Algorithmen der Bioinformatik

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 AlmaIllias
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.

https://www.nature.com/articles/s41592-018-0176-y

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.

https://www.nature.com/articles/s41592-019-0437-4

CP XC
23. June

05 Machine learning in metagenomics.

https://www.nature.com/articles/s41467-019-12669-6

MG XC
23. June

06 How antibiotics changes gut microbiome, which further weakened immunogenicity, resulting in different responses to influenza vaccine.

https://www.cell.com/cell/fulltext/S0092-8674(19)30898-0

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.

https://www.nature.com/articles/nbt.3988

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.

https://www.nature.com/articles/s41467-019-10649-4

PE XC
  Alternative topics:    
Alt-a

Bacterial recombination rates. https://www.nature.com/articles/s41592-018-0293-7

   
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