Published in Bioinformatics (Oxford, England)
MicroRNAs have been shown to be able to modulate the tumor microenvironment and the immune response and hence could be interesting biomarkers and therapeutic targets in immuno-oncology, however, dedicated analysis tools are missing. Here we present a user-friendly web platform MIO and a Python toolkit miopy integrating various methods for visualiza...
Published in Bioinformatics (Oxford, England)
A widely applicable strategy to create cell factories is to knock out (KO) genes or reactions to redirect cell metabolism so that chemical synthesis is made obligatory when the cell grows at its maximum rate. Synthesis is thus growth-coupled, and the stronger the coupling the more deleterious any impediments in synthesis are to cell growth, making ...
Published in Bioinformatics (Oxford, England)
In the exploratory data analysis of single-cell or spatial genomic data, single cells or spatial spots are often visualized using a two-dimensional plot where cell clusters or spot clusters are marked with different colors. With tens of clusters, current visualization methods often assign visually similar colors to spatially neighboring clusters, m...
Published in Bioinformatics (Oxford, England)
Mutation is the key for a variant of concern (VOC) to overcome selective pressures, but this process is still unclear. Understanding the association of the mutational process with VOCs is an unmet need. Here we developed VOC-alarm, a method to predict VOCs and their caused COVID surges, using mutations of about 5.7 million SARS-CoV-2 complete seque...
Published in Bioinformatics (Oxford, England)
Published in Bioinformatics (Oxford, England)
Selecting the optimal cancer cell line for an experiment can be challenging given the diversity of lines available. Here, we present CNpare, which identifies similar cell line models based on genome-wide DNA copy number. CNpare is available as an R package at https://github.com/macintyrelab/CNpare. All analysis performed in the manuscript can be re...
Published in Bioinformatics (Oxford, England)
Metal binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal binding proteins is thus crucial for understanding the mechanisms of cellular activity...
Published in Bioinformatics (Oxford, England)
Testing for pathway enrichment is an important aspect in the analysis of untargeted metabolomics data. Due to the unique characteristics of untargeted metabolomics data, some key issues have not been fully addressed in existing pathway testing algorithms: (1) matching uncertainty between data features and metabolites; (2) lacking of method to analy...
Published in Bioinformatics (Oxford, England)
Protein design has become increasingly important for medical and biotechnological applications. Because of the complex mechanisms underlying protein formation, the creation of a novel protein requires tedious and time-consuming computational or experimental protocols. At the same time, machine learning has enabled the solving of complex problems by...
Published in Bioinformatics (Oxford, England)
Lattice light sheet microscopy is revolutionizing cell biology since it enables fast, high-resolution extended imaging in three dimensions combined with a drastic reduction in photo-toxicity and bleaching. However analysis of such data sets still remains a major challenge. Automated tracking of kinetochores, the protein complex facilitating and con...
