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