A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

NIH Image to ImageJ: 25 years of image analysis

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PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer

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Adverse Renal Effects of Immune Checkpoint Inhibitors: A Narrative Review

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Chromatin modifications and their function

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Combined Nivolumab and Ipilimumab or Monotherapy in Untreated Melanoma

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Cancer immunotherapy using checkpoint blockade

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Myeloid-derived-suppressor cells as regulators of the immune system

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PD-1 blockade induces responses by inhibiting adaptive immune resistance

Tumeh, P. C., Harview, C. L., Yearley, J. H., Shintaku, I. P., Taylor, E. J. M., Robert, L., Chmielowski, B., Spasic, M., Henry, G., Ciobanu, V., et al. (2014) · Nature · doi:10.1038/nature13954 · Cited by 6,609

Elements of cancer immunity and the cancer–immune set point

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Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients

Herbst, R. S., Soria, J.-C., Kowanetz, M., Fine, G. D., Hamid, O., Gordon, M. S., Sosman, J. A., McDermott, D. F., Powderly, J. D., Gettinger, S. N., et al. (2014) · Nature · doi:10.1038/nature14011 · Cited by 5,231

Position-informed contrastive learning for spatially resolved omics deciphers hierarchical tissue structure at both cellular and niche levelsPreprint

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Editorial: Defining the Spatial Organization of Immune Responses to Cancer and Viruses In Situ

Phillips, D. J., Rodig, S. J., & Jiang, S. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.847582 · Cited by 3

Four tumor micro-environmental niches explain a continuum of inter-patient variation in the macroscopic cellular composition of breast tumorsPreprint

Marrahi, A. E., Lipreri, F., Alber, D. M., & Hausser, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.04.482793 · Cited by 3

A Versatile Deep Graph Contrastive Learning Framework for Single-cell Proteomics EmbeddingPreprint

Li, W., Yang, F., Wang, F., Rong, Y., Wu, B., Zhang, H., & Yao, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.14.520366 · Cited by 3

Pseudo-spectral angle mapping for automated pixel-level analysis of highly multiplexed tissue image dataPreprint

Durkee, M. S., Ai, J., Casella, G., Cao, T., Chang, A., Halper-Stromberg, A., Jabrì, B., Clark, M. R., & Giger, M. L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.09.574920 · Cited by 3

Spatial Single-Cell Transcriptomic Analysis in Breast Cancer Reveals Potential Biomarkers for PD-1 Blockade TherapyPreprint

Wang, N., Song, Y., Hong, W., Mo, H., Song, Z., Dai, W., Wang, L., Zhang, H., Zhang, Y., Zhang, Q., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4376986/v1 · Cited by 3

A spatial atlas of human gastro-intestinal acute GVHD reveals epithelial and immune dynamics underlying disease pathophysiologyPreprint

Azulay, N., Milo, I., Bussi, Y., Ben-Uri, R., Haran, T. K., Eldar, M., Elhanani, O., Harnik, Y., Yakubovsky, O., Nachmany, I., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.02.610085 · Cited by 3

Kontextual: Reframing analysis of spatial omics data reveals consistent cell relationships across imagesPreprint

Ameen, F., Robertson, N., Lin, D. M., Ghazanfar, S., & Patrick, E. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.03.611109 · Cited by 3

Decoding Spatial Tissue Architecture: A Scalable Bayesian Topic Model for Multiplexed Imaging AnalysisPreprint

Peng, X., Smithy, J. W., Yosofvand, M., Kostrzewa, C. E., Bleile, M., Ehrich, F. D., Lee, J., Postow, M. A., Callahan, M. K., Panageas, K. S., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.08.617293 · Cited by 3

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomicsPreprint

Avraham‐Davidi, I., Mages, S., Klughammer, J., Moriel, N., Imada, S., Hofree, M., Murray, E. M., Chen, J. H., Pelka, K., Mehta, A., et al. (2025) · eLife · doi:10.7554/elife.104815 · Cited by 5

