Integrated analysis of multimodal single-cell data

Cited by (1,144)

Items 201–300 of 1,144

1. Normalizing and denoising protein expression data from droplet-based single cell profiling
   Mulè, Matthew P., Martins, Andrew J., Tsang, John S. · 2022 · Nature Communications
2. Cerebrospinal fluid immune dysregulation during healthy brain aging and cognitive impairment
   Natalie Piehl, Lynn van Olst, Abhirami Ramakrishnan, Victoria Teregulova, Brooke Simonton, Ziyang Zhang, Emma Tapp, Divya Channappa, Hamilton Se‐Hwee Oh, Patricia Morán Losada et al. · 2022 · Cell
3. Integration of whole transcriptome spatial profiling with protein markers
   Nir Ben‐Chetrit, Xiang Niu, Ariel D. Swett, Jesus Sotelo, Maria S. Jiao, Caitlin M. Stewart, Catherine J. Potenski, Paulius Mielinis, Patrick Roelli, Marlon Stoeckius et al. · 2023 · Nature Biotechnology
4. Single-cell sequencing to multi-omics: technologies and applications
   Wu, Xiangyu, Yang, Xin, Dai, Yunhan, Zhao, Zihan, Zhu, Junmeng, Guo, Hongqian, Yang, Rong · 2024 · Biomarker Research
5. An integrated single cell and spatial transcriptomic map of human white adipose tissue
   Massier, Lucas, Jalkanen, Jutta, Elmastas, Merve, Zhong, Jiawei, Wang, Tongtong, Nono Nankam, Pamela A., Frendo-Cumbo, Scott, Bäckdahl, Jesper, Subramanian, Narmadha, Sekine, Takuya et al. · 2023 · Nature Communications
6. The interaction between STING and NCOA4 exacerbates lethal sepsis by orchestrating ferroptosis and inflammatory responses in macrophages
   Jie Wu, Qinjie Liu, Xufei Zhang, Miaomiao Tan, Xuanheng Li, Peizhao Liu, Lei Wu, Fan Jiao, Zhaoyu Lin, Xiuwen Wu et al. · 2022 · Cell Death and Disease
7. Adoptive Cellular Therapy with Autologous Tumor-Infiltrating Lymphocytes and T-cell Receptor–Engineered T Cells Targeting Common p53 Neoantigens in Human Solid Tumors
   Sanghyun Peter Kim, Nolan R. Vale, Nikolaos Zacharakis, Sri Krishna, Zhiya Yu, Billel Gasmi, Jared J. Gartner, Sivasish Sindiri, Parisa Malekzadeh, Drew C. Deniger et al. · 2022 · Cancer Immunology Research
8. Clonal expansion and epigenetic inheritance of long-lasting NK cell memory
   Timo Rückert, Caleb A. Lareau, Mir‐Farzin Mashreghi, Leif S. Ludwig, Chiara Romagnani · 2022 · Nature Immunology
9. Tumour evolution and microenvironment interactions in 2D and 3D space
   Chia-Kuei Mo, Jingxian Liu, Siqi Chen, Erik P. Storrs, André Luiz N. Targino da Costa, Andrew Houston, Michael C. Wendl, Reyka G. Jayasinghe, Michael D. Iglesia, Cong Ma et al. · 2024 · Nature
10. Long-primed germinal centres with enduring affinity maturation and clonal migration
    Jeong Hyun Lee, Henry J. Sutton, Christopher A. Cottrell, Ivy Phung, Gabriel Ozorowski, Leigh M. Sewall, Rebecca Nedellec, Catherine Nakao, Murillo Silva, Sara T. Richey et al. · 2022 · Nature
11. Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression
    Junyi Hu, Shaogang Wang, Yaxin Hou, Zhaohui Chen, Lilong Liu, Ruizhi Li, Nisha Li, Lijie Zhou, Yu Yang, Liping Wang et al. · 2024 · Nature Genetics
12. Blockade of LAG-3 and PD-1 leads to co-expression of cytotoxic and exhaustion gene modules in CD8+ T cells to promote antitumor immunity
