Algorithmen der Bioinformatik

BIOINF4322 Seminar Microbiome Analysis

Teachers Prof Daniel Huson and Xi Chen
Date Tuesdays, 8:15-10:00h
Starts April 27, 2021
Register via Ilias, already full
Language English
Links Alma Ilias

 

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 biological problems that are currently 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. 

 

  Date Topic Student Supervisor
  27-April Overview and topic selection    
  1-June

MGnify: the microbiome analysis resource

https://academic.oup.com/nar/article/48/D1/D570/5614179

   
  1-June

A new genomic blueprint of the human gut microbiota

https://www.nature.com/articles/s41586-019-0965-1

   
  8-June

Studying the gut virome in the metagenomic era: challenges and perspectives

https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-019-0704-y

   
  8-June

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog https://academic.oup.com/nargab/article/3/1/lqab009/6155872

   
  15-June Raven: a de novo genome assembler for long reads https://www.biorxiv.org/content/10.1101/2020.08.07.242461v2.full    
  15-June

Characteristics of bacterial and yeast microbiomes in spontaneous and mixed-fermentation beer and cider

https://www.sciencedirect.com/science/article/pii/S0740002020302471

   
  22-June

Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02303-4

   
  22-June

Strobemers: an alternative to k-mers for sequence comparison
https://www.biorxiv.org/content/10.1101/2021.01.28.428549v3

   
  29-June

A critical assessment of gene catalogs for metagenomic analysis https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab216/6207961

   
  29-June

SetSketch: Filling the Gap between MinHash and HyperLogLog

https://arxiv.org/abs/2101.00314

   
  6-July Fast and sensitive taxonomic assignment to metagenomic contigs
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab184/6178277
   
  6-July Taxonomic analysis of metagenomic data with kASA https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab200/6204649    

Additional topics: