Algorithmen der Bioinformatik

BIOINF4322 Seminar Microbiome Analysis -2

Teachers Prof Daniel Huson and Wenhuan Zeng
Date Mondays, 8:15-10:00h
Starts April 26, 2021
Register via Ilias, closed
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
  26-April Overview and topic selection    
  31-May

Genetic determinants of the gut microbiome in UK Twins https://pubmed.ncbi.nlm.nih.gov/27173935/

JB DH
  31-May

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007859

  WZ
  7-June

DeepMicrobes: taxonomic classification for metagenomics with deep learning https://academic.oup.com/nargab/article/2/1/lqaa009/5740226

GOG WZ
  7-June

Species abundance information improves sequence taxonomy classification accuracy https://www.nature.com/articles/s41467-019-12669-6

MOH DH
  14-June

CoCoNet: An Efficient Deep Learning Tool for Viral Metagenome Binning https://doi.org/10.1093/bioinformatics/btab213

LM WZ
  14-June

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps https://www.nature.com/articles/s41467-019-10934-2

MH DH
  21-June

Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital https://elifesciences.org/articles/53886

NK DH
         
  28-June

DeepNOG: fast and accurate protein orthologous group assignment https://academic.oup.com/bioinformatics/article/36/22-23/5304/6050698

CS WZ
  28-June

PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data https://academic.oup.com/bioinformatics/article/36/22-23/5499/6042705

FL DH
  5-July

Identity: rapid alignment-free prediction of sequence alignment identity scores using self-supervised general linear models https://academic.oup.com/nargab/article/3/1/lqab001/6125549?login=true

KCC DH
  5-July

Gut microbiome, big data and machine learning to promote precision medicine for cancer https://www.nature.com/articles/s41575-020-0327-3

EB WZ
  12-July Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences https://www.nature.com/articles/s41598-021-83922-6 AM WZ

 

Additional topics: