[HTML][HTML] Foundation models in molecular biology

Y Si, J Zou, Y Gao, G Chuai, Q Liu… - Biophysics …, 2024 - biophysics-reports.org
Determining correlations between molecules at various levels is an important topic in
molecular biology. Large language models have demonstrated a remarkable ability to …

Towards a universal spatial molecular atlas of the mouse brain

Y He, H Sheng, H Shi, WX Wang, Z Tang, J Liu… - bioRxiv, 2024 - biorxiv.org
Spatially mapping a comprehensive brain at the single-cell level with molecular resolution is
crucial for understanding its biological structure, mechanisms, and functions. Recent …

PAST: latent feature extraction with a prior-based self-attention framework for spatial transcriptomics

Z Li, X Chen, X Zhang, S Chen, R Jiang - bioRxiv, 2022 - biorxiv.org
Rapid advances in spatial transcriptomics (ST) have revolutionized the interrogation of
spatial heterogeneity and increased the demand for comprehensive methods to effectively …

[HTML][HTML] Spatial motifs reveal patterns in cellular architecture of complex tissues

Z Samadi, A Askary - bioRxiv, 2024 - ncbi.nlm.nih.gov
Spatial organization of cells is crucial to both proper physiological function of tissues and
pathological conditions like cancer. Recent advances in spatial transcriptomics have …

Hexagonal image segmentation on spatially resolved transcriptomics

J Gao, K Hu, F Zhang, X Cui - Methods, 2023 - Elsevier
Spatial transcriptomics is a rapidly evolving field that enables researchers to capture
comprehensive molecular profiles while preserving information about the physical locations …

Identification of Key Biomarkers Associated with Ductal Breast Cancer in Spatial Transcriptomics Data

E Xi, L Shang, T Hu, X Zhou, C Yu… - 2023 IEEE International …, 2023 - ieeexplore.ieee.org
Spatial transcriptomics (ST) is a collection of groundbreaking genomic technologies that
allows the measurement of gene expression with spatial localization information on tissues …

[HTML][HTML] 通过图注意力网络识别空间转录组中的空间域

瀚文吴, 洁高 - Sheng Wu Yi Xue Gong Cheng Xue Za Zhi= Journal …, 2024 - ncbi.nlm.nih.gov
由于数据的高维和复杂性, 空间转录组数据的分析一直是一个具有挑战性的问题,
而聚类分析则是空间转录组数据分析的核心问题。 本文提出了一种基于图注意力网络的深度 …

A multi-view comparative learning method for spatial transcriptomics data clustering

W Peng, Z Zhang, W Dai, X Fu, L Liu… - … on Bioinformatics and …, 2023 - ieeexplore.ieee.org
Clustering individual cells or spots based on their gene expression profiles in a spatial
context is a powerful approach to uncovering the underlying biological diversity and …

Spatial domains identification in spatial transcriptomics by domain knowledge-aware and subspace-enhanced graph contrastive learning

Y Gui, C Li, Y Xu - bioRxiv, 2024 - biorxiv.org
Spatial transcriptomics (ST) technologies have emerged as an effective tool to identify the
spatial architecture of the tissue, facilitating a comprehensive understanding of organ …

Dimensionality Reduction and Denoising of Spatial Transcriptomics Data Using Dual-Channel Masked Graph Autoencoder

W Min, D Fang, J Chen, S Zhang - bioRxiv, 2024 - biorxiv.org
Recent advances in spatial transcriptomics (ST) technology allow researchers to
comprehensively measure gene expression patterns at the level of individual cells or even …