| Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus | PNAS | 11.1 | Q1 | 2023 | Peking University Institute of Advanced Agricultural Sciences | Plant | Tomato | Callus | S1000 | 10.1073/pnas.2310163120 |
| Opportunities and Challenges in Advancing Plant Research with Single cell Omics | Genomics, Proteomics & Bioinformatics | 11.5 | Q2 | 2024 | Peking University Institute of Advanced Agricultural Sciences | Plant | Review | Review | S1000 | 10.1093/gpbjnl/qzae026 |
| Harnessing spatial transcriptomics for advancing plant regeneration research | Trends in Plant Science | 17.3 | Q1 | 2024 | Hong Kong Baptist University | Plant | Review | Review | S1000 | 10.1016/j.tplants.2024.02.004 |
| Spatial transcriptomics: Technologies, applications and experimental considerations | Genomics | 4.4 | Q2 | 2023 | Qingdao Central Hospital Affiliated to Qingdao University Medical College | Medicine | Review | Review | S1000 | 10.1016/j.ygeno.2023.110671 |
| Integrative molecular and spatial analysis reveals evolutionary dynamics and tumor-immune interplay of in situ and invasive acral melanoma | Cancer Cell | 50.1 | Q1 | 2024 | Peking University Health Science Center | Medicine | Human | Plantar acral melanoma samples (n=10) | S1000 (cell segmentation) | 10.1016/j.ccell.2024.04.012 |
| Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat | Genome Biology | 10.1 | Q1 | 2025 | Peking University Institute of Advanced Agricultural Sciences | Plant | Wheat | Wheat grain — longitudinal sections at 4, 8 and 12 days of grain filling plus a transverse section at 12 days | S1000 | 10.1186/s13059-025-03569-8 |
| Systematic comparison of sequencing-based spatial transcriptomic methods | nature methods | 36.1 | Q1 | 2024 | Guangzhou Laboratory, Westlake University | Medicine | Mouse | Mouse embryo (eyeball); adult mouse brain (hippocampus) | S1000 | 10.1038/s41592-024-02325-3 |
| Spatial transcriptome analysis reveals de novo regeneration of poplar roots | Horticulture Research | 7.6 | Q1 | 2024 | Peking University Institute of Advanced Agricultural Sciences | Plant | Poplar | Root | S1000 | 10.1093/hr/uhae237 |
| haCCA: Multi-module Integrating of spatial transcriptomes and metabolomes | bioRxiv | / | / | 2024 | Huashan Hospital, Institute of Cancer Metastasis, Fudan University | Medicine | Mouse | Intrahepatic cholangiocarcinoma model | S1000 | https://doi.org/10.1101/2024.08.20.608773 |
| Molecular and spatial signatures of human and rat corpus cavernosum physiopathological processes at single-cell resolutio | Cell Reports | 7.5 | Q1 | 2024 | The Fifth Affiliated Hospital of Sun Yat-sen University | Medicine | Rat | Corpus cavernosum | S1000 | 10.1016/j.celrep.2024.114760 |
| Spatiotemporal transcriptomic analyses reveal molecular gradient patterning during development and the tonotopic organization along cochlear axis | bioRxiv | / | / | 2025 | Chengdu Institute of Biology | Medicine | Mouse | Mouse cochlea at E17.5, P8 and 2 months of age | S1000 | https://doi.org/10.1101/2024.10.30.621022 |
| Tracing the evolutionary and genetic footprints of atmospheric tillandsioids transition from land to air | Nature Communications | 15.7 | Q1 | 2024 | Zhejiang University | Plant | Vriesea (red-bracted bromeliad) | Root | S1000 | 10.1038/s41467-024-53756-7 |
| Single-cell and spatial transcriptomics uncover the role of B chromosomes in driving plant invasiveness | Genome Biology | 10.1 | Q1 | 2026 | Shandong University | Plant | Reed | Shoot | S3000 | 10.1186/s13059-026-04079-x |
| Spatiotemporal dynamics of early oogenesis in pigs | Genome Biology | 10.1 | Q1 | 2025 | Qingdao Agricultural University | Animal | Pig | Porcine embryonic ovary at E45, E55, E65 and E75 | S1000 | 10.1186/s13059-024-03464-8 |
| Cross-species single-nucleus analysis reveals the potential role of whole-genome duplication in the evolution of maize flower development | BMC Genomics | 3.5 | Q2 | 2025 | Peking University Institute of Advanced Agricultural Sciences | Plant | Maize | Female + male inflorescence | S1000 | 10.1186/s12864-024-11186-1 |
| Obstacles in sugar transportation lead to blank nut formation in hazel (Corylus heterophylla) | Industrial Crops & Products | 6.2 | Q1 | 2025 | Jilin Normal University | Plant | Hazel | Ovule | S1000 | https://doi.org/10.1016/j.indcrop.2024.120365 |
| Spatial and single-cell transcriptomics reveal cellular heterogeneity and a novel cancer-promoting Treg cell subset in human clear-cell renal cell carcinoma | Journal for ImmunoTherapy of Cancer | 10.3 | Q1 | 2025 | Fourth Military Medical University | Medicine | Human | Surgically resected tumor tissue from clear cell renal cell carcinoma patients (n=4) | DG1000、S1000 | 10.1136/jitc-2024-010183 |
| Next-generation spatial transcriptomics: unleashing the power to gear up translational oncology | MedComm | 10.7 | Q3 | 2024 | Hangzhou Institute of Medicine, Chinese Academy of Sciences | Medicine | Review | Review | S1000 | 10.1002/mco2.765 |
| Single-cell transcriptomics reveals the heterogeneity and function of mast cells in human ccRCC | Frontiers in immunology | 5.7 | Q2 | 2025 | Fourth Military Medical University | Medicine | Human | Surgically resected tumor tissue from clear cell renal cell carcinoma patients | DG1000、S1000 | 10.3389/fimmu.2024.1494025 |
| Improving Spatial Transcriptomics with Membrane-Based Boundary Definition and Enhanced Single-Cell Resolution | Small Methods | 10.7 | Q2 | 2025 | Guangdong Provincial People's Hospital | Medicine | Cell segmentation algorithm | Cell-membrane-based segmentation algorithm — mouse and salamander: liver, brain, intestine | S1000 | 10.1002/smtd.202401056 |
| Single-Cell and Spatial Transcriptomics Reveals a Stereoscopic Response of Rice Leaf Cells to Mag aportheoryzae Infection | Advanced Science | 14.3 | Q1 | 2025 | China Agricultural University | Plant | Rice | Rice leaves 0, 6, 12 and 24 hours after Magnaporthe oryzae infection | S1000 | 10.1002/advs.202416846 |
| Entering the era of spatial transcriptomics: opportunities and challenges for pathology | Diagnostic Histopathology | / | / | 2025 | Oxford University Hospitals | Medicine | Review | Review | S1000 | 10.1016/j.mpdhp.2025.04.001 |
| Integrated multi-omics analyses provide new insights into genomic variation landscape and regulatory network candidate genes associated with walnut endocarp | the plant journal | 6.2 | Q1 | 2025 | Northwest University | Plant | Walnut | Walnut shell 44 days after flowering (longitudinal section) | S1000 | 10.1111/tpj.70113 |
| A distinct subgroup with Schwann-like differentiation presents immune resistance and poor prognosis in plantar melanoma | Theranostics | 12.4 | Q1 | 2025 | Peking University First Hospital | Medicine | Human | Plantar melanoma tissue | S1000 | 10.7150/thno.99526 |
| Single-cell and spatial transcriptomics reveal the pathogenesis of chronic granulomatous disease in a natural model | cell reports | 7.5 | Q1 | 2025 | School of Basic Medical Sciences, Tianjin Medical University | Medicine | Mouse | Granuloma structures of chronic granulomatous disease — mouse lung tissue | S1000 | 10.1016/j.celrep.2025.115612 |
| Dissection of the global responses of mandarin fish pyloric cecum to an acute ranavirus (MRV) infection reveals the formation of serositis and then ascites | Journal of Virology | 4 | Q2 | 2025 | State Key Laboratory for Aquatic Animal Disease Control and Healthy Aquaculture, School of Life Sciences, Sun Yat-sen University | Animal | Mandarin fish | Pyloric caeca of infected mandarin fish | S1000 | 10.1128/jvi.02308-24 |
| CCR2+ monocytes promote memory CD8+ T-cell differentiation via membrane-bound TGF-β | Cellular & Molecular Immunology | 21.8 | Q1 | 2025 | Xi'an Jiaotong University | Medicine | Mouse | WT mouse spleen on days 0 and 5 after adoptive T-cell transfer and Listeria infection | S1000、10X | 10.1038/s41423-025-01299-2 |
| Spatiotemporal Transcriptomic Atlas Reveals the Regulatory Mechanisms Underlying Early Inflorescence Development and Sex Differentiation in Spinach | Advanced Science | 14.1 | Q1 | 2025 | Henan Normal University, Henan Agricultural University | Plant | Spinach | Shoot apices of female/male plants at 4 developmental stages | S1000 | 10.1002/advs.202507818 |
| Cancer-Associated Fibroblasts Establish Spatially Distinct Prognostic Niches in Subcutaneous Colorectal Cancer Mouse Model | Cancers | 4.4 | Q3 | 2025 | School of Medicine, Xi'an Jiaotong University | Medicine | Mouse | Subcutaneous colon tumor in mice (n=1) | S1000 | 10.3390/cancers17142402 |
| New insights into liver injury and regeneration from single-cell transcriptomics | eGastroenterology | / | / | 2025 | University of Texas Health Science Center at Houston | Medicine | Review | Review | S1000 | |
| The Liquid Crystal Monomer 3cH2B Affects the Visual System via Neural-Cell-Specific Retinoic Acid Disruption in the Optic Tectum | Environmental Science & Technology | 11.3 | Q1 | 2025 | College of Plant Protection, Shenyang Agricultural University; Institute of Quality Standard and Testing Technology for Agro-Products, CAAS; Freshwater Fisheries Research Center, CAFS | Animal | Zebrafish | Adult zebrafish exposed to environmental concentrations for 40 days as the core model, with systematic collection of live specimens, eyes, brain and other samples | DG1000、S1000 | |
| Dissecting cross-lineage tumourigenesis under p53 inactivation through single-cell multi-omics and spatial transcriptomics | Clinical and Translational Medicine | 6.8 | Q1 | 2025 | Bone Marrow Transplantation Center and Stem Cell and Regenerative Medicine Center, The First Affiliated Hospital, Zhejiang University School of Medicine, et al. | Medicine | Mouse | Mouse thymus | S1000 | 10.1002/ctm2.70461 |
| Single-nucleus transcriptomics reveal the morphogenesis and artemisinin biosynthesis in Artemisia annua glandular trichomes | Nature Communications | 15.7 | Q1 | 2025 | Shanghai Key Laboratory for Pharmaceutical Metabolite Research, School of Pharmacy, Naval Medical University | Plant | Artemisia annua | Four leaves: 4 developmental stages (S1–S4) | S3000, 10X single-nucleus transcriptome | 10.1038/s41467-025-63770-y |
| Advances in plant spatial multi-omics data analysis | Trends in Plant Science | 20.8 | Q1 | 2025 | Zhejiang University, University of Georgia, University of Michigan, BGI Life Science Institute | Plant | Review | Review | BMKMANU | 10.1016/j.tplants.2025.10.005 |
| Cellular and molecular mechanisms of seahorse male pregnancy | nature ecology & evolution | 14.5 | Q1 | 2025 | South China Sea Institute of Oceanology; University of Chinese Academy of Sciences; Shanghai Institute of Biochemistry and Cell Biology; ShanghaiTech University; Southern Medical University; Kunming Institute of Zoology; Harvard University | Animal | Seahorse / Pipefish | Single-cell transcriptome; single-cell ATAC-seq; spatial transcriptome-seq: brood-pouch sample from one seahorse in early pregnancy (stage V) | S1000 | 10.1038/s41559-025-02883-5 |
| Spatial transcriptomics provide insights into the secondary lateral rooting difficulties of tetraploid forsythia cuttings | Industrial Crops & Products | 6.2 | Q1 | 2025 | Inner Mongolia Normal University, Henan Agricultural University | Plant | Forsythia | Cutting stems of annual diploid and tetraploid forsythia | S3000 | 10.1016/j.indcrop.2025.122182 |
| Spatially resolved single-cell transcriptome analysis of murine Salmonella infection reveals the role of distal colonocytes in the inflammatory response | Gut Microbes | 11 | Q1 | 2025 | The First Affiliated Hospital of Xi'an Jiaotong University Health Science Center | Medicine | Mouse | Focusing on 5 key time points in the mouse colon after Salmonella Typhimurium (S. Tm) infection: Days 0, 1, 3, 5, and 7 | S1000 | 10.1080/19490976.2025.2579909 |
| Electron Microscopy and Multi-Omics Reveal Mitochondrial Dysfunction and Structural Remodeling in the Hearts of Elderly Mice | Aging Cell | 7.1 | Q1 | 2025 | University of Campania "Luigi Vanvitelli"; IRCCS INRCA National Institute of Health and Science on Aging; Marche Polytechnic University | Medicine | Mouse | Heart | S1000 | 10.1111/acel.70286 |
| Acquired resistance to immunotherapy by physical barriers with cancer cell-expressing collagens in non-small cell lung cancer | PNAS | 11.1 | Q1 | 2025 | West China Hospital of Sichuan University; State Key Laboratory of Biotherapy, Sichuan University; Chengdu University of Traditional Chinese Medicine; Macau University of Science and Technology, et al. | Medicine | Mouse | Lung cancer | S1000 | 10.1073/pnas.2500019122 |
| A Single-Cell-Resolution Spatial Transcriptomic Atlas Decodes Wheat Spike Development and Yield Potential | Molecular Plant | 24.1 | Q1 | 2025 | College of Life Sciences, Shandong Agricultural University; Peking University Institute of Advanced Agricultural Sciences | Plant | Wheat | Wheat spike — key early stages of spike architecture establishment | S3000 | 10.1016/j.molp.2025.12.020 |
| A single-nucleus and spatial transcriptomic atlas of the shoot apex reveals insights into the vegetative-to-reproductive transition in loquat | Journal of Integrative Agriculture | 4.4 | Q1 | 2025 | South China Agricultural University; Fruit Research Institute, Fujian Academy of Agricultural Sciences | Plant | Loquat | Shoot apex | S3000 | 10.1016/j.jia.2025.12.031 |
| Single-Cell Transcriptomic Atlases of Camels and Cattle Unravel Molecular Evolution of Digestive and Metabolic Systems | Advanced Science | 14.1 | Q1 | 2026 | College of Animal Science and Technology, Northwest A&F University | Animal | Camel | scRNA-seq (C4): liver, kidney, complex stomach, testis; snRNA-seq (C4): hump fat, tongue, frontal lobe, cerebellum; spatial transcriptome: kidney sample from one adult female Bactrian camel | S1000 | 10.1002/advs.202519346 |
| Integrated Single-Cell and Spatial Transcriptomics Reveal Cell-Type-Specific Immune Regulatory Networks in Maize Responding to Southern Corn Rust | Advanced Science | 14.1 | Q1 | 2026 | Cereal Crops Institute of Henan Academy of Agricultural Sciences; College of Plant Protection, Henan Agricultural University; Institute of Crop Sciences / State Key Laboratory of Crop Gene Resources and Breeding, Chinese Academy of Agricultural Sciences; Henan Agricultural University | Plant | Maize | Maize leaf | S1000 | 10.1002/advs.202512295 |
| The SWI/SNF chromatin-remodeling subunit DPF2 regulates macrophage inflammation in intestinal injury via CACNA1D-mediated MAPK pathway | PNAS | 9.4 | Q1 | 2025 | Fudan University, Soochow University | Medicine | Mouse | scRNA-seq; spatial transcriptome: mouse intestinal tissue after irradiation | S3000 | 10.1073/pnas.2518762122 |
| Chromatin remodeling in pericentral hepatocytes modulates MASH through CYP450 activity | Journal of Hepatology | 33 | Q1 | 2026 | Soochow University, Fudan University, Southern University of Science and Technology | Medicine | Mouse | scRNA-seq and snRNA-seq; spatial transcriptome: WT and Dpf2^ΔLgr5 mice fed an FPC diet for 4 weeks. | S3000 | 10.1016/j.jhep.2026.03.035 |
| Laminar patterning transcription factors orchestrate spatial metabolite partitioning in Capsicum fruit | Nature plants | 13.6 | Q1 | 2026 | Peking University Institute of Advanced Agricultural Sciences | Plant | Pepper (Capsicum) | snRNA-seq: pepper hypocotyl, root, stem, leaf and fruits at different developmental stages; | S1000/S3000+DG1000+ISSeq Kit v.1.0 | 10.1038/s41477-026-02293-w |
| Single-cell multiomic and spatial landscape of the primate pineal gland reveals circadian and melatonin regulatory architecture | PNAS | 9.4 | Q1 | 2026 | Shanghai Jiao Tong University School of Medicine | Animal | Cynomolgus monkey | Cynomolgus monkey pineal gland — 21 healthy cynomolgus monkeys (9 females, 12 males, 4–5 years old), used to resolve the pineal cell atlas and regulatory landscape | 10X single-nucleus RNA-seq, 10X single-cell ATAC, BMKMANU S3000 | 10.1073/pnas.2524839123 |
| Super-resolution multimodal spatial transcriptomics reveals an ovoid stem-cell niche structuring de novo shoot regeneration | Molecular Plant | 24.1 | Q1 | 2026 | Peking University Institute of Advanced Agricultural Sciences | Plant | Tomato | Cotyledons of 6-day-old seedlings | S1000/S3000+DG1000+ISSeq+Stereo‑seq+10× Xenium | 10.1016/j.molp.2026.05.008 |
| Cross-species comparison of amniote single-cell transcriptomes reveals evolutionary conservation and divergence in the chicken immune system | Nature Communications | 15.7 | Q1 | 2026 | Northwest A&F University | Animal | Chicken | Bursa of Fabricius and tonsil | S3000 | 10.1038/s41467-026-72642-y |
| Spatiotemporal transcriptome atlas reveals the dynamic cellular and molecular characteristics of ovule development in gymnosperms | PNAS | 9.4 | Q1 | 2026 | Fudan University, Shanghai | Plant | Ovules of gymnosperms (Ginkgo, Gnetum, Chinese pine, Cycas panzhihuaensis) | Spatial transcriptome | S1000 | 10.1073/pnas.2524858123 |
| Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution | nature methods | 36.1 | Q1 | 2026 | Westlake University | Medicine | Mouse: small intestine, brain | Spatial transcriptome | S3000 | 10.1038/s41592-026-03151-5 |
| Single-nucleus multi-omics dissection of dysregulated trophoblast development and disrupted immune microenvironment in complete hydatidiform moles | Science China. Life sciences | 9.6 | Q1 | 2026 | Center for Reproductive Medicine, Shandong University | Medicine | Human grape embryo | Spatial transcriptome | S1000 | 10.1007/s11427-025-3191-5 |
| Interrogation of the cellular hierarchies reveals neoplastic evolution and therapeutic vulnerability in craniopharyngioma | Neuro-Oncology | 13.1 | Q1 | 2026 | Sichuan University, West China Hospital | Medicine | Human craniopharyngioma (CP) tumor tissue | Spatial transcriptome | S1000 | 10.1093/neuonc/noaf249 |
| Mitochondrial-impaired ductal epithelium fuels TLS formation in Sjögren's disease | Annals of the rheumatic diseases | 24 | Q1 | 2026 | Ruijin Hospital, Shanghai Jiao Tong University | Medicine | Human salivary gland | Spatial transcriptome | S1000 | 10.1016/j.ard.2026.05.014 |