    Anthony Richard Cillo, Carly Cardello, Feng Shan, Lilit Karapetyan, Sheryl R. Kunning, Cindy Sander, Elizabeth A. Rush, Arivarasan D. Karunamurthy, Ryan Campbell Massa, Anjali Rohatgi et al. · 2024 · Cell
13. scPerturb: harmonized single-cell perturbation data
    Peidli, Stefan, Green, Tessa D., Shen, Ciyue, Gross, Torsten, Min, Joseph, Garda, Samuele, Yuan, Bo, Schumacher, Linus J., Taylor-King, Jake P., Marks, Debora S. et al. · 2024 · Nature Methods
14. Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE
    Yupei You, Yair D. J. Prawer, Ricardo De Paoli‐Iseppi, Cameron P. J. Hunt, Clare L. Parish, Heejung Shim, Michael B. Clark · 2023 · Genome biology
15. An atlas of cells in the human tonsil
    Ramon Massoni-Badosa, Sergio Aguilar-Fernández, Juan Camilo Nieto, Paula Soler-Vila, Marc Elosua-Bayés, Doménica Marchese, Marta Kulis, Amaia Vilas‐Zornoza, Marco Matteo Bühler, Sonal Rashmi et al. · 2024 · Immunity
16. Single-cell atlas of the human brain vasculature across development, adulthood and disease
    Thomas Wälchli, Moheb Ghobrial, Marc Schwab, Shigeki Takada, Hang Zhong, Samuel Suntharalingham, Sandra Vetiska, Daymé González Rodríguez, Ruilin Wu, Hubert Rehrauer et al. · 2024 · Nature
17. A fast, scalable and versatile tool for analysis of single-cell omics data
    Zhang, Kai, Zemke, Nathan R., Armand, Ethan J., Ren, Bing · 2024 · Nature Methods
18. Recent advances in droplet microfluidics for single-cell analysis
    Zhenqi Jiang, Haoran Shi, Xiaoying Tang, Jieling Qin · 2023 · TrAC Trends in Analytical Chemistry
19. A genome-scale screen for synthetic drivers of T cell proliferation
    Mateusz Legut, Zoran Z. Gajic, Maria Guarino, Zharko Daniloski, Jahan A. Rahman, Xinhe Xue, Congyi Lu, Lu Lu, Eleni P. Mimitou, Stephanie Hao et al. · 2022 · Nature
20. Single-cell biological network inference using a heterogeneous graph transformer
    Ma, Anjun, Wang, Xiaoying, Li, Jingxian, Wang, Cankun, Xiao, Tong, Liu, Yuntao, Cheng, Hao, Wang, Juexin, Li, Yang, Chang, Yuzhou et al. · 2023 · Nature Communications
21. The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts
    Shimrit Mayer, Tomer Milo, Achinoam Isaacson, Coral Halperin, Shoval Miyara, Yaniv Stein, Chen Lior, Meirav Pevsner‐Fischer, Eldad Tzahor, Avi Mayo et al. · 2023 · Nature Communications
22. AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships
    You Wu, Lei Xie · 2025 · Computational and Structural Biotechnology Journal
23. Phenotypic plasticity and genetic control in colorectal cancer evolution
    Jacob Househam, Timon Heide, George D. Cresswell, Inmaculada Spiteri, Christopher Kimberley, Luis Zapata, Claire Lynn, Chela T. James, Maximilian Mossner, Javier Fernández-Mateos et al. · 2022 · Nature
24. Active eosinophils regulate host defence and immune responses in colitis
    Alessandra Gurtner, Costanza Borrelli, Ignacio Gonzalez-Perez, Karsten Bach, İlhan E. Acar, Nicolás Gonzalo Núñez, Daniel Crepaz, Kristina Handler, Vivian Pham Vu, Atefeh Lafzi et al. · 2022 · Nature
25. Cancer cell-derived arginine fuels polyamine biosynthesis in tumor-associated macrophages to promote immune evasion
