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Nature Papers Present Framework for Convolutional Neural Networks for Genomics, Single-Cell Atlas of Brain Development

A Princeton University research team reports in Nature Machine Intelligence this week a new framework to facilitate the use of convolutional neural networks (CNNs) in genomics. Artificial neural networks such as CNNs represent powerful tools for analyzing biological sequences, but the need to tune network architectures, which is time-consuming and requires machine learning expertise, limits their application. To address this, the scientists developed Automated Modelling for Biological Evidence-based Research, or AMBER, which automates the design and application of optimal CNNs for genomic sequences through the state-of-the-art neural architecture search. Its developers show that AMBER-designed models outperform equivalent non-neural architecture search models, even published ones designed by experts, and demonstrate it using established benchmarks.

A single-cell atlas of early-stage human brain development is published in Nature Neuroscience this week, providing insights into the first trimester of human brain development and the subpopulations of progenitor cells that form the basis for creating the human cortex. To build the atlas, researchers from the University of California, San Francisco performed single-cell RNA sequencing across regions of the developing human brain including the telencephalon, diencephalon, midbrain, hindbrain, and cerebellum. They uncovered progenitor populations located near the telencephalon, suggesting more heterogeneity than previously known. A comparison of human and mouse progenitor populations at similar developmental timepoints, meanwhile, revealed two progenitor clusters that are enriched in the early stages of human cortical development.

The Scan

Genetic Ancestry of South America's Indigenous Mapuche Traced

Researchers in Current Biology analyzed genome-wide data from more than five dozen Mapuche individuals to better understand their genetic history.

Study Finds Variants Linked to Diverticular Disease, Presents Polygenic Score

A new study in Cell Genomics reports on more than 150 genetic variants associated with risk of diverticular disease.

Mild, Severe Psoriasis Marked by Different Molecular Features, Spatial Transcriptomic Analysis Finds

A spatial transcriptomics paper in Science Immunology finds differences in cell and signaling pathway activity between mild and severe psoriasis.

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.