Integrated analysis of multimodal single-cell data

Cited by (1,144)

Items 301–400 of 1,144

1. Spatial metatranscriptomics resolves host–bacteria–fungi interactomes
   Sami Saarenpää, Or Shalev, Haim Ashkenazy, Vanessa Carlos, Derek S. Lundberg, Detlef Weigel, Stefania Giacomello · 2023 · Nature Biotechnology
2. Single-cell transcriptomic profiling reveals the tumor heterogeneity of small-cell lung cancer
   Yanhua Tian, Qingqing Li, Zhenlin Yang, Shu Zhang, Jiachen Xu, Zhijie Wang, Hua Bai, Jianchun Duan, Bo Jian Zheng, Wen Li et al. · 2022 · Signal Transduction and Targeted Therapy
3. Spatial cellular architecture predicts prognosis in glioblastoma
   Yuanning Zheng, Francisco Carrillo‐Pérez, Marija Pizurica, Dieter Henrik Heiland, Olivier Gevaert · 2023 · Nature Communications
4. Early cellular mechanisms of type I interferon-driven susceptibility to tuberculosis
   Dmitri Ivanovich Kotov, Ophelia V. Lee, Stefan A. Fattinger, Charlotte A. Langner, Jaresley V. Guillen, Joshua M. Peters, Andres Moon, Eileen M. Burd, Kristen C. Witt, Daniel B. Stetson et al. · 2023 · Cell
5. A mixture-of-experts deep generative model for integrated analysis of single-cell multiomics data
   Kodai Minoura, Ko Abe, Hyunha Nam, Hiroyoshi Nishikawa, Teppei Shimamura · 2021 · Cell Reports Methods
6. Engraftment of allogeneic iPS cell-derived cartilage organoid in a primate model of articular cartilage defect
   Kengo Abe, Akihiro Yamashita, Miho Morioka, Nanao Horike, Yoshiaki Takei, Saeko Koyamatsu, Keisuke Okita, Shuichi Matsuda, Noriyuki Tsumaki · 2023 · Nature Communications
7. Integrated vector genomes may contribute to long-term expression in primate liver after AAV administration
   Jenny A. Greig, Kelly M. Martins, Camilo Ayala Breton, Jason Lamontagne, Yanqing Zhu, Zhenning He, John White, Jingxu Zhu, Jessica A. Chichester, Qi Zheng et al. · 2023 · Nature Biotechnology
8. Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag
   Bartosovic, Marek, Castelo-Branco, Gonçalo · 2023 · Nature Biotechnology
9. Human skeletal muscle CD90+ fibro-adipogenic progenitors are associated with muscle degeneration in type 2 diabetic patients
   Jean Farup, Jesper Just, Frank Vincenzo de Paoli, Lin Lin, Jonas Jensen, Tine Borum Billeskov, Inés Sánchez-Román, Cagla Cömert, Andreas Buch Møller, Luca Madaro et al. · 2021 · Cell Metabolism
10. Next-Generation Morphometry for pathomics-data mining in histopathology
    David Laurin Hölscher, Nassim Bouteldja, Mehdi Joodaki, María Luisa Russo, Yu-Chia Lan, Alireza Vafaei Sadr, Mingbo Cheng, Vladimı́r Tesař, Saskia Freifrau von Stillfried, Barbara M. Klinkhammer et al. · 2023 · Nature Communications
11. Towards a comprehensive evaluation of dimension reduction methods for transcriptomic data visualization
    Haiyang Huang, Yingfan Wang, Cynthia D Rudin, Edward P. Browne · 2022 · Communications Biology
12. Lipid-associated macrophages transition to an inflammatory state in human atherosclerosis, increasing the risk of cerebrovascular complications
    Lea H. Dib, Lada A. Koneva, Andreas Edsfeldt, Yasemin-Xiomara Zurke, Jiangming Sun, Mihaela Nitulescu, Moustafa Attar, Esther Lutgens, Steffen Schmidt, Marie Lindholm et al. · 2023 · Nature Cardiovascular Research
