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Bioinformatics (Oxford, England)
Nov 1, 2023
MOTIVATION: Accurate prediction of change in protein stability due to point mutations is an attractive goal that remains unachieved. Despite the high interest in this area, little consideration has been given to the transformer architecture, which is...
Bioinformatics (Oxford, England)
Nov 1, 2023
MOTIVATION: Recent frameworks based on deep learning have been developed to identify cancer subtypes from high-throughput gene expression profiles. Unfortunately, the performance of deep learning is highly dependent on its neural network architecture...
Bioinformatics (Oxford, England)
Nov 1, 2023
MOTIVATION: The origins of replication sites (ORIs) are precise regions inside the DNA sequence where the replication process begins. These locations are critical for preserving the genome's integrity during cell division and guaranteeing the faithfu...
Bioinformatics (Oxford, England)
Nov 1, 2023
MOTIVATION: Quantitative determination of protein thermodynamic stability is a critical step in protein and drug design. Reliable prediction of protein stability changes caused by point variations contributes to developing-related fields. Over the pa...
Bioinformatics (Oxford, England)
Nov 1, 2023
MOTIVATION: The rapid and extensive transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an unprecedented global health emergency, affecting millions of people and causing an immense socioeconomic impact. The id...
Bioinformatics (Oxford, England)
Oct 3, 2023
MOTIVATION: The usefulness of supervised molecular property prediction (MPP) is well-recognized in many applications. However, the insufficiency and the imbalance of labeled data make the learning problem difficult. Moreover, the reliability of the p...
Bioinformatics (Oxford, England)
Oct 3, 2023
MOTIVATION: In recent years, there has been a breakthrough in protein structure prediction, and the AlphaFold2 model of the DeepMind team has improved the accuracy of protein structure prediction to the atomic level. Currently, deep learning-based pr...
Bioinformatics (Oxford, England)
Oct 3, 2023
MOTIVATION: Reliable label-free methods are needed for detecting and profiling apoptotic events in time-lapse cell-cell interaction assays. Prior studies relied on fluorescent markers of apoptosis, e.g. Annexin-V, that provide an inconsistent and lat...
Bioinformatics (Oxford, England)
Oct 3, 2023
MOTIVATION: Cell-cell interactions (CCIs) play critical roles in many biological processes such as cellular differentiation, tissue homeostasis, and immune response. With the rapid development of high throughput single-cell RNA sequencing (scRNA-seq)...
Bioinformatics (Oxford, England)
Sep 2, 2023
MOTIVATION: Living a Big Data era in Biomedicine, there is an unmet need to systematically assess experimental observations in the context of available information. This assessment would offer a means for a comprehensive and robust validation of biom...