Journal Club

Chaos game representation and its applications in bioinformatics

Hannah Franziska Löchel ¹, Dominik Heider ¹

Comput Struct Biotechnol J. 2021 Nov 10;19:6263-6271 [PMD34900136] [PDF] [my notes]

(preparation for Jan 19 presentation)

For the canonical representation discussion - encoding sequence storage, and encoding for deep learning:

Fractal construction of constrained code words for DNA storage systems
Hannah F Löchel, Marius Welzel, Georges Hattab, Anne-Christin Hauschild, Dominik Heider

Nucleic Acids Res 2021 Dec 15;gkab1209. https://doi.org/10.1093/nar/gkab1209. Online ahead of print.

Deep learning on chaos game representation for proteins
Hannah F Löchel, Dominic Eger, Theodor Sperlea, Dominik Heider
Bioinformatics, Volume 36, Issue 1, 1 January 2020, Pages 272–279, https://doi.org/10.1093/bioinformatics/btz493

Live SDK in

• notebook: https://observablehq.com/@episphere/usm

• and web application: https://usm.github.io/2

Hackathon - epiTracker

For CGR's see notebook and web application at https://github.com/usm/2,

Open SDK hack with epiTracker in mind.

Other topics

FAIR Friday this week is open