arXiv:2608. 14330v1 Announce Type: new Abstract: Spatial transcriptomics (ST) enables genome-wide gene expression profiling while preserving tissue architecture, but its cost and limited scalability remain major bottlenecks.
By Ruyter Swann, Dorent Reuben, Racoceanu Daniel
SpaFactor is a lightweight framework that predicts spatial gene expression from hematoxylin and eosin images by fusing central spot visuals with multiscale neighborhood context. It uses a residual MLP to map tissue microenvironment to low‑dimensional latent gene programs, which are decoded into coordinated multi‑gene predictions. Across five public cohorts, SpaFactor outperforms existing methods, especially for spatially variable genes, and better recovers biologically organized spatial patterns.
By Shiting Ruan, Xitong Ling, Qiming He, Ziyou Yan, Huaitian Yuan, Tian Guan, Ying Xiao, Xu Guan, Yonghong He
arXiv:2606. 08712v1 Announce Type: cross Abstract: Purpose: Spatial transcriptomics (ST) enables gene expression measurements within the tissue context.
By Hongyi Yu, Yaoyu Fang, Jiahe Qian, Xinkun Wang, Lee A. Cooper, Bo Zhou
arXiv:2507. 04704v3 Announce Type: replace-cross Abstract: Understanding how cellular morphology, gene expression, and spatial context jointly shape tissue function is a central challenge in biology.
By Zhenglun Kong, Mufan Qiu, John Boesen, Xiang Lin, Sukwon Yun, Tianlong Chen, Manolis Kellis, Marinka Zitnik
arXiv:2606. 03644v1 Announce Type: new Abstract: Comprehensive molecular profiling is essential for modern precision oncology but remains hindered by prohibitive costs, specimen exhaustion, and protracted turnaround times.
By Fengtao Zhou, Yingxue Xu, Zhengyu Zhang, Yihui Wang, Zhengrui Guo, Ling Liang, Jiabo Ma, Cheng Jin, Ziyi Liu, Huajun Zhou, Hongyi Wang, Du Cai, Chenglong Zhao, Xi Wang, Can Yang, Yu Wang, Wenbin Li, Feng Gao, Zhe Wang, Zhenhui Li, Xiuming Zhang, Li Liang, Hao Chen
arXiv:2607. 09166v1 Announce Type: new Abstract: Spatial transcriptomics enables profiling of spatial gene expression but is limited by high cost and low throughput, motivating prediction from H&E histopathology images.
By Keunho Byeon, Sunhong Park, Jeewoo Lim, Jin Tae Kwak