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Gene panel selection aims to identify the most informative genomic biomarkers in label-free genomic datasets. Traditional approaches, which rely on domain expertise, embedded machine learning models, or heuristic-based iterative…
This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a…
Fragment-based drug design is a promising strategy leveraging the binding of small chemical moieties that can efficiently guide drug discovery. The initial step of fragment identification remains challenging, as fragments often bind weakly…
Single-cell RNA sequencing (scRNA-seq) has revealed complex cellular heterogeneity, but recent studies emphasize that understanding biological function also requires modeling cell-cell communication (CCC), the signaling interactions…
How a single fertilized cell gives rise to a complex array of specialized cell types in development is a central question in biology. The cells grow, divide, and acquire differentiated characteristics through poorly understood molecular…
Open-set biometrics faces challenges with probe subjects who may not be enrolled in the gallery, as traditional biometric systems struggle to detect these non-mated probes. Despite the growing prevalence of multi-sample galleries in…
This paper reports some experimental results validating in a broader context a variant of PCR, called XPCR, previously introduced and tested on relatively short synthetic DNA sequences. Basic XPCR technique confirmed to work as expected, to…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
Deep convolutional neural networks (CNNs) have demonstrated dominant performance in person re-identification (Re-ID). Existing CNN based methods utilize global average pooling (GAP) to aggregate intermediate convolutional features for…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…
Electron tomography (ET) allows high-resolution reconstructions of macromolecular complexes at nearnative state. Cellular structures segmentation in the reconstruction data from electron tomographic images is often required for analyzing…
Current in vivo microscopy allows us detailed spatiotemporal imaging (3D+t) of complete organisms and offers insights into their development on the cellular level. Even though the imaging speed and quality is steadily improving,…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
We offer new high-performance label-free electrochemical impedimetric DNA sensors of non-faradaic type. The DNA sensors based on a platform of crystalline carbon nanotube (CNT) arrays are fabricated by the Langmuir--Blodgett (LB) deposition…
A chloroplast is a subcellular organelle of photosynthesis in plant and algal cells. A chloroplast genome encodes proteins of the photosynthetic electron transport chain and ribosomal proteins required to express them. Chloroplast-encoded…
Many efforts have been made to discover tumor-specific microenvironment elements (TMEs) from immunostained tissue sections. However, the identification of yet unknown but relevant TMEs from multiplex immunostained tissues remains a…
We define BioScapeL, a stochastic pi-calculus in 3D-space. A novel aspect of BioScapeL is that entities have programmable locations. The programmer can specify a particular location where to place an entity, or a location relative to the…
The pivotal storage density win achieved by solid-state devices over magnetic devices in 2015 is a result of multiple innovations in physics, architecture, and signal processing. One of the most important innovations in that regard is…