Spatiotemporal dynamics of tumor microenvironment remodelingPreprint

Lisek, K., Pentimalli, T. M., Theurillat, I., Beier, S., León-Periñán, D., Boltengagen, A., Antonatou, A., Dubnov, S., Muller, M., Hubl, F., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.15.662972 · Cited by 3

AMICI: Attention Mechanism Interpretation of Cell-cell InteractionsPreprint

Hong, J., Desai, K., Nguyen, T. D., Nazaret, A., Levy, N., Ergen, C., Plitas, G., & Azizi, E. (2025) · bioRxiv · doi:10.1101/2025.09.22.677860 · Cited by 4

Stem cell-like T cell depletion in the recurrent head and neck cancer immune microenvironment

Chen, L., Lee, N. Y., Sarkar, R. R., Katabi, N., Li, Y., Morris, L. G. T., Wong, R. J., Sherman, E. J., Reis-Filho, J. S., Hollmann, T. J., et al. (2023) · OncoImmunology · doi:10.1080/2162402x.2023.2230666 · Cited by 2

Quantitative analysis of T cell subsets in a population of Black women with invasive breast cancer

Omilian, A. R., Mendicino, L., George, A., Darabnoushtehrani, T., Ondracek, R. P., Bshara, W., Hong, C., Qin, B., Bandera, E. V., Khoury, T., et al. (2025) · npj Breast Cancer · doi:10.1038/s41523-025-00780-5 · Cited by 2

DDX27 in cancer: molecular mechanisms, clinical implications, and therapeutic potential

Yang, L., Mok, S. W.-F., Li, H., Wong, I. N., & Yang, L. J. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-025-07004-1 · Cited by 2

Spatial Distribution of Senescent Cells and Their Proximity to Immune Subsets in the Human Endometrium During the Implantation Window

Parvanov, D. A., Ganeva, R., Ruseva, M., Handzhiyska, M., Safir, J., Jelezarsky, L., Vidolova, N., Metodiev, D., Stamenov, G., & Hadjidekova, S. P. (2025) · Diagnostics · doi:10.3390/diagnostics15212679 · Cited by 2

Growth differentiation factor 11 modulates metabolism, mitigating the pro-tumoral behavior provided by M2-like macrophages in hepatocellular carcinoma-derived cells

Escobedo‐Calvario, A., Chávez-Rodríguez, L., Souza-Arroyo, V., Bucio, L., Miranda-Labra, R. U., Massó, F., Páez, A., Hernández‐Pando, R., Marquardt, J. U., Gutiérrez‐Ruíz, M. C., et al. (2025) · World Journal of Gastroenterology · doi:10.3748/wjg.v31.i40.111307 · Cited by 2

Connectogenomics: edges-first spatial biology

Yasser, R., Yu, M., Qian, N., Chang, H., & Weinstein, J. A. (2025) · Trends in biotechnology · doi:10.1016/j.tibtech.2025.10.012 · Cited by 2

A transformer-based pathomics model using endoscopic biopsy WSIs for predicting pathological complete response to preoperative immunotherapy in colorectal cancer

Xiao, C., Zhang, W., Qiu, M., He, D., Jiang, D., Wang, Z., Shen, Y., & Chen, H. (2025) · European Journal of Surgical Oncology · doi:10.1016/j.ejso.2025.111182 · Cited by 2

Dendritic Cells at the Center of Reactive Tumor Immunity

Pass, L. F., & Krummel, M. F. (2025) · Immunological Reviews · doi:10.1111/imr.70072 · Cited by 2

Immune and non-immune cell fencing of tumor cells is a widespread and functionally relevant spatial pattern in solid cancers

Giuliani, G., Chavan, D., Gaddam, R., Stewart, W. C., Li, Z., Jayaprakash, C., & Das, J. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.11.062 · Cited by 2

Detecting clinically relevant topological structures in multiplexed spatial proteomics using TopKAT

Samorodnitsky, S., Campbell, K. M., Little, A., Ling, W., Zhao, N., Chen, Y., & Wu, M. C. (2026) · Patterns · doi:10.1016/j.patter.2025.101456 · Cited by 2

