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Bioinformatics (Oxford, England)
Jan 12, 2022
MOTIVATION: The acid dissociation constant (pKa) is a critical parameter to reflect the ionization ability of chemical compounds and is widely applied in a variety of industries. However, the experimental determination of pKa is intricate and time-co...
Bioinformatics (Oxford, England)
Jan 12, 2022
MOTIVATION: Single-cell RNA-seq (scRNA-seq) has been widely used to resolve cellular heterogeneity. After collecting scRNA-seq data, the natural next step is to integrate the accumulated data to achieve a common ontology of cell types and states. Thu...
Bioinformatics (Oxford, England)
Jan 3, 2022
MOTIVATION: With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding ...
Bioinformatics (Oxford, England)
Jan 3, 2022
MOTIVATION: Applications in synthetic and systems biology can benefit from measuring whole-cell response to biochemical perturbations. Execution of experiments to cover all possible combinations of perturbations is infeasible. In this paper, we prese...
Bioinformatics (Oxford, England)
Jan 3, 2022
MOTIVATION: Drug response prediction (DRP) plays an important role in precision medicine (e.g. for cancer analysis and treatment). Recent advances in deep learning algorithms make it possible to predict drug responses accurately based on genetic prof...
Bioinformatics (Oxford, England)
Jan 3, 2022
MOTIVATION: Antibodies are one of the most important classes of pharmaceuticals, with over 80 approved molecules currently in use against a wide variety of diseases. The drug discovery process for antibody therapeutic candidates however is time- and ...
Bioinformatics (Oxford, England)
Dec 22, 2021
MOTIVATION: Protein-protein interactions (PPI) play crucial roles in many biological processes, and identifying PPI sites is an important step for mechanistic understanding of diseases and design of novel drugs. Since experimental approaches for PPI ...
Bioinformatics (Oxford, England)
Dec 22, 2021
MOTIVATION: The solvent accessible surface is an essential structural property measure related to the protein structure and protein function. Relative solvent accessible area (RSA) is a standard measure to describe the degree of residue exposure in t...
Bioinformatics (Oxford, England)
Dec 22, 2021
MOTIVATION: N4-acetylcytidine (ac4C) is the only acetylation modification that has been characterized in eukaryotic RNA, and is correlated with various human diseases. Laboratory identification of ac4C is complicated by factors, such as sample hydrol...
Bioinformatics (Oxford, England)
Dec 22, 2021
MOTIVATION: Human proteins that are secreted into different body fluids from various cells and tissues can be promising disease indicators. Modern proteomics research empowered by both qualitative and quantitative profiling techniques has made great ...