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Most human protein-coding genes can be transcribed into multiple possible distinct mRNA isoforms. These alternative splicing patterns encourage molecular diversity and dysregulation of isoform expression plays an important role in disease…

Many machine learning models have been proposed to classify phenotypes from gene expression data. In addition to their good performance, these models can potentially provide some understanding of phenotypes by extracting explanations for…

In differential expression (DE) analysis of RNA-seq count data, it is known that genes with a larger read number are more likely to be differentially expressed. This bias has a profound effect on the subsequent Gene Ontology (GO) analysis…

Biological oscillations are periodic changes in various signaling processes crucial for the proper functioning of living organisms. These oscillations are modeled by ordinary differential equations, with coefficient variations leading to…

Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have…

Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…

Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…

Scientists often use a paired comparison of the areas under the receiver operating characteristic curves to decide which continuous cancer screening test has the best diagnostic accuracy. In the paired design, all participants are screened…

Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based…

Variant calling, the problem of estimating whether a position in a DNA sequence differs from a reference sequence, given noisy, redundant, overlapping short sequences that cover that position, is fundamental to genomics. We propose a deep…

We exploit Surface-Enhanced Raman Scattering (SERS) to investigate aqueous droplets of genomic DNA deposited onto silver-coated silicon nanowires and we show that it is possible to efficiently discriminate between spectra of tumoral and…

The DNA microarray technology has modernized the approach of biology research in such a way that scientists can now measure the expression levels of thousands of genes simultaneously in a single experiment. Gene expression profiles, which…

Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D…

Single-cell RNA sequencing (scRNA-seq) determines RNA expression at single-cell resolution. It provides a powerful tool for studying immunity, regulation, and other life activities of cells. However, due to the limitations of the sequencing…

Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE…

The advent of high--throughput transcription profiling technologies has enabled identification of genes and pathways associated with disease, providing new avenues for precision medicine. A key challenge is to analyze this data in the…

Sequencing costs currently prohibit the application of single-cell mRNA-seq to many biological and clinical analyses. Targeted single-cell mRNA-sequencing reduces sequencing costs by profiling reduced gene sets that capture biological…

Single-cell RNA sequencing (scRNA-seq) data simulation is limited by classical methods that rely on linear correlations, failing to capture the intrinsic, nonlinear dependencies. No existing simulator jointly models gene-gene and cell-cell…

Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…

Cancer is a term that denotes a group of diseases caused by abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after…