BIOINF2110AB Proseminar Foundations of Bioinformatics
| Teachers | Prof Daniel Huson and Timo Lucas |
| Date | Tuesdays, 8:15-10 a.m. |
| Starts | 26th October 8:15-10:00 a.m. |
| Register | via Ilias |
| Language | English |
| Links | Alma Ilias |
Description
The aim of this proseminar is to obtain an overview and introduction to some of the fundamental topics in bioinformatics.
In the first session of the proseminar, 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 20-25 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 adjust 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. The write-up is due two weeks after the presentation, at the latest.
| Date | Topic | Student | Supervisor |
| 26th October | Overview and topic selection | ||
| 30th Nov. | Community profiling using QIIME | K.H. | DH |
| 30th Nov. | Metagenome analysis using MEGAN https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004957 | Y.X. | TL |
| 7th Dec. | Taxonomic metagenome analysis using MetaPhlAn | J.K. | TL |
| 7th Dec. | Functional metagenome analysis using HUMAnN2 | G.R. | DH |
| 14th Dec. | Microbiome analysis using Kraken https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1891-0 | J.F. | DH |
| 14th Dec. | Metagenome asssembly using MegaHit https://www.sciencedirect.com/science/article/pii/S1046202315301183?via%3Dihub | E.K. | TL |
| 21st Dec. | MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | A.B. | DH |
| 21st Dec. | CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes | J.N. | TL |
| 11th Jan. 2022 | Minimap2: pairwise alignment for nucleotide sequences https://academic.oup.com/bioinformatics/article/34/18/3094/4994778 | M.P. | DH |
| 11th Jan. 2022 | Mash: fast genome and metagenome distance estimation using MinHash https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x | M.A.A. | TL |
| 18th Jan. 2022 | Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega | V.B. | DH |
| 18th Jan. 2022 | Prokka: rapid prokaryotic genome annotation https://academic.oup.com/bioinformatics/article/30/14/2068/2390517 | M.C. | TL |
Additional possible topics:
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998144/
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Phylogenetic networks using Neighbor-net (https://academic.oup.com/mbe/article/21/2/255/1187993),
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Bayesian analysis using BEAST (https://bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-7-214), or
- Multiple alignment using MAFFT (https://academic.oup.com/nar/article/30/14/3059/2904316).
Remarks
- Topics are handed out in class.
- Students are first required to determine literature and other sources that are suitable to address their topic. The result of the literature search should be discussed with the tutor before students starts working on their report and presentation.
- The first page of the report and the first slide should contain the title of the seminar and the presentation, the student's name and email address and the tutor's name and the date.
- If figures, formulations or whole sentences are taken verbally from the references it has to be marked as a citation; this is also the case if the reference is a WWW document, there the exact url and the author of the text have to be cited.
- Presentation and report in English.
Assessment
- The quality of the presentation and the report will be assessed on content and presentation and a total grade will be given by the tutors.