Related papers: A New DNA Sequences Vector Space on a Genetic Code…
Variational encoder-decoders (VEDs) have shown promising results in dialogue generation. However, the latent variable distributions are usually approximated by a much simpler model than the powerful RNN structure used for encoding and…
We present a deep-learning Variational Encoder-Decoder (VED) framework for learning data-driven low-dimensional representations of the relationship between high-dimensional parameters of a physical system and the system's high-dimensional…
We explore the sensitivity of flavour changing b -> s transitions to a (sub-)GeV hidden sector with generic couplings to the Standard Model through the Higgs, vector and axion portals. The underlying two-body decays of B mesons, B -> X_s S…
The frequencies of A, C, G and T in mitochondrial DNA vary among species due to unequal rates of mutation between the bases. The frequencies of bases at four-fold degenerate sites respond directly to mutation pressure. At 1st and 2nd…
In previous papers we have described with strong experimental support, the organising role that CoHSI (Conservation of Hartley-Shannon Information) plays in determining important global properties of all known proteins, from defining the…
Genome-wide proximity placement analysis of 10,598 HSGRL within the context of the principal regulatory structures of the interphase chromatin, namely topologically-associating domains (TADs) and specific sub-TAD structures termed…
Generalized parton distributions (GPDs) characterize the 3-dimensional structure of hadrons, combining information about their internal quark and gluon longitudinal momentum distributions and transverse position within the hadron. The…
Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu}) across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and found substantial variation among genes in the density of synonymous polymorphisms. They…
Heaps' or Herdan's law is a linguistic law describing the relationship between the vocabulary/dictionary size (type) and word counts (token) to be a power-law function. Its existence in genomes with certain definition of DNA words is…
We present a high-fidelity 3D generative adversarial network (GAN) inversion framework that can synthesize photo-realistic novel views while preserving specific details of the input image. High-fidelity 3D GAN inversion is inherently…
Generalized Parton Distributions (GPDs) have emerged as a powerful framework for exploring the internal structure of hadrons in terms of their partonic constituents. Over the past three decades, the field has witnessed significant…
We revisit the notion of gene regulatory code in embryonic development in the light of recent findings about genome spatial organisation. By analogy with the genetic code, we posit that the concept of code can only be used if the…
Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying…
We define a new class of Convolutional Codes in terms of fibrations of algebraic varieties generalizaing our previous constructions of Convolutional Goppa Codes. Using this general construction we can give several examples of Maximum…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
Protein-fragment seqlets typically feature about 10 amino acid residue positions that are fixed to within conservative substitutions but usually separated by a number of prescribed gaps with arbitrary residue content. By quantifying a…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
DNA segments and sequences have been studied thoroughly during the past decades. One of the main problems in computational biology is the identification of exon-intron structures inside genes using mathematical techniques. Previous studies…
We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…