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Team Shares Marker Detection Method for Single-Cell Data

In Nucleic Acids Research, investigators in Germany outline a "single-cell marker identification by enrichment scoring," or SEMITONES, approach for finding informative markers in single-cell RNA sequence, single-cell ATAC-seq, or other single-cell omics datasets without a clustering assignment step. Along with analyses of simulated datasets, the team used the SEMITONES method to find cell identity insights from publicly available scRNA-seq and scATAC-seq data for human hematopoietic cells and through an analysis of published spatial transcriptomic data from the mouse brain. "The method allows for the identification of both local markers, i.e. features that are only detected in a small group of highly similar cells, and global markers, i.e. features that are detected in a larger group of cells covering several cell states," the authors write, noting that SEMITONES "qualitatively and quantitatively outperforms existing methods for the retrieval of cell identity markers from single-cell omics data."

The Scan

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.

Sequencing Analysis Examines Gene Regulatory Networks of Honeybee Soldier, Forager Brains

Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role.

Analysis of Ashkenazi Jewish Cohort Uncovers New Genetic Loci Linked to Alzheimer's Disease

The study in Alzheimer's & Dementia highlighted known genes, but also novel ones with biological ties to Alzheimer's disease.

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.