Related papers: Di-nucleotide Entropy as a Measure of Genomic Sequ…
Reporting extensions of a recently developed approach to density functional theory with correct long-range be-havior (Phys. Rev. Lett. 94, 043002 (2005)). The central quantities are a splitting functional gamma[n] and a complementary…
Motivation: Methods are needed to test pre-defined genomic regions such as promoters for differential methylation in genome-wide association studies, where the number of samples is limited and the data have large amounts of measurement…
While standard computational protocols for density functional theory (DFT) have universal applicability, differences exist in code implementations. Specific applications require manual parameter optimization, whereas high-throughput…
Background: Prior to the current genomic era it was suggested that the number of protein-coding genes that an organism made use of was a valid measure of its complexity. It is now clear, however, that major incongruities exist and that…
Secondary contact between divergent populations or incipient species may result in the exchange and introgression of genomic material. We develop a simple DNA sequence measure, called Gmin, which is designed to identify genomic regions…
Density-functional theory is a formally exact description of a many-body quantum system in terms of its density; in practice, however, approximations to the universal density functional are required. In this work, a model based on deep…
The spatial location of cells within tissues and organs is crucial for the manifestation of their specific functions.Spatial transcriptomics technology enables comprehensive measurement of the gene expression patterns in tissues while…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
Communication of quantized information is frequently followed by a computation. We consider situations of \emph{distributed functional scalar quantization}: distributed scalar quantization of (possibly correlated) sources followed by…
Geographic data is fundamentally local. Disease outbreaks cluster in population centers, ecological patterns emerge along coastlines, and economic activity concentrates within country borders. Machine learning models that encode geographic…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
In recent deep image compression neural networks, the entropy model plays a critical role in estimating the prior distribution of deep image encodings. Existing methods combine hyperprior with local context in the entropy estimation…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Graph transformation that predicts graph transition from one mode to another is an important and common problem. Despite much progress in developing advanced graph transformation techniques in recent years, the fundamental assumption…
Deep learning has proven to successfully learn variations in tissue and cell morphology. Training of such models typically relies on expensive manual annotations. Here we conjecture that spatially resolved gene expression, e.i., the…
The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely…
The nature of the quantitative distribution of the 64 DNA codons in the human genome has been an issue of debate for over a decade. Some groups have proposed that the quantitative distribution of the DNA codons ordered as a rank-frequency…
Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior…
A key challenge in systems biology is the elucidation of the underlying principles, or fundamental laws, which determine the cellular phenotype. Understanding how these fundamental principles are altered in diseases like cancer is important…