Genetic code
View article: DNA damage reflected in the evolution of G-runs in genomes
DNA damage reflected in the evolution of G-runs in genomes Open
DNA oxidation is one of the main types of damage to the genetic material of living organisms. Of the many dozens of oxidative lesions, the most abundant is 8-oxoguanine (8-oxoG), a premutagenic base that leads to G→T transversions during r…
View article: TrevorZandi/FKBP-CIP-DEL: DEL analysis code for publication "Discovery of molecular glues that bind FKBP12 and structurally distinct targets using DNA-encoded libraries"
TrevorZandi/FKBP-CIP-DEL: DEL analysis code for publication "Discovery of molecular glues that bind FKBP12 and structurally distinct targets using DNA-encoded libraries" Open
"This release contains the minimal code required to reproduce the analyses in the manuscript, namely decoding of NGS data.
View article: TrevorZandi/FKBP-CIP-DEL: DEL analysis code for publication "Discovery of molecular glues that bind FKBP12 and structurally distinct targets using DNA-encoded libraries"
TrevorZandi/FKBP-CIP-DEL: DEL analysis code for publication "Discovery of molecular glues that bind FKBP12 and structurally distinct targets using DNA-encoded libraries" Open
"This release contains the minimal code required to reproduce the analyses in the manuscript, namely decoding of NGS data.
View article: Data and analysis code for the manuscript titled "Direct Optical Activation of Human IRE1 Identifies Unique Patterns of Transcriptional and Post-Transcriptional mRNA Regulation in the Unfolded Protein Response""
Data and analysis code for the manuscript titled "Direct Optical Activation of Human IRE1 Identifies Unique Patterns of Transcriptional and Post-Transcriptional mRNA Regulation in the Unfolded Protein Response"" Open
This repository contains the raw data and analysis code for our manuscript (Smith et. al.), tittled "Direct Optical Activation of Human IRE1 Identifies Unique Patterns of Transcriptional and Post-Transcriptional mRNA Regulation in the Unfo…
View article: Data preparation (A) and EPAM framework for assessing model performance (B,C).
Data preparation (A) and EPAM framework for assessing model performance (B,C). Open
(A) BCR DNA sequences from repertoires of multiple individuals (colors) were clustered into clonal families, a phylogenetic tree was reconstructed for each lineage, and the branches provided as parent-child pairs (PCPs) for analysis. PCPs …
View article: yxwang-fudan/Whole-genome-landscape-of-plasma-metabolome: Code
yxwang-fudan/Whole-genome-landscape-of-plasma-metabolome: Code Open
This release contains Linux/R code for the analysis implemented in the genetic atlas of the human plasma metabolome, as described in the paper 'Whole-genome sequencing analysis of plasma metabolome unveils genetic determinants and clinical…
View article: yxwang-fudan/Whole-genome-landscape-of-plasma-metabolome: Code
yxwang-fudan/Whole-genome-landscape-of-plasma-metabolome: Code Open
This release contains Linux/R code for the analysis implemented in the genetic atlas of the human plasma metabolome, as described in the paper 'Whole-genome sequencing analysis of plasma metabolome unveils genetic determinants and clinical…
View article: The Neural Genome Hypothesis
The Neural Genome Hypothesis Open
This preprint presents the Neural Genome Hypothesis, a speculative framework proposing that genomes exhibit functional properties akin to distributed, memory-bearing neural networks, including attractors, latent representations, and contex…
View article: The Neural Genome Hypothesis
The Neural Genome Hypothesis Open
This preprint presents the Neural Genome Hypothesis, a speculative framework proposing that genomes exhibit functional properties akin to distributed, memory-bearing neural networks, including attractors, latent representations, and contex…
View article: Triadic Topological Resonance in Eukaryotic Genomes: Evidence for a Discrete Toroidal Origin of the Genetic Code and Its Relation to the Yang-Mills Mass Gap
Triadic Topological Resonance in Eukaryotic Genomes: Evidence for a Discrete Toroidal Origin of the Genetic Code and Its Relation to the Yang-Mills Mass Gap Open
We report that the autocorrelation spectrum of human genomic DNA exhibits precise triadic peaks at lags 3, 6, and 9, with ratios matching predictions from the 9×9 Shelbydon toroidal orbifold endowed with Z₃×Z₃ symmetry. Analysis of a 100 k…
View article: Triadic Topological Resonance in Eukaryotic Genomes: Evidence for a Discrete Toroidal Origin of the Genetic Code and Its Relation to the Yang-Mills Mass Gap
Triadic Topological Resonance in Eukaryotic Genomes: Evidence for a Discrete Toroidal Origin of the Genetic Code and Its Relation to the Yang-Mills Mass Gap Open
We report that the autocorrelation spectrum of human genomic DNA exhibits precise triadic peaks at lags 3, 6, and 9, with ratios matching predictions from the 9×9 Shelbydon toroidal orbifold endowed with Z₃×Z₃ symmetry. Analysis of a 100 k…
View article: Ribosomal Structural Dynamics Orchestrate Degenerate Codon Decoding Kinetics.