    Yinghua Zhu, Ziwei Zhou, Xin Du, Xiaorong Lin, Zhi-Mei Liang, Si Chen, Yiwei Sun, Yue Wang, Zhenkun Na, Zhi‐Yong Wu et al. · 2025 · Cancer Cell
26. Multi-omic profiling highlights factors associated with resistance to immuno-chemotherapy in non-small-cell lung cancer
    Yilv Yan, Dongqing Sun, Junjie Hu, Yue Chen, Liangdong Sun, Huansha Yu, Yicheng Xiong, Zhida Huang, Haoran Xia, Xinsheng Zhu et al. · 2024 · Nature Genetics
27. Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer
    Peipei Zhou, Hao Shi, Hongling Huang, Xiang Sun, Sujing Yuan, Nicole M. Chapman, Jon P. Connelly, Seon Ah Lim, Jordy Saravia, Anil KC et al. · 2023 · Nature
28. Unveiling inflammatory and prehypertrophic cell populations as key contributors to knee cartilage degeneration in osteoarthritis using multi-omics data integration
    Yue Fan, Xuzhao Bian, Xiaogao Meng, Lei Li, Laiyi Fu, Yanan Zhang, Long Wang, Yan Zhang, Dalong Gao, Xiong Guo et al. · 2024 · Annals of the Rheumatic Diseases
29. Tumour vasculature at single-cell resolution
    Xu Pan, Xin Li, Liang Dong, Teng Liu, Min Zhang, Lining Zhang, Xiyuan Zhang, Lingjuan Huang, Wensheng Shi, Hongyin Sun et al. · 2024 · Nature
30. Guided construction of single cell reference for human and mouse lung
    Minzhe Guo, Michael P. Morley, Cheng Jiang, Yixin Wu, Guangyuan Li, Yina Du, Shuyang Zhao, Andrew F. Wagner, Adnan Cihan Cakar, Michal Kouril et al. · 2023 · Nature Communications
31. Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain
    Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin Aubin, Charles C. White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt–Rosen, Devan Phillips, Liat Amir-Zilberstein et al. · 2024 · Nature Genetics
32. Long-term histone lactylation connects metabolic and epigenetic rewiring in innate immune memory
    Athanasios Ziogas, Boris Novakovic, Lorenzo Ventriglia, Noriko Galang, Kim A. Tran, Wenchao Li, Vasiliki Matzaraki, Nienke van Unen, Titus Schlüter, Anaísa V. Ferreira et al. · 2025 · Cell
33. Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress
    Michael Hagemann-Jensen, Christoph Ziegenhain, Rickard Sandberg · 2022 · Nature Biotechnology
34. Tumor heterogeneity: preclinical models, emerging technologies, and future applications
    Marco Proietto, Martina Crippa, Chiara Damiani, Valentina Pasquale, Elena Sacco, Marco Vanoni, Mara Gilardi · 2023 · Frontiers in Oncology
35. Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq
    Zhiyuan Liu, Yujie Chen, Qimin Xia, Menghan Liu, Heming Xu, Yi Chi, Yujing Deng, Dong Xing · 2023 · Science
36. Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes
    Tuo Shi, Marielle O Beaulieu, Lauren M. Saunders, Péter Fábián, Cole Trapnell, Neil Segil, Justin Gage Crump, David W. Raible · 2023 · eLife
37. A comparative atlas of single-cell chromatin accessibility in the human brain
    Li, Yang Eric, Preissl, Sebastian, Miller, Michael, Johnson, Nicholas D., Wang, Zihan, Jiao, Henry, Zhu, Chenxu, Wang, Zhaoning, Xie, Yang, Poirion, Olivier et al. · 2023 · Science
38. Single-cell atlases: shared and tissue-specific cell types across human organs
    Rasa Elmentaite, Cecilia Domínguez Conde, Lu Yang, Sarah Amalia Teichmann · 2022 · Nature Reviews Genetics
39. Directed evolution of adeno-associated virus for efficient gene delivery to microglia
    Lin, Rui, Zhou, Youtong, Yan, Ting, Wang, Ruiyu, Li, Heng, Wu, Zhaofa, Zhang, Xinshuang, Zhou, Xiangyu, Zhao, Fei, Zhang, Li et al. · 2022 · Nature Methods
40. Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation
    Zhijian Liu, Xiangying Kong, Yanping Long, Sirui Liu, Hong Zhang, Jinbu Jia, Wenhui Cui, Zunmian Zhang, Xianwei Song, Lijuan Qiu et al. · 2023 · Nature Plants
41. Advances in spatial transcriptomics and its applications in cancer research
    Yang Jin, Yuanli Zuo, Gang Li, Wenrong Liu, Yitong Pan, Ting Fan, Xin Fu, Xiaojun Yao, Yong Peng · 2024 · Molecular Cancer
42. Molecular and cellular dynamics of the developing human neocortex
    Li Wang, Cheng Wang, Juan Moriano, Songcang Chen, Guolong Zuo, Arantxa Cebrián‐Silla, Shaobo Zhang, Tanzila Mukhtar, Shaohui Wang, Mengyi Song et al. · 2025 · Nature
43. Lifelong multilineage contribution by embryonic-born blood progenitors
    Sachin H Patel, Constantina Christodoulou, Caleb Weinreb, Qi Yu, Edroaldo Lummertz da Rocha, Brian J. Pepe-Mooney, Sarah Bowling, Li Li, Fernando G. Osorio, George Q. Daley et al. · 2022 · Nature
44. Integration, exploration, and analysis of high‐dimensional single‐cell cytometry data using Spectre
    Thomas M. Ashhurst, Felix Marsh‐Wakefield, Givanna Putri, Alanna Gabrielle Spiteri, Diana Shinko, Mark Norman Read, Adrian Lloyd Smith, Nicholas J. C. King · 2021 · Cytometry Part A
45. Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer’s disease
    Na Sun, Leyla Anne Akay, Mitchell H. Murdock, Yongjin Park, Fabiola Galiana-Melendez, Adele Bubnys, Kyriaki Galani, Hansruedi Mathys, Xueqiao Jiang, Ayesha P. Ng et al. · 2023 · Nature Neuroscience
46. Obesity induces PD-1 on macrophages to suppress anti-tumour immunity
    Jackie E. Bader, Melissa M. Wolf, Gian Luca Lupica-Tondo, Matthew Z. Madden, Bradley I. Reinfeld, Emily Nicole Arner, Emma S. Hathaway, KayLee K. Steiner, Gabriel A. Needle, Zaid Hatem et al. · 2024 · Nature
47. Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis
    Annika Vannan, Ruqian Lyu, Arianna L. Williams-Katek, Nicholas M. Negretti, Evan D. Mee, Joseph Hirsh, Samuel Hirsh, Niran Hadad, David S. Nichols, Carla L. Calvi et al. · 2025 · Nature Genetics
48. Mitochondrial integrated stress response controls lung epithelial cell fate
    SeungHye Han, Minho Lee, Youngjin Shin, Regina Giovanni, Ram Prosad Chakrabarty, Mariana M. Herrerias, Laura A. Dada, Annette S. Flozak, Paul A. Reyfman, Basil Khuder et al. · 2023 · Nature
49. Single-cell genomics and regulatory networks for 388 human brains
    Prashant S. Emani, Jason J. Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che-Yu Lee, Siwei Xu, Cagatay Dursun et al. · 2024 · Science
50. irGSEA: the integration of single-cell rank-based gene set enrichment analysis
    Chuiqin Fan, Fuyi Chen, Yuanguo Chen, Liangping Huang, Manna Wang, Yulin Liu, Yu Wang, Huijie Guo, Nanpeng Zheng, Yanbing Liu et al. · 2024 · Briefings in Bioinformatics
51. Adenosine signalling to astrocytes coordinates brain metabolism and function
