Residue co-evolution has become the primary principle for estimating inter-residue distances of a protein, which are crucially important for predicting protein structure. Most existing approaches adopt an indirect strategy, i.e., inferring residue co...
Recent advances in machine learning promise to yield novel insights by interrogation of large datasets ranging from gene expression and mutation data to CRISPR knockouts and drug screens. We combined existing and new algorithms with available experim...
This short article describes the method of digital cytopathology using Z-stack scanning with or without extended focusing. This technology is suitable to observe such thick clusters as adenocarcinoma on cytologic specimens. Artificial intelligence (A...
BACKGROUND: Tumor mutational burden-high (TMB-H), which is detected with gene panel testing, is a promising biomarker for immune checkpoint inhibitors (ICIs) in colorectal cancer (CRC). However, in clinical practice, not every patient is tested for T...
Accurate prediction of cancer stage is important in that it enables more appropriate treatment for patients with cancer. Many measures or methods have been proposed for more accurate prediction of cancer stage, but recently, machine learning, especia...
The ability to design functional sequences and predict effects of variation is central to protein engineering and biotherapeutics. State-of-art computational methods rely on models that leverage evolutionary information but are inadequate for importa...
Deregulation of the protein secretory pathway (PSP) is linked to many hallmarks of cancer, such as promoting tissue invasion and modulating cell-cell signaling. The collection of secreted proteins processed by the PSP, known as the secretome, is ofte...
OBJECTIVE: H3K27M mutation in gliomas has prognostic implications. Previous magnetic resonance imaging (MRI) studies have reported variable rates of tumoral enhancement, necrotic changes, and peritumoral edema in H3K27M-mutant gliomas, with no distin...
Journal of chemical theory and computation
Mar 30, 2021
Drug resistance threatens many critical therapeutics through mutations in the drug target. The molecular mechanisms by which combinations of mutations, especially those remote from the active site, alter drug binding to confer resistance are poorly u...
Journal of chemical information and modeling
Mar 23, 2021
Mutational effects predictions continue to improve in accuracy as advanced artificial intelligence (AI) algorithms are trained on exhaustive experimental data. The next natural questions to ask are if it is possible to gain insights into which attrib...