Ribosomal Structural Dynamics Orchestrate Degenerate Codon Decoding Kinetics. Open
The ribosome, as the central machinery of protein synthesis, plays a critical role in translating genetic information encoded in mRNA into functional proteins. This process is highly accurate yet remarkably efficient, despite the degenerac…
View article: DNA as a Resonance Code System – Codons as an Electronic Coding System
DNA as a Resonance Code System – Codons as an Electronic Coding System Open
This work presents a theoretical framework that interprets DNA as a carbon-based resonance coding system in which energy, rather than chemistry alone, governs information storage and transmission. It proposes that the four DNA bases (A, T,…
View article: DNA as a Resonance Code System – Codons as an Electronic Coding System
DNA as a Resonance Code System – Codons as an Electronic Coding System Open
This work presents a theoretical framework that interprets DNA as a carbon-based resonance coding system in which energy, rather than chemistry alone, governs information storage and transmission. It proposes that the four DNA bases (A, T,…
View article: Ribosomal Structural Dynamics Orchestrate Degenerate Codon Decoding Kinetics.
Ribosomal Structural Dynamics Orchestrate Degenerate Codon Decoding Kinetics. Open
The ribosome, as the central machinery of protein synthesis, plays a critical role in translating genetic information encoded in mRNA into functional proteins. This process is highly accurate yet remarkably efficient, despite the degenerac…
View article: Fluoride-TriggeredProtein Activation via a GeneticallyEncoded Tyrosine Analogue
Fluoride-TriggeredProtein Activation via a GeneticallyEncoded Tyrosine Analogue Open
Fluoride is orthogonal to cellular metabolism and can serve as an effective chemical trigger for modulating biological systems. Here, we present a genetically encoded actuator platform based on the site-specific incorporation of a fluoride…
View article: Fluoride-TriggeredProtein Activation via a GeneticallyEncoded Tyrosine Analogue
Fluoride-TriggeredProtein Activation via a GeneticallyEncoded Tyrosine Analogue Open
Fluoride is orthogonal to cellular metabolism and can serve as an effective chemical trigger for modulating biological systems. Here, we present a genetically encoded actuator platform based on the site-specific incorporation of a fluoride…
View article: Supporting text.
Supporting text. Open
The genetic code, a unifying principle in biology, ensures that all organisms, stemming from a Last Universal Common Ancestor (LUCA), share fundamental rules for translating DNA into proteins. However, codon usage varies across the tree o…
View article: Zoom view of the lower-left corner of Fig 7.
Zoom view of the lower-left corner of Fig 7. Open
The genetic code, a unifying principle in biology, ensures that all organisms, stemming from a Last Universal Common Ancestor (LUCA), share fundamental rules for translating DNA into proteins. However, codon usage varies across the tree o…
View article: Species with larger distances to medians.
