Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides

K Boone, C Wisdom, K Camarda, P Spencer… - BMC …, 2021 - Springer
Background Current methods in machine learning provide approaches for solving
challenging, multiple constraint design problems. While deep learning and related neural …

Mathematical fundamentals for the noise immunity of the genetic code

E Fimmel, L Strüngmann - Biosystems, 2018 - Elsevier
Symmetry is one of the essential and most visible patterns that can be seen in nature.
Starting from the left–right symmetry of the human body, all types of symmetry can be found …

Circular codes, symmetries and transformations

E Fimmel, S Giannerini, DL Gonzalez… - Journal of Mathematical …, 2015 - Springer
Circular codes, putative remnants of primeval comma-free codes, have gained considerable
attention in the last years. In fact they represent a second kind of genetic code potentially …

Beyond crystals: the dialectic of materials and information

JHE Cartwright, AL Mackay - … Transactions of the …, 2012 - royalsocietypublishing.org
We argue for a convergence of crystallography, materials science and biology, that will
come about through asking materials questions about biology and biological questions …

On dichotomic classes and bijections of the genetic code

E Fimmel, A Danielli, L Strüngmann - Journal of Theoretical Biology, 2013 - Elsevier
Dichotomic classes arising from a recent mathematical model of the genetic code allow to
uncover many symmetry properties of the code, and although theoretically derived, they …

Yury Borisovich Rumer and his 'biological papers' on the genetic code

E Fimmel, L Strüngmann - Philosophical Transactions of …, 2016 - royalsocietypublishing.org
Yury Borisovich Rumer was one of the most important theoretical physicists of the former
Soviet Union in the early 1930s. However, he also wrote a few 'biological papers' on the …

On models of the genetic code generated by binary dichotomic algorithms

M Gumbel, E Fimmel, A Danielli, L Strüngmann - Biosystems, 2015 - Elsevier
In this paper we introduce the concept of a BDA-generated model of the genetic code which
is based on binary dichotomic algorithms (BDAs). A BDA-generated model is based on …

The non-power model of the genetic code: a paradigm for interpreting genomic information

DL Gonzalez, S Giannerini… - … Transactions of the …, 2016 - royalsocietypublishing.org
In this article, we present a mathematical framework based on redundant (non-power)
representations of integer numbers as a paradigm for the interpretation of genomic …

A permuted set of a trinucleotide circular code coding the 20 amino acids in variant nuclear codes

CJ Michel, G Pirillo - Journal of Theoretical Biology, 2013 - Elsevier
We identify here a combinatorial property between circular code and genetic code. A circular
code of 20 trinucleotides which allows to retrieve the reading frame has a permuted set of 20 …

Maximal dinucleotide comma-free codes

E Fimmel, L Strüngmann - Journal of Theoretical Biology, 2016 - Elsevier
The problem of retrieval and maintenance of the correct reading frame plays a significant
role in RNA transcription. Circular codes, and especially comma-free codes, can help to …