Scenic: single-cell regulatory network inference and clustering.

Cited by (1,038)

Items 601–700 of 1,038

1. 3D reconstruction of a gastrulating human embryo
   Zhenyu Xiao, Lina Cui, Yang Yuan, Nannan He, Xinwei Xie, Sirui Lin, Xiaolong Yang, Xin Zhang, Peifu Shi, Zhifeng Wei et al. · 2024 · Cell
2. SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells
   Kearney, Conor J., Vervoort, Stephin J., Ramsbottom, Kelly M., Todorovski, Izabela, Lelliott, Emily J., Zethoven, Magnus, Pijpers, Lizzy, Martin, Ben P., Semple, Timothy, Martelotto, Luciano et al. · 2021 · Science Advances
3. SARS-CoV-2 activates lung epithelial cell proinflammatory signaling and leads to immune dysregulation in COVID-19 patients
   Huarong Chen, Weixin Liu, Yifei Wang, Dabin Liu, Liuyang Zhao, Jun Qing Yu · 2021 · EBioMedicine
4. Modeling human multi-lineage heart field development with pluripotent stem cells
   Donghe Yang, Juliana Gomez-Garcia, Shunsuke Funakoshi, Thinh Ngoc Tran, Ian M. Fernandes, Gary D. Bader, Michael A. Laflamme, Gordon M. Keller · 2022 · Cell stem cell
5. Sex differences in resilience to ferroptosis underlie sexual dimorphism in kidney injury and repair
   Shintaro Ide, Kana Ide, Koki Abe, Yoshihiko Kobayashi, Hiroki Kitai, Jennifer McKey, Sarah A. Strausser, Lori L. O’Brien, Aleksandra Tata, Purushothama Rao Tata et al. · 2022 · Cell Reports
6. Single-cell transcriptomic Atlas of mouse cochlear aging
   Guoqiang Sun, Yandong Zheng, Xiaolong Fu, Weiqi Zhang, Jie Ren, Shuai Ma, Shuhui Sun, Xiaojuan He, Qiaoran Wang, Zhejun Ji et al. · 2022 · Protein & Cell
7. Multi-omics analysis of human mesenchymal stem cells shows cell aging that alters immunomodulatory activity through the downregulation of PD-L1
   Yuchen Gao, Ying Chi, Yunfei Chen, Wentian Wang, Huiyuan Li, Wenting Zheng, Ping Zhu, Jinying An, Yanan Duan, Ting Sun et al. · 2023 · Nature Communications
8. Spatiotemporal insight into early pregnancy governed by immune-featured stromal cells
   Min Yang, Jennie Ong, Fanju Meng, Feixiang Zhang, Hui Shen, Kerstin Kitt, Tengfei Liu, Wei Tao, Peng Du · 2023 · Cell
9. Endothelial sensing of AHR ligands regulates intestinal homeostasis
   Wiggins, Benjamin G., Wang, Yi-Fang, Burke, Alice, Grunberg, Nil, Vlachaki Walker, Julia M., Dore, Marian, Chahrour, Catherine, Pennycook, Betheney R., Sanchez-Garrido, Julia, Vernia, Santiago et al. · 2023 · Nature
10. Computational Methods for Single-Cell RNA Sequencing
    Brian Hie, Joshua M. Peters, Sarah K. Nyquist, Alex K. Shalek, Bonnie Berger, Bryan D. Bryson · 2020 · Annual Review of Biomedical Data Science
11. Identification and characterization of cellular heterogeneity within the developing renal interstitium
    Alicia R. England, Christopher P. Chaney, Amrita Das, Mohita Patel, Alicia Malewska, Daniel A. Armendariz, Gary C. Hon, Douglas W. Strand, Keri A. Drake, Thomas J. Carroll · 2020 · Development
12. Single-Cell RNA Sequencing of Childhood Ependymoma Reveals Neoplastic Cell Subpopulations That Impact Molecular Classification and Etiology
    Austin E. Gillen, Kent A. Riemondy, Vladimir M. Amani, Andrea M. Griesinger, Ahmed Gilani, Sujatha Venkataraman, Krishna P.C. Madhavan, Eric W. Prince, Bridget L. Sanford, Todd Cameron Hankinson et al. · 2020 · Cell Reports
13. PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle
    Tongbin Wu, Zhengyu Liang, Zengming Zhang, Canzhao Liu, Lunfeng Zhang, Yusu Gu, Kirk L. Peterson, Sylvia M. Evans, Xiang‐Dong Fu, Ju Chen · 2021 · Circulation
14. Sequential Single-Cell Transcriptional and Protein Marker Profiling Reveals TIGIT as a Marker of CD19 CAR-T Cell Dysfunction in Patients with Non-Hodgkin Lymphoma
    Zachary Jackson, Changjin Hong, Robert Schauner, Boro Dropulić, Paolo Fabrizio Caimi, Marcos J. G. De Lima, Maria Florencia Giraudo, Kalpana Gupta, Jane Reese, Tae Hyun Hwang et al. · 2022 · Cancer Discovery
15. Tumor immunogenicity dictates reliance on TCF1 in CD8+ T cells for response to immunotherapy
    Giulia Escobar, Katherine Tooley, Joan Pagès Oliveras, Linglin Huang, Hanning Cheng, Michelle L. Bookstaver, Camilla Edwards, Eugene Froimchuk, Chang Xue, Davide Mangani et al. · 2023 · Cancer Cell
16. Decoding aging-dependent regenerative decline across tissues at single-cell resolution
    Yusheng Cai, Muzhao Xiong, Zijuan Xin, Chengyu Liu, Jie Ren, Xiying Yang, Jinghui Lei, Wei Li, Fei‐Fei Liu, Qun Chu et al. · 2023 · Cell stem cell
17. An immune cell map of human lung adenocarcinoma development reveals an anti-tumoral role of the Tfh-dependent tertiary lymphoid structure
    Wei Liu, Wenhua You, Zhenwei Lan, Yijiu Ren, Shuangshu Gao, Shuchao Li, Weiwei Chen, Chunyu Huang, Yong Zeng, Nengming Xiao et al. · 2024 · Cell Reports Medicine
18. Causal identification of single-cell experimental perturbation effects with CINEMA-OT
    Dong, Mingze, Wang, Bao, Wei, Jessica, de O. Fonseca, Antonio H., Perry, Curtis J., Frey, Alexander, Ouerghi, Feriel, Foxman, Ellen F., Ishizuka, Jeffrey J., Dhodapkar, Rahul M. et al. · 2023 · Nature Methods
19. Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
    Bravo González‐Blas, Carmen, Quan, Xiao‐Jiang, Duran‐Romaña, Ramon, Taskiran, Ibrahim Ihsan, Koldere, Duygu, Davie, Kristofer, Christiaens, Valerie, Makhzami, Samira, Hulselmans, Gert, de Waegeneer, Maxime et al. · 2020 · Molecular Systems Biology
20. Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells
    Thi Xuan Ai Pham, Amitesh Panda, Harunobu Kagawa, San Kit To, Cankat Ertekin, Grigorios Georgolopoulos, Sam Samuel Franciscus Allegonda van Knippenberg, Ryan Allsop, Alexandre Bruneau, Jonathan Sai‐Hong Chui et al. · 2022 · Cell stem cell
21. Biomedical Big Data Technologies, Applications, and Challenges for Precision Medicine: A Review
    Xue Yang, Kexin Huang, Dewei Yang, Weiling Zhao, Xiaobo Zhou · 2023 · Global Challenges
22. Single-cell tumor heterogeneity landscape of hepatocellular carcinoma: unraveling the pro-metastatic subtype and its interaction loop with fibroblasts
    De‐Zhen Guo, Xin Zhang, Sen-Quan Zhang, Shiyu Zhang, Xiangyu Zhang, Jiayan Yan, San-Yuan Dong, Kai Zhu, Xin-Rong Yang, Jia Fan et al. · 2024 · Molecular Cancer
23. Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis
    Jonas C. Schupp, Sara Khanal, José L. Gómez, Maor Sauler, Taylor Sterling Adams, Geoffrey Lowell Chupp, Xiting Yan, Sergio Poli, Yujiao Zhao, Ruth R. Montgomery et al. · 2020 · American Journal of Respiratory and Critical Care Medicine
24. DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data