Informed spatially aware patterns for multiplexed immunofluorescence data

Bhadury, S., Peruzzi, M., Acharyya, S., Eliason, J., di Magliano, M. P., Frankel, T. L., Ravikumar, V., Krishnan, S., & Rao, A. (2026) · Scientific Reports · doi:10.1038/s41598-026-35341-8 · Cited by 2

Meningioma microenvironment harbors a rich immune landscape that evolves with biological state

Guo, X., Moynihan, Z. A., Driver, J., Patel, R. V., Bhave, V. M., Maury, E. A., Knelson, E. H., Guo, H., Lin, J., Coy, S., et al. (2026) · Neuro-Oncology · doi:10.1093/neuonc/noag022 · Cited by 3

Neoadjuvant Endocrine Treatment plus Mammaglobin-A DNA Vaccine Induces Antitumor Immune Responses in the Primary Tumor and Peripheral Blood of Patients with Breast Cancer: Insights from a Phase Ib Clinical Trial

Mishra, R., Ademuyiwa, F. O., Yang, Y., Herndon, J. M., Li, L., Street, C., Myers, N. B., Chen, I., Zhang, X., Hagemann, I. S., et al. (2026) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-25-0666 · Cited by 2

Omics-Based Functional Fingerprinting of Nanoparticles in Cancer: Toward Predictive Nanomedicine

Marchiò, S. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27041960 · Cited by 2

Spatial AI in cancer: mapping immune evasion topology through multi-modal omics and deep learning

Lang, L., Cui, Y., Wang, H., & Xiao, Y. (2026) · Frontiers in Oncology · doi:10.3389/fonc.2026.1762907 · Cited by 3

Identification of cycling regulatory T cell precursors as conductors of immune escape during breast carcinoma progression

Bui, T. M., Rojas-Jiménez, E. A., Li, Z., Foidart, P., Puleo, J. I., Yan, P., Jhaveri, A., Yang, L., Nishida, J., Seehawer, M., et al. (2026) · Cancer Cell · doi:10.1016/j.ccell.2026.03.015 · Cited by 3

Insights From Spatiality: Accelerating Pharmaceutical Research Using Mass Spectrometry Imaging

Zou, Y., Yan, Z., Tang, W., & Li, B. (2026) · Medicinal Research Reviews · doi:10.1002/med.70061 · Cited by 2

Proof-of-principle 4-marker spatial profiling reveals distinct, location-independent immune clusters in biliary tract cancers

Rossari, F., Sala, M., Rimini, M., Camera, S., Persano, M., Tonon, G., Bonini, C., Cangi, M. G., Pecciarini, L., Doglioni, C., et al. (2026) · Pathology & Oncology Research · doi:10.3389/pore.2026.1612389 · Cited by 3

Artificial Intelligence in Oncology: Clinical Applications, Challenges, and Opportunities

Parkinson, G., Patel, R. D., Bergstrom, C. P., Vadasz, B., Amgad, M., Cooper, L. A. D., Sparano, J. A., & Lu, J. (2026) · American Society of Clinical Oncology Educational Book · doi:10.1200/edbk-26-520716 · Cited by 4

Targeting macrophage-driven NK cell immunosuppression to improve cancer immunotherapy

Redavid, A. R., Cifaldi, L., Bei, R., de Billy, E., & Fruci, D. (2026) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2026-014840 · Cited by 2

3D multi-omics tumour atlases: from technology to biology and clinical translation

Liu, M., Villazon, J. I., Forjaz, A., Tian, X., Fan, R., Wang, S., Shi, L., Wirtz, D., & Kiemen, A. L. (2026) · Nature reviews. Cancer · doi:10.1038/s41568-026-00940-0 · Cited by 3

Epitranscriptomic circuits wiring the tumor microenvironment: A pharmacodynamic framework for clinical translation

Izadpanah, R., Izadpanah, A., & Alt, E. U. (2026) · Pharmacological Research · doi:10.1016/j.phrs.2026.108304 · Cited by 2

Decoding the tumor-aging axis: from bench to clinical

Wang, Y., Lv, G., Gao, X., Zheng, J. H., Huang, J., & Wang, Z. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1823423 · Cited by 2

