Comprehensive Integration of Single-Cell Data

Cited by (513)

Items 401–500 of 513

1. Evaluating the Utilities of Foundation Models in Single-cell Data Analysis
   Liu, Tianyu, Li, Kexing, Wang, Yuge, Li, Hongyu, Zhao, Hongyu · 2023
2. Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination
   Huang, Yaping, Li, Lin, An, Geng, Yang, Xinyan, Cui, Manman, Song, Xiuling, Lin, Jing, Zhang, Xiaoling, Yao, Zhaokai, Wan, Cong et al. · 2023 · Nature Cell Biology
3. Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis
   Mandric, Igor, Schwarz, Tommer, Majumdar, Arunabha, Hou, Kangcheng, Briscoe, Leah, Perez, Richard, Subramaniam, Meena, Hafemeister, Christoph, Satija, Rahul, Ye, Chun Jimmie et al. · 2020 · Nature Communications
4. Single-cell transcriptomic landscape of the developing human spinal cord
   Andersen, Jimena, Thom, Nicholas, Shadrach, Jennifer L., Chen, Xiaoyu, Onesto, Massimo Mario, Amin, Neal D., Yoon, Se-Jin, Li, Li, Greenleaf, William J., Müller, Fabian et al. · 2023 · Nature Neuroscience
5. B cells drive neuropathic pain–related behaviors in mice through IgG–Fc gamma receptor signaling
   Lacagnina, Michael J., Willcox, Kendal F., Boukelmoune, Nabila, Bavencoffe, Alexis, Sankaranarayanan, Ishwarya, Barratt, Daniel T., Zuberi, Younus A., Dayani, Dorsa, Chavez, Melissa V., Lu, Jonathan T. et al. · 2024 · Science Translational Medicine
6. ASGARD is a single-cell guided pipeline to aid repurposing of drugs
   He, Bing, Xiao, Yao, Liang, Haodong, Huang, Qianhui, Du, Yuheng, Li, Yijun, Garmire, David, Sun, Duxin, Garmire, Lana X. · 2023 · Nature Communications
7. Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types
   Li, Jiaqi, Wang, Jingjing, Zhang, Peijing, Wang, Renying, Mei, Yuqing, Sun, Zhongyi, Fei, Lijiang, Jiang, Mengmeng, Ma, Lifeng, E, Weigao et al. · 2022 · Nature Genetics
8. Intermittent clearance of p21-highly-expressing cells extends lifespan and confers sustained benefits to health and physical function
   Wang, Binsheng, Wang, Lichao, Gasek, Nathan S., Kuo, Chia-Ling, Nie, Jia, Kim, Taewan, Yan, Pengyi, Zhu, Junyu, Torrance, Blake L., Zhou, Yueying et al. · 2024 · Cell Metabolism
9. Nicotinamide phosphoribosyltransferase prompts bleomycin-induced pulmonary fibrosis by driving macrophage M2 polarization in mice
   Chen, Yaling, Wang, Tong, Liang, Fuxiang, Han, Jia, Lou, Zhiling, Yu, Yifan, Li, Jinsheng, Zhan, Tianwei, Gu, Yuqing, Dong, Lingjun et al. · 2024 · Theranostics
10. Resident macrophages restrain pathological adipose tissue remodeling and protect vascular integrity in obese mice
    Chen, Qi, Lai, Si Min, Xu, Shaohai, Tan, Yingrou, Leong, Keith, Liu, Dehua, Tan, Jia Chi, Naik, Roshan Ratnakar, Barron, Anna M, Adav, Sunil S et al. · 2021 · The EMBO Reports
11. The chromatin landscape of Th17 cells reveals mechanisms of diversification of regulatory and pro-inflammatory states
    Thakore, Pratiksha I., Schnell, Alexandra, Zhao, Maryann, Huang, Linglin, Hou, Yu, Christian, Elena, Zaghouani, Sarah, Wang, Chao, Singh, Vasundhara, Ma, Sai et al. · 2022
12. Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens
    Xu, Zihan, Sziraki, Andras, Lee, Jasper, Zhou, Wei, Cao, Junyue · 2024 · Nature Biotechnology
13. Single-cell RNA sequencing reveals the pro-inflammatory roles of liver-resident Th1-like cells in primary biliary cholangitis
    Jin, Ciliang, Jiang, Penglei, Zhang, Zhaoru, Han, Yingli, Wen, Xue, Zheng, Lin, Kuang, Wei, Lian, Jiangshan, Yu, Guodong, Qian, Xinyue et al. · 2024 · Nature Communications
14. Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq
    Mylka, Viacheslav, Matetovici, Irina, Poovathingal, Suresh, Aerts, Jeroen, Vandamme, Niels, Seurinck, Ruth, Verstaen, Kevin, Hulselmans, Gert, Van den Hoecke, Silvie, Scheyltjens, Isabelle et al. · 2022 · Genome Biology
15. Integrative analysis of cross-modal features for the prognosis prediction of clear cell renal cell carcinoma
    Ning, Zhenyuan, Pan, Weihao, Chen, Yuting, Xiao, Qing, Zhang, Xinsen, Luo, Jiaxiu, Wang, Jian, Zhang, Yu · 2020 · Bioinformatics
16. Single-cell transcriptomics reveals opposing roles of Shp2 in Myc-driven liver tumor cells and microenvironment
    Chen, Wendy S., Liang, Yan, Zong, Min, Liu, Jacey J., Kaneko, Kota, Hanley, Kaisa L., Zhang, Kun, Feng, Gen-Sheng · 2021 · Cell Reports
17. Whole genome sequencing identifies genetic variants associated with neurogenic inflammation in rosacea
    Deng, Zhili, Chen, Mengting, Zhao, Zhixiang, Xiao, Wenqin, Liu, Tangxiele, Peng, Qinqin, Wu, Zheng, Xu, San, Shi, Wei, Jian, Dan et al. · 2023 · Nature Communications
18. Delineating the early dissemination mechanisms of acral melanoma by integrating single-cell and spatial transcriptomic analyses
    Wei, Chuanyuan, Sun, Wei, Shen, Kangjie, Zhong, Jingqin, Liu, Wanlin, Gao, Zixu, Xu, Yu, Wang, Lu, Hu, Tu, Ren, Ming et al. · 2023 · Nature Communications
19. Review of multi-omics data resources and integrative analysis for human brain disorders
    Dong, Xianjun, Liu, Chunyu, Dozmorov, Mikhail · 2021 · Briefings in Functional Genomics
20. Single-Cell RNA Profiling of Human Skin Reveals Age-Related Loss of Dermal Sheath Cells and Their Contribution to a Juvenile Phenotype
    Ahlers, Juliane M. D., Falckenhayn, Cassandra, Holzscheck, Nicholas, Solé-Boldo, Llorenç, Schütz, Sabrina, Wenck, Horst, Winnefeld, Marc, Lyko, Frank, Grönniger, Elke, Siracusa, Annette · 2022 · Frontiers in Genetics
21. CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks
    Buterez, David, Bica, Ioana, Tariq, Ifrah, Andrés-Terré, Helena, Liò, Pietro · 2022 · Bioinformatics
22. Gliotransmission of D-serine promotes thirst-directed behaviors in Drosophila
    Park, Annie, Croset, Vincent, Otto, Nils, Agarwal, Devika, Treiber, Christoph D., Meschi, Eleonora, Sims, David, Waddell, Scott · 2022 · Current Biology
23. Using Single-Cell and Spatial Transcriptomes to Understand Stem Cell Lineage Specification During Early Embryo Development
    Peng, Guangdun, Cui, Guizhong, Ke, Jincan, Jing, Naihe · 2020 · Annual Review of Genomics and Human Genetics
24. Spatial transcriptomics reveals metabolic changes underly age-dependent declines in digit regeneration
    Tower, Robert J, Busse, Emily, Jaramillo, Josue, Lacey, Michelle, Hoffseth, Kevin, Guntur, Anyonya R, Simkin, Jennifer, Sammarco, Mimi C · 2022 · eLife
25. Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism
    Cheng, Yurong, Schlosser, Pascal, Hertel, Johannes, Sekula, Peggy, Oefner, Peter J., Spiekerkoetter, Ute, Mielke, Johanna, Freitag, Daniel F., Schmidts, Miriam, GCKD Investigators et al. · 2021 · Nature Communications
26. Regulation of cell distancing in peri-plaque glial nets by Plexin-B1 affects glial activation and amyloid compaction in Alzheimer’s disease
    Huang, Yong, Wang, Minghui, Ni, Haofei, Zhang, Jinglong, Li, Aiqun, Hu, Bin, Junqueira Alves, Chrystian, Wahane, Shalaka, Rios de Anda, Mitzy, Ho, Lap et al. · 2024 · Nature Neuroscience
