BIOINF4362 - Seminar Algorithms in Bioinformatics
Online seminar
Lecturer | Xi Chen and Daniel Huson |
Venue | Start date: April 28th, 2020 Tuesdays, 8:15-10h, dates: see below, online using Zoom (both audio and video required) |
Signup | April 14-24 on Ilias. |
Links | Alma, Illias |
Language | English |
Description
The aim of this seminar is to present and discuss some of the interesting recent algorithms and approaches in bioinformatics.
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.
Topics:
Date | Topic | Student | Supervisor |
28. April | Introduction and topic assignment | ||
26. May | (01 Metadata and gut microbiome diversity. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0747-x) | ||
26. May | 02 Metagenomic functional profiling. | LB | DH |
16. June | 03 DeepMAsED: evaluating the quality of metagenomic assemblies. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa124/5756210 | KM | DH |
16. June | 04 Protein level assembly from metagenomic short reads. | CP | XC |
23. June |
| MG | XC |
23. June | 06 How antibiotics changes gut microbiome, which further weakened immunogenicity, resulting in different responses to influenza vaccine. | TN | XC |
30. June | 07 Synteny paths for assembly graphs comparison. https://drops.dagstuhl.de/opus/volltexte/2019/11054/pdf/LIPIcs-WABI-2019-24.pdf | SJ | DH |
30. June | (08 Viral quasispecies assembly. https://genome.cshlp.org/content/27/5/835.ful https://academic.oup.com/bioinformatics/article-abstract/35/24/5086/5506652) | ||
7. July | 09 Methods for automatic reference trees and multilevel phylogenetic placement. https://academic.oup.com/bioinformatics/article/35/7/1151/5088318 | ED | XC |
7. July | 10 Efficient algorithms for protein alignments. | MOH | DH |
14. July | 11 Homology-aware phylogenomics. https://academic.oup.com/sysbio/article/66/4/590/2957051 | AS | DH |
14. July | 12 Improving the diagnostic yield of exome-sequencing by predicting gene–phenotype associations using large-scale gene expression analysis. | PE | XC |
Alternative topics: | |||
Alt-a | Machine learning in metagenomics. | ||
Alt-b | Long-read metagenomics. https://www.nature.com/articles/s41467-019-10934-2 | ||
Alt-c | Long-read assembly. https://www.nature.com/articles/s41587-019-0072-8 |