Genetic disorders are the result of mutation in the deoxyribonucleic acid (DNA) sequence which can be developed or inherited from parents. Such mutations may lead to fatal diseases such as Alzheimer's, cancer, Hemochromatosis, etc. Recently, the use ...
The binding of microRNAs (miRNAs) to their target sites is a complex process, mediated by the Argonaute (Ago) family of proteins. The prediction of miRNA:target site binding is an important first step for any miRNA target prediction algorithm. To dat...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent responsible for coronavirus disease 2019 (COVID-19), has affected the lives of billions and killed millions of infected people. This virus has been demonstrated t...
The high dimensionality of genotype data available for genomic evaluations has presented a motivation for developing strategies to identify subsets of markers capable of increasing the accuracy of predictions compared to the current commercial single...
Cancer prognosis analysis is of essential interest in clinical practice. In order to explore the prognostic power of computational histopathology and genomics, this paper constructs a multi-modality prognostic model for survival prediction. We collec...
Analysis of data with a censored survival response and high-dimensional omics measurements is now common. Most of the existing analyses are based on specific (semi)parametric models, in particular the Cox model. Such analyses may be limited by not ha...
A common goal in the convolutional neural network (CNN) modeling of genomic data is to discover specific sequence motifs. Post hoc analysis methods aid in this task but are dependent on parameters whose optimal values are unclear and applying the dis...
DNA methylation is a process that can affect gene accessibility and therefore gene expression. In this study, a machine learning pipeline is proposed for the prediction of breast cancer and the identification of significant genes that contribute to t...
Cancer is a complex disease caused by genomic and epigenetic alterations; hence, identifying meaningful cancer drivers is an important and challenging task. Most studies have detected cancer drivers with mutated traits, while few studies consider mul...
Mapping chromatin insulator loops is crucial to investigating genome evolution, elucidating critical biological functions, and ultimately quantifying variant impact in diseases. However, chromatin conformation profiling assays are usually expensive, ...