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This thesis develops computational methods in similarity-preserving hashing, classification, and cancer genomics. Standard space partitioning-based hashing relies on Binary Search Trees (BSTs), but their exponential growth and sparsity…
A new type of microfluidic system for biological cell manipulation, a CMOS/microfluidic hybrid, is demonstrated. The hybrid system starts with a custom-designed CMOS (complementary metal-oxide semiconductor) chip fabricated in a…
The explosion of biobank data offers immediate opportunities for gene-environment (GxE) interaction studies of complex diseases because of the large sample sizes and the rich collection in genetic and non-genetic information. However, the…
Multi-hop networks become popular network topologies in various emerging Internet of things applications. Batched network coding (BNC) is a solution to reliable communications in such networks with packet loss. By grouping packets into…
Cellular nuclei recognition serves as a fundamental and essential step in the workflow of digital pathology. However, with disparate source organs and staining procedures among histology image clusters, the scanned tiles inherently conform…
DNA cloning methods are fundamental tools in molecular biology, synthetic biology, and genetic engineering that enable precise DNA manipulation for various scientific and biotechnological applications. This review systematically summarizes…
Phylogenomic approaches developed thus far are either too time-consuming or lack a solid evolutionary basis. Moreover, no phylogenomic approach is capable of constructing a tree directly from unassembled raw sequencing data. A new…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Wireless indoor localization has attracted significant amount of attention in recent years. Using received signal strength (RSS) obtained from WiFi access points (APs) for establishing fingerprinting database is a widely utilized method in…
Regenerating codes and codes with locality are two schemes that have recently been proposed to ensure data collection and reliability in a distributed storage network. In a situation where one is attempting to repair a failed node,…
Localization in the environment is an essential navigational capability for animals and mobile robots. In the indoor environment, the global localization problem remains challenging to be perfectly solved with probabilistic methods.…
The renaissance of neural architecture search (NAS) has seen classical methods such as genetic algorithms (GA) and genetic programming (GP) being exploited for convolutional neural network (CNN) architectures. While recent work have…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
The emergence of complex behaviors in cellular automata is an area that has been widely developed in recent years with the intention to generate and analyze automata that produce space-moving patterns or gliders that interact in a periodic…
In this research, a reflection-based nanohole array sensor system is presented for discriminating between migration-competent cancer cells that maintain the integrity of the actin cortex and those cells lacking the actin cortex and thus…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
CARTEpigenoQC is an R-based toolkit designed to streamline quality control (QC) for single-cell epigenomic datasets involving Chimeric Antigen Receptor (CAR)-engineered T cells. With the growing application of scATAC-seq, scCUT&Tag, and…
Accurately segmenting and individualizing cells in SEM images is a highly promising technique for elucidating tissue architecture in oncology. While current AI-based methods are effective, errors persist, necessitating time-consuming manual…
Designing full-length, epitope-specific TCR {\alpha}\b{eta} remains challenging due to vast sequence space, data biases and incomplete modeling of immunogenetic constraints. We present LSMTCR, a scalable multi-architecture framework that…