Chang, R. Y. | bioRxiv Science

bioRxiv2024

mRNArchitect: optimized design of mRNA sequences

Sequence design is the critical first step in developing a new mRNA medicine. The mRNA primary sequence is assembled from multiple elements, including the coding sequence of the target protein or gene, flanking untranslated regions that impact expression, and the poly(A) tail, which improves stability. The mRNA primary sequence can be optimized to improve the performance of an mRNA medicine, including increasing translation and stability, and reducing reactogenicity. Here, we introduce mRNArchitect, a software toolkit to assist in the design of mRNA sequences. mRNArchitect can rapidly assemble and optimize mRNA sequences based on user requirements, including GC content, secondary structure, codon optimization, and uridine depletion. The sequences generated by mRNArchitect can also be readily synthesized and have been experimentally validated across a variety of applications. We present mRNArchitect as a software toolkit to help scientists design new mRNA medicines. Availability and implementationmRNArchitect is available via a web portal at www.basefacility.org.au/software/ and Github at https://github.com/BaseUQ/mRNArchitect. mRNArchitect is open-source and freely available under MIT License.

bioinformatics↗

bioRxiv2020

Segmentation boosting with compensation methods in optical coherence tomography angiography images

Optical coherence tomography angiography is a noninvasive imaging modality to establish the diagnosis of retinal vascular diseases. However, angiography images are significantly interfered if patients jitter or blink. In this study, a novel retinal image analysis method to accurately detect blood vessels and compensate the effect of interference was proposed. We call this the patch U-Net compensation (PUC) system, which is based on the famous U-Net. Several techniques, including a better training mechanism, direction criteria, area criteria, gap criteria, and probability map criteria, have been proposed to improve its accuracy. Simulations show that the proposed PUC achieves much better performance than state-of-art methods.

bioengineering↗