Robust enumeration of cell subsets from tissue expression profiles

Cited by (135)

Items 101–135 of 135

1. Identification of TYROBP and C1QB as Two Novel Key Genes With Prognostic Value in Gastric Cancer by Network Analysis
   Jiang, Junjie, Ding, Yongfeng, Wu, Mengjie, Lyu, Xiadong, Wang, Haifeng, Chen, Yanyan, Wang, Haiyong, Teng, Lisong · 2020 · Frontiers in Oncology
2. Targeting <i>HER2</i> Exon 20 Insertion–Mutant Lung Adenocarcinoma with a Novel Tyrosine Kinase Inhibitor Mobocertinib
   Han, Han, Li, Shuai, Chen, Ting, Fitzgerald, Michael, Liu, Shengwu, Peng, Chengwei, Tang, Kwan Ho, Cao, Shougen, Chouitar, Johara, Wu, Jiansheng et al. · 2021 · Cancer Research
3. Genetic variants associated with Alzheimer’s disease confer different cerebral cortex cell-type population structure
   The Dominantly Inherited Alzheimer Network (DIAN), Li, Zeran, Del-Aguila, Jorge L., Dube, Umber, Budde, John, Martinez, Rita, Black, Kathleen, Xiao, Qingli, Cairns, Nigel J., Dougherty, Joseph D. et al. · 2018 · Genome Medicine
4. Atherosclerosis in the single-cell era
   Winkels, Holger, Ehinger, Erik, Ghosheh, Yanal, Wolf, Dennis, Ley, Klaus · 2018 · Current Opinion in Lipidology
5. Towards artificial intelligence to multi-omics characterization of tumor heterogeneity in esophageal cancer
   Li, Junyu, Li, Lin, You, Peimeng, Wei, Yiping, Xu, Bin · 2023 · Seminars in Cancer Biology
6. DNA methylation-based prognostic subtypes of chordoma tumors in tissue and plasma
   Zuccato, Jeffrey A, Patil, Vikas, Mansouri, Sheila, Liu, Jeffrey C, Nassiri, Farshad, Mamatjan, Yasin, Chakravarthy, Ankur, Karimi, Shirin, Almeida, Joao Paulo, Bernat, Anne-Laure et al. · 2022 · Neuro-Oncology
7. Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women With Alzheimer’s Disease
   Paranjpe, Manish D., Belonwu, Stella, Wang, Jason K., Oskotsky, Tomiko, Gupta, Aarzu, Taubes, Alice, Zalocusky, Kelly A., Paranjpe, Ishan, Glicksberg, Benjamin S., Huang, Yadong et al. · 2021 · Frontiers in Aging Neuroscience
8. Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago
   Natri, Heini M., Bobowik, Katalina S., Kusuma, Pradiptajati, Crenna Darusallam, Chelzie, Jacobs, Guy S., Hudjashov, Georgi, Lansing, J. Stephen, Sudoyo, Herawati, Banovich, Nicholas E., Cox, Murray P. et al. · 2020 · PLoS Genetics
9. Viral Status and Efficacy of Immunotherapy in Hepatocellular Carcinoma: A Systematic Review With Meta-Analysis
   Ding, Ziniu, Dong, Zhaoru, Chen, Zhiqiang, Hong, Jianguo, Yan, Lunjie, Li, Haichao, Yao, Shengyu, Yan, Yuchuan, Yang, Yafei, Yang, Chuncheng et al. · 2021 · Frontiers in Immunology
10. CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology
    Bernstein, Matthew N., Ma, Zhongjie, Gleicher, Michael, Dewey, Colin N. · 2021 · iScience
11. A tumor microenvironment-specific gene expression signature predicts chemotherapy resistance in colorectal cancer patients
    Zhu, Xiaoqiang, Tian, Xianglong, Ji, Linhua, Zhang, Xinyu, Cao, Yingying, Shen, Chaoqin, Hu, Ye, Wong, Jason W. H., Fang, Jing-Yuan, Hong, Jie et al. · 2021 · npj Precision Oncology
12. Mesothelioma Malignancy and the Microenvironment: Molecular Mechanisms
    Cersosimo, Francesca, Barbarino, Marcella, Lonardi, Silvia, Vermi, William, Giordano, Antonio, Bellan, Cristiana, Giurisato, Emanuele · 2021 · Cancers
13. A biomimetic liver cancer on-a-chip reveals a critical role of LIPOCALIN-2 in promoting hepatocellular carcinoma progression
    Shen, Peiliang, Jia, Yuanyuan, Zhou, Weijia, Zheng, Weiwei, Wu, Yueyao, Qu, Suchen, Du, Shiyu, Wang, Siliang, Shi, Huilian, Sun, Jia et al. · 2023 · Acta Pharmaceutica Sinica B
