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Nucleotide sequence variation can induce significant shifts in functional fitness. Recent nucleotide foundation models promise to predict such fitness effects directly from sequence, yet heterogeneous datasets and inconsistent preprocessing…
The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
Hybrid Foreground Residual Subtraction (HyFoReS) is a new family of algorithms designed to remove systematics-induced foreground contamination for 21-cm intensity mapping data. Previously, the algorithm was shown to be effective in…
Electronic DNA sequencing using two-dimensional (2D) materials such as graphene has recently emerged as the next-generation of DNA sequencing technology. Owing to its commercial availability and remarkable physical and conductive…
In previous work, a novel supervised framework implementing a binary classifier was presented that obtained excellent results for side effect discovery. Interestingly, unique side effects were identified when different binary classifiers…
Background Remover (BGR) is a novel software tool developed as a plugin to the well-known ImageJ program and designed to address the challenges of analysing fluorescent microscopy images characterized by low signal-to-noise ratios and…
Data complexity analysis quantifies the hardness of constructing a predictive model on a given dataset. However, the effectiveness of existing data complexity measures can be challenged by the existence of irrelevant features and feature…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
We consider the problem of imaging a crack network embedded in some homogeneous background from measured multi-static far field data generated by acoustic plane waves. We propose two novel approaches that can be seen as extensions of linear…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
A wide variety of application domains are concerned with data consisting of entities and their relationships or connections, formally represented as graphs. Within these diverse application areas, a common problem of interest is the…
Most finger vein feature extraction algorithms achieve satisfactory performance due to their texture representation abilities, despite simultaneously ignoring the intensity distribution that is formed by the finger tissue, and in some…
Functional near-infrared spectroscopy (fNIRS) is a non-invasive optical technique that measures brain activity by estimating blood oxygenation using near-infrared light. Traditionally, PsychoPy is used in many studies to send task-specific…
Spectroscopic anomaly detection and isotope identification algorithms are integral components in nuclear nonproliferation applications such as search operations. The task is especially challenging in the case of mobile detector systems due…
Fine-grained anomaly detection has recently been dominated by segmentation based approaches. These approaches first classify each element of the sample (e.g., image patch) as normal or anomalous and then classify the entire sample as…
21cm tomography promises to be a powerful tool for estimating cosmological parameters, constraining the epoch of reionization, and probing the so-called dark ages. However, realizing this promise will require the extraction of a…
Background fluorescence, especially when it exhibits undesired spatial features, is a primary factor for reduced image quality in optical microscopy. Structured background is particularly detrimental when analyzing single-molecule images…
The RMA, since its introduction in \cite{Iri03a, Iri03b, Iri06}, has gained popularity among bioinformaticians. It has evolved from the exponential-normal convolution to the gamma-normal convolution, from single to two channels and from the…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…