Related papers: Modeling association between DNA copy number and g…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
Inspired by the complexity of certain real-world datasets, this article introduces a novel flexible linear spline index regression model. The model posits piecewise linear effects of an index on the response, with continuous changes…
In this report a systematic approach is used to determine the approximate genetic network and robust dependencies underlying differentiation. The data considered is in the form of a binary matrix and represent the expression of the nine…
When nanoparticles (NPs) are introduced into a biological solution, layers of biomolecules form on their surface, creating a corona. Understanding how the structure of the protein evolves into the corona is essential for evaluating the…
In a recent paper Siegfried et al. published a new sequence-based structural RNA assay that utilizes mutational profiling to detect base pairing (MaP). Output from MaP provides information about both pairing (via reactivities) and contact…
We propose a method for detecting differential gene expression that exploits the correlation between genes. Our proposal averages the univariate scores of each feature with the scores in correlation neighborhoods. In a number of real and…
Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the…
We present a quantitative, multi-scale coarse-grained model of DNA coated colloids. The parameters of this model are transferable and are solely based on experimental data. As a test case, we focus on nano-sized colloids carrying…
The differential network (DN) analysis identifies changes in measures of association among genes under two or more experimental conditions. In this article, we introduce a Pseudo-value Regression Approach for Network Analysis (PRANA). This…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
We introduce the Poisson Log-Normal Graphical Model for count data, and present a normality transformation for data arising from this distribution. The model and transformation are feasible for high-throughput microRNA (miRNA) sequencing…
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…
Understanding the phenotypic drug response on cancer cell lines plays a vital rule in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data for researchers in phenotypic…
DNA copy number aberrations (CNAs) can be found in the majority of cancer genomes, and are crucial for understanding the potential mechanisms underlying tumor initiation and progression. Since the first release in 2001, the Progenetix…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
Late diagnosis and high costs are key factors that negatively impact the care of cancer patients worldwide. Although the availability of biological markers for the diagnosis of cancer type is increasing, costs and reliability of tests…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and…
Motivated by the important problem of detecting association between genetic markers and binary traits in genome-wide association studies, we present a novel Bayesian model that establishes a hierarchy between markers and genes by defining…
Standard approaches to analysing data in genome-wide association studies (GWAS) ignore any potential functional relationships between genetic markers. In contrast gene pathways analysis uses prior information on functional structure within…