Related papers: Non-alignment comparison of human and high primate…
Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from…
Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small alpha protein domains have hidden…
Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis. We show that the…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Mass spectrometry (MS) is used widely in biomolecular structural analysis and is particularly dominant in the study of proteins. Despite its considerable power, state-of-the-art protein MS frequently suffers from limited reliability of…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
The conventional way of identifying DNA motifs, solely based on match alignment information, is susceptible to a high number of spurious sites. A novel scoring system has been introduced by taking both match and mismatch alignment…
One of the ubiquitous representation of long DNA sequence is dividing it into shorter k-mer components. Unfortunately, the straightforward vector encoding of k-mer as a one-hot vector is vulnerable to the curse of dimensionality. Worse yet,…
We investigate the large-scale geometry of the DNA-protein complex of chromatin using a generalized optimality principle, which requires that not only should all sub-parts of a natural process be optimal but also the unfolding of higher…
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…
A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…
Many developmental processes in biology utilize Notch-Delta signaling to construct an ordered pattern of cellular differentiation. This signaling modality is based on nearest-neighbor contact, as opposed to the more familiar mechanism…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
Over the recent years, the field of whole metagenome shotgun sequencing has witnessed significant growth due to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster, and with better coverage than…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large genomes that have undergone complex genome rearrangements,…