14. Generation of synthetic whole-slide image tiles of tumours from RNA-sequencing data via cascaded diffusion models
    Carrillo-Perez, Francisco, Pizurica, Marija, Zheng, Yuanning, Nandi, Tarak Nath, Madduri, Ravi, Shen, Jeanne, Gevaert, Olivier · 2024 · Nature Biomedical Engineering
15. Gene expression in cord blood links genetic risk for neurodevelopmental disorders with maternal psychological distress and adverse childhood outcomes
    Breen, Michael S., Wingo, Aliza P., Koen, Nastassja, Donald, Kirsten A., Nicol, Mark, Zar, Heather J., Ressler, Kerry J., Buxbaum, Joseph D., Stein, Dan J. · 2018 · Brain, Behavior, and Immunity
16. A curated human cellular microRNAome based on 196 primary cell types
    Patil, Arun H, Baran, Andrea, Brehm, Zachary P, McCall, Matthew N, Halushka, Marc K · 2022 · GigaScience
17. Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma
    Mitra, Akash, Andrews, Miles C., Roh, Whijae, De Macedo, Marianna Petaccia, Hudgens, Courtney W., Carapeto, Fernando, Singh, Shailbala, Reuben, Alexandre, Wang, Feng, Mao, Xizeng et al. · 2020 · Nature Communications
18. Identification of metabolism-related subtypes and feature genes in Alzheimer’s disease
    Lian, Piaopiao, Cai, Xing, Wang, Cailin, Liu, Ke, Yang, Xiaoman, Wu, Yi, Zhang, Zhaoyuan, Ma, Zhuoran, Cao, Xuebing, Xu, Yan · 2023 · Journal of Translational Medicine
19. A transcriptome-based human universal senescence index (hUSI) robustly predicts cellular senescence under various conditions
    Wang, Jing, Zhou, Xiaolan, Yu, Peng, Yao, Jun, Guo, Pengfei, Xu, Qiushi, Zhao, Yuqi, Wang, Guanlong, Li, Qianru, Zhu, Xiaofeng et al. · 2025 · Nature Aging
20. Antiretroviral therapy potentiates high-fat diet induced obesity and glucose intolerance
    Pepin, Mark E., Padgett, Lindsey E., McDowell, Ruth E., Burg, Ashley R., Brahma, Manoja K., Holleman, Cassie, Kim, Teayoun, Crossman, David, Kutsch, Olaf, Tse, Hubert M. et al. · 2018 · Molecular Metabolism
21. Signaling networks in inflammatory pathways and risk for suicidal behavior
    Rengasamy, Manivel, Zhong, Yongqi, Marsland, Anna, Chen, Kehui, Douaihy, Antoine, Brent, David, Melhem, Nadine M. · 2020 · Brain, Behavior, &amp; Immunity - Health
22. A multicenter, randomized, non-comparative, phase II study of nivolumab ± ipilimumab for patients with metastatic sarcoma (Alliance A091401): expansion cohorts and correlative analyses
    Seligson, Nathan D, Chen, James L, Goodrich, Austin C, Van Tine, Brian A, Campbell, Jordan D, Richards, Allison L, Antonescu, Cristina R, Liebner, David A, Milhem, Mohammed M, Streicher, Howard et al. · 2024 · Journal for ImmunoTherapy of Cancer
23. Identification and Validation of the Prognostic Panel in Clear Cell Renal Cell Carcinoma Based on Resting Mast Cells for Prediction of Distant Metastasis and Immunotherapy Response
    Su, Yang, Zhang, Tianxiang, Lu, Jinsen, Qian, Lei, Fei, Yang, Zhang, Li, Fan, Song, Zhou, Jun, Tang, Jieqiong, Chen, Haige et al. · 2023 · Cells
24. Immune phenotype of tumor microenvironment predicts response to bevacizumab in neoadjuvant treatment of <scp>ER</scp>‐positive breast cancer
    von der Lippe Gythfeldt, Hedda, Lien, Tonje, Tekpli, Xavier, Silwal‐Pandit, Laxmi, Borgen, Elin, Garred, Øystein, Skjerven, Helle, Schlichting, Ellen, Lundgren, Steinar, Wist, Erik et al. · 2020 · International Journal of Cancer
25. Activation of innate-adaptive immune machinery by poly(I:C) exposes a therapeutic vulnerability to prevent relapse in stroma-rich colon cancer
    Corry, Shania M, McCorry, Amy MB, Lannagan, Tamsin RM, Leonard, Niamh A, Fisher, Natalie C, Byrne, Ryan M, Tsantoulis, Petros, Cortes-Lavaud, Xabier, Amirkhah, Raheleh, Redmond, Keara L et al. · 2022 · Gut