13. Signature of long-lived memory CD8+ T cells in acute SARS-CoV-2 infection
    Sarah Adamo, Jan Michler, Yves Zurbuchen, Carlo Cervia, Patrick Taeschler, Miro E. Raeber, Simona Baghai Sain, Jakob Nilsson, Andreas E. Moor, Onur Boyman · 2021 · Nature
14. Comparative analysis of cell–cell communication at single-cell resolution
    Aaron J. Wilk, Alex K. Shalek, Susan Holmes, Catherine A. Blish · 2023 · Nature Biotechnology
15. SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor
    Dario Righelli, Lukas M. Weber, Helena Lucia Crowell, Brenda Pardo, Leonardo Collado‐Torres, Shila Ghazanfar, Aaron T. L. Lun, Stephanie C. Hicks, Davide Risso · 2022 · Bioinformatics
16. Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq
    Vincent Hahaut, Dinko Pavlinić, Walter Carbone, Sven Schuierer, Pierre Balmer, Mathieu Quinodoz, Magdalena Renner, Guglielmo Roma, Cameron S. Cowan, Simone Picelli · 2022 · Nature Biotechnology
17. Deep learning applications in single-cell genomics and transcriptomics data analysis
    Nafiseh Erfanian, A. Ali Heydari, Adib Miraki Feriz, Pablo Iáñez Picazo, Afshin Derakhshani, Mohammad GhasemiGol, Mohsen Farahpour, Seyyed Mohammad Razavi, Saeed Nasseri, Hossein Safarpour et al. · 2023 · Biomedicine & Pharmacotherapy
18. Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics
    Bozeng Tang, Feng Li, Michelle T. Hulin, Pingtao Ding, Wenbo Ma · 2023 · Cell Host & Microbe
19. CZ CELL×GENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data
    CZI Single-Cell Biology Program, Abdulla, Shibla, Aevermann, Brian, Assis, Pedro, Badajoz, Seve, Bell, Sidney M., Bezzi, Emanuele, Cakir, Batuhan, Chaffer, Jim, Chambers, Signe et al. · 2023
20. Acquisition of epithelial plasticity in human chronic liver disease
    Gribben, Christopher, Galanakis, Vasileios, Calderwood, Alexander, Williams, Eleanor C., Chazarra-Gil, Ruben, Larraz, Miguel, Frau, Carla, Puengel, Tobias, Guillot, Adrien, Rouhani, Foad J. et al. · 2024 · Nature
21. Periodic formation of epithelial somites from human pluripotent stem cells
    Marina Sanaki-Matsumiya, Mitsuhiro Matsuda, Nicola Gritti, Fumio Nakaki, James A. Sharpe, Vikas Trivedi, Miki Ebisuya · 2022 · Nature Communications
22. Single‐Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma
    Zhihua Ou, Shitong Lin, Jiaying Qiu, Wencheng Ding, Peidi Ren, Dongsheng Chen, Jiaxuan Wang, Yihan Tong, Di Wu, Ao Chen et al. · 2022 · Advanced Science
23. Beiging of perivascular adipose tissue regulates its inflammation and vascular remodeling
    Yusuke Adachi, Kazutaka Ueda, Seitaro Nomura, Kaoru Ito, Manami Katoh, Mikako Katagiri, Shintaro Yamada, Masaki Hashimoto, Bowen Zhai, Genri Numata et al. · 2022 · Nature Communications
24. Interrogating glioma-M2 macrophage interactions identifies Gal-9/Tim-3 as a viable target against PTEN -null glioblastoma
    Xiangrong Ni, Wei-Chi Wu, Xiaoqiang Sun, Jun-Xiao Ma, Zhihui Yü, Xinwei He, Jinyu Cheng, Pengfei Xu, Haoxian Liu, Tengze Shang et al. · 2022 · Science Advances
25. PHGDH-mediated endothelial metabolism drives glioblastoma resistance to chimeric antigen receptor T cell immunotherapy
