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.
|27-April||Overview and topic selection|
MGnify: the microbiome analysis resource
A new genomic blueprint of the human gut microbiota
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||PE||DH|
Characteristics of bacterial and yeast microbiomes in spontaneous and mixed-fermentation beer and cider
Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis
Strobemers: an alternative to k-mers for sequence comparison
A critical assessment of gene catalogs for metagenomic analysis https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab216/6207961
Studying the gut virome in the metagenomic era: challenges and perspectives
|6-July||Fast and sensitive taxonomic assignment to metagenomic contigs |
|6-July||Taxonomic analysis of metagenomic data with kASA https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab200/6204649||JVT||DH|
- Computing the Rearrangement Distance of Natural Genomes https://link.springer.com/chapter/10.1007%2F978-3-030-45257-5_1
- Minimally overlapping words for sequence similarity search https://academic.oup.com/bioinformatics/article/36/22-23/5344/6042707
- eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses https://academic.oup.com/nar/article/47/D1/D309/5173662
- AnnoTree: visualization and exploration of a functionally annotated microbial tree of life https://academic.oup.com/nar/article/47/9/4442/5432638
SetSketch: Filling the Gap between MinHash and HyperLogLog https://arxiv.org/abs/2101.00314