    Jiaxing Chen, ChinWang Cheong, Liang Lan, Xin Zhou, Jiming Liu, Aiping Lü, William K. Cheung, Lu Zhang · 2021 · Briefings in Bioinformatics
25. Single-cell RNA-sequencing analysis of the developing mouse inner ear identifies molecular logic of auditory neuron diversification
    Charles Petitpré, Louis Faure, Phoebe Uhl, Paula Fontanet, Iva Filová, Gabriela Pavlínková, Igor I. Adameyko, Saïda Hadjab, François Lallemend · 2022 · Nature Communications
26. Single-Cell RNA Sequencing Reveals Potential for Endothelial-to-Mesenchymal Transition in Tetralogy of Fallot
    Zulibiya Aisa, Jing Wen, Huiqing Yu, Xiaoming Chen, Lei Xu, Xiao Ma, Baojian Zhang · 2023 · Congenital Heart Disease
27. Coordinated chemokine expression defines macrophage subsets across tissues
    Xin Li, Arlind B. Mara, Shawn C. Musial, Kavita Rawat, William T. King, Fred W. Kolling, Nikita Gerebtsov, Claudia Jakubzick · 2024 · Nature Immunology
28. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Alessandro Pastore, Federico Gaiti, Sydney X. Lu, Ryan M. Brand, Scott Kulm, Ronan Chaligné, Hongcang Gu, Kevin Y. Huang, Elena K. Stamenova, Wendy Béguelin et al. · 2019 · Nature Communications
29. Revealing dynamics of gene expression variability in cell state space
    Dominic Grün · 2019 · Nature Methods
30. Single-cell transcriptome atlas of lung adenocarcinoma featured with ground glass nodules
    Tao Lu, Xiaodong Yang, Yu Shi, Mengnan Zhao, Guoshu Bi, Jiaqi Liang, Zhencong Chen, Yiwei Huang, Wei Jiang, Zongwu Lin et al. · 2020 · Cell Discovery
31. Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations
    Zhao-Zhe Hao, Jia-Ru Wei, Dongchang Xiao, Ruifeng Liu, Nana Xu, Lei Tang, Mengyao Huang, Yuhui Shen, Changsheng Xing, Wanjing Huang et al. · 2022 · Nature Neuroscience
32. Single-Cell RNA Sequencing of Coronary Perivascular Adipose Tissue From End-Stage Heart Failure Patients Identifies SPP1 + Macrophage Subpopulation as a Target for Alleviating Fibrosis
    Mengxia Fu, Songren Shu, Zhiming Peng, Xiaorui Liu, Xiao Chen, Zhiwei Zeng, Yicheng Yang, Hao Cui, Ruojin Zhao, Xiaohu Wang et al. · 2023 · Arteriosclerosis Thrombosis and Vascular Biology
33. Mapping and modeling human colorectal carcinoma interactions with the tumor microenvironment
    Ning Li, Qin Zhu, Yuhua Tian, Kyung Jin Ahn, Xin Wang, Zvi Cramer, Justine Jou, Ian Wesley Folkert, Pengfei Yu, Stephanie Adams‐Tzivelekidis et al. · 2023 · Nature Communications
34. Single‐Cell Atlas of Human Ovaries Reveals The Role Of The Pyroptotic Macrophage in Ovarian Aging
    Chuanchuan Zhou, Qi Guo, Jiayu Lin, Meng Wang, Zhi Zeng, Yujie Li, Xiaolan Li, Yuting Xiang, Qiqi Liang, Jiawen Liu et al. · 2023 · Advanced Science
35. Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis
    Niklas Jonathan Lang, Janine Gote-Schniering, Diana Porras-Gonzalez, Lin Yang, Laurens De Sadeleer, R. Christoph Jentzsch, Vladimir A. Shitov, Shuhong Zhou, Meshal Ansari, Ahmed Agami et al. · 2023 · Science Translational Medicine
36. Spatial Transcriptomic and Metabolomic Landscapes of Oral Submucous Fibrosis‐Derived Oral Squamous Cell Carcinoma and its Tumor Microenvironment
    Yuan Zhi, Qian Wang, Moxin Zi, Shanshan Zhang, Junshang Ge, Keyue Liu, Linsong Lu, Chunmei Fan, Qijia Yan, Lei Shi et al. · 2024 · Advanced Science
37. Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains
    Rachel K. Zwick, Petr Kašpárek, Brisa Palikuqi, Sara Viragova, Laura Weichselbaum, Christopher S. McGinnis, Kara L. McKinley, Asoka Rathnayake, Dedeepya Vaka, Vinh Q Nguyen et al. · 2024 · Nature Cell Biology
38. Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges
    Hung Nguyen, Ha Nguyen, Duc Tran, Sorin Drăghici, Tin Nguyen · 2024 · Nucleic Acids Research
39. Nanoceria-Mediated Cyclosporin A Delivery for Dry Eye Disease Management through Modulating Immune–Epithelial Crosstalk
    Wenyu Cui, Sheng Chen, Tianyi Hu, Tinglian Zhou, Chen Qiu, Luyang Jiang, Xiaoyu Cheng, Jian Ji, Ke Yao, Haijie Han · 2024 · ACS Nano
40. Single-cell spatial multiomics reveals tumor microenvironment vulnerabilities in cancer resistance to immunotherapy
    Camelia Y. J. Quek, Aditya Pratapa, Xinyu Bai, Ghamdan Al‐Eryani, Inês Pires da Silva, Aaron T. Mayer, Nenad Bartoniček, Kate Harvey, Nigel Gordon Maher, Jordan W. Conway et al. · 2024 · Cell Reports
41. KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection
    Eric Fagerberg, John Attanasio, Christine Dien, Jaiveer Singh, Emily Kessler, Leena Abdullah, Jian Shen, Brian G. Hunt, Kelli A. Connolly, Edward De Brouwer et al. · 2025 · Science
42. Single cell approaches to address adipose tissue stromal cell heterogeneity
    Elizabeth Ann Rondini, James G. Granneman · 2020 · Biochemical Journal
43. Heme oxygenase-1 orchestrates the immunosuppressive program of tumor-associated macrophages
    Emmanuelle Alaluf, Benoît Vokaer, Aurélie Detavernier, Abdulkader Azouz, Marion Splittgerber, Alice Carrette, Louis Boon, Frédérick Libert, Miguel Parreira Soares, Alaín Le Moine et al. · 2020 · JCI Insight
44. Distinct human Langerhans cell subsets orchestrate reciprocal functions and require different developmental regulation
    Xiaochun Liu, Ronghui Zhu, Yang Luo, Shangshang Wang, Yi Zhao, Zhuoqiong Qiu, Yu Xin Zhang, Xiao Liu, Xu Yao, Xiao Li et al. · 2021 · Immunity
45. Single-Cell Transcriptomic Analysis Revealed a Critical Role of SPP1/CD44-Mediated Crosstalk Between Macrophages and Cancer Cells in Glioma
    Cong He, Luoyan Sheng, Deshen Pan, Shuai Jiang, Li Ding, Xiaojun Ma, Yaohua Liu, Deshui Jia · 2021 · Frontiers in Cell and Developmental Biology
46. Discovery and Application of Postnatal Nucleus Pulposus Progenitors Essential for Intervertebral Disc Homeostasis and Degeneration
    Bo Gao, Bo Jiang, Wenhui Xing, Zaiqi Xie, Zhuojing Luo, Weiguo Zou · 2022 · Advanced Science
47. A single-cell transcriptomic landscape of mouse testicular aging
    Wei Zhang, Siyu Xia, Wei Lie Xiao, Yali Song, Li Tang, Min Cao, Jing Yang, Shuang Wang, Zhijie Li, Chengchao Xu et al. · 2022 · Journal of Advanced Research
48. Transcription factors in fibroblast plasticity and CAF heterogeneity
    Roberta Melchionna, Paola Trono, Anna Di Carlo, Francesca Di Modugno, Paola Nisticò · 2023 · Journal of Experimental & Clinical Cancer Research
49. A transcriptional rheostat couples past activity to future sensory responses
    Tatsuya Tsukahara, David H. Brann, Stan L. Pashkovski, Grigori Guitchounts, Thomas C. Bozza, Sandeep Robert Datta · 2021 · Cell
50. Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis
    David van Bruggen, Fabio Baldivia Pohl, Christoffer Mattsson Langseth, Petra Kukanja, Hower Lee, Alejandro Mossi Albiach, Mukund Kabbe, Mandy Meijer, Sten Linnarsson, Markus M. Hilscher et al. · 2022 · Developmental Cell
51. Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity
    Antoine E. Roux, Chunlian Zhang, Jonathan S. Paw, Jose Zavala‐Solorio, Evangelia Malahias, Twaritha Vijay, Ganesh A. Kolumam, Cynthia J. Kenyon, Jacob C. Kimmel · 2022 · Cell Systems
52. Single-cell RNA-seq of heart reveals intercellular communication drivers of myocardial fibrosis in diabetic cardiomyopathy
    Wei Li, Xinqi Lou, Yingjie Zha, Yinyin Qin, Jun Zha, Lei Hong, Zhanli Xie, Shu-di Yang, Chen Wang, Jianzhong An et al. · 2023 · eLife
53. Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis
    Juan Du, Junlei Zhang, Lin Wang, Xun Wang, Yaxing Zhao, Jiaoying Lu, Tingmin Fan, Meng Niu, Jie Zhang, Fei Cheng et al. · 2023 · Nature Communications
54. Cancer‐Associated Fibroblast‐Induced Remodeling of Tumor Microenvironment in Recurrent Bladder Cancer
    Ting Liang, Tao Tao, Kai Wu, Lisha Liu, Wuwu Xu, Dewang Zhou, Fang Hu, Qiuxia Ding, Guixiao Huang, Song Wu · 2023 · Advanced Science
55. Transitional cell states sculpt tissue topology during lung regeneration
    Arvind Konkimalla, Satoshi Konishi, Lauren Macadlo, Yoshihiko Kobayashi, Zachary J. Farino, Naoya Miyashita, Léa El Haddad, Jeremy M. Morowitz, Christina E. Barkauskas, Pankaj Agarwal et al. · 2023 · Cell stem cell
56. Phenotypic signatures of circulating neoantigen-reactive CD8+ T cells in patients with metastatic cancers
    Rami Yossef, Sri Krishna, Sivasish Sindiri, Frank J. Lowery, Amy R. Copeland, Jared J. Gartner, Maria R. Parkhurst, Neilesh B. Parikh, Kyle Joseph Hitscherich, Shoshana T. Levi et al. · 2023 · Cancer Cell
57. Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges
    Jiajia Liu, Zhiwei Fan, Weiling Zhao, Xiaobo Zhou · 2021 · Frontiers in Genetics
58. Single-Cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells
    Chen Zhang, Xueshuai Han, Jingkun Liu, Lei Chen, Ying Lei, Kunying Chen, Jia Si, Tian-yi Wang, Hui Fang Zhou, Xiaoyun Zhao et al. · 2022 · Genomics Proteomics & Bioinformatics
59. An interactive murine single-cell atlas of the lung responses to radiation injury
    Sandra Curras-Alonso, Juliette Soulier, Thomas Defard, Christian Weber, Sophie Heinrich, Hugo Laporte, Sophie Leboucher, Sonia Lameiras, Marie Dutreix, Vincent Favaudon et al. · 2023 · Nature Communications
60. Stepwise emergence of the neuronal gene expression program in early animal evolution
    Sebastián R. Najle, Xavier Grau‐Bové, Anamaria Elek, Cristina Navarrete, Damiano Cianferoni, Cristina Chiva, Didac Cañas-Armenteros, Arrate Mallabiabarrena, Kai Kamm, Eduard Sabidó et al. · 2023 · Cell
61. Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon
    Nicola Micali, Shaojie Ma, Mingfeng Li, Suel–Kee Kim, Xoel Mato-Blanco, Suvimal Kumar Sindhu, Jon I. Arellano, Tianliuyun Gao, Mikihito Shibata, Kevin T. Gobeske et al. · 2023 · Science
62. A pancreatic cancer organoid platform identifies an inhibitor specific to mutant KRAS
    Xiaohua Duan, Tuo Zhang, Lingling Feng, Neranjan de Silva, Benjamin C. Greenspun, Xing Wang, Jenna E. Moyer, M. Laura Martin, Rohit Chandwani, Olivier Elemento et al. · 2023 · Cell stem cell
63. Single cell deciphering of progression trajectories of the tumor ecosystem in head and neck cancer
