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Peak picking is a fundamental preprocessing step in Mass Spectrometry Imaging (MSI), where each sample is represented by hundreds to thousands of ion images. Existing approaches require careful dataset-specific hyperparameter tuning, and…
Protein-ligand binding affinity (PLBA) prediction is the fundamental task in drug discovery. Recently, various deep learning-based models predict binding affinity by incorporating the three-dimensional structure of protein-ligand complexes…
Metabolites, small molecules that are involved in cellular reactions, provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually relies on tandem mass spectrometry to identify the thousands of…
This study introduces a novel approach for early Type 2 Diabetes Mellitus (T2DM) risk prediction using a tabular transformer (TabTrans) architecture to analyze longitudinal patient data. By processing patients` longitudinal health records…
The accurate segmentation of medical images is a crucial step in obtaining reliable morphological statistics. However, training a deep neural network for this task requires a large amount of labeled data to ensure high-accuracy results. To…
{\it De novo} protein sequencing is essential for understanding cellular processes that govern the function of living organisms and all post-translational events and other sequence modifications that occur after a protein has been…
Limited spectrum coverage is a problem in shotgun proteomics. Replicates are generated to improve the spectrum coverage. When integrating peptide identification results obtained from replicates, the state-of-the-art algorithm PeptideProphet…
Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
Magnetic Resonance Imaging (MRI) plays an important role in diagnosing the parotid tumor, where accurate segmentation of tumors is highly desired for determining appropriate treatment plans and avoiding unnecessary surgery. However, the…
The segmentation of pelvic fracture fragments in CT and X-ray images is crucial for trauma diagnosis, surgical planning, and intraoperative guidance. However, accurately and efficiently delineating the bone fragments remains a significant…
Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the…
Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as…
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells.…
The diagnosis and segmentation of tumors using any medical diagnostic tool can be challenging due to the varying nature of this pathology. Magnetic Reso- nance Imaging (MRI) is an established diagnostic tool for various diseases and…
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single…
We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo- and heterolevels involving possibly different RHF and…
Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor…
Tumor protein P53 is believed to be involved in over half of human cancers cases, the prediction of malignancies plays essential roles not only in advance detection for cancer, but also in discovering effective prevention and treatment of…
Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular…