Nanopore Direct
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Related Articles from SNS
Nanopore Direct RNA Sequencing Enables Reproducible, Site-Resolved Pseudouridine Quantification in Human Ribosomal RNA
Pseudouridine is the most abundant post-transcriptional modification in human ribosomal RNA, with over 110 annotated sites and variable stoichiometry across biological contexts. Existing quantification methods are low-throughput or constrained to predefined panels. We benchmarked nanopore direct RNA sequencing using the Dorado v5.1 model against mass spectrometry-validated sites in human liver tissue, induced pluripotent stem cells, and HeLa cells.
Information Rate Decomposition for Noisy Nanopore Channels with Geometric Duplication
arXiv:2606.06808v1 Announce Type: new Abstract: This paper studies information rates of noisy duplication channels with memory, motivated by nanopore DNA sequencing. In nanopore sequencing, the measured signal is affected by both inter-symbol interference (ISI), caused by multiple DNA bases residing in the pore, and random sample duplications, where variable translocation speed causes each base to generate a random number of samples.
A Low-Cost, High-Throughput Design-Build-Test Pipeline for Engineering Genetic Systems: Stress Testing with Complex Structural Proteins
Genetic systems engineering is constrained by high DNA synthesis costs, assembly inefficiencies, and challenges in expressing complex proteins. To address these limitations, we developed a highly parallel, low-cost pipeline for the design, assembly, and functional screening of genetic systems, which we stress-tested on highly repetitive structural proteins, including spider silk, biocements, reflectins, and talins. The integrated pipeline combines computational genetic systems design,...