    Duo Zhang, Albert Mao Li, Guanghui Hu, Menggui Huang, Fan Yang, Lin Zhang, Kathryn E. Wellen, Xiaowei Xu, Crystal S. Conn, Wei Zou et al. · 2023 · Cell Metabolism
26. Stat5 opposes the transcription factor Tox and rewires exhausted CD8+ T cells toward durable effector-like states during chronic antigen exposure
    Jean‐Christophe Beltra, Mohamed S. Abdel-Hakeem, Sasikanth Manne, Zhen Zhang, Hua Huang, Makoto Kurachi, Leon Su, Lora K. Picton, Shin Foong Ngiow, Yuki Muroyama et al. · 2023 · Immunity
27. Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence
    Zhang, Shuming, Yuan, Long, Danilova, Ludmila, Mo, Guanglan, Zhu, Qingfeng, Deshpande, Atul, Bell, Alexander T. F., Elisseeff, Jennifer, Popel, Aleksander S., Anders, Robert A. et al. · 2023 · Genome Medicine
28. Astrocyte transcriptomic changes along the spatiotemporal progression of Alzheimer’s disease
    Serrano-Pozo, Alberto, Li, Huan, Li, Zhaozhi, Muñoz-Castro, Clara, Jaisa-aad, Methasit, Healey, Molly A., Welikovitch, Lindsay A., Jayakumar, Rojashree, Bryant, Annie G., Noori, Ayush et al. · 2024 · Nature Neuroscience
29. Single-Cell RNA Sequencing Reveals the Heterogeneity of Tumor-Associated Macrophage in Non-Small Cell Lung Cancer and Differences Between Sexes
    Qi Yang, Hongman Zhang, Ting Wei, Anqi Lin, Yueqin Sun, Peng Luo, Jian Zhang · 2021 · Frontiers in Immunology
30. IFNγ and GM-CSF control complementary differentiation programs in the monocyte-to-phagocyte transition during neuroinflammation
    Amorim, Ana, De Feo, Donatella, Friebel, Ekaterina, Ingelfinger, Florian, Anderfuhren, Cyrill Dimitri, Krishnarajah, Sinduya, Andreadou, Myrto, Welsh, Christina A., Liu, Zhaoyuan, Ginhoux, Florent et al. · 2022 · Nature Immunology
31. Secondary influenza challenge triggers resident memory B cell migration and rapid relocation to boost antibody secretion at infected sites
    Andrew J. MacLean, Niamh Richmond, Lada A. Koneva, Moustafa Attar, Cesar A. Prada‐Medina, Emily E. Thornton, Ariane Cruz Gomes, Aadil El-Turabi, Martin F. Bachmann, Pramila Rijal et al. · 2022 · Immunity
32. The antioxidant enzyme Peroxiredoxin-1 controls stroke-associated microglia against acute ischemic stroke
    Sinai Kim, Wonhyo Lee, Huiju Jo, Seongkeun Sonn, Se‐Jin Jeong, Seungwoon Seo, Joowon Suh, Jing Jin, Hyae Yon Kweon, Tae Kyeong Kim et al. · 2022 · Redox Biology
33. Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data
    Lijia Yu, Yue Cao, Jean Yee Hwa Yang, Pengyi Yang · 2022 · Genome biology
34. Engineered CD47 protects T cells for enhanced antitumour immunity
    Sean A. Yamada‐Hunter, Johanna Lena Theruvath, Brianna J. McIntosh, Katherine A. Freitas, Frank H. S. Lin, Molly Radosevich, Amaury Leruste, Shaurya Dhingra, Naiara Martínez-Vélez, Peng Xu et al. · 2024 · Nature
35. Multimodal decoding of human liver regeneration
    Matchett, K. P., Wilson-Kanamori, J. R., Portman, J. R., Kapourani, C. A., Fercoq, F., May, S., Zajdel, E., Beltran, M., Sutherland, E. F., Mackey, J. B. G. et al. · 2024 · Nature
36. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia
    Ferran Nadeu, Romina Royo, Ramon Massoni-Badosa, Heribert Playà-Albinyana, Beatriz García-Torre, Martí Duran‐Ferrer, Kevin J. Dawson, Marta Kulis, Ander Díaz‐Navarro, Neus Villamor et al. · 2022 · Nature Medicine
37. The transcription factor IRF2 drives interferon-mediated CD8+ T cell exhaustion to restrict anti-tumor immunity
    Sabelo Lukhele, Diala Abd-Rabbo, Mengdi Guo, Jian Shen, Heidi J. Elsaesser, Rene Quevedo, Madeleine Carew, Ramy Gadalla, Laura M. Snell, Lawanya Mahesh et al. · 2022 · Immunity
38. The type 2 cytokine Fc–IL-4 revitalizes exhausted CD8+ T cells against cancer
    Bing Feng, Zhiliang Bai, Xiaolei Zhou, Yang Zhao, Yuqing Xie, Xinyi Huang, Yang Liu, Tom Enbar, Rongrong Li, Yi Wang et al. · 2024 · Nature
39. Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma
    Daniel H. Shu, Won Jin Ho, Luciane Tsukamoto Kagohara, Alexander A. Girgis, Sarah M. Shin, Ludmila Danilova, Jae Woo Lee, Dimitrios N. Sidiropoulos, Sarah Mitchell, Kabeer Munjal et al. · 2024 · Nature Immunology
40. A spatially resolved multi-omic single-cell atlas of soybean development
    Xuan Zhang, Ziliang Luo, Alexandre P. Marand, Haidong Yan, Hosung Jang, Sohyun Bang, John Pablo Mendieta, Mark A.A. Minow, Robert J. Schmitz · 2024 · Cell
41. Reconstituting human somitogenesis in vitro
    Yoshihiro Yamanaka, Sofiane Hamidi, Kumiko Yoshioka-Kobayashi, Sirajam Munira, Kazunori Sunadome, Yi Zhang, Yuzuru Kurokawa, Rolf Ericsson, Ai Mieda, Jamie Louise Thompson et al. · 2022 · Nature
42. Multimodal spatiotemporal phenotyping of human retinal organoid development
    Philipp Wahle, Giovanna Brancati, Christoph Harmel, Zhisong He, Gabriele Gut, Jacobo Sarabia del Castillo, Aline Xavier da Silveira dos Santos, Qianhui Yu, Pascal Noser, Jonas Simon Fleck et al. · 2023 · Nature Biotechnology
43. MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
    Robin Browaeys, Jeroen Gilis, Chananchida Sang-aram, Pieter De Bleser, Levi Hoste, Simon Jan Tavernier, Diether Lambrechts, Ruth Seurinck, Yvan Saeys · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
44. A population-level digital histologic biomarker for enhanced prognosis of invasive breast cancer
    Amgad, Mohamed, Hodge, James M., Elsebaie, Maha A. T., Bodelon, Clara, Puvanesarajah, Samantha, Gutman, David A., Siziopikou, Kalliopi P., Goldstein, Jeffery A., Gaudet, Mia M., Teras, Lauren R. et al. · 2024 · Nature Medicine
45. Systematic single-cell pathway analysis to characterize early T cell activation
    Jack A. Bibby, Divyansh Agarwal, Tilo Freiwald, Natalia Kunz, Nicolas S. Merle, Erin E. West, Parul Singh, André Larochelle, Fariba Chinian, Somabha Mukherjee et al. · 2022 · Cell Reports
46. The developmental basis of fingerprint pattern formation and variation
    Glover, James D., Sudderick, Zoe R., Shih, Barbara Bo-Ju, Batho-Samblas, Cameron, Charlton, Laura, Krause, Andrew L., Anderson, Calum, Riddell, Jon, Balic, Adam, Li, Jinxi et al. · 2023 · Cell
47. Transcriptional and spatial profiling of the kidney allograft unravels a central role for FcyRIII+ innate immune cells in rejection
    Baptiste Lamarthée, Jasper Callemeyn, Yannick Van Herck, Asier Antoranz, Dany Anglicheau, Patrick Boada, Jan Ulrich Becker, Tim Debyser, Frederik De Smet, Katrien De Vusser et al. · 2023 · Nature Communications