    Shefeeq M. Theparambil, Olga Kopach, Alice Braga, Shereen Nizari, Patrick Steven Hosford, Virág Sági‐Kiss, Anna Hadjihambi, Christos Konstantinou, Noemí Esteras, Ana Gutierrez del Arroyo et al. · 2024 · Nature
52. Dissociable hindbrain GLP1R circuits for satiety and aversion
    Huang, Kuei-Pin, Acosta, Alisha A., Ghidewon, Misgana Y., McKnight, Aaron D., Almeida, Milena S., Nyema, Nathaniel T., Hanchak, Nicholas D., Patel, Nisha, Gbenou, Yenoukoume S. K., Adriaenssens, Alice E. et al. · 2024 · Nature
53. FOXA2 drives lineage plasticity and KIT pathway activation in neuroendocrine prostate cancer
    Han, Ming, Li, Fei, Zhang, Yehan, Dai, Pengfei, He, Juan, Li, Yunguang, Zhu, Yiqin, Zheng, Junke, Huang, Hai, Bai, Fan et al. · 2022 · Cancer Cell
54. Cobolt: integrative analysis of multimodal single-cell sequencing data
    Gong, Boying, Zhou, Yun, Purdom, Elizabeth · 2021 · Genome Biology
55. scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning
    Lin, Yingxin, Wu, Tung-Yu, Wan, Sheng, Yang, Jean Y. H., Wong, Wing H., Wang, Y. X. Rachel · 2022 · Nature Biotechnology
56. Monocyte-derived alveolar macrophages autonomously determine severe outcome of respiratory viral infection
    Fengqi Li, Federica Piattini, Lea Maria Pohlmeier, Qian Feng, Hubert Rehrauer, Manfred Köpf · 2022 · Science Immunology
57. Interferon-stimulated neutrophils as a predictor of immunotherapy response
    Madeleine Benguigui, Tim J. Cooper, Prajakta Kalkar, Sagie Schif‐Zuck, Ruth Halaban, Antonella Bacchiocchi, Iris Kamer, Abhilash Deo, Bar Manobla, Menachem Rottem et al. · 2024 · Cancer Cell
58. 8C-like cells capture the human zygotic genome activation program in vitro
    Jasmin Taubenschmid, Maria Rostovskaya, Fátima Santos, Sebastian Ljung, Ricard Argelaguet, Felix Krueger, Jennifer Nichols, Wolf Reik · 2022 · Cell stem cell
59. Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis
    Zhenzhen Xun, Xinyu Ding, Yao Zhang, Benyan Zhang, Shujing Lai, Duowu Zou, Junke Zheng, Guoqiang Chen, Bing Su, Leng Han et al. · 2023 · Nature Communications
60. Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology
    Thomas Hu, Mayar Allam, Shuangyi Cai, Walter E. Henderson, Brian Yueh, Aybuke Alici-Garipcan, Anton V. Ievlev, Maryam Afkarian, Semir Beyaz, Ahmet F. Coskun · 2023 · Nature Communications
61. Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory
    Sun, Wenfei, Liu, Zhihui, Jiang, Xian, Chen, Michelle B., Dong, Hua, Liu, Jonathan, Südhof, Thomas C., Quake, Stephen R. · 2024 · Nature
62. A lactate-SREBP2 signaling axis drives tolerogenic dendritic cell maturation and promotes cancer progression
    Plebanek, Michael P., Xue, Yue, Nguyen, Y-Van, DeVito, Nicholas C., Wang, Xueying, Holtzhausen, Alisha, Beasley, Georgia M., Theivanthiran, Balamayooran, Hanks, Brent A. · 2024 · Science Immunology
63. A census of the lung: CellCards from LungMAP
    Xin Sun, Anne‐Karina T. Perl, Rongbo Li, Sheila M. Bell, Enikö Sajti, Vladimir V. Kalinichenko, Tanya V. Kalin, Ravi S. Misra, Hitesh S. Deshmukh, Gérémy Clair et al. · 2021 · Developmental Cell
64. Independent origins of fetal liver haematopoietic stem and progenitor cells
