Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns by Nghia Millard, Jonathan H. Chen, Mukta G. Palshikar, Karin Pelka, Maxwell Spurrell, Colles Price, Jiang He, Nir Hacohen, Soumya Raychaudhuri, Ilya Korsunsky

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Comprehensive single-cell pan-cancer atlas unveils IFI30+ macrophages as key modulators of intra-tumoral immune dynamics by Lihe Jiang, Lihe Jiang, Lihe Jiang, Peili Wang, Peili Wang, Yixuan Hou, Jingying Chen, Hua Li, Hua Li

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Advanced omics approaches in liver transplant settings: current applications and future prospectives by Huijuan Wang, Huijuan Wang, Huijuan Wang, Yifeng Zhou, Lu Yu, Lu Yu, Lu Yu, Zhengtao Liu, Zhengtao Liu, Zhengtao Liu, Zhengtao Liu, Shusen Zheng, Shusen Zheng, Shusen Zheng, Shusen Zheng, Shusen Zheng

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STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition by Chuhanwen Sun, Yi Zhang

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EMGP-Net: A Hybrid Deep Learning Architecture for Breast Cancer Gene Expression Prediction by Oumeima Thâalbi, Moulay A. Akhloufi

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Spatial relationships and interactions of immune cell niches are linked to the pathologic response of muscle-invasive bladder cancer to neoadjuvant therapy by Wasilijiang Wahafu, Quan Zhou, Xihua Yang, Yongming Yang, Yuanyuan Zhao, Zhu Wang, Xiangpeng Kang, Xiongjun Ye, Nianzeng Xing

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Spatial transcriptome analysis of myenteric plexus and intestinal epithelium of colon in patients with Parkinson’s disease by Chaewon Shin, Karoliina Eliisa Ruhno, Jung Hwan Shin, Sanha Hwang, Jasper Roldan Go, Minji Kang, Hyun Je Kim, Ji Hwan Moon, Han-Joon Kim

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stGRL: spatial domain identification, denoising, and imputation algorithm for spatial transcriptome data based on multi-task graph contrastive representation learning by Xin Lu, Murong Zhou, Bo Gao, Fang Wang, Shuilin Jin, Qiaoming Liu, Guohua Wang

Subjects: “…Spatial transcriptomics…”
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mNSF: multi-sample non-negative spatial factorization by Yi Wang, Kyla Woyshner, Chaichontat Sriworarat, Genevieve Stein-O’Brien, Loyal A. Goff, Kasper D. Hansen

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CRP deposition in human abdominal aortic aneurysm is associated with transcriptome alterations toward aneurysmal pathogenesis: insights from in situ spatial whole transcriptomic an... by Eun Na Kim, Hee Young Seok, Joon Seo Lim, Jiwon Koh, Jeong Mo Bae, Chong Jai Kim, Ga-Hyeon Ryu, You Jung Ok, Jae-Sung Choi, Chung-Hyun Cho, Se Jin Oh

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Ginsenoside Rb1 and berberine synergistically protect against type 2 diabetes mellitus via GDF15/HAMP pathway throughout the liver lobules: Insights from spatial transcriptomics an... by Rongfang Guo, Shuying Zhang, Anyao Li, Ping Zhang, Xin Peng, Xiaoyan Lu, Xiaohui Fan

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Spatially resolved transcriptomic signatures of hippocampal subregions and Arc-expressing ensembles in active place avoidance memory by Isaac Vingan, Shwetha Phatarpekar, Victoria Sook Keng Tung, Alejandro Iván Hernández, Alejandro Iván Hernández, Alejandro Iván Hernández, Oleg V. Evgrafov, Oleg V. Evgrafov, Oleg V. Evgrafov, Oleg V. Evgrafov, Juan Marcos Alarcon, Juan Marcos Alarcon, Juan Marcos Alarcon

Subjects: “…spatial transcriptomics…”
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Spatial transcriptomics and scRNA-seq: decoding tumor complexity and constructing prognostic models in colorectal cancer by Wei Song, Yatao Wang, Min Zhou, Fengqin Guo, Yanliang Liu

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Current status, hotspots and frontiers of ion channel-related research in glioblastoma: a bibliometric analysis from 2005 to 2024 by Zefeng He, Jing Liu, Qianxu Jin, Shangkun Ren, Liang Liu, Yingzi Liu

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A Bayesian hierarchical model with spatially varying dispersion for reference-free cell type deconvolution in spatial transcriptomics by Xuan Li, Yincai Tang, Jingsi Ming, Xingjie Shi

Subjects: “…Spatial transcriptomics…”
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Spatially resolved gene expression profiles of fibrosing interstitial lung diseases by Seung J. Kim, Matthew J. Cecchini, Elissa Woo, Nathashi Jayawardena, Daniel T. Passos, Frederick A. Dick, Marco Mura

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Extracellular vesicle-derived miRNA-mediated cell–cell communication inference for single-cell transcriptomic data with miRTalk by Xin Shao, Lingqi Yu, Chengyu Li, Jingyang Qian, Xinyu Yang, Haihong Yang, Jie Liao, Xueru Fan, Xiao Xu, Xiaohui Fan

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Telmisartan modulates exercise responses in peripheral artery disease: Analyses of skeletal muscle from the TELEX Trial by Kate Kosmac, PhD, Jai K. Joshi, BS, Mary M. McDermott, MD, Jada C. Stewart, BS, Dongxue Zhang, MS, Shujun Xu, MS, Karen J. Ho, MD, Robert Sufit, MD, Luigi Ferrucci, MD, Charlotte A. Peterson, PhD, Ahmed Ismaeel, PhD

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Multiscale Dissection of Spatial Heterogeneity by Integrating Multi‐Slice Spatial and Single‐Cell Transcriptomics by Yuqi Chen, Caiwei Zhen, Yuanyuan Mo, Juan Liu, Lihua Zhang

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Novel insights into kidney disease: the scRNA-seq and spatial transcriptomics approaches: a literature review by Mingming Ma, Qiao Luo, Liangmei Chen, Fanna Liu, Lianghong Yin, Baozhang Guan

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