48. SOX9 switch links regeneration to fibrosis at the single-cell level in mammalian kidneys
    Shikhar Aggarwal, Zhanxiang Wang, David Rincon Fernandez Pacheco, Anna Rinaldi, Alex C. Rajewski, Jasper Callemeyn, Elisabet Van Loon, Baptiste Lamarthée, Ambart E. Covarrubias, Jean Hou et al. · 2024 · Science
49. Modeling embryo-endometrial interface recapitulating human embryo implantation
    Shun Shibata, Shun Endo, Luís Augusto Eijy Nagai, Eri H. Kobayashi, Akira Oike, Norio Kobayashi, Akane Kitamura, Takeshi Hori, Yuji Nashimoto, Ryuichiro Nakato et al. · 2024 · Science Advances
50. Spatial transcriptomics in health and disease
    Sanjay R. Jain, Michael T. Eadon · 2024 · Nature Reviews Nephrology
51. Divergent roles for the gut intraepithelial lymphocyte GLP-1R in control of metabolism, microbiota, and T cell-induced inflammation
    Wong, Chi Kin, Yusta, Bernardo, Koehler, Jacqueline A., Baggio, Laurie L., McLean, Brent A., Matthews, Dianne, Seeley, Randy J., Drucker, Daniel J. · 2022 · Cell Metabolism
52. Clustering of single-cell multi-omics data with a multimodal deep learning method
    Lin, Xiang, Tian, Tian, Wei, Zhi, Hakonarson, Hakon · 2022 · Nature Communications
53. Spatial transcriptomics atlas reveals the crosstalk between cancer-associated fibroblasts and tumor microenvironment components in colorectal cancer
    Zhiwei Peng, Manping Ye, Huiming Ding, Zhenyou Feng, Kongwang Hu · 2022 · Journal of Translational Medicine
54. Single cell sequencing identifies clonally expanded synovial CD4+ TPH cells expressing GPR56 in rheumatoid arthritis
    Alexandra Argyriou, Marc H. Wadsworth, Adrian Lendvai, Stephen M. Christensen, Aase Haj Hensvold, Christina Gerstner, Annika van Vollenhoven, Kellie M. Kravarik, Aaron R. Winkler, Vivianne Malmström et al. · 2022 · Nature Communications
55. Periportal macrophages protect against commensal-driven liver inflammation
    Miyamoto, Yu, Kikuta, Junichi, Matsui, Takahiro, Hasegawa, Tetsuo, Fujii, Kentaro, Okuzaki, Daisuke, Liu, Yu-chen, Yoshioka, Takuya, Seno, Shigeto, Motooka, Daisuke et al. · 2024 · Nature
56. Pan-cancer landscape of T-cell exhaustion heterogeneity within the tumor microenvironment revealed a progressive roadmap of hierarchical dysfunction associated with prognosis and therapeutic efficacy
    Zicheng Zhang, Lu Chen, Hongyan Chen, Jing Zhao, Ke Li, Jie Sun, Meng Zhou · 2022 · EBioMedicine
57. ARID1A suppresses R-loop-mediated STING-type I interferon pathway activation of anti-tumor immunity
    Matthew B. Maxwell, Marianne S. Hom, Jawoon Yi, Shitian Li, Samuel A. Rivera, Jingting Yu, Mannix J. Burns, Helen M. McRae, Braden T. Stevenson, Katherine E. Coakley et al. · 2024 · Cell
58. Detection of cell–cell interactions via photocatalytic cell tagging
    Oslund, Rob C., Reyes-Robles, Tamara, White, Cory H., Tomlinson, Jake H., Crotty, Kelly A., Bowman, Edward P., Chang, Dan, Peterson, Vanessa M., Li, Lixia, Frutos, Silvia et al. · 2022 · Nature Chemical Biology
59. Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age
    Yufei Wang, Ronghong Li, Renyang Tong, Taiwei Chen, Mingze Sun, Lingjie Luo, Zheng Li, Yifan Chen, Yichao Zhao, Chensheng Zhang et al. · 2025 · Nature Immunology