CAR-T and TIL therapies in solid tumors: barriers, clinical lessons, and convergent solutions

Bach, D., Hoang, V. H., Pham, T. V., Huong, & Nguyen, D. D. (2026) · Cancer Cell International · doi:10.1186/s12935-026-04425-w · Cited by 2

Single-nucleus multimodal spatial transcriptomics reveals spatial colocalization of neoantigen-expressing tumor cells and cognate T cells

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P2X7 blockade inhibits the growth of breast cancer in 4T1 breast cancer-bearing mice by NLRP3/caspase 1 pathway

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Autoimmunity in motion: Mechanisms of immune regulation and destruction revealed by in vivo imaging*

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Deep learning to detect lymphocytes with high phenotypic resolution in highly multiplexed fluorescence microscopy images of triple-negative breast cancer biopsies

Durkee, M. S., Abraham, R., Clark, M. R., & Giger, M. L. (2022) · Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues · doi:10.1117/12.2610260 · Cited by 2

Pediatric Sarcomas: The Next Generation of Molecular Studies

Giannikopoulos, P., & Parham, D. M. (2022) · Cancers · doi:10.3390/cancers14102515 · Cited by 4

eaQTLdb : An atlas of enhancer activity quantitative trait loci across cancer types

Yuan, J., Tong, Y., Liu, X., Li, M. J., Zhang, Q., & Yang, Y. (2023) · International Journal of Cancer · doi:10.1002/ijc.34481 · Cited by 2

Beyond the Lab and Into the Hospital: An Outlook on the Clinical Utility of Spatial Omics Technologies

Pucciarelli, D. M., Lu, B. Y., Zlobec, I., & DiStasio, M. (2023) · GEN Biotechnology · doi:10.1089/genbio.2023.0030 · Cited by 2

Modulatory Effects of XIAOPI Formula on CXCL1 and Selected Outcomes in Triple-Negative Breast Cancer: A Randomized Controlled Clinical Trial

Guo, L., Hong, S., Wang, X., Wang, S., Wang, N., Wei, X., Situ, H., & Wang, Z. (2024) · Breast Cancer Targets and Therapy · doi:10.2147/bctt.s462296 · Cited by 2

Dissection of the cell communication interactions in lung adenocarcinoma identified a prognostic model with immunotherapy efficacy assessment and a potential therapeutic candidate gene ITGB1

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Breast Cancer Heterogeneity and Its Implication in Precision Therapy

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Isolation of a tumor neoantigen specific CD8+ TCR from a skin biopsy of a vaccination site

Roberti, M. P., Charoentong, P., Lyu, Y., Meyer, M., Eichmüller, S. B., Schmidt, P., Momburg, F., Cetin, M., Hartmann, F. J., Valous, N. A., et al. (2025) · OncoImmunology · doi:10.1080/2162402x.2025.2457793 · Cited by 2

Tumor microenvironment response to neoadjuvant therapy in breast cancer: insights from single-cell and spatial omics

Wu, Q., Yang, J., Zhang, D., Xu, H., Yu, Y., & Zheng, Y. (2025) · Medical Oncology · doi:10.1007/s12032-025-03028-1 · Cited by 2

Use of Imaging Mass Cytometry in Studies of the Tissue Microenvironment

Herdlevær, I., Petrilli, L. L., Qosaj, F., Vinci, M., Bressan, D., & Gavasso, S. (2022) · Springer eBooks · doi:10.1007/978-3-030-98950-7_20 · Cited by 2

Proliferative Tumor-Infiltrating Lymphocytes' Abundance within the Microenvironment Impacts Clinical Outcome in Cutaneous B-Cell Lymphomas

Menguy, S., Prochazkova‐Carlotti, M., Martin, L. A., Ferté, T., Bresson‐Bepoldin, L., Rey, C. C., Vergier, B., Merlio, J., Beylot-Barry, M., & Pham‐Ledard, A. (2022) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2022.06.027 · Cited by 2

Quantile Index Biomarkers Based on Single-Cell Expression Data

Yi, M., Zhan, T., Peck, A. R., Hooke, J. A., Kovatich, A. J., Shriver, C. D., Hu, H., Sun, Y., Rui, H., & Chervoneva, I. (2023) · Laboratory Investigation · doi:10.1016/j.labinv.2023.100158 · Cited by 2

