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RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…
Electromagnetic hot-spots at ultra-narrow plasmonic nanogaps carry immense potential to drive detection limits down to few molecules in sensors based on surface enhanced Raman or Fluorescence spectroscopies. However, leveraging the EM…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
Precise analysis of nanoparticles for characterization in electron microscopy images is essential for advancing nanomaterial development. Yet it remains challenging due to the time-consuming nature of manual methods and the shortcomings of…
We propose a new label-free ultrasonic sensor, which comprises a slot wave-guide and double silicon-on-insulator (SOI) slot micro-ring resonators. The all-optical sensors do not suffer from electromagnetic interference. We choose to…
Optical metasurfaces provide novel solutions to label-free biochemical sensing by localizing light resonantly beyond the diffraction limit, thereby selectively enhancing light-matter interactions for improved analytical performance.…
The applications of traditional statistical feature selection methods to high-dimension, low sample-size data often struggle and encounter challenging problems, such as overfitting, curse of dimensionality, computational infeasibility, and…
Highly sensitive and selective label free devices for real-time identification of specific biomarkers are expected to significantly impact the biosensing field. The ability of plasmonic systems to confine the light in nanometer volume and…
Metasurfaces provide a versatile and compact approach to free-space optical manipulation and wavefront shaping. Comprised of arrays of judiciously-arranged dipolar resonators, metasurfaces precisely control the amplitude, polarization, and…
Optical sensing is one of the key-enablers of modern diagnostics. Especially label-free imaging modalities hold great promise as they eliminate labeling procedures prior to analysis. However, scattering signals of nanometric particles scale…
Magnetic resonance imaging (MRI) is a non-invasive and label-free technique widely used in medical diagnosis and life science research, and its success has benefited greatly from continuing efforts on enhancing contrast and resolution. Here…
Recent advances in nanotechnology have led to the development of nano-electro-mechanical systems (NEMS) such as nanomechanical resonators, which have recently received significant attention from the scientific community. This has not only…
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…
Nonlinear optical phenomena in nanostructured materials have been challenging our perceptions of nonlinear optical processes that have been explored since the invention of lasers. For example, the ability to control optical field…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…
This work presents an innovative magnetoelastic (ME) biosensor using graphene functionalized with the SARS-CoV-2 N protein for antibody detection via magnetoelastic resonance. Graphene was chosen for its biocompatibility and high surface…