Related papers: Estimation of the methylation pattern distribution…
Mixture interpretation is a central challenge in forensic science, where evidence often contains contributions from multiple sources. In the context of DNA analysis, biological samples recovered from crime scenes may include genetic…
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…
Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Broadly categorized in three types (i.e., sequences, images, and signals), these…
Metagenomic binning aims to cluster DNA fragments from mixed microbial samples into their respective genomes, a critical step for downstream analyses of microbial communities. Existing methods rely on deterministic representations, such as…
A key focus in current cancer research is the discovery of cancer biomarkers that allow earlier detection with high accuracy and lower costs for both patients and hospitals. Blood samples have long been used as a health status indicator,…
Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last…
Probabilistic mixture models have been widely used for different machine learning and pattern recognition tasks such as clustering, dimensionality reduction, and classification. In this paper, we focus on trying to solve the most common…
Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder characterized by progressive cognitive decline and widespread epigenetic dysregulation in the brain. DNA methylation, as a stable yet dynamic epigenetic modification,…
Motivation: In silico methods for the prediction of antigenic peptides binding to MHC class I molecules play an increasingly important role in the identification of T-cell epitopes. Statistical and machine learning methods, in particular,…
Recent breakthroughs in cancer research have come via the up-and-coming field of pathway analysis. By applying statistical methods to prior known gene and protein regulatory information, pathway analysis provides a meaningful way to…
As global warming intensifies, increased attention is being paid to monitoring fugitive methane emissions and detecting gas plumes from landfills. We have divided methane emission monitoring into three subtasks: methane concentration…
Motivation: Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patterns along the…
In this paper, distributed Bayesian detection problems with unknown prior probabilities of hypotheses are considered. The sensors obtain observations which are conditionally dependent across sensors and their probability density functions…
Background: Trace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
Hematopoiesis is the process of blood cell formation, through which progenitor stem cells differentiate into mature forms, such as white and red blood cells or mature platelets. While the precursors of the mature forms share many regulatory…
Methane is a potent greenhouse gas and a major driver of climate change, making its timely detection critical for effective mitigation. Machine learning (ML) deployed onboard satellites can enable rapid detection while reducing downlink…
Protein complexes involved in DNA mismatch repair appear to diffuse along dsDNA in order to locate a hemimethylated incision site via a dissociative mechanism. Here, we study the probability that these complexes locate a given target site…