Pseudo-spectral angle mapping to improve immune cell classification in highly multiplexed fluorescence microscopy images

Durkee, M. S., Ai, J., Casella, G., Cao, T., Clark, M. R., & Giger, M. L. (2024) · Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues · doi:10.1117/12.3003486 · Cited by 2

Cell metabolism: Functional and phenotypic single cell approaches

Biasi, S. D., Gigan, J. P., Borella, R., Santacroce, E., Tartaro, D. L., Neroni, A., Paschalidis, N., Piwocka, K., Argüello, R. J., Gibellini, L., et al. (2024) · Methods in cell biology · doi:10.1016/bs.mcb.2024.02.024 · Cited by 2

cmIF: A Python Library for Scalable Multiplex Imaging Pipelines

Eng, J. R., Bucher, E., Gray, E., Campbell, L. G., Thibault, G., Heiser, L. M., Gibbs, S. L., Gray, J. W., Chin, K., & Chang, Y. H. (2019) · Lecture notes in computer science · doi:10.1007/978-3-030-35210-3_3 · Cited by 2

Microscopic and nanoscopic protein imaging by SIMS and helium ion microscopy

Lim, H., & Moon, D. (2020) · Biointerphases · doi:10.1116/6.0000220 · Cited by 2

Design and Optimization of the Circulatory Cell-Driven Drug Delivery Platform

Gao, P., Zou, D., Zhao, A., & Yang, P. (2021) · Stem Cells International · doi:10.1155/2021/8502021 · Cited by 2

Multiplexing Immunohistochemistry

McLaughlin, K. (2019) · Materials and Methods · doi:10.13070/mm.en.9.2846 · Cited by 3

IMCell XMBD : A statistical approach for robust cell identification and quantification from imaging mass cytometry imagesPreprint

Xu, X., Su, N., Kong, Y., Zhang, L., Ding, X., Yang, W., & Yu, R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.27.461899 · Cited by 2

Spatially Resolved and Highly Complexed Protein and RNA in situ Detection by Combining CODEX with RNAscope In Situ HybridizationPreprint

Cheng, Y., Burrack, R. M., & Li, Q. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.10.479971 · Cited by 2

Single-cell mapping links neurogenesis and angiogenesis in aggressive breast cancerPreprint

Wik, E., Aziz, S. M., Finne, K., Kleftogiannis, D., Askeland, C., Knutsvik, G., Krüger, K., Svanøe, A. A., Birkeland, E., Kjølle, S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.28.477898 · Cited by 3

Exploring the Landscape of Spatial Transcriptome Analysis: Introducing STASH, a Database of Spatial Transcriptome ToolsPreprint

Chu, H., Wang, K., Cheng, H., Ma, W., Dong, L., Gou, Y., Yang, J., & Cai, H. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.20.537419 · Cited by 2

Spatial Single-Cell Transcriptomic Analysis in Breast Cancer Reveals Potential Biomarkers for PD1 Blockade TherapyPreprint

Wang, N., Song, Y., Hong, W., Mo, H., Song, Z., Dai, W., Wang, L., Zhang, H., Zhang, Y., Zhang, Q., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4376986/v2 · Cited by 2

Tumor Landscape Analysis: An Ecologically Informed Framework to Understand Tumor MicroenvironmentsPreprint

Cisneros, L. H., Toruner, M. D., Fernández-Zapico, M. E., Maley, C. C., & Carr, R. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.22.646608 · Cited by 2

POLQ-driven repair scars shape the immunogenic landscape of homologous recombination-deficient pancreatic cancerPreprint

Park, W., Umeda, S., Hilmi, M., O'Connor, C. A., Sharma, R., Tezcan, N., Zhang, H., Zhu, Y., Schwartz, C., Yaqubie, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.15.711961 · Cited by 2

Tumor-immune trajectory context connects static tissue architecture to clinical outcomesPreprint

Cramer, E. M., Heiland, R. W., da Rocha, H. L., Bergman, D. R., Gray, J. W., Mills, G. B., Fertig, E. J., Macklin, P., Heiser, L. M., & Chang, Y. H. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.26.714521 · Cited by 2

High-definition CODEX for 3D multiplex spatial cell phenotyping

Hu, T., Zhang, N. Y., Venkatesan, M., Schürch, C. M., Nolan, G. P., & Coskun, A. F. (2024) · Elsevier eBooks · doi:10.1016/b978-0-12-822209-6.00008-4 · Cited by 1

Mass Spectrometry Imaging for Cellular-level Analysis: Advances and Applications on Medical Research

Yu, Y., Fan, J., Liu, H., & Nie, Z. (2025) · Chemical Research in Chinese Universities · doi:10.1007/s40242-025-4251-5 · Cited by 1

Functional protein biomarkers based on distributions of expression levels in single-cell imaging data

Yi, M., Zhan, T., Rui, H., & Chervoneva, I. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf182 · Cited by 1

Spatial immune profiling of Crohn’s disease fistula carcinomas—defining a distinct cancer subtype

Lehmann, M., Paclik, D., Huck, A., Arnold, A., Kurth-Stavenhagen, C., Vieth, M., Treese, C., Kühl, A. A., Siegmund, B., German IBD Study Group (GISG), et al. (2025) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjaf086 · Cited by 1

MAX Eraser: An affordable and simple reagent for antibody removal cycle in multiplex immunohistochemistry

Park, S.-H., Lee, B., Kim, I., Seo, J., Kim, J., Ryu, J. R., Chang, J., Kim, H., & Sun, W. (2025) · Cell Biomaterials · doi:10.1016/j.celbio.2025.100096 · Cited by 1

Vitiligo Signature‐Based Drug Screening Identifies Fulvestrant as a Novel Immunotherapy Combination Strategy

Zhu, J., Huang, L., Bi, S., Kong, W., Feng, W., Li, Y., Xie, Z., Shan, P., & Zhu, S. (2025) · Advanced Science · doi:10.1002/advs.202503979 · Cited by 1

From innovation to application: Pioneering advances in mass spectrometry imaging for spatially resolved single-cell omics

Lai, X., Xu, H., Chen, X., Ke, J., & Lin, S. (2025) · Chinese Chemical Letters · doi:10.1016/j.cclet.2025.111932 · Cited by 1

Expression of carcinoma ecotypes in the tumor microenvironment predicts response to neoadjuvant therapy in early-stage breast cancer

Asleh, K., Bethune, G. C., & Marcato, P. (2025) · Scientific Reports · doi:10.1038/s41598-025-28810-z · Cited by 1

Infiltration of CXCL9+ macrophages confers a favorable prognosis in breast cancer: Insights from an integrated single-cell RNA and bulk RNA sequencing study

Liang, B., Duan, Z., Long, S., & Zhou, P. (2025) · PLoS ONE · doi:10.1371/journal.pone.0337175 · Cited by 1

Implementing spatial single-cell omics in immuno-oncology clinical trials: Challenges and opportunities

Caprioli, C., Morscio, J., Chui, J. S., González‐Blas, C. B., Vandereyken, K., Voet, T., Antoranz, A., Vleeschouwer, S. D., Clement, P., Bosisio, F. M., et al. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-14064-8.00053-9 · Cited by 1

The interplay between cytokines and immune checkpoints in breast cancer therapy

Wu, Y., Zhu, Y. F., Cang, Q., Shaibu, Z., Kong, L., Zhou, Q., Li, X., & Yin, L. (2026) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2026.189539 · Cited by 1

smoppix: unified nonparametric analysis of single-molecule spatial omics data using probabilistic indices

Hawinkel, S., Yang, X., Poelmans, W., Motte, H., Beeckman, T., & Maere, S. (2026) · Genome biology · doi:10.1186/s13059-026-03976-5 · Cited by 1

ITGB1 Regulates Triple‐Negative Breast Cancer Development by Modulating the Tumor Microenvironment

Song, N., Chen, S., Wang, L., Dang, J., Cao, X., Singh, S., Yang, L., Wang, J., Rosen, S. T., Wang, Y., et al. (2026) · Advanced Science · doi:10.1002/advs.202513672 · Cited by 2

DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks

Zhang, X., Wu, Z., Wang, T., Zhou, Y., Ding, W., Zhu, H., & Zhang, Q. (2026) · Communications Biology · doi:10.1038/s42003-026-09659-y · Cited by 1

HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps

Xie, R., Wang, Z., Liu, J., Xu, H., Xu, Y., Lin, J., Hu, Y., & Gao, L. (2026) · Nature Communications · doi:10.1038/s41467-026-70069-z · Cited by 1

AI-driven deciphering of cell niches with single-cell and spatial omics: a new perspective for traditional Chinese medicine research

Qian, J., Bao, H., Yang, H., Zhang, J., Shao, X., & Fan, X. (2026) · Targetome · doi:10.48130/targetome-0026-0009 · Cited by 1

Harnessing innate lymphoid cells (ILCs) for cancer immunotherapy: A new frontier in precision immuno-oncology

Ghezel, M. A., Aram, C., Alishvandi, A., Barancheshmeh, M., Firuzpour, F., Khodabandehloo, M. H., Mohammadian, S., Rahimi, M., & Keikha, M. (2026) · Translational research · doi:10.1016/j.trsl.2026.03.001 · Cited by 1

Research progress on the compositional characteristics of the tumor immune microenvironment and immunopredictive models in esophageal squamous cell carcinoma

Wang, G., Li, Z., Tan, S., Ma, J., Yin, Z., Du, J., & Fan, L. (2026) · Cancer Biology & Therapy · doi:10.1080/15384047.2026.2641263 · Cited by 1

Spatial Immune Profiling and AI-Based Classifiers Identify Predictors of BCG Therapy Outcomes in High-Risk Non-Muscle-Invasive Bladder Cancer

Lillesand, M., Austdal, M., Mroz, J., Skaland, I., Gudlaugsson, E. G., de Jong, F. C., Zuiverloon, T. C. M., Engan, K., & Janssen, E. A. (2026) · Cancers · doi:10.3390/cancers18060938 · Cited by 1

The pathological landscape of tumor evolution: a paradigm shift from morphology to functional networks

Yuan, Y., Sun, Y., Ma, Y., Liu, H., & Sun, K. (2026) · Frontiers in Oncology · doi:10.3389/fonc.2026.1842639 · Cited by 1

Single-cell phenotype-associated subpopulation identification via transfer foundation model and statistical ensemble learning

Zhao, Y., Pan, X., Luo, Z., & Liu, Q. (2026) · BMC Biology · doi:10.1186/s12915-026-02613-8 · Cited by 2

The ARTEMIS trial identifies immune activation as a key predictor of neoadjuvant chemotherapy response in triple-negative breast cancer

Seth, S., Yam, C., Huo, L., Lim, B., Rinkenbaugh, A. L., White, J. B., Ravenberg, E. E., Song, X., Litton, J. K., Tripathy, D., et al. (2026) · Breast Cancer Research · doi:10.1186/s13058-026-02290-z · Cited by 3

Multi-parametric MRI habitat radiomics with interpretable machine learning for early prediction of axillary lymph node metastasis in triple-negative breast cancer

Xie, B., Peng, X., Wang, Y., Wen, X., Hu, Y., 李浥涵, You, X., & Ma, Y. (2026) · Frontiers in Medicine · doi:10.3389/fmed.2026.1808030 · Cited by 1

Ferroptosis in breast cancer: From adipocyte–immune–iron regulation to therapeutic application

Sun, J., Qu, Y., Ru, Y., & Zhou, Y. (2026) · Clinical and Translational Medicine · doi:10.1002/ctm2.70707 · Cited by 1

Precision immuno-oncology in oral cancer: latest trends in biomarkers, novel drug development and nanoparticle-based therapeutic platforms

Augustine, D., Sowmya, S., Pushpalatha, C., Prasad, K., & Khatoon, H. (2026) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2026.1839508 · Cited by 1

Spatial omics: current advances, biomedical applications, and future perspectives

Kim, M.-H., & Cha, H. (2026) · Kosin Medical Journal · doi:10.7180/kmj.26.165 · Cited by 1

Integration of multi-omics for precision therapy in breast cancer

Chen, P., Lo, C., Ou, D., Li, J., Hsu, C.-C., Lin, C.-H., & Wang, M.-Y. (2026) · Drug Discovery Today · doi:10.1016/j.drudis.2026.104722 · Cited by 1

Integration of artificial intelligence in stem cell research: a comprehensive bibliometric and emerging trend analysis

Ogra, I., Obasa, O. D., Adaji, J. Z., Usman, S., Tizhe, D., Nebo, P. E., Opoku, F. N., Apollos, S. D., Ladan, D. J. B., Johnson, N. A., et al. (2026) · Beni-Suef University Journal of Basic and Applied Sciences · doi:10.1186/s43088-026-00797-0

Cross-scale bioanalytical integration for decoding tumour regulatory plasticity in oncology

Kumar, S., Mondal, A., & Dubey, V. K. (2026) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2026.105466 · Cited by 1

Single-cell mass spectrometry imaging: platform advances for multimodal spatial omics

Hill, L. E., Young, L. E. A., Dressman, J. W., Angel, P. M., Mehta, A. S., & Drake, R. R. (2026) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-026-06644-6 · Cited by 1

Agentic AI for Spatial Omics

Pavilion, G. L., Mbigidde, C., Tubelleza, R., Ramarao-Milne, P., & Kulasinghe, A. (2026) · Immunology and Cell Biology · doi:10.1111/imcb.70146 · Cited by 1

Spatial organization of the TNBC tumor microenvironment: multicellular niches, T-cell bottlenecks, and therapeutic opportunities

Wu, J., Fan, J., Sha, T., & Li, H. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-026-08602-3 · Cited by 2

ConGAT: Context-aware graph attention network for 3D region of interest discovery in multiplexed microscopy images

Fathollahian, H., Zhao, S., Nipu, N., Salahshour, M., Duan, L., Tang, W., Boorboor, S., & Marai, G. E. (2026) · Computers & Graphics · doi:10.1016/j.cag.2026.104728 · Cited by 1

Humoral immunity in cancer

Leonard, J., Duhamel, M., & Salzet, M. (2026) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-026-02902-2 · Cited by 2

Research Status of Immune Microenvironment in Triple Negative Breast Cancer

Liang, B. (2023) · SHS Web of Conferences · doi:10.1051/shsconf/202317403004 · Cited by 1

Multiplexed imaging analysis of the tumor-immune microenvironment reveals predictors of outcome in triple-negative breast cancer

Patwa, A., Yamashita, R., Long, J., Risom, T., Angelo, M., Keren, L., & Rubin, D. L. (2021) · Communications Biology · doi:10.1038/s42003-021-02361-1 · Cited by 49

Abstract 1535: Differential immune microenvironments in triple-negative breast cancer and hormone receptor-positive HER2-negative breast cancer: A spatial analysis via multiplex immunofluorescence

Cha, Y. J., Park, I. H., & Shin, S. (2024) · Cancer Research · doi:10.1158/1538-7445.am2024-1535

Spatial and Compositional Biomarkers in Tumor Microenvironment Predicts Clinical Outcomes in Triple-Negative Breast CancerPreprint

Mi, H., Varadhan, R., Cimino‐Mathews, A., Emens, L. A., Santa-Maria, C. A., & Popel, A. S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.18.572234 · Cited by 10

A multiplexed view of immune infiltration

Seton-Rogers, S. E. (2018) · Nature reviews. Cancer · doi:10.1038/s41568-018-0063-y · Cited by 4

Multiplexed ion beam imaging (MIBI) for characterization of the tumor microenvironment across tumor types

Ptacek, J., Locke, D., Finck, R., Cvijic, M. E., Li, Z., Tarolli, J. G., Aksoy, M., Sigal, Y. M., Zhang, Y., Newgren, M., et al. (2020) · Laboratory Investigation · doi:10.1038/s41374-020-0417-4 · Cited by 112