Related papers: Estimation of the methylation pattern distribution…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
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…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
Feature engineering has become one of the most important steps to improve model prediction performance, and to produce quality datasets. However, this process requires non-trivial domain-knowledge which involves a time-consuming process.…
We investigate the distribution of the depth of a node containing a specific key or, equivalently, the number of steps needed to retrieve an item stored in a randomly grown binary search tree. Using a representation in terms of mixed and…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
Modeling the diameter distribution of trees in forest stands is a common forestry task that supports key biologically and economically relevant management decisions. The choice of model used to represent the diameter distribution and how to…
Quantitatively predictive models of biomolecular circuits are important tools for the design of synthetic biology and molecular communication circuits. The information content of typical time-lapse single-cell data for the inference of…
The rapid development of high-throughput sequencing technologies has led to an explosive increase in biological sequence data, making sequence clustering a fundamental task in large-scale bioinformatics analyses. Unlike traditional…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
We define a new morphology metric called "patchiness" ($P$) that is sensitive to deviations from the average of a resolved distribution, does not require the galaxy center to be defined, and can be used on the spatially-resolved…
Major Depressive Disorder (MDD) is a clinically heterogeneous syndrome with diverse etiological pathways. Traditional Epigenome-Wide Association Studies (EWAS) have successfully identified risk loci based on differential methylation…
Colorectal cancer remains a major global health concern, with early detection being pivotal for improving patient outcomes. In this study, we leveraged high throughput methylation profiling of cellfree DNA to identify and validate…
Ultra-weak photon emission (UPE) from living systems is widely hypothesized to reflect un-derlying self-organization and long-range coordination in biological dynamics. However, distin-guishing biologically driven correlations from trivial…
We describe an expert system, MAIES, developed for analysing forensic identification problems involving DNA mixture traces using quantitative peak area information. Peak area information is represented by conditional Gaussian distributions,…
Sensitive and reliable methylation assay is important for oncogentic studies and clinical applications. Here, a new methylation assay was developed by the use of adapter-dependent adapter in library preparation. This new assay avoids the…
Diffuse Reflectance Spectroscopy has demonstrated a strong aptitude for identifying and differentiating biological tissues. However, the broadband and smooth nature of these signals require algorithmic processing, as they are often…
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…