Nature Search

A benchmark of expert-level academic questions to assess AI capabilities

Humanity’s Last Exam, a multi-modal benchmark at the frontier of human knowledge, is designed to be an expert-level closed-ended academic benchmark with broad subject coverage.

Long Phan
Alice Gatti
Davide Scaramuzza
ResearchOpen Access28 Jan 2026
Nature

Volume: 649, P: 1139-1146
Harnessing the power of single-cell large language models with parameter-efficient fine-tuning using scPEFT

He et al. present a parameter-efficient fine-tuning method for single-cell language models that improves performance on unseen diseases, treatments and cell types.

Fei He
Ruixin Fei
Dong Xu
Research31 Dec 2025
Nature Machine Intelligence

Volume: 8, P: 118-133
Systematic evidence grading evaluates multisystemic associations and risks of vitiligo

Vitiligo, a chronic autoimmune skin disorder, has inconsistent associations with various biomarkers and diseases due to confounding factors. Here, the authors conduct an umbrella review and comparative analysis of meta-analyses and Mendelian randomization studies to evaluate the strength and validity of evidence on multisystemic associations with vitiligo.

Lin Liu
Yuzhou Xue
Jianmin Chang
ResearchOpen Access03 Nov 2025
Nature Communications

Volume: 16, P: 1-12
Graph Fourier transform for spatial omics representation and analyses of complex organs

SpaGFT is a spatial omics representation method. It identifies spatially variable genes, enhances gene imputation, detects immunological regions, and characterises variations in secondary lymphoid organs. This method improves predictive power in wide downstream machine-learning tasks.

Yuzhou Chang
Jixin Liu
Qin Ma
ResearchOpen Access29 Aug 2024
Nature Communications

Volume: 15, P: 1-22
Author Correction: A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

Mor Kenigsbuch
Pierre Bost
Ido Amit
Amendments and Corrections31 Jan 2023
Nature Neuroscience

Volume: 26, P: 528
Author Correction: scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

Juexin Wang
Anjun Ma
Dong Xu
Amendments and CorrectionsOpen Access04 May 2022
Nature Communications

Volume: 13, P: 1-2
scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

Single-cell RNA-Seq suffers from heterogeneity in sequencing sparsity and complex differential patterns in gene expression. Here, the authors introduce a graph neural network based on a hypothesis-free deep learning framework as an effective representation of gene expression and cell–cell relationships.

Juexin Wang
Anjun Ma
Dong Xu
ResearchOpen Access25 Mar 2021
Nature Communications

Volume: 12, P: 1-11
Dimension-agnostic and granularity-based spatially variable gene identification using BSP

Identifying spatially variable genes (SVGs) is essential for linking molecular cell functions with tissue phenotypes. Here, authors introduce a non-parametric model that detects SVGs from two or three-dimensional spatial transcriptomics data by comparing gene expression patterns at granularities.

Juexin Wang
Jinpu Li
Dong Xu
ResearchOpen Access14 Nov 2023
Nature Communications

Volume: 14, P: 1-15
Single-cell biological network inference using a heterogeneous graph transformer

Single-cell multi-omics and deep learning could lead to the inference of biological networks across specific cell types. Here, the authors develop DeepMAPS, a deep learning, graph-based approach for cell-type specific network inference from single-cell multi-omics data that is tested on healthy and tumour tissue datasets.

Anjun Ma
Xiaoying Wang
Qin Ma
ResearchOpen Access21 Feb 2023
Nature Communications

Volume: 14, P: 1-18
A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

We identified an oligodendrocyte signature associated with brain pathology in the 5xFAD model of amyloidosis, which we termed disease-associated oligodendrocytes. This signature was found to be shared by oligodendrocytes across pathologies.

Mor Kenigsbuch
Pierre Bost
Ido Amit
Research27 Jun 2022
Nature Neuroscience

Volume: 25, P: 876-886
SENP3 maintains the stability and function of regulatory T cells via BACH2 deSUMOylation

Regulatory T cells are crucial for the establishment and maintenance of peripheral immune tolerance, yet the mechanisms regulating their stability and function remain to be fully elucidated. Here the authors show SENP3 maintains Treg cell stability and function via BACH2 deSUMOylation.

Xiaoyan Yu
Yimin Lao
Qiang Zou
ResearchOpen Access08 Aug 2018
Nature Communications

Volume: 9, P: 1-11
Multi-omics analysis reveals the evolution, function, and regulatory mechanisms of SPF pheromones in Anurans

Multi-omics techniques facilitate a comprehensive understanding of the function and regulatory mechanisms of SPF pheromones in Anurans, shedding lights on the protein pheromones evolutionary and multi-modal communication in vertebrates.

Puyang Zheng
Yunyun Lv
Feng Xie
ResearchOpen Access20 Dec 2024
Communications Biology

Volume: 7, P: 1-13
Principle of Tibetan medicine fluoritum processing by vinegar based on the change of microstructure and chemical composition

Yuzhou Zhuo
Chang Lin
Jing Hu
ResearchOpen Access04 Mar 2025
Scientific Reports

Volume: 15, P: 1-17
Identification and verification of the molecular mechanisms and prognostic values of the cadherin gene family in gastric cancer

Shanshan Luo
Rujing Lin
Yuzhou Qin
ResearchOpen Access08 Dec 2021
Scientific Reports

Volume: 11, P: 1-21

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