    Z. L. Liu, Xiangyan Meng, Rujuan Bao, M. Y. Shen, J. J. Sun, W. D. Chen, Fei‐Fei Liu, Yue He · 2024 · Nature Communications
64. BCG vaccination alters the epigenetic landscape of progenitor cells in human bone marrow to influence innate immune responses
    Sarah J. Sun, Raúl Aguirre‐Gamboa, L. Charlotte J. de Bree, Joaquín Sanz, Anne Dumaine, Walter J. F. M. van der Velden, Leo A. B. Joosten, Shabaana A. Khader, Maziar Divangahi, Mihai Gheorghe Netea et al. · 2024 · Immunity
65. Single-Cell RNA Sequencing With Combined Use of Bulk RNA Sequencing to Reveal Cell Heterogeneity and Molecular Changes at Acute Stage of Ischemic Stroke in Mouse Cortex Penumbra Area
    Kang Guo, Jianing Luo, Dayun Feng, Lin Wu, Xin Wang, Xia Li, Kai Xiong Tao, Xun Wu, Wenxing Cui, Yixuan He et al. · 2021 · Frontiers in Cell and Developmental Biology
66. Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing
    Júber Herrera-Uribe, Jayne E Wiarda, Sathesh Kumar Sivasankaran, Lance Daharsh, Haibo Liu, Kristen A. Byrne, Timothy P. L. Smith, Joan K. Lunney, Crystal Lynn Loving, Christopher Keith Tuggle · 2021 · Frontiers in Genetics
67. Transitions in lineage specification and gene regulatory networks in hematopoietic stem/progenitor cells over human development
    Anindita Roy, Guanlin Wang, Deena Iskander, Sorcha O’Byrne, Natalina Elliott, Jennifer O’Sullivan, Gemma Buck, Elisabeth F. Heuston, Wei Xiong Wen, Alba Rodríguez-Meira et al. · 2021 · Cell Reports
68. Aging compromises human islet beta cell function and identity by decreasing transcription factor activity and inducing ER stress
    Shristi Shrestha, Galina A. Erikson, J. Lyon, A. Spigelman, Austin Bautista, J. E. Manning Fox, Cristiane dos Santos, M. Shokhirev, Jean-Philippe Cartailler, M. Hetzer et al. · 2022 · Science Advances
69. Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease
    Theodore S. Kapellos, Kevin E. Bassler, Wataru Fujii, Christina Nalkurthi, Anna Christina Schaar, Lorenzo Bonaguro, Tal Pecht, Izabela Galvão, Shobhit Agrawal, Adem Saglam et al. · 2023 · Cell Reports
70. Decoding the temporal and regional specification of microglia in the developing human brain
    Yanxin Li, Zhong‐Qiu Li, Min Yang, Feiyang Wang, Yuehong Zhang, Rong Li, Qian Li, Yunxia Gong, Binhong Wang, Baoguang Fan et al. · 2022 · Cell stem cell
71. IL-2Rα-biased agonist enhances antitumor immunity by invigorating tumor-infiltrating CD25+CD8+ T cells
    Weiwei Wu, Tiongsun Chia, Jia Lu, Xue Li, Jian Guan, Yaning Li, Fenggen Fu, Shuaixiang Zhou, Ye Feng, Junjie Deng et al. · 2023 · Nature Cancer
72. Single-cell assessment of primary and stem cell-derived human trophoblast organoids as placenta-modeling platforms
    Matthew James Shannon, Gina L. McNeill, Burak Koksal, Jennet Baltayeva, Jasmin Wächter, Bárbara Castellana, Maria S. Peñaherrera, Wendy P. Robinson, Peter C. K. Leung, Alexander G. Beristain · 2024 · Developmental Cell
73. CellOracle: Dissecting cell identity via network inference and in silico gene perturbation
    Kamimoto, Kenji, Hoffmann, Christy M., Morris, Samantha A. · 2020
74. Single-cell sequencing and its applications in head and neck cancer
    Zongtai Qi, Thomas F. Barrett, Anuraag S. Parikh, Itay Tirosh, Sidharth V. Puram · 2019 · Oral Oncology