Species with larger distances to medians. Open
The genetic code, a unifying principle in biology, ensures that all organisms, stemming from a Last Universal Common Ancestor (LUCA), share fundamental rules for translating DNA into proteins. However, codon usage varies across the tree o…
View article: Groups of species included in this study.
Groups of species included in this study. Open
The genetic code, a unifying principle in biology, ensures that all organisms, stemming from a Last Universal Common Ancestor (LUCA), share fundamental rules for translating DNA into proteins. However, codon usage varies across the tree o…
View article: Sampling informational properties of codon usage through the tree of life
Sampling informational properties of codon usage through the tree of life Open
The genetic code, a unifying principle in biology, ensures that all organisms, stemming from a Last Universal Common Ancestor (LUCA), share fundamental rules for translating DNA into proteins. However, codon usage varies across the tree of…
View article: Second-Order Code: The Universal Meta-Code Linking the Cosmos and Life
Second-Order Code: The Universal Meta-Code Linking the Cosmos and Life Open
In modern biology, the genetic code (DNA/RNA) is often viewed as the fundamental informational substrate of life. However, increasing evidence from molecular biology, epigenetic regulation, quantum coherence in enzymes, collective FIR/THz …
View article: Second-Order Code: The Universal Meta-Code Linking the Cosmos and Life
Second-Order Code: The Universal Meta-Code Linking the Cosmos and Life Open
In modern biology, the genetic code (DNA/RNA) is often viewed as the fundamental informational substrate of life. However, increasing evidence from molecular biology, epigenetic regulation, quantum coherence in enzymes, collective FIR/THz …
View article: A global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles
A global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles Open
Supplementary code and data for the manuscript "A global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles". v1.0.3: Dataset fix — includes the comp…
View article: Data and code for "Population genetic structure and patterns of hybridization of the rare Lupinus tidestromii and its congener L. chamissonis (Fabaceae) inform seed sourcing strategies for population augmentation and reintroduction"
Data and code for "Population genetic structure and patterns of hybridization of the rare Lupinus tidestromii and its congener L. chamissonis (Fabaceae) inform seed sourcing strategies for population augmentation and reintroduction" Open
Data and code for the article "Population genetic structure and patterns of hybridization of the rare Lupinus tidestromii and its congener L. chamissonis (Fabaceae) inform seed sourcing strategies for population augmentation and reintroduc…
View article: tRNA-dependent conformational dynamics and folding coordinate translational regulation by a full-length T-box riboswitch
tRNA-dependent conformational dynamics and folding coordinate translational regulation by a full-length T-box riboswitch Open
T-box riboswitches regulate gene expression by sensing tRNA aminoacylation status, but their dynamic mechanisms remain elusive. Here, we present single-molecule FRET studies of a full-length translational ileS T-box, showing that its decod…
View article: Data and code from: Sex-biased duplicates are rapidly generated during Drosophila tRNA repertoire evolution
Data and code from: Sex-biased duplicates are rapidly generated during Drosophila tRNA repertoire evolution Open
Eukaryotic genomes encode hundreds of transfer RNA genes ostensibly to ensure efficient translation. How these seemingly redundant tRNA copies arise and are naturally selected in metazoan genomes and populations remains largely unexplored,…
View article: Sex-biased duplicates are rapidly generated during <i>Drosophila</i> tRNA repertoire evolution
Sex-biased duplicates are rapidly generated during <i>Drosophila</i> tRNA repertoire evolution Open
Eukaryotic genomes encode hundreds of transfer RNA genes ostensibly to ensure efficient translation. How these seemingly redundant tRNA copies arise and are naturally selected in metazoan genomes and populations remains largely unexplored,…
View article: Full Genetic Code Emergence From Physics Alone: A Complete Proto-Codon & Replicator System Formed Naturally
Full Genetic Code Emergence From Physics Alone: A Complete Proto-Codon & Replicator System Formed Naturally Open
This study presents the first full-scale simulation demonstrating the spontaneous emergence of a proto-genetic coding system from purely physical and chemical rules. No biological assumptions, enzymes, or classical origin-of-life models we…