26. Sex differences in expression of immune elements emerge in children, young adults and mice with osteosarcoma.
    Mills, Lauren J., Spector, Logan G., Largaespada, David A., Williams, Lindsay A. · 2021 · Biology of Sex Differences
27. Identification and validation of efferocytosis-related biomarkers for the diagnosis of metabolic dysfunction-associated steatohepatitis based on bioinformatics analysis and machine learning
    Cao, Chenghui, Liu, Wenwu, Guo, Xin, Weng, Shuwei, Chen, Yang, Luo, Yonghong, Wang, Shuai, Zhu, Botao, Liu, Yuxuan, Peng, Daoquan · 2024 · Frontiers in Immunology
28. Phosphoserine phosphatase as a prognostic biomarker in patients with gastric cancer and its potential association with immune cells
    Huang, Ma-Yan, Liu, Xiao-Yun, Shao, Qiong, Zhang, Xu, Miao, Lei, Wu, Xiao-Yan, Xu, Yu-Xia, Wang, Fang, Wang, Hai-Yun, Zeng, Liang et al. · 2022 · BMC Gastroenterology
29. Osteosarcoma neutrophil extracellular trap network-associated gene recurrence and metastasis model
    Tang, Hao, Xie, Jiang, Du, Yu-Xuan, Tan, Ze-Jiu, Liang, Zhuo-Tao · 2024 · Journal of Cancer Research and Clinical Oncology
30. TP53 Mutational Status-Based Genomic Signature for Prognosis and Predicting Therapeutic Response in Pancreatic Cancer
    Zhang, Feng, Zhong, Wenhui, Li, Honghao, Huang, Kaijun, Yu, Min, Liu, Yubin · 2021 · Frontiers in Cell and Developmental Biology
31. MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
    Schaafsma, Evelien, Zhao, Yanding, Zhang, Lanjing, Li, Yong, Cheng, Chao · 2021 · Molecular Cancer Research
32. Machine-learning algorithm-based prediction of a diagnostic model based on oxidative stress-related genes involved in immune infiltration in diabetic nephropathy patients
    Zhu, Heng-Mei, Liu, Na, Sun, Dong-Xuan, Luo, Liang · 2023 · Frontiers in Immunology
33. Expression quantitative trait locus studies in the era of single-cell omics
    Luo, Jie, Wu, Xinyi, Cheng, Yuan, Chen, Guang, Wang, Jian, Song, Xijiao · 2023 · Frontiers in Genetics
34. SpaHE-Infil: A spatial heterogeneity framework for decoding TME infiltration from H&amp;E-stained slides
    Wang, Fang, Xu, Hejia, Wang, Xue, Wu, Mengyin, Ding, Sisi, Duan, Lian, Yang, Chen, Li, Jiaxuan, Ge, Xiaosong, Qin, Yan et al. · 2026 · iScience
35. Genome-Wide Network Analysis of DRG-Sciatic Nerve Network-Inferred Cellular Senescence and Senescence Phenotype in Peripheral Sensory Neurons
    Kawabata, Sora, Iijima, Hirotaka, Kanemura, Naohiko, Murata, Kenji · 2025 · Molecular Neurobiology