27. Region-specific cellular and molecular basis of liver regeneration after acute pericentral injury.
    Wang, Shuyong, Wang, Xuan, Shan, Yiran, Tan, Zuolong, Su, Yuxin, Cao, Yannan, Wang, Shuang, Dong, Jiahong, Gu, Jin, Wang, Yunfang · 2024 · Cell Stem Cell
28. Cholangiocyte organoids from human bile retain a local phenotype and can repopulate bile ducts in vitro
    Roos, Floris J. M., Wu, Haoyu, Willemse, Jorke, Lieshout, Ruby, Albarinos, Laura A. Muñoz, Kan, Yik‐Yang, Poley, Jan‐Werner, Bruno, Marco J., de Jonge, Jeroen, Bártfai, Richard et al. · 2021 · Clinical and Translational Medicine
29. Single-cell microglial transcriptomics during demyelination defines a microglial state required for lytic carcass clearance
    Zia, Sameera, Hammond, Brady P., Zirngibl, Martin, Sizov, Anastasia, Baaklini, Charbel S., Panda, Sharmistha P., Ho, Madelene F. S., Lee, Kelly V., Mainali, Apurba, Burr, Mena K. et al. · 2022 · Molecular Neurodegeneration
30. Multidirectional characterization of cellular composition and spatial architecture in human multiple primary lung cancers
    Wang, Yawei, Chen, Di, Liu, Yu, Shi, Daiwang, Duan, Chao, Li, Jinghan, Shi, Xiang, Zhang, Yong, Yu, Zhanwu, Sun, Nan et al. · 2023 · Cell Death & Disease
31. Single‐cell RNAseq provides insight into altered immune cell populations in human fracture nonunions
    Avin, Keith G., Dominguez, James M., Chen, Neal X., Hato, Takashi, Myslinski, Jered J., Gao, Hongyu, Liu, Yunlong, McKinley, Todd O., Brown, Krista M., Moe, Sharon M. et al. · 2023 · Journal of Orthopaedic Research
32. Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency
    Jakab, Moritz, Lee, Ki Hong, Uvarovskii, Alexey, Ovchinnikova, Svetlana, Kulkarni, Shubhada R., Jakab, Sevinç, Rostalski, Till, Spegg, Carleen, Anders, Simon, Augustin, Hellmut G. · 2024 · Nature Cancer
33. Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues
    Saul, Dominik, Jurk, Diana, Doolittle, Madison L, Kosinsky, Robyn Laura, Han, Yeaeun, Zhang, Xu, Franco, Ana Catarina, Kim, Sung Y, Wyles, Saranya P, Prakash, Y S et al. · 2025 · The EMBO Journal
34. SCING: Inference of robust, interpretable gene regulatory networks from single cell and spatial transcriptomics
    Littman, Russell, Cheng, Michael, Wang, Ning, Peng, Chao, Yang, Xia · 2023 · iScience
35. Spatially resolved gene signatures of white matter lesion progression in multiple sclerosis
    Alsema, Astrid M., Wijering, Marion H. C., Miedema, Anneke, Kotah, Janssen M., Koster, Mirjam, Rijnsburger, Merel, van Weering, Hilmar R. J., de Vries, Helga E., Baron, Wia, Kooistra, Susanne M. et al. · 2024 · Nature Neuroscience
36. Advancing biological understanding of cellular senescence with computational multiomics
    Li, Sheng, Agudelo Garcia, Paula A., Aliferis, Constantin, Becich, Michael J., Calyeca, Jazmin, Cosgrove, Benjamin D., Elisseeff, Jennifer, Farzad, Negin, Fertig, Elana J., Glass, Carolyn et al. · 2025 · Nature Genetics
37. Molecular blueprints for spinal circuit modules controlling locomotor speed in zebrafish
    Pallucchi, Irene, Bertuzzi, Maria, Madrid, David, Fontanel, Pierre, Higashijima, Shin-ichi, El Manira, Abdeljabbar · 2024 · Nature Neuroscience
38. 4D marmoset brain map reveals MRI and molecular signatures for onset of multiple sclerosis–like lesions