60. Neuronal APOE4 removal protects against tau-mediated gliosis, neurodegeneration and myelin deficits
    Koutsodendris, Nicole, Blumenfeld, Jessica, Agrawal, Ayushi, Traglia, Michela, Grone, Brian, Zilberter, Misha, Yip, Oscar, Rao, Antara, Nelson, Maxine R., Hao, Yanxia et al. · 2023 · Nature Aging
61. Homeostatic IL-13 in healthy skin directs dendritic cell differentiation to promote TH2 and inhibit TH17 cell polarization
    Johannes U. Mayer, Kerry L. Hilligan, Jodie S. Chandler, David Eccles, Samuel I. Old, Rita G. Domingues, Jianping Yang, Greta R. Webb, Luis Munoz‐Erazo, Evelyn J. Hyde et al. · 2021 · Nature Immunology
62. Interleukin-10 receptor signaling promotes the maintenance of a PD-1int TCF-1+ CD8+ T cell population that sustains anti-tumor immunity
    Bola S. Hanna, Laura Llaó Cid, Murat Iskar, Philipp M. Roessner, Lara C. Klett, John Wong, Yashna Paul, Nikolaos Ioannou, Selcen Öztürk, Norman L. Mack et al. · 2021 · Immunity
63. Prenatal immune stress blunts microglia reactivity, impairing neurocircuitry
    Lindsay N. Hayes, Kyongman An, Elisa Carloni, Fangze Li, Elizabeth Vincent, Chloë Trippaers, Manish D. Paranjpe, Gül Dölen, Loyal A. Goff, Adriana Ramos et al. · 2022 · Nature
64. An exhausted-like microglial population accumulates in aged and APOE4 genotype Alzheimer’s brains
    Millet, Alon, Ledo, Jose Henrique, Tavazoie, Sohail F. · 2024 · Immunity
65. The multilayered transcriptional architecture of glioblastoma ecosystems
    Masashi Nomura, Avishay Spitzer, Kevin C. Johnson, Luciano Garofano, Djamel Nehar-Belaid, Noam Galili Darnell, Alissa Greenwald, Lillian Bussema, Young Taek Oh, Frederick S. Varn et al. · 2025 · Nature Genetics
66. The gut microbiota promotes distal tissue regeneration via RORγ+ regulatory T cell emissaries
    Hanna, Bola S., Wang, Gang, Galván-Peña, Silvia, Mann, Alexander O., Ramirez, Ricardo N., Muñoz-Rojas, Andrés R., Smith, Kathleen, Wan, Min, Benoist, Christophe, Mathis, Diane · 2023 · Immunity
67. Radiation exposure elicits a neutrophil-driven response in healthy lung tissue that enhances metastatic colonization
    Emma Nolan, Victoria Louise Bridgeman, Luigi Ombrato, Adam Karoutas, Nicolas Rabas, Celine Angeli Natascha Sewnath, Marcos Vásquez, Felipe Silva Rodrigues, Stuart D. Horswell, Peter Allen Faull et al. · 2022 · Nature Cancer
68. Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis
    Tomohito Doke, Amin Abedini, Daniel L. Aldridge, Ya‐Wen Yang, Jihwan Park, Christina M. Hernandez, Michael S. Balzer, Rojesh Shrestra, Gaia Coppock, Juan Manuel Inclan-Rico et al. · 2022 · Nature Immunology
69. Upregulation of PD-L1 in Senescence and Aging
    Angelique Onorati, Aaron P. Havas, Brian Lin, Jayaraj Rajagopal, Payel Sen, Peter D. Adams, Zhixun Dou · 2022 · Molecular and Cellular Biology
70. Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer
    Kelsy C. Cotto, Yang-Yang Feng, Avinash Ramu, Megan M. Richters, Sharon L. Freshour, Zachary L. Skidmore, Huiming Xia, Joshua F. McMichael, Jason Kunisaki, Katie Marie Campbell et al. · 2023 · Nature Communications
