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UCLA Team Develops Computational Tool for Generating Realistic Single-Cell, Spatial Omics Data

A statistical simulator that can generate realistic single-cell and spatial omics data including cell latent structures, feature modalities, spatial locations, and experimental designs is presented in Nature Biotechnology this week. Called scDesign3, the simulator learns interpretable parameters from real data, according to the University of California, Los Angeles researchers who developed it. ScDesign3 offers a probabilistic model that unifies the generation and inference for single-cell and spatial omics data, they write, inferring biologically meaningful parameters and assessing the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations. The model also generates in silico negative and positive controls for benchmarking computational tools. "Although the scDesign3 model should not be treated as the true model, its interpretable parameters precede functionalities besides data simulation," the researchers add.

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.