    Lin, Jing-Ping, Brake, Alexis, Donadieu, Maxime, Lee, Amanda, Smith, Ginger, Hu, Kevin, Nair, Govind, Kawaguchi, Riki, Sati, Pascal, Geschwind, Daniel H. et al. · 2025 · Science
39. Obesity medication lorcaserin activates brainstem GLP-1 neurons to reduce food intake and augments GLP-1 receptor agonist induced appetite suppression
    Wagner, Stefan, Brierley, Daniel I., Leeson-Payne, Alasdair, Jiang, Wanqing, Chianese, Raffaella, Lam, Brian Y.H., Dowsett, Georgina K.C., Cristiano, Claudia, Lyons, David, Reimann, Frank et al. · 2023 · Molecular Metabolism
40. Developmental trajectories of thalamic progenitors revealed by single-cell transcriptome profiling and Shh perturbation
    Govek, Kiya W., Chen, Sixing, Sgourdou, Paraskevi, Yao, Yao, Woodhouse, Steven, Chen, Tingfang, Fuccillo, Marc V., Epstein, Douglas J., Camara, Pablo G. · 2022 · Cell Reports
41. Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease
    Gupta, Chirag, Xu, Jielin, Jin, Ting, Khullar, Saniya, Liu, Xiaoyu, Alatkar, Sayali, Cheng, Feixiong, Wang, Daifeng · 2022 · PLOS Computational Biology
42. AAV vectors trigger DNA damage responses and STING-dependent inflammation in human CNS cells
    Costa-Verdera, Helena, Meneghini, Vasco, Fitzpatrick, Zachary, Alezz, Monah Abou, Fabyanic, Emily, Huang, Xin, Dzhashiashvili, Yulia, Ahiya, Avantika, Mangiameli, Elisabeth, Valeri, Erika et al. · 2024
43. AAV vectors trigger DNA damage response-dependent pro-inflammatory signalling in human iPSC-derived CNS models and mouse brain
    Costa-Verdera, Helena, Meneghini, Vasco, Fitzpatrick, Zachary, Abou Alezz, Monah, Fabyanic, Emily, Huang, Xin, Dzhashiashvili, Yulia, Ahiya, Avantika, Mangiameli, Elisabeth, Valeri, Erika et al. · 2025 · Nature Communications
44. Variation of Human Neural Stem Cells Generating Organizer States In Vitro before Committing to Cortical Excitatory or Inhibitory Neuronal Fates
    Micali, Nicola, Kim, Suel-Kee, Diaz-Bustamante, Marcelo, Stein-O’Brien, Genevieve, Seo, Seungmae, Shin, Joo-Heon, Rash, Brian G., Ma, Shaojie, Wang, Yanhong, Olivares, Nicolas A. et al. · 2020 · Cell Reports
45. The Wnt/TCF7L1 transcriptional repressor axis drives primitive endoderm formation by antagonizing naive and formative pluripotency
    Athanasouli, Paraskevi, Balli, Martina, De Jaime-Soguero, Anchel, Boel, Annekatrien, Papanikolaou, Sofia, van der Veer, Bernard K., Janiszewski, Adrian, Vanhessche, Tijs, Francis, Annick, El Laithy, Youssef et al. · 2023 · Nature Communications
46. Single-cell transcriptomics of human-skin-equivalent organoids
    Stabell, Adam R., Lee, Grace E., Jia, Yunlong, Wong, Kirsten N., Wang, Shuxiong, Ling, Ji, Nguyen, Sandrine D., Sen, George L., Nie, Qing, Atwood, Scott X. · 2023 · Cell Reports
47. Multifactorial Role of Mitochondria in Echinocandin Tolerance Revealed by Transcriptome Analysis of Drug-Tolerant Cells
    Garcia-Rubio, Rocio, Jimenez-Ortigosa, Cristina, DeGregorio, Lucius, Quinteros, Christopher, Shor, Erika, Perlin, David S. · 2021 · mBio
48. scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links
    Wang, Gefei, Zhao, Jia, Lin, Yingxin, Liu, Tianyu, Zhao, Yize, Zhao, Hongyu · 2025 · Nature Communications
