A signal processing and deep learning framework for methylation detection using Oxford Nanopore sequencing.

Oxford Nanopore sequencing can detect DNA methylations from ionic current signal of single molecules, offering a unique advantage over conventional methods. Additionally, adaptive sampling, a software-controlled enrichment method for targeted sequencing, allows reduced representation methylation sequencing that can be applied to CpG islands or imprinted regions. Here we present DeepMod2, a comprehensive deep-learning framework for methylation detection using ionic current signal from Nanopore sequencing.

DELongSeq for efficient detection of differential isoform expression from long-read RNA-seq data.

Conventional gene expression quantification approaches, such as microarrays or quantitative PCR, have similar variations of estimates for all genes. However, next-generation short-read or long-read sequencing use read counts to estimate expression levels with much wider dynamic ranges. In addition to the accuracy of estimated isoform expression, efficiency, which measures the degree of estimation uncertainty, is also an important factor for downstream analysis.

BepiTBR: T-B reciprocity enhances B cell epitope prediction.

The ability to predict B cell epitopes is critical for biomedical research and many clinical applications. Investigators have observed the phenomenon of T-B reciprocity, in which candidate B cell epitopes with nearby CD4 T cell epitopes have higher chances of being immunogenic. To our knowledge, existing B cell epitope prediction algorithms have not considered this interesting observation.

Impact of pH on efficacy of peroxy acetic acid against Salmonella, Campylobacter, and Escherichia coli on chicken wings.

Peroxy acetic acid (PAA) is widely used as an antimicrobial in poultry processing, specifically in the chiller. While the natural pH of PAA at the concentrations used is between 4.5 and 6.