75. Single-cell RNA-seq dissects the intratumoral heterogeneity of triple-negative breast cancer based on gene regulatory networks
    Shunheng Zhou, Yue Huang, Haizhou Liu, Xu Zhou, Mengqin Yuan, Fei Hou, Lihong Wang, Wei Jiang · 2020 · Molecular Therapy — Nucleic Acids
76. DAMPs/PAMPs induce monocytic TLR activation and tolerance in COVID-19 patients; nucleic acid binding scavengers can counteract such TLR agonists
    Ibtehaj A. Naqvi, Nicholas S. Giroux, Lyra B. Olson, Sarah Ahn Morrison, Telmo Llanga, Tolulope Akinade, Yuefei Zhu, Yiling Zhong, Shree Bose, Stephanie Arvai et al. · 2022 · Biomaterials
77. Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types
    Methodios Ximerakis, Kristina M. Holton, Richard M. Giadone, Ceren Ozek, Monika Saxena, Samara Santiago, Xian Adiconis, Danielle Ashley Dionne, Lan Nguyễn, Kavya M. Shah et al. · 2023 · Nature Aging
78. Redox signals at the ER–mitochondria interface control melanoma progression
    Xin Zhang, Christine Silvia Gibhardt, Thorsten Will, Hedwig Stanisz, Christina Körbel, Mišo Mitkovski, Ioana Stejerean‐Todoran, Sabrina Cappello, David Pacheu‐Grau, Jan Dudek et al. · 2019 · The EMBO Journal
79. Immunology in the Era of Single-Cell Technologies
    Mirjana Efremova, Roser Vento‐Tormo, Jong-Eun Park, Sarah Amalia Teichmann, Kylie Renee James · 2020 · Annual Review of Immunology
80. Benchmarking algorithms for pathway activity transformation of single-cell RNA-seq data
    Zhang, Yaru, Ma, Yunlong, Huang, Yukuan, Zhang, Yan, Jiang, Qi, Zhou, Meng, Su, Jianzhong · 2020 · Computational and Structural Biotechnology Journal
81. ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Shen‐Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew D Sharrocks · 2019 · Cell Reports
82. Antibody-secreting cell destiny emerges during the initial stages of B-cell activation
    Christopher D. Scharer, Dillon G. Patterson, Mi Tian, Madeline J. Price, Sakeenah L. Hicks, Jeremy M. Boss · 2020 · Nature Communications
83. Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration
    Chen, Tianyi, Oh, Sehhoon, Gregory, Simon, Shen, Xiling, Diehl, Anna Mae · 2020 · JCI Insight
84. Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data
    Michael J. Geuenich, Jinyu Hou, Lee Sunyun, Shanza Ayub, Hartland Warren Jackson, Kieran R. Campbell · 2021 · Cell Systems
85. A Cuproptosis Activation Scoring model predicts neoplasm-immunity interactions and personalized treatments in glioma
    Bo Chen, Xiaoxi Zhou, Liting Yang, Hongshu Zhou, Ming Meng, Liyang Zhang, Jian Li · 2022 · Computers in Biology and Medicine
86. The molecular classification of cancer‐associated fibroblasts on a pan‐cancer single‐cell transcriptional atlas
    Bonan Chen, Wai Nok Chan, Fuda Xie, Chun Wai Mui, Xiaoli Liu, Alvin H.K. Cheung, Raymond Wai Ming Lung, Chit Chow, Zhenhua Zhang, Canbin Fang et al. · 2023 · Clinical and Translational Medicine
87. Runx1 negatively regulates inflammatory cytokine production by neutrophils in response to Toll-like receptor signaling
    Dana C. Bellissimo, Chia-Hui Chen, Qin Zhu, Sumedha Bagga, Chung-Tsai Lee, Bing He, Gerald B. W. Wertheim, Martha S. Jordan, Kai Tan, George Scott Worthen et al. · 2020 · Blood Advances
88. An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development
