Related papers: Predicting genome-wide DNA methylation using methy…
In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…
The past decade has seen a rapid growth in omics technologies. Genome-wide association studies (GWAS) have uncovered susceptibility variants for a variety of complex traits. However, the functional significance of most discovered variants…
Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in…
Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…
Protein-DNA interaction is critical for life activities such as replication, transcription, and splicing. Identifying protein-DNA binding residues is essential for modeling their interaction and downstream studies. However, developing…
Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
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…
Rapid sequencing of individual human genome is prerequisite to genomic medicine, where diseases will be prevented by preemptive cures. Quantum-mechanical tunneling through single-stranded DNA in a solid-state nanopore has been proposed for…
In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the bloodstream and contribute to a pool of…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
We propose a new approach for clustering DNA features using array CGH data from multiple tumor samples. We distinguish data-collapsing: joining contiguous DNA clones or probes with extremely similar data into regions, from clustering:…
Cancer and its subtypes constitute approximately 30% of all causes of death globally and display a wide range of heterogeneity in terms of clinical and molecular responses to therapy. Molecular subtyping has enabled the use of precision…
Determining the primary site of origin for metastatic tumors is one of the open problems in cancer care because the efficacy of treatment often depends on the cancer tissue of origin. Classification methods that can leverage tumor genomic…
Deep learning has become the mainstream methodological choice for analyzing and interpreting whole-slide digital pathology images (WSIs). It is commonly assumed that tumor regions carry most predictive information. In this paper, we…
In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to the discovery of biological pathways associated to the disease. As a cancer progresses, its signalling…
Identifying differentially methylated regions is an important task in epigenome-wide association studies, where differential signals often arise across groups of neighboring CpG sites. Many existing methods detect differentially methylated…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…
Background Precise prediction of cancer types is vital for cancer diagnosis and therapy. Important cancer marker genes can be inferred through predictive model. Several studies have attempted to build machine learning models for this task…
Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "chromophoresis", the dynamics of…