Journal Club

Fractal Encoding of sequences

Hannah Löchel

• 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]

• Fractal construction of constrained code words for DNA storage systems

Hannah F Löchel, Marius Welzel, Georges Hattab, Anne-Christin Hauschild, Dominik Heider (2021)

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

Notes:

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https://en.wikipedia.org/wiki/The_Fractal_Geometry_of_Nature

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On Michael Barnsley fractals work: https://en.wikipedia.org/wiki/Michael_Barnsley

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the original CGR paper: https://academic.oup.com/nar/article/18/8/2163/2383530

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order = log2 (sequence length)

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https://en.wikipedia.org/wiki/Kronecker_product

Susana Vinga to Everyone

variable lenght Markov Models - https://www.jstor.org/stable/1391185

Balasubramanian, Jeya (NIH/NCI) [F] to Everyone

https://www.nature.com/articles/s41586-020-1943-3

Susana Vinga to Everyone

and the link to e.g. suffix trees https://almob.biomedcentral.com/articles/10.1186/1748-7188-7-10

Entropy of DNA sequences: https://www.sciencedirect.com/science/article/abs/pii/S0022519304003224?via%3Dihub

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