    Laura B. Chopp, Vishaka Gopalan, Thomas Ciucci, Allison J. Ruchinskas, Zachary Rae, Manon Lagarde, Yayi Gao, Caiyi Li, Marita Bosticardo, Francesca Pala et al. · 2020 · Immunity
89. Molecular identity of human limbal heterogeneity involved in corneal homeostasis and privilege
    Shengqian Dou, Qun Wang, Xia Qi, Bin Zhang, Hui Jiang, Shengwen Chen, Haoyun Duan, Yao Lu, Jiaoyang Dong, Yihai Cao et al. · 2021 · The Ocular Surface
90. Transcriptional and Immune Landscape of Cardiac Sarcoidosis
    Liu, Jing, Ma, Pan, Lai, Lulu, Villanueva, Ana, Koenig, Andrew, Bean, Gregory R., Bowles, Dawn E., Glass, Carolyn, Watson, Michael, Lavine, Kory J. et al. · 2022 · Circulation Research
91. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays
    Ao Chen, Sha Liao, Mengnan Cheng, Kailong Ma, Liang Wu, Yiwei Lai, Xiaojie Qiu, Jin Yang, Wenjiao Li, Jiangshan Xu et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
92. Network modeling of single-cell omics data: challenges, opportunities, and progresses
    Blencowe, Montgomery, Arneson, Douglas, Ding, Jessica, Chen, Yen-Wei, Saleem, Zara, Yang, Xia · 2019 · Emerging Topics in Life Sciences
93. Single nucleus multi-omics regulatory landscape of the murine pituitary
    Frederique Murielle Ruf-Zamojski, Zidong Zhang, Michel Zamojski, Gregory R. Smith, Natalia Mendelev, Hanqing Liu, German Nudelman, Mika Moriwaki, Hanna Pinças, Rosa Castanon et al. · 2021 · Nature Communications
94. Single‐cell transcriptomes reveal heterogeneity of high‐grade serous ovarian carcinoma
    Qian Hao, Jiajia Li, Qinghua Zhang, Fei Xu, Bangxiang Xie, Hua Lu, Xiaohua Wu, Xiang Yu Zhou · 2021 · Clinical and Translational Medicine
95. Nonbone Marrow CD34 + Cells Are Crucial for Endothelial Repair of Injured Artery
    Liujun Jiang, Ting Chen, Shasha Sun, Ruilin Wang, Jiacheng Deng, Lingxia Lyu, Hong Wu, Mei Yang, Xiangyuan Pu, Luping Du et al. · 2021 · Circulation Research
96. Deciphering endothelial heterogeneity in health and disease at single-cell resolution: progress and perspectives
    Lisa M. Becker, Shiau-Haln Chen, Julie Rodor, Laura P. M. H. de Rooij, Andrew Howard Baker, Peter Carmeliet · 2022 · Cardiovascular Research
97. Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities
    Tobias Roider, Marc‐Andrea Baertsch, Donnacha Fitzgerald, Harald S. Vöhringer, Berit J. Brinkmann, Felix Czernilofsky, Mareike Knoll, Laura Llaó Cid, Anna Mathioudaki, Bianca Faßbender et al. · 2024 · Nature Cell Biology
98. Interleukin-1α release during necrotic-like cell death generates myeloid-driven immunosuppression that restricts anti-tumor immunity
    Kay Hänggi, Jie Li, Achintyan Gangadharan, Xiaoxian Liu, Daiana Pamela Celias, Olabisi Osunmakinde, Aysenur Keske, Joshua Davis, Faiz F. Ahmad, Auriane Giron et al. · 2024 · Cancer Cell
99. Dysregulated hematopoiesis in bone marrow marks severe COVID-19
    Xin Wang, Yanling Wen, Xiaowei Xie, Yang Liu, Xiao-Hua Tan, Qing-Xian Cai, Ya-Wen Zhang, Lin Cheng, Gang Xu, Shengyuan Zhang et al. · 2021 · Cell Discovery
100. Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity
     Rémi Fiancette, Conor M. Finlay, Claire Willis, Sarah L. Bevington, Jake K. Soley, Sky T. H. Ng, Syed Murtuza Baker, Simon Andrews, Matthew R. Hepworth, David R. Withers · 2021 · Nature Immunology