    Tomomasa Yokomizo, Takako Ideue, Saori Morino‐Koga, Cheng Yong Tham, Tomohiko Sato, Naoki Takeda, Yoshiaki Kubota, Mineo Kurokawa, Norio Komatsu, Minetaro Ogawa et al. · 2022 · Nature
65. Cell type specific transcriptomic differences in depression show similar patterns between males and females but implicate distinct cell types and genes
    Malosree Maitra, Haruka Mitsuhashi, Reza Rahimian, Anjali Chawla, Jennie Yang, Laura M. Fiori, Maria Antonietta Davoli, Kelly Perlman, Zahia Aouabed, Deborah C. Mash et al. · 2023 · Nature Communications
66. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)
    Sanjay R. Jain, Liming Pei, Jeffrey M. Spraggins, Michael Angelo, James P. Carson, Nils Gehlenborg, Fiona Ginty, Joana P. Gonçalves, James S. Hagood, John W. Hickey et al. · 2023 · Nature Cell Biology
67. The Human Cell Atlas from a cell census to a unified foundation model
    Jennifer Rood, Samantha Wynne, Lucia Robson, Anna Hupalowska, John Randell, Sarah Amalia Teichmann, Aviv Regev · 2024 · Nature
68. Stem-cell-derived trophoblast organoids model human placental development and susceptibility to emerging pathogens
    Rowan M. Karvas, Shafqat Ali Khan, Sonam Verma, Yan Yin, Devesha Hrishikesh Kulkarni, Chen Dong, Kyoung‐mi Park, Brian Chew, Eshan S. Sane, Laura A. Fischer et al. · 2022 · Cell stem cell
69. Single-Cell Analysis Reveals the Range of Transcriptional States of Circulating Human Neutrophils
    Gustaf Wigerblad, Qilin Cao, Stephen R. Brooks, Faiza Naz, Manasi Gadkari, Kan Jiang, Sarthak Gupta, Liam J. O’Neil, Stefania Dell’Orso, Mariana J. Kaplan et al. · 2022 · The Journal of Immunology
70. Chemically defined cytokine-free expansion of human haematopoietic stem cells
    Masatoshi Sakurai, Kantaro Ishitsuka, Ryoji Ito, Adam C. Wilkinson, Takaharu Kimura, Eiji Mizutani, Hidekazu Nishikii, Kazuhiro Sudo, H. Becker, Hiroshi Takemoto et al. · 2023 · Nature
71. Stretchable Mesh Nanoelectronics for 3D Single‐Cell Chronic Electrophysiology from Developing Brain Organoids
    Paul Le Floch, Qiang Li, Zuwan Lin, Siyuan Zhao, Ren Liu, Kazi Tasnim, Han Jiang, Jia Liu B · 2022 · Advanced Materials
72. Overlapping transcriptional programs promote survival and axonal regeneration of injured retinal ganglion cells
    Anne Jacobi, Nicholas M. Tran, Wenjun Yan, Inbal Benhar, Feng Tian, Rebecca Schaffer, Zhigang He, Joshua R. Sanes · 2022 · Neuron
73. Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain
    Fu, Xiaonan, Sun, Li, Dong, Runze, Chen, Jane Y., Silakit, Runglawan, Condon, Logan F., Lin, Yiing, Lin, Shin, Palmiter, Richard D., Gu, Liangcai · 2022 · Cell
74. Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID
    Akira Cortal, Loredana Martignetti, Emmanuelle M. Six, Antonio Rausell · 2021 · Nature Biotechnology
75. Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy
    Keyu Li, Joseph A. Tandurella, Jessica Gai, Qingfeng Zhu, Su Jin Lim, Dwayne L. Thomas, Tao Xia, Guanglan Mo, Jacob T. Mitchell, Janelle Marie Montagne et al. · 2022 · Cancer Cell
76. A disease-associated gene desert directs macrophage inflammation through ETS2
    Christina T. Stankey, Christophe Bourges, Lea-Maxie Haag, Tabitha Turner‐Stokes, A. P. Piedade, Christopher Palmer-Jones, Ilenia Papa, Mariana Silva dos Santos, Q. Zhang, Andrew J. Cameron et al. · 2024 · Nature
