Fractal and DNA sequence analysis

DNA nullomers as a statistical phenomenon

The paper shows that nullomers in genomes arise from statistical properties rather than evolutionary pressures or lethal effects.

UniWave-2: A Hybrid Model for Nucleic Acid Waveform Feature Extraction Enhanced by Fourier and Wavelet Transforms

UniWave-2 improves nucleic acid sequence analysis by integrating hydrophobicity, enhancing waveform resolution with Fourier and wavelet transforms, and using a lightweight GRU model for efficient feature extraction.

Genome-wide mapping of persistent long-range correlation in the complete telomere-to-telomere human reference genome

The paper maps long-range correlations in the complete telomere-to-telomere human genome, revealing heterogeneous genomic structure and chromosome-specific scaling.

Genome-wide Pervasiveness and Localized Variation of k-mer-based Genomic Signatures in Eukaryotes

This study investigates the pervasiveness and variation of genomic signatures across eukaryotic genomes using k-mer-based FCGR analysis, identifying localized exceptions and developing tools for improved taxonomic classification.

Entropy Fusion DNA: Alignment-Free Gene Fusion Detection through Entropy and Mutual Information Descriptors

This paper introduces an alignment-free method using information-theoretic features to detect gene fusions, achieving strong performance in classification and partner prediction.

In silico restriction site analysis of whole genome sequences shows patterns caused by selection and sequence duplications

The paper analyzes whole genome sequences to identify non-random patterns in restriction site distributions, showing deviations from random sequences and effects of GC content and repetitive elements.

A deterministic computational kernel encoded in the human genome

The paper demonstrates that the human genome encodes a deterministic computational kernel with four properties, validated through analysis of proteome and chromosome data.

Quaternion Spectral Fingerprinting of DNA: GPU-Accelerated Multi-Channel Fourier Analysis for Alignment-Free Genomics

This paper introduces a quaternion Fourier transform framework for DNA sequence analysis, demonstrating its ability to detect structural periodicities and spectral signatures across multiple species.

Proteins as Statistical Languages: Information-Theoretic Signatures of Proteomes Across the Tree of Life

The paper introduces information-theoretic descriptors to analyze protein sequences as statistical languages, showing that real proteomes exhibit structured dependencies beyond simple compositional models.

dna-parser: a Python library written in Rust for fast encoding of DNA and RNA sequences

dna-parser encodes DNA and RNA sequences into numerical features efficiently using Rust and Python, offering fast and parallel processing.

UniWave: A Waveform-Based Encoding Framework for Nucleic Acid Feature Extraction

UniWave converts nucleotide sequences into continuous waveforms for improved genomic analysis, outperforming traditional methods in multiple tasks.

Efficient training of neural networks using natural vectors with covariates for the plant microRNA precursor prediction.

This study evaluates neural networks trained with natural vectors incorporating covariance for predicting plant microRNA precursors, showing improved performance in feature prediction and classification.

High dimensional tissue specific regulatory codes embedded in viral coding regions

This study shows that high dimensional silent patterns in viral coding regions encode regulatory codes related to viral tropism using a novel computational measure.

Solving the gene classification problem with a novel Gene Space approach

This paper introduces a Gene Space framework to characterize genome organization by analyzing nucleotide token frequencies, enabling species-specific gene classification and evolutionary pathway constraints.

Discovery of Inverted Repeats and Palindromes in Viral Genomes

The paper identifies over 19 million inverted repeats in 14,000 viral genomes using BLMT, highlighting their prevalence and potential biological significance.

Positional frequency chaos game representation for machine learning-based classification of crop lncRNAs

This paper introduces PFCGR, a new encoding method for classifying plant lncRNAs using machine learning, achieving high accuracy with significantly reduced computational time compared to DNABERT.

A DNA Sequence Imaging Approach to Predict Splice Sites Using Deep Learning

This paper introduces a DNA sequence imaging method for splice site prediction, showing that DFCP outperforms FCGR using deep learning on Arabidopsis and human data.

Alignment Free Viral Sequence Classification

This study evaluates alignment-free methods for viral sequence classification, showing high accuracy and efficiency on SARS-CoV-2, dengue, and HIV datasets.

Frequency Chaos Game Representation - Singular Value Decomposition for Alignment-Free Phylogenetic Analysis

This paper introduces SVD-FCGR, an alignment-free phylogenetic analysis method using SVD on FCGR, showing improved resolution and scalability over MEGA for viral datasets.

Musical Insights into Protein Sequences and Functions via NMR Data

This paper converts protein sequences into music using NMR data, assigning notes based on amino acid frequencies and relaxation periods, and applies set theory to analyze homologous beta-globin sequences.

TIPs-VF: An augmented vector-based representation for variable-length DNA fragments with sequence, length, and positional awareness

TIPs-VF provides a variable-length DNA sequence encoding framework that improves representation of genetic sequences for machine learning by incorporating sequence, length, and positional awareness.

DNA walk of specific fused oncogenes exhibit distinct fractal geometric characteristics in nucleotide patterns

The paper uses fractal geometry and DNA walk analysis to identify distinct geometric features in nucleotide patterns of oncogenes and tumour-suppressor genes, highlighting their potential in cancer research.

Preserving Hidden Hierarchical Structure: Poincare Distance for Enhanced Genomic Sequence Analysis

This paper introduces Poincare distance measures for genomic and proteomic sequence analysis, showing improved performance in classification tasks compared to existing methods.

Prioritization of Lung Cancer Candidate Genes using Moment of Inertia Tensor Analysis

This study prioritizes lung cancer candidate genes using moment of inertia tensor analysis of amino acid physicochemical properties, identifying four genes linked to poor survival.

DNA N-gram Analysis Framework (DNAnamer): A generalized N-gram frequency analysis framework for the supervised classification of DNA sequences

DNAnamer is a framework that uses N-gram frequency analysis to classify DNA sequences, identifying species, functional elements, and contamination.

Quantum mechanical electronic and geometric parameters for DNA k-mers as features for machine learning

The paper provides a database of quantum mechanical and geometric features for DNA k-mers and demonstrates their use in predicting A to C mutation rate constants.

Laws of genome nucleotide composition

The paper proposes and validates three mathematical laws of genome nucleotide composition across three domains of life.

Improved Python Package for DNA Sequence Encoding using Frequency Chaos Game Representation

The paper introduces a Python package for DNA sequence encoding using Frequency Chaos Game Representation (FCGR), showing improved accuracy and efficiency over an R-based library for DNA sequences.

The determinants of the rarity of nucleic and peptide short sequences in nature

The paper calculates the rarity of short nucleic and peptide sequences across genomes and proteomes, finds dipeptide rarity in peptides but not dinucleotides, and develops predictive models for sequence frequency.

Complexity And Ergodicity In Chaos Game Representation Of Genomic Sequences

The paper analyzes the Chaos Game Representation of genomic sequences to assess ergodicity and finds that CGRs are non-ergodic due to distribution properties of nucleotide sequences.