MOTIVATION: The investigation of the structure of biological systems at the molecular level gives insights about their functions and dynamics. Shape and surface of biomolecules are fundamental to molecular recognition events. Characterizing their geo...
Application of machine and deep learning methods in drug discovery and cancer research has gained a considerable amount of attention in the past years. As the field grows, it becomes crucial to systematically evaluate the performance of novel computa...
The goal of precision oncology is to tailor treatment for patients individually using the genomic profile of their tumors. Pharmacogenomics datasets such as cancer cell lines are among the most valuable resources for drug sensitivity prediction, a cr...
Drug combinations have exhibited promising therapeutic effects in treating cancer patients with less toxicity and adverse side effects. However, it is infeasible to experimentally screen the enormous search space of all possible drug combinations. Th...
Mitochondria are membrane-bound organelles containing over 1000 different proteins involved in mitochondrial function, gene expression and metabolic processes. Accurate localization of those proteins in the mitochondrial compartments is critical to t...
The biomedical literature is growing rapidly, and the extraction of meaningful information from the large amount of literature is increasingly important. Biomedical named entity (BioNE) identification is one of the critical and fundamental tasks in b...
MOTIVATION: Over the past 50 years, our ability to model protein sequences with evolutionary information has progressed in leaps and bounds. However, even with the latest deep learning methods, the modelling of a critically important class of protein...
MOTIVATION: Tumor tile selection is a necessary prerequisite in patch-based cancer whole slide image analysis, which is labor-intensive and requires expertise. Whole slides are annotated as tumor or tumor free, but tiles within a tumor slide are not....
PURPOSE: The molecular subtype of breast cancer is an important component of establishing the appropriate treatment strategy. In clinical practice, molecular subtypes are determined by receptor expressions. In this study, we developed a model using d...
Recent pharmacogenomic studies that generate sequencing data coupled with pharmacological characteristics for patient-derived cancer cell lines led to large amounts of multi-omics data for precision cancer medicine. Among various obstacles hindering ...
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