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Colocalization analyses assess whether two traits are affected by the same or distinct causal genetic variants in a single gene region. A class of Bayesian colocalization tests are now routinely used in practice; for example, for genetic…
Chromosomal crossovers play a crucial role in meiotic cell division, as they ensure proper chromosome segregation and increase genetic variability. Experiments have consistently revealed two key observations across species: (i) the number…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
Genome-wide gene expression profiles, as measured with microarrays or RNA-Seq experiments, have revolutionized biological and biomedical research by providing a quantitative measure of the entire mRNA transcriptome. Typically, researchers…
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
Data privacy is a core tenet of responsible computing, and in the United States, differential privacy (DP) is the dominant technical operationalization of privacy-preserving data analysis. With this study, we qualitatively examine one class…
The ability to classify images is dependent on having access to large labeled datasets and testing on data from the same domain that the model can train on. Classification becomes more challenging when dealing with new data from a different…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an…
In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping…
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…
Differential conductance spectroscopy performed in the high bias regime -- in which the applied voltage exceeds the sample work function -- is a poor measure of the local density of states due to the effects of the changing tunnel barrier.…
Deep learning models are prone to learning shortcut solutions to problems using spuriously correlated yet irrelevant features of their training data. In high-risk applications such as medical image analysis, this phenomenon may prevent…
Visual place recognition in changing environments is the problem of finding matchings between two sets of observations, a query set and a reference set, despite severe appearance changes. Recently, image comparison using CNN-based…
Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…
Automatic classification of Human Epithelial Type-2 (HEp-2) cells staining patterns is an important and yet a challenging problem. Although both shallow and deep methods have been applied, the study of deep convolutional networks (CNNs) on…
High-throughput sequencing of RNA transcripts (RNA-seq) has become the method of choice for detection of differential expression (DE). Concurrent with the growing popularity of this technology there has been a significant research effort…
Medical image segmentation, which is essential for many clinical applications, has achieved almost human-level performance via data-driven deep learning technologies. Nevertheless, its performance is predicated upon the costly process of…