Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework.

Direct nanopore-based RNA sequencing can be used to detect posttranscriptional base modifications, such as N6-methyladenosine (m6A) methylation, based on the electric current signals produced by the distinct chemical structures of modified bases. A key challenge is the scarcity of adequate training data with known methylation modifications. We present Xron, a hybrid encoder-decoder framework that delivers a direct methylation-distinguishing basecaller by training on synthetic RNA data and immunoprecipitation (IP)-based experimental data in two steps.

Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework.

Direct nanopore-based RNA sequencing can be used to detect post-transcriptional base modifications, such as m6A methylation, based on the electric current signals produced by the distinct chemical structures of modified bases. A key challenge is the scarcity of adequate training data with known methylation modifications. We present Xron, a hybrid encoder-decoder framework that delivers a direct methylation-distinguishing basecaller by training on synthetic RNA data and immunoprecipitation-based experimental data in two steps.

Clustering spatial transcriptomics data.

Motivation: Recent advancements in fluorescence in situ hybridization (FISH) techniques enable them to concurrently obtain information on the location and gene expression of single cells. A key question in the initial analysis of such spatial transcriptomics data is the assignment of cell types. To date, most studies used methods that only rely on the expression levels of the genes in each cell for such assignments.

Templated-Assisted Synthesis of Structurally Ordered Intermetallic PtCo with Ultralow Loading Supported on 3D Porous Carbon for Oxygen Reduction Reaction.

Simple and reliable mass production of platinum-based alloy catalysts with excellent activity and stability is an enormous challenge for the wide commercialization of proton-exchange membrane fuel cells (PEMFC), especially those with ultralow loading of Pt. Herein, an economical, highly durable, and efficient catalyst consisting of structurally ordered intermetallic PtCo alloy nanoparticles with ultralow Pt loading (1.4 wt %) supported on hierarchically porous carbon structure (three-dimensional, 3D PtCo/C) were synthesized with large-scale production by the NaCl-template-assisted approach.

Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing.

Background: Klebsiella pneumoniae frequently harbours multidrug resistance, and current diagnostics struggle to rapidly identify appropriate antibiotics to treat these bacterial infections. The MinION device can sequence native DNA and RNA in real time, providing an opportunity to compare the utility of DNA and RNA for prediction of antibiotic susceptibility. However, the effectiveness of bacterial direct RNA sequencing and base-calling has not previously been investigated.

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning.

Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step.

Spontaneous Activity in the Zebrafish Tectum Reorganizes over Development and Is Influenced by Visual Experience.

Spontaneous patterns of activity in the developing visual system may play an important role in shaping the brain for function. During the period 4-9 dpf (days post-fertilization), larval zebrafish learn to hunt prey, a behavior that is critically dependent on the optic tectum. However, how spontaneous activity develops in the tectum over this period and the effect of visual experience are unknown.