Related papers: Spectral concepts in genome informational analysis
This paper provides a comprehensive review of recent advancements in k-mer-based data structures representing collections of several samples (sometimes called colored de Bruijn graphs) and their applications in large-scale sequence indexing…
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…
This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is…
It is basic question in biology and other fields to identify the char- acteristic properties that on one hand are shared by structures from a particular realm, like gene regulation, protein-protein interaction or neu- ral networks or…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
Spectral sampling is associated with the group of unitary transformations acting on matrices in much the same way that simple random sampling is associated with the symmetric group acting on vectors. This parallel extends to symmetric…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Some spectral data analysis methods that are useful for the two-dimensional imaging diagnostics data are introduced. It is shown that the frequency spectrum, the local dispersion relation, the flow shear, and the nonlinear energy transfer…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
Statistical moments of the intensity distributions are used as molecular descriptors. They are used as a basis for defining similarity distances between two model spectra. Parameters which carry the information derived from the comparison…
This survey gives an overview over different techniques used for pixel-level semantic segmentation. Metrics and datasets for the evaluation of segmentation algorithms and traditional approaches for segmentation such as unsupervised methods,…
Spectrogram-based representations have grown to dominate the feature space for deep learning audio analysis systems, and are often adopted for speech analysis also. Initially, the primary motivator for spectrogram-based representations was…
Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…
The explicit solution to the spectral problem of quantum graphs is used to obtain the exact distributions of several spectral statistics, such as the oscillations of the quantum momentum eigenvalues around the average, $\delta…
We present a data model describing the structure of spectrophotometric datasets with spectral and temporal coordinates and associated metadata. This data model may be used to represent spectra, time series data, segments of SED (Spectral…
We study numerically the spectrum and eigenfunctions of the quantum Neumann model, illustrating some general properties of a non trivial integrable model.
To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a…
We discuss a model of genome as a program with functional architecture and consider the approach to Darwinian evolution as a learning problem for functional programming. In particular we introduce a model of learning for some class of…
We study k-positive maps on operators. Proofs are given to different positivity criteria. Special attention is on positive maps arising in the study of quantum information science. Results of other researchers are extended and improved. New…