Mining for missed sORF-encoded peptides

X Yin, Y Jing, H Xu - Expert review of proteomics, 2019 - Taylor & Francis
Introduction: Small open reading frames (sORFs) with potential protein-coding capacity have
been disclosed in various transcripts, including long noncoding RNAs (LncRNAs), mRNAs …

Why is AUG the start codon? Theoretical minimal RNA rings: Maximizing coded information biases 1st codon for the universal initiation codon AUG

J Demongeot, H Seligmann - Bioessays, 2020 - Wiley Online Library
The rational design of theoretical minimal RNA rings predetermines AUG as the universal
start codon. This design maximizes coded amino acid diversity over minimal sequence …

Spontaneous evolution of circular codes in theoretical minimal RNA rings

J Demongeot, H Seligmann - Gene, 2019 - Elsevier
Small circular RNAs occur in many cells. Theoretical considerations designed to mimick
primordial RNAs designed 25 theoretical, minimal 22-nucleotide long circular RNAs (RNA …

[HTML][HTML] Genetic code optimization for cotranslational protein folding: codon directional asymmetry correlates with antiparallel betasheets, tRNA synthetase classes

H Seligmann, G Warthi - Computational and Structural Biotechnology …, 2017 - Elsevier
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a
biologically meaningful genetic code dimension: palindromic codons (first and last …

The uroboros theory of life's origin: 22-nucleotide theoretical minimal RNA rings reflect evolution of genetic code and tRNA-rRNA translation machineries

J Demongeot, H Seligmann - Acta Biotheoretica, 2019 - Springer
Theoretical minimal RNA rings attempt to mimick life's primitive RNAs. At most 25 22-
nucleotide-long RNA rings code once for each biotic amino acid, a start and a stop codon …

Bijective transformation circular codes and nucleotide exchanging RNA transcription

CJ Michel, H Seligmann - Biosystems, 2014 - Elsevier
The C 3 self-complementary circular code X identified in genes of prokaryotes and
eukaryotes is a set of 20 trinucleotides enabling reading frame retrieval and maintenance, ie …

Stem-loop RNA hairpins in giant viruses: invading rRNA-like repeats and a template free RNA

H Seligmann, D Raoult - Frontiers in Microbiology, 2018 - frontiersin.org
We examine the hypothesis that de novo template-free RNAs still form spontaneously, as
they did at the origins of life, invade modern genomes, contribute new genetic material …

RNA rings strengthen hairpin accretion hypotheses for tRNA evolution: a reply to commentaries by ZF Burton and M. Di Giulio

J Demongeot, H Seligmann - Journal of Molecular Evolution, 2020 - Springer
Theoretical minimal RNA ring design ensures coding over the shortest length once for each
coding signal (start and stop codons, and each amino acid) and their hairpin configuration …

[HTML][HTML] Protein sequences recapitulate genetic code evolution

H Seligmann - Computational and Structural Biotechnology Journal, 2018 - Elsevier
Several hypotheses predict ranks of amino acid assignments to genetic code's codons.
Analyses here show that average positions of amino acid species in proteins correspond to …

Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case

H Seligmann - Computational Biology and Chemistry, 2012 - Elsevier
Mitochondrial genes code for additional proteins after+ 2 frameshifts by reassigning stops to
code for amino acids, which defines overlapping genetic codes for overlapping genes …