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Purpose: Thyroid cancer has been a common cancer. Papillary thyroid cancer and follicular thyroid cancer are the two most common types of thyroid cancer. Follicular thyroid cancer lacks distinctive ultrasound signs and is more difficult to…
Peptide compounds demonstrate considerable potential as therapeutic agents due to their high target affinity and low toxicity, yet their drug development is constrained by their low membrane permeability. Molecular weight and peptide length…
As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across…
The segmentation of lesions in Moderate to Severe Traumatic Brain Injury (msTBI) presents a significant challenge in neuroimaging due to the diverse characteristics of these lesions, which vary in size, shape, and distribution across brain…
The diverse nature of protein prediction tasks has traditionally necessitated specialized models, hindering the development of broadly applicable and computationally efficient Protein Language Models (PLMs). In this work, we introduce…
Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a…
In this paper, a new descriptor selection method for selecting an optimal combination of important descriptors of sulfonamide derivatives data, named self tuned reweighted sampling (STRS), is developed. descriptors are defined as the…
Size measurements of tumor manifestations on follow-up CT examinations are crucial for evaluating treatment outcomes in cancer patients. Efficient lesion segmentation can speed up these radiological workflows. While numerous benchmarks and…
Proteolysis-targeting chimeras (PROTACs) represent a promising therapeutic modality that induces targeted protein degradation by hijacking the ubiquitin-proteasome system. However, rational PROTAC design remains challenging due to the…
Peptide microarrays have emerged as a powerful technology in immunoproteomics as they provide a tool to measure the abundance of different antibodies in patient serum samples. The high dimensionality and small sample size of many…
Over the last ten years, Patient-Derived Organoids (PDOs) emerged as the most reliable technology to generate ex-vivo tumor avatars. PDOs retain the main characteristics of their original tumor, making them a system of choice for…
Pathology image segmentation is crucial in computational pathology for analyzing histological features relevant to cancer diagnosis and prognosis. However, current methods face major challenges in clinical applications due to limited…
Background: In the field of radiology and radiotherapy, accurate delineation of tissues and organs plays a crucial role in both diagnostics and therapeutics. While the gold standard remains expert-driven manual segmentation, many automatic…
Cardiovascular disease and chronic kidney disease are major complications of diabetes, leading to high morbidity and mortality. Early detection of these conditions is critical, yet traditional diagnostic markers often lack sensitivity in…
In comparative proteomics studies, LC-MS/MS data is generally quantified using one or both of two measures: the spectral count, derived from the identification of MS/MS spectra, or some measure of ion abundance derived from the LC-MS data.…
One of the central challenges in the computational analysis of liquid chromatography-tandem mass spectrometry (LC-MS/MS) data is to identify the compounds underlying the output spectra. In recent years, this problem is increasingly tackled…
Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the progression of aggregation diseases. Predicting exposed…
Electrospray tandem mass spectrometry (ESI-MS/MS) is commonly used in high throughput metabolomics. One of the key obstacles to the effective use of this technology is the difficulty in interpreting measured spectra to accurately and…
Quantitative measurements produced by mass spectrometry proteomics experiments offer a direct way to explore the role of proteins in molecular mechanisms. However, analysis of such data is challenging due to the large proportion of missing…
The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD…