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Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic…
Aptamers are single-stranded DNA/RNAs or short peptides with unique tertiary structures that selectively bind to specific targets. They have great potential in the detection and medical fields. Here, we present SelfTrans-Ensemble, a deep…
In this paper, we present the design and the analysis of an electrochemical circuit for measuring the concentrations of therapeutic drugs using structure-switching aptamers. Aptamers are single-stranded nucleic acids, whose sequence is…
This report describes the development of an aptamer for sensing azole antifungal drugs for therapeutic drug monitoring. Modified Synthetic Evolution of Ligands through Exponential Enrichment (SELEX) was used to discover a DNA aptamer…
Nucleic acid-based drugs like aptamers have recently demonstrated great therapeutic potential. However, experimental platforms for aptamer screening are costly, and the scarcity of labeled data presents a challenge for supervised methods to…
The development of an aptamer-based impedimetric sensor for typing of bacteria (AIST-B) is presented. Highly specific DNA aptamers to Salmonella enteritidis were selected via Cell-SELEX technique. Twelve rounds of selection were performed;…
Machine-learning methods in biochemistry commonly represent molecules as graphs of pairwise intermolecular interactions for property and structure predictions. Most methods operate on a single graph, typically the minimal free energy (MFE)…
Optical fiber sensing carries a number of potential advantages for diagnostics and biomarker detection and monitoring, yet particular challenges persist in linking molecular recognition events to a change in the refractive index. DNA…
Aptamers, short synthetic RNA/DNA molecules binding specific targets with high affinity and specificity, are utilized in an increasing spectrum of bio-medical applications. Aptamers are identified in vitro via the Systematic Evolution of…
In drug discovery, predicting the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of small-molecule drugs is critical for ensuring safety and efficacy. However, the process of accurately predicting these…
There is an urgent need for economical blood based, noninvasive molecular biomarkers to assist in the detection and diagnosis of cancers in a cost effective manner at an early stage, when curative interventions are still possible. Serum…
Mycotoxins comprise a frequent type of toxins present in food and feed. The problem of mycotoxin contamination has been recently aggravated due to the increased complexity of the farm-to-fork chains, resulting in negative effects on human…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Simple and low-cost biosensing solutions are suitable for point-of-care applications aiming to overcome the gap between scientific concepts and technological production. To compete with sensitivity and selectivity of golden standards, such…
We study the electronic properties of a linear trans-polyacetylene (tPA) molecule capacitively coupled to an external gate voltage $V_g$ of width $d$. We describe this system using the Takayama-Lin-Liu-Maki (TLM) model in the continuum, and…
Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo environment with physiological ionic concentrations. In…
A dielectric-modulated double gate bilayer electrodes organic thin-film transistor (DMDGBE-OTFT) based sensor is proposed for label-free biomolecule detection. The double gate of DMDGBE-OTFT is used for creating two symmetrical gates…
Efficient encoding and representation of large 3D molecular structures with high fidelity is critical for biomolecular design applications. Despite this, many representation learning approaches restrict themselves to modeling smaller…
Electrochemical biosensors ("E-AB" or "E-DNA" type sensors) that utilize square-wave voltammetry originated in academic labs with a few standard experimental configurations for the electrochemical cell and data analysis. We report here on…
Hemoglobin (Hgb) forms tetramers (dimerized dimers), which enhance its globular stability and may also facilitate small gas molecule transport, as shown by recent all-atom Newtonian solvated simulations. Hydropathic bioinformatic scaling…