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Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a…
Cre-lox and other systems are used as genetic tools to control site-specific recombination (SSR) events in genomic DNA. If multiple recombination sites are organized in a compact cluster within the same genome, a series of random…
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…
A method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing is presented. The manuscript focuses on…
DNA barcoding has emerged as a cost-effective approach for species identification. However, the scarcity of tools used for searching the booming reference database becomes an obstacle, currently with BLAST as the only practical choice.…
Cell imaging and analysis are fundamental to biomedical research because cells are the basic functional units of life. Among different cell-related analysis, cell counting and detection are widely used. In this paper, we focus on one common…
Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
Detection of rare variants by resequencing is important for the identification of individuals carrying disease variants. Rapid sequencing by new technologies enables low-cost resequencing of target regions, although it is still prohibitive…
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…
In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained comparisons among organisms within the same kingdom of…
Bacterial biofilm segmentation poses significant challenges due to lack of apparent structure, poor imaging resolution, limited contrast between conterminous cells and high density of cells that overlap. Although there exist bacterial…
The ability to measure or manipulate network connectivity is the main challenge in the field of connectomics. Recently, a set of approaches has been developed that takes advantage of next generation DNA sequencing to scan connections…
Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of the data. Identification of barcodes is one of the crucial steps in the process and can be accomplished…
Evaluating the performance of generative models in image synthesis is a challenging task. Although the Fr\'echet Inception Distance is a widely accepted evaluation metric, it integrates different aspects (e.g., fidelity and diversity) of…
Cell segmentation and tracking allow us to extract a plethora of cell attributes from bacterial time-lapse cell movies, thus promoting computational modeling and simulation of biological processes down to the single-cell level. However, to…
In the age of data revolution, a modern storage~or transmission system typically requires different levels of protection. For example, the coding technique used to fortify data in a modern storage system when the device is fresh cannot be…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…
Detection of extremely rare variant alleles, such as tumour DNA, within a complex mixture of DNA molecules is experimentally challenging due to sequencing errors. Barcoding of target DNA molecules in library construction for next-generation…
Modern spatial microscopy has provided developmental biology with powerful research tools. However, the recent significant technological breakthroughs have inevitably led to technical "bottlenecks" for the application of the new procedures…