71. SPACEL: deep learning-based characterization of spatial transcriptome architectures
    Hao Xu, Shuyan Wang, Minghao Fang, Songwen Luo, Chunpeng Chen, Siyuan Wan, Rirui Wang, Meifang Tang, Tian Xue, Bin Li et al. · 2023 · Nature Communications
72. Circadian control of tumor immunosuppression affects efficacy of immune checkpoint blockade
    Bridget M. Fortin, Shannon M. Pfeiffer, Jacob Insua‐Rodríguez, Hamad S. Alshetaiwi, Alexander Moshensky, Wei A. Song, Alisa L. Mahieu, Sung Kook Chun, Amber N. Lewis, Alex Hsu et al. · 2024 · Nature Immunology
73. Spatial transcriptomic analysis of primary and metastatic pancreatic cancers highlights tumor microenvironmental heterogeneity
    Ateeq Muhammed Khaliq, Meenakshi Rajamohan, Omer Abdelaziz Mohammed Saeed, Kimia Mansouri, Asif Adil, Chi Zhang, Anita Ahmed Turk, Julienne L. Carstens, Michael Garrett House, Sikander Hayat et al. · 2024 · Nature Genetics
74. Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction
    Li, Chen, Virgilio, Maria C., Collins, Kathleen L., Welch, Joshua D. · 2023 · Nature Biotechnology
75. Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics
    Valdeolivas, Alberto, Amberg, Bettina, Giroud, Nicolas, Richardson, Marion, Gálvez, Eric J. C., Badillo, Solveig, Julien-Laferrière, Alice, Túrós, Demeter, Voith von Voithenberg, Lena, Wells, Isabelle et al. · 2024 · npj Precision Oncology
76. Chronic type I interferon signaling promotes lipid-peroxidation-driven terminal CD8+ T cell exhaustion and curtails anti-PD-1 efficacy
    Weixin Chen, Jia Ming Nickolas Teo, Siu Wah Yau, Melody Yee‐Man Wong, Chun‐Nam Lok, Chi‐Ming Che, Asif Javed, Yuanhua Huang, Stephanie Ma, Guang Sheng Ling · 2022 · Cell Reports
77. Targeting pancreatic cancer by TAK-981: a SUMOylation inhibitor that activates the immune system and blocks cancer cell cycle progression in a preclinical model
    Sumit Kumar, Mark J.A. Schoonderwoerd, Jessie S. Kroonen, Ilona J. de Graaf, Marjolein Sluijter, Dina Ruano, Román González‐Prieto, Matty Verlaan–de Vries, Jasper Rip, Ramon Arens et al. · 2022 · Gut
78. Lipid-laden lung mesenchymal cells foster breast cancer metastasis via metabolic reprogramming of tumor cells and natural killer cells
    Zheng Gong, Qing Li, Jiayuan Shi, Edison T. Liu, Leonard D. Shultz, Guangwen Ren · 2022 · Cell Metabolism
79. Molecular and metabolic heterogeneity of astrocytes and microglia
    Philip Hasel, William H. Aisenberg, F. Chris Bennett, Shane Antony Liddelow · 2023 · Cell Metabolism
80. Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus
    Xiehai Song, Pengru Guo, Keke Xia, Meiling Wang, Yongqi Liu, Lichuan Chen, Jinhui Zhang, Mengyuan Xu, Naixu Liu, Zhi-Liang Yue et al. · 2023 · Proceedings of the National Academy of Sciences
81. Integrated single-cell and spatial transcriptomics uncover distinct cellular subtypes involved in neural invasion in pancreatic cancer
    Minmin Chen, Qinhang Gao, Huiheng Ning, Kang Chen, Yang Gao, Min Yu, Chaoqun Liu, Wei Zhou, Jieying Pan, Lusheng Wei et al. · 2025 · Cancer Cell
82. Lithium deficiency and the onset of Alzheimer’s disease
    Liviu Aron, Zhen‐Kai Ngian, Chenxi Qiu, Jaejoon Choi, Marianna Liang, Derek Drake, Sara E Hamplova, Ella K. Lacey, Perle Roche, Monlan Yuan et al. · 2025 · Nature
83. Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES
    Micha Sam Brickman Raredon, Junchen Yang, Neeharika Kothapalli, Wesley Lewis, Naftali Kaminski, Laura E. Niklason, Yuval Kluger · 2022 · Bioinformatics
84. Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
    Lőrinc Sándor Pongor, Christopher William Schultz, Lorenzo Rinaldi, Darawalee Wangsa, Christophe E. Redon, Nobuyuki Takahashi, Gavriel Fialkoff, Parth Anil Desai, Yang Zhang, Sandra Sczerba Burkett et al. · 2023 · Cancer Discovery
85. Integrated multi-omics profiling to dissect the spatiotemporal evolution of metastatic hepatocellular carcinoma
    Yun‐Fan Sun, Pin Wu, Zefan Zhang, Zejian Wang, Kaiqian Zhou, Minfang Song, Yuan Ji, Fenglin Zang, Limu Lou, Keqiang Rao et al. · 2023 · Cancer Cell
86. Stroke induces disease-specific myeloid cells in the brain parenchyma and pia
    Carolin Beuker, David Schafflick, Jan‐Kolja Strecker, Michael Heming, Xiaolin Li, Jolien Wolbert, Antje Schmidt‐Pogoda, Christian Thomas, Tanja Kuhlmann, Irene Aranda-Pardos et al. · 2022 · Nature Communications
87. Single-cell transcriptomics identifies Mcl-1 as a target for senolytic therapy in cancer
    Martina Troiani, Manuel Colucci, Mariantonietta D’Ambrosio, Ilaria Guccini, Emiliano Pasquini, Angelica Varesi, Aurora Valdata, Simone Mosole, Ajinkya Revandkar, Giuseppe Attanasio et al. · 2022 · Nature Communications
88. Inhalable Stem Cell Exosomes Promote Heart Repair After Myocardial Infarction
    Junlang Li, Shenghuan Sun, Dashuai Zhu, Xuan Mei, Yongbo Lyu, Ke Huang, Yuan Li, Shuo Liu, Zhenzhen Wang, Shiqi Hu et al. · 2024 · Circulation
89. CancerSCEM: a database of single-cell expression map across various human cancers
    Jingyao Zeng, Yadong Zhang, Yunfei Shang, Jialin Mai, Shuo Shi, Mingming Lu, Congfan Bu, Zhewen Zhang, Zaichao Zhang, Yang Li et al. · 2021 · Nucleic Acids Research
90. Gene function and cell surface protein association analysis based on single-cell multiomics data
    Huan Hu, Zhen Feng, Hai Lin, Jinyan Cheng, Jie Lyu, Yaru Zhang, Junjie Zhao, Fei Xu, Tao Lin, Qi Zhao et al. · 2023 · Computers in Biology and Medicine
91. A platform for efficient establishment and drug-response profiling of high-grade serous ovarian cancer organoids
    Wojciech Senkowski, Laura Gall-Mas, Matías Marín Falco, Yilin Li, Kari Lavikka, Mette C. Kriegbaum, Jaana Oikkonen, Daria R. Bulanova, Elin J. Pietras, Karolin Voßgröne et al. · 2023 · Developmental Cell
92. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels
    Natalia Eberhardt, Maria Gabriela Noval, Ravneet Kaur, Letizia Amadori, Michael A. Gildea, Swathy Sajja, Dayasagar Das, Burak Cılhoroz, O’Jay Stewart, Dawn M. Fernandez et al. · 2023 · Nature Cardiovascular Research
93. Proteomic changes in Alzheimer’s disease associated with progressive Aβ plaque and tau tangle pathologies
    Alexa Pichet Binette, Chris Gaiteri, Malin Wennström, Atul Kumar, Inès Hristovska, Nicola Spotorno, Gemma Salvadó, Olof T. Strandberg, Hansruedi Mathys, Li‐Huei Tsai et al. · 2024 · Nature Neuroscience
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