MOTIVATION: Single-cell Chromatin ImmunoPrecipitation DNA-Sequencing (scChIP-seq) analysis is challenging due to data sparsity. High degree of sparsity in biological high-throughput single-cell data is generally handled with imputation methods that c...
This article uses Deep Learning technologies to safeguard DNA sequencing against Bio-Cyber attacks. We consider a hybrid attack scenario where the payload is encoded into a DNA sequence to activate a Trojan malware implanted in a software tool used i...
Nanopore sequencing is an emerging technology that reads DNA by utilizing a unique method of detecting nucleic acid sequences and identifies the various chemical modifications they carry. Deep learning has increased in popularity as a useful techniqu...
Computational methods based on whole genome linked-reads and short-reads have been successful in genome assembly and detection of structural variants (SVs). Numerous variant callers that rely on linked-reads and short reads can detect genetic variati...
Complex structural variants (CSVs) encompass multiple breakpoints and are often missed or misinterpreted. We developed SVision, a deep-learning-based multi-object-recognition framework, to automatically detect and haracterize CSVs from long-read sequ...
MOTIVATION: Genome sequencing experiments have revolutionized molecular biology by allowing researchers to identify important DNA-encoded elements genome wide. Regions where these elements are found appear as peaks in the analog signal of an assay's ...
De novo mutations (DNMs) are an important cause of genetic disorders. The accurate identification of DNMs from sequencing data is therefore fundamental to rare disease research and diagnostics. Unfortunately, identifying reliable DNMs remains a major...
MOTIVATION: Metagenomics is the study of microbiomes using DNA sequencing. A microbiome consists of an assemblage of microbes that is associated with a 'theater of activity' (ToA). An important question is, to what degree does the taxonomic and funct...
Massively parallel reporter assay (MPRA) is a high-throughput method that enables the study of the regulatory activities of tens of thousands of DNA oligonucleotides in a single experiment. While MPRA experiments have grown in popularity, their small...
Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair res...