77. Prognostic genome and transcriptome signatures in colorectal cancers
    Luís Nunes, Fuqiang Li, Meizhen Wu, Tian Luo, Klara Hammarström, Emma Torell, Ingrid Ljuslinder, Artur Mezheyeuski, Per-Henrik D. Edqvist, Anna Löfgren‐Burström et al. · 2024 · Nature
78. Computational approaches and challenges in spatial transcriptomics
    Fang, Shuangsang, Chen, Bichao, Zhang, Yong, Sun, Haixi, Liu, Longqi, Liu, Shiping, Li, Yuxiang, Xu, Xun · 2023 · Genomics, Proteomics & Bioinformatics
79. Unified rhombic lip origins of group 3 and group 4 medulloblastoma
    Kyle S. Smith, Laure Bihannic, Brian L. Gudenas, Parthiv Haldipur, Ran Tao, Qingsong Gao, Yiran Li, Kimberly A. Aldinger, Igor Y. Iskusnykh, Victor V. Chizhikov et al. · 2022 · Nature
80. Failure of human rhombic lip differentiation underlies medulloblastoma formation
    Liam D. Hendrikse, Parthiv Haldipur, Olivier Saulnier, Jake Millman, Alexandria H. Sjoboen, Anders Wilder Erickson, Winnie Ong, Victor Dela Gordon, Ludivine Coudière-Morrison, Audrey L. Mercier et al. · 2022 · Nature
81. The choroid plexus synergizes with immune cells during neuroinflammation
    Huixin Xu, Peter Lotfy, Sivan Gelb, Aja Pragana, Christine Hehnly, Lillian I.J. Byer, Frederick B. Shipley, Miriam E. Zawadzki, Jin Cui, Liwen Deng et al. · 2024 · Cell
82. Brainstem ADCYAP1+ neurons control multiple aspects of sickness behaviour
    Anoj Ilanges, Rani Shiao, Jordan T. Shaked, Ji‐Dung Luo, Xiaofei Yu, Jeffrey M. Friedman · 2022 · Nature
83. Multiomic spatial landscape of innate immune cells at human central nervous system borders
    Sankowski, Roman, Süß, Patrick, Benkendorff, Alexander, Böttcher, Chotima, Fernandez-Zapata, Camila, Chhatbar, Chintan, Cahueau, Jonathan, Monaco, Gianni, Gasull, Adrià Dalmau, Khavaran, Ashkan et al. · 2024 · Nature Medicine
84. Mapping cells through time and space with moscot
    Dominik Klein, Giovanni Palla, Marius Lange, Michal Klein, Zoe Piran, Manuel Gander, Laetitia Meng-Papaxanthos, Michael Sterr, Lama Saber, Changying Jing et al. · 2025 · Nature
85. A human breast atlas integrating single-cell proteomics and transcriptomics
    G. Kenneth Gray, Carman Man-Chung Li, Jennifer M. Rosenbluth, Laura M. Selfors, Nomeda Girnius, Jia‐Ren Lin, Ron C.J. Schackmann, Walter L. Goh, Kaitlin Moore, Hana Shapiro et al. · 2022 · Developmental Cell
86. Spatial transcriptomic landscape unveils immunoglobin-associated senescence as a hallmark of aging
    Ma, Shuai, Ji, Zhejun, Zhang, Bin, Geng, Lingling, Cai, Yusheng, Nie, Chao, Li, Jiaming, Zuo, Yuesheng, Sun, Yuzhe, Xu, Gang et al. · 2024 · Cell
87. LGR5 expressing skin fibroblasts define a major cellular hub perturbed in scleroderma
    Chamutal Gur, Shuang-Yin Wang, Fadi Sheban, Mor Zada, Baoguo Li, Fadi Kharouf, Hagit Peleg, Suhail Aamar, Adam Yalin, Daniel Kirschenbaum et al. · 2022 · Cell
88. An immune cell atlas reveals the dynamics of human macrophage specification during prenatal development
    Zeshuai Wang, Zhisheng Wu, Hao Wang, Ruoqing Feng, Guanlin Wang, Muxi Li, Shuang-Yin Wang, Xiaoyan Chen, Yiyi Su, Jun Wang et al. · 2023 · Cell
