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In Genome Biology, Researchers Share Algorithm for Reference-Free Nanopore-Based Transcript Analyses

A team from Australia, Spain, and Portugal has come up with a reference-free "greedy clustering" algorithm called RATTLE for putting together and quantifying transcript data based on Nanopore sequencing reads. As they report in the journal Genome Biology, the researchers applied RATTLE to simulated and real RNA sequence data on a variety of sample types, including human tissue samples. "Using simulated data, isoform spike-ins, and sequencing data from human tissues and cell lines, we show that RATTLE is competitive at recovering transcript sequences and their abundance, despite not using any information from the reference," the authors write, adding that their RATTLE method "lays the foundation for a multitude of potential new applications of Nanopore transcriptomics."

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.