyroHMMvar: a sensitive and accurate method to call short INDELs and SNPs for Ion Torrent and 454 data link
10:00-10:45 De novo assembly and genotyping of variants using colored de Bruijn graphs link
11:00-11:45 IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels link
12:00-13:00 Lunch Break
13:00-13:45 Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data link
14:00-14:45 Differential analysis of gene regulation at transcript resolution with RNA-seq link
15:00-15:45 Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms link
Epigenetics Thursday 20th March
9:00-9:45 Unsupervised pattern discovery in human chromatin structure through genomic segmentation link
10:00-10:45 Inferring nucleosome positions with their histone mark annotation from ChIP data link
11:00-11:45 Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data link
12:00-13:00 Lunch Break
13:00-13:45 HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data link