Category: Bioinformatics
- tskit 1.0 formalizes stable infrastructure for population-scale genetic ancestry research ()
Published October 31, 2026. A correspondence published October 29 in Nature Methods marks the release of tskit 1.0, software infrastructure for working with ancestral recombination graphs. These graphs represent genetic ancestry across recombining genomes. Shared data representations let researchers connect simulation and inference tools rather than treating each analysis as a separate, incompatible workflow. The […]
- ATLAS maps 40 million mouse brain cells for comparative spatial biology ()
Published October 31, 2026. ATLAS, a tissue mapping method reported October 30 in Nature Methods, enables large comparative studies of cell distributions in mouse brains. The method learns transcriptional signatures from single-cell RNA sequencing, encodes them within tissue using oligonucleotide probes, and decodes the measurements to infer cell types and imputed transcriptomes. Those inferred transcriptomes […]
- Self-supervised models improve Cell Painting profiling in drug-discovery benchmarks ()
Published October 31, 2026. Self-supervised AI models can extract useful cellular profiles directly from microscopy images, according to a large benchmark published October 29 in Nature Methods. Researchers pretrained four model families on roughly 1.77 million Cell Painting images covering 119,876 compounds from seven laboratories. Their pipeline operates without the cell segmentation and handcrafted feature […]
- Thyra connects mass spectrometry imaging with SpatialData for multimodal biology ()
Published October 31, 2026. Thyra is an open-source Python library designed to connect mass spectrometry imaging with other spatial biology measurements. A report published October 28 in Nature Methods describes its conversion of continuous raw vendor datasets and imzML data into the SpatialData format. Mass spectrometry imaging maps where molecules occur within samples. Combining those […]
- AbOptimizer uses AI to improve multiple antibody properties in laboratory tests ()
Published October 29, 2026. Researchers have introduced AbOptimizer, an artificial intelligence framework that searches for antibody variants with several desirable properties at once. The study appeared in Nature Communications on October 26. The system combines protein language models with reinforcement learning to choose editing sites and amino-acid changes. It can edit several positions together and, […]
- JEEPERS corrects cell-free DNA methylation errors for molecular profiling ()
Published October 29, 2026. A computational framework called JEEPERS corrects a source of error in cell-free DNA methylation analysis. Wang and colleagues describe the method today in Nature Methods. Circulating DNA fragments often have uneven ends. During sequencing-library preparation, repairing those ends can introduce unmethylated bases that distort the molecule’s original epigenetic pattern. This can […]
- Alzheimer’s genetic study identifies 48 new risk loci and cellular pathways ()
Published October 29, 2026. A large genetic study published in Nature on October 28 identifies additional Alzheimer’s disease risk regions and highlights links to microglial and neuronal biology. The analysis combined 30 cohorts, including 109,479 cases and 74,141 proxy cases, alongside more than two million controls and additional proxy controls. Proxy cases were genotyped people […]
- ProBEiT combines protein sequence and structure for efficient engineering predictions ()
Published October 28, 2026. An October 26 paper in Communications Biology introduces ProBEiT, a protein language model that combines amino-acid sequences with structural information. Li and colleagues aim to improve protein-property prediction without relying solely on increasing model size. ProBEiT jointly represents sequences and tokenized structures through an architecture that specializes parts of the model […]
- Imaging-genetics study identifies distinct brain patterns linked to mental health ()
Published October 28, 2026. Research published today in Nature Communications combines brain imaging, behavioral measures and genetics to investigate links between brain structure and mental health. Hu and colleagues developed an analysis framework using UK Biobank data and evaluated its findings in the independent Human Connectome Project cohort. The analysis identified two reproducible patterns of […]
- Spatial midbrain atlas maps cellular vulnerability in Parkinson’s disease ()
Published October 27, 2026. A study published October 26 in Signal Transduction and Targeted Therapy maps cellular and regional differences in the human midbrain associated with Parkinson’s disease. Sooyeon Yoo and colleagues combined single-nucleus RNA sequencing with spatial transcriptomics in postmortem tissue from Korean donors. The study included controls, incidental Lewy body disease and advanced […]