Related papers: Mapping to a Reference Genome Structure
A systematic mapping is a way to identify, evaluate and interpret all relevant research available to a matter of particular research. One of the reasons for conducting systematic reviews is that it summarizes the existing evidence regarding…
The aim of this study is to investigate the relation that can be found between the phylogeny of a large set of complete chloroplast genomes, and the evolution of gene content inside these sequences. Core and pan genomes have been computed…
When the same set of genes appear in two top ranking gene lists in two different studies, it is often of interest to estimate the probability for this being a chance event. This overlapping probability is well known to follow the…
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a greater length increases the chance for reads being…
We consider multivariate two-sample tests of means, where the location shift between the two populations is expected to be related to a known graph structure. An important application of such tests is the detection of differentially…
Machine learning provides a broad framework for addressing high-dimensional prediction problems in classification and regression. While machine learning is often applied for imaging problems in medical physics, there are many efforts to…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
As science advances, the academic community has published millions of research papers. Researchers devote time and effort to search relevant manuscripts when writing a paper or simply to keep up with current research. In this paper, we…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation…
We define a Frame of reference as a two ingredients concept: A meta-rigid motion, which is a generalization of a Born motion, and a chorodesic synchronization, which is an adapted foliation. At the end of the line we uncover a low-level…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…