89. Lymphatic-localized Treg-mregDC crosstalk limits antigen trafficking and restrains anti-tumor immunity
    Siyuan You, Shuqin Li, Lingsu Zeng, Jinsheng Song, Zifeng Li, Weiyun Li, Hengxiao Ni, Xiao Xu, Wenbo Deng, Hongye Li et al. · 2024 · Cancer Cell
90. High-throughput single-сell sequencing in cancer research
    Qingzhu Jia, Han Chu, Zheng Jin, Haixia Long, Bo Zhu · 2022 · Signal Transduction and Targeted Therapy
91. The choroid plexus links innate immunity to CSF dysregulation in hydrocephalus
    Stephanie M. Robert, Benjamin C. Reeves, Emre Kiziltug, Phan Q. Duy, Jason K. Karimy, Mohammad Shahid Mansuri, Arnaud Marlier, Garrett Allington, Ana B.W. Greenberg, Tyrone DeSpenza et al. · 2023 · Cell
92. scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
    Dongyuan Song, Qingyang Wang, Guanao Yan, Tianyang Liu, Tianyi Sun, Jingyi Jessica Li · 2023 · Nature Biotechnology
93. Tertiary lymphoid structures critical for prognosis in endometrial cancer patients
    Nanda Horeweg, Hagma H. Workel, Dominik Loiero, David N. Church, Lisa Vermij, Alicia León‐Castillo, Ricki T. Krog, Stephanie M. de Boer, Remi A. Nout, Melanie E. B. Powell et al. · 2022 · Nature Communications
94. Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis
    Coulis, Gerald, Jaime, Diego, Guerrero-Juarez, Christian, Kastenschmidt, Jenna M., Farahat, Philip K., Nguyen, Quy, Pervolarakis, Nicholas, McLinden, Katherine, Thurlow, Lauren, Movahedi, Saba et al. · 2023 · Science Advances
95. Integrative single-cell analysis of human colorectal cancer reveals patient stratification with distinct immune evasion mechanisms
    Xiaojing Chu, Xiangjie Li, Yu Zhang, Guohui Dang, Yuhui Miao, Wenbin Xu, Jinyu Wang, Zemin Zhang, Sijin Cheng · 2024 · Nature Cancer
96. Programs, origins and immunomodulatory functions of myeloid cells in glioma
    Tyler E. Miller, Chadi A. El Farran, Charles Couturier, Zeyu Chen, Joshua P. D’Antonio, Julia A. Verga, Martin Arreola Villanueva, L. Nicolas Gonzalez Castro, Yuzhou Evelyn Tong, Tariq Dhiyab Al-Saadi et al. · 2025 · Nature
97. Multimodal single-cell chromatin analysis with Signac
    Tim Stuart, Avi Srivastava, Caleb A. Lareau, Rahul Satija · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
98. Monocytes re-enter the bone marrow during fasting and alter the host response to infection
    Janssen, Henrike, Kahles, Florian, Liu, Dan, Downey, Jeffrey, Koekkoek, Laura L., Roudko, Vladimir, D’Souza, Darwin, McAlpine, Cameron S., Halle, Lennard, Poller, Wolfram C. et al. · 2023 · Immunity
99. Analysis of Donor Pancreata Defines the Transcriptomic Signature and Microenvironment of Early Neoplastic Lesions
    Eileen S. Carpenter, Ahmed M. Elhossiny, Padma Kadiyala, Jay Li, Jake J. McGue, Brian D. Griffith, Yaqing Zhang, Jacob Edwards, Sarah Nelson, Fatima Lima et al. · 2023 · Cancer Discovery
100. Modeling post-implantation stages of human development into early organogenesis with stem-cell-derived peri-gastruloids
     Lizhong Liu, Seiya Oura, Zachary Markham, James N. Hamilton, Robin M. Skory, Leijie Li, Masahiro Sakurai, Lei Wang, Carlos A. Pinzón-Arteaga, Nicolas Plachta et al. · 2023 · Cell