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Bioinformatics (Oxford, England)
Mar 4, 2022
MOTIVATION: In proteomics, database search programs are routinely used for peptide identification from tandem mass spectrometry data. However, many low-quality spectra cannot be interpreted by any programs. Meanwhile, certain high-quality spectra may...
Bioinformatics (Oxford, England)
Mar 4, 2022
MOTIVATION: Structural genomic variants account for much of human variability and are involved in several diseases. Structural variants are complex and may affect coding regions of multiple genes, or affect the functions of genomic regions in differe...
Bioinformatics (Oxford, England)
Feb 7, 2022
MOTIVATION: Protein-protein interactions (PPIs) are key elements in numerous biological pathways and the subject of a growing number of drug discovery projects including against infectious diseases. Designing drugs on PPI targets remains a difficult ...
Bioinformatics (Oxford, England)
Feb 7, 2022
MOTIVATION: Viruses, the most abundant biological entities on earth, are important components of microbial communities, and as major human pathogens, they are responsible for human mortality and morbidity. The identification of viral sequences from m...
Bioinformatics (Oxford, England)
Feb 7, 2022
MOTIVATION: Molecule generation, which is to generate new molecules, is an important problem in bioinformatics. Typical tasks include generating molecules with given properties, molecular property improvement (i.e. improving specific properties of an...
Bioinformatics (Oxford, England)
Feb 7, 2022
MOTIVATION: Algorithms for classifying chromosomes, like convolutional deep neural networks (CNNs), show promise to augment cytogeneticists' workflows; however, a critical limitation is their inability to accurately classify various structural chromo...
Bioinformatics (Oxford, England)
Feb 7, 2022
MOTIVATION: With the development of single-cell RNA sequencing (scRNA-seq) techniques, increasingly more large-scale gene expression datasets become available. However, to analyze datasets produced by different experiments, batch effects among differ...
Bioinformatics (Oxford, England)
Feb 7, 2022
MOTIVATION: Clustering spatial-resolved gene expression is an essential analysis to reveal gene activities in the underlying morphological context by their functional roles. However, conventional clustering analysis does not consider gene expression ...
Bioinformatics (Oxford, England)
Feb 7, 2022
SUMMARY: DeepKG is an end-to-end deep learning-based workflow that helps researchers automatically mine valuable knowledge in biomedical literature. Users can utilize it to establish customized knowledge graphs in specified domains, thus facilitating...
Bioinformatics (Oxford, England)
Feb 7, 2022
MOTIVATION: DNA methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational methods have been developed to ...