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In distributed storage systems, locally repairable codes (LRCs) are designed to reduce disk I/O and repair costs by enabling recovery of each code symbol from a small number of other symbols. To handle multiple node failures,…
In many tissues, cell type varies over single-cell length-scales, creating detailed spatial heterogeneities fundamental to physiological function. To gain understanding of this relationship between tissue function and detailed structure,…
This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes…
Designing regulatory DNA sequences that achieve precise cell-type-specific gene expression is crucial for advancements in synthetic biology, gene therapy and precision medicine. Although transformer-based language models (LMs) can…
The locations of different mRNA molecules can be revealed by multiplexed in situ RNA detection. By assigning detected mRNA molecules to individual cells, it is possible to identify many different cell types in parallel. This in turn enables…
Wireless indoor localization has been a pivotal area of research over the last two decades, becoming a cornerstone for numerous sensing applications. However, conventional wireless localization methods rely on channel state information to…
Automatic 3D neuron reconstruction is critical for analysing the morphology and functionality of neurons in brain circuit activities. However, the performance of existing tracing algorithms is hinged by the low image quality. Recently, a…
The rapid emergence of single-cell data has facilitated the study of many different biological conditions at the cellular level. Cluster analysis has been widely applied to identify cell types, capturing the essential patterns of the…
"Epigenetic Tracking" is the name of a model of cellular development that, coupled with an evolutionary technique, becomes an evo-devo (or "artificial embryology", or "computational development") method to generate 2d or 3d sets of…
Cooperative relay systems have become an active area of research during recent years since they help cellular networks to enhance data rate and coverage. In this paper we develop a method to jointly optimize precoding matrices for…
Counterfeiting poses a significant challenge across multiple industries, leading to financial losses and health risks. While DNA-based molecular tagging has emerged as a promising anti-counterfeiting strategy, existing methods rely on…
Spectral clustering is a key research topic in the field of machine learning and data mining. Most of the existing spectral clustering algorithms are built upon Gaussian Laplacian matrices, which are sensitive to parameters. We propose a…
Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing any heterogeneous tissues, such as blood, tumor systems. Due to inevitable sequencing errors and other…
Recent advances in microphysiological systems have underscored the need for novel sensing and monitoring systems specifically designed for three-dimensional (3D) cell culture. In this article, an original architecture of a cell-culture…
Locating the center of convex objects is important in both image processing and unsupervised machine learning/data clustering fields. The automated analysis of biological images uses both of these fields for locating cell nuclei and for…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
We investigate fully self-consistent multiscale quantum-classical algorithms on current generation superconducting quantum computers, in a unified approach to tackle the correlated electronic structure of large systems in both quantum…
Cell counting in microscopy images is vital in medicine and biology but extremely tedious and time-consuming to perform manually. While automated methods have advanced in recent years, state-of-the-art approaches tend to increasingly…
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such…