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Seminar Microbiome Analysis

Title   BIOINF4322 Seminar Microbiome Analysis
Teachers   Prof. Daniel Huson  and Prof. Ruth Ley (MPI-DB)
Time and place Tuesdays, 8:15-11:00h,  A104
Signup Email to:  Daniel Huson  until Sunday, 22nd April
 First Session
(Assignment of topics)
Tuesday, 24 April, 2018
Language
English
Links Campus
 
 

Description

 
The aim of this interdisciplinary seminar is to obtain an overview and understanding of the current state of the art in microbiome research.  On the one hand, we will look at some of the most interesting biological problems that are being studied. On the other hand, we will survey the bioinformatics approaches that are being used to help solve these questions.
 
In the first session of the seminar, we will provide an overview over the topics to be discussed in the seminar and then the topics will be assigned to the participants. Each participant will be provided with one or more papers on their topic. In addition, participants are expected to also survey the literature so as to identify additional papers that are useful for their topic.
 
Each participant will give a 25 minute oral presentation, followed by questions and discussion, and then feedback. Sessions will be chaired by a participant of the seminar. In addition, each participant will provide a write-up of their topic (~12 pages) in which they present the content of their presentation in their own words. 
 
Grading will be based on the quality of the oral presentation. The quality of the writeup and the level of participation in discussions will used to push the grade up or down. Participation in all sessions is mandatory.
 
To ensure a high quality of presentations and write-ups, each participant must discuss their presentation with their supervisor at least one week before the scheduled presentation. 
 
 
Topics

 

Here is a list of topics, each with a "seed" paper introduce you to the topic:
 
  1. QIIME and QIIME2, Caporaso et al, 2010
  2. 16S clustering and deblurring, Amir et al, 2017
  3. MetaPhlAn2, Truong et al, 2015
  4. MEGAN Community Edition, Huson et al, 2016
  5. Kraken, Centrifuge and Kaiju, Wood et al, 2014Kim et al, 2016 and Menzel et al (2016)
  6. Metabolic and microbiome changes during pregnancy, Koren et al, 2012
  7. Immunity and gut microbiome, Cullender et al, 2013
  8. The Tara Oceans voyage, Gimmler et al, 2016 
  9. Microbes in an aquifer system, Anantharaman et al, 2016
  10. Strain-level analysis,  Smillie et al, 2018 (or contact RL)
  11. Ancient microbiomes, Weyrich et al, 2017
  12. Ancient pathogens, Vågene et al, 2017  (or contact DH)
 

Time table

 
 
Date Topic Name Supervisor
24. Apr  Introduction to seminar, assignment of topics   DH & RL
 5. June  QIIME and QIIME2, Caporaso et al, 2010 Jennifer Bödker RL
 5. June  MetaPhlAn2, Truong et al, 2015 Manuel Kreutzer DH 
5. June Metabolic and microbiome changes during pregnancy, Koren et al, 2012 Sylvia Siegel RL
26. June 16S clustering and deblurring, Amir et al, 2017
Pia Rautenstrauch DH
26. June Kraken, Centrifuge and Kaiju, Wood et al, 2014Kim et al, 2016 and Menzel et al (2016)
DH
26. June Immunity and gut microbiome, Cullender et al, 2013

3. July The Tara Oceans voyage, Gimmler et al, 2016  Lakshmipriya Thrukonda DH
3. July Microbes in an aquifer system, Anantharaman et al, 2016 Yangpeng Li  RL
 3. July Strain-level analysis,  Smillie et al, 2018
RL
17. July Ancient microbiomes, Weyrich et al, 2017  Jan Prosi DH
17. July Ancient pathogens, Vågene et al, 2017  Steffen Kienzler DH






 
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