49. From tissue architecture to clinical insights: Spatial transcriptomics in solid tumor studies
    Sharma, Arpit, Raut, Shruti S., Shukla, Alok, Gupta, Shivani, Mishra, Abha, Singh, Amit · 2025 · Seminars in Oncology
50. An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum
    Li, Yang Eric, Preissl, Sebastian, Hou, Xiaomeng, Zhang, Ziyang, Zhang, Kai, Fang, Rongxin, Qiu, Yunjiang, Poirion, Olivier, Li, Bin, Liu, Hanqing et al. · 2020
51. Alternative splicing downstream of EMT enhances phenotypic plasticity and malignant behavior in colon cancer
    Xu, Tong, Verhagen, Mathijs, Joosten, Rosalie, Sun, Wenjie, Sacchetti, Andrea, Munoz Sagredo, Leonel, Orian-Rousseau, Véronique, Fodde, Riccardo · 2022 · eLife
52. Single-Cell RNA Sequencing for Studying Human Cancers
    Aran, Dvir · 2023 · Annual Review of Biomedical Data Science
53. Angiopoietin–TIE2 feedforward circuit promotes PIK3CA-driven venous malformations
    Kraft, Marle, Schoofs, Hans, Petkova, Milena, Andrade, Jorge, Grosso, Ana Rita, Benedito, Rui, De Roo, An-Katrien, Boon, Laurence M., Vikkula, Miikka, Kapp, Friedrich G. et al. · 2025 · Nature Cardiovascular Research
54. CMOT: cross-modality optimal transport for multimodal inference
    Alatkar, Sayali Anil, Wang, Daifeng · 2023 · Genome biology
55. Oxytocin receptor behavioral effects and cell types in the bed nucleus of the stria terminalis
    Luo, Pei X., Zakharenkov, Hannah Cortez, Torres, Lisette Y., Rios, Roberto A., Gegenhuber, Bruno, Black, Alexis M., Xu, Christine K., Minie, Vanessa A., Tran, Amy M., Tollkuhn, Jessica et al. · 2022 · Hormones and Behavior
56. Differential gene expression analysis for multi-subject single-cell RNA-sequencing studies with aggregateBioVar
    Thurman, Andrew L, Ratcliff, Jason A, Chimenti, Michael S, Pezzulo, Alejandro A · 2021 · Bioinformatics
57. Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics
    Ma, Cong, Chitra, Uthsav, Zhang, Shirley, Raphael, Benjamin J. · 2022 · Cell Systems
58. Single-Nucleus RNA-seq of Normal-Appearing Brain Regions in Relapsing-Remitting vs. secondary Progressive Multiple Sclerosis: implications for the Efficacy of fingolimod
    Kihara, Yasuyuki, Zhu, Yunjiao, Jonnalagadda, Deepa, Romanow, William, Palmer, Carter, Siddoway, Benjamin, Rivera, Richard, Dutta, Ranjan, Trapp, Bruce D., Chun, Jerold · 2022 · Frontiers in Cellular Neuroscience
59. Spatial transcriptome sequencing of FFPE tissues at cellular level
    Liu, Yang, Enninful, Archibald, Deng, Yanxiang, Fan, Rong · 2020
60. Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1
    Shangguan, Shida, Ehrenberg, Philip K, Geretz, Aviva, Yum, Lauren, Kundu, Gautam, May, Kelly, Fourati, Slim, Nganou-Makamdop, Krystelle, Williams, LaTonya D, Sawant, Sheetal et al. · 2021 · eLife
61. In vivo transcriptional analysis of mice infected with Leishmania major unveils cellular heterogeneity and altered transcriptomic profiling at single-cell resolution
    Venugopal, Gopinath, Bird, Jordan T., Washam, Charity L., Roys, Hayden, Bowlin, Anne, Byrum, Stephanie D., Weinkopff, Tiffany · 2022 · PLOS Neglected Tropical Diseases
62. Attenuation of SARS-CoV-2 infection by losartan in human kidney organoids
    Rahmani, Waleed, Chung, Hyunjae, Sinha, Sarthak, Bui-Marinos, Maxwell P., Arora, Rohit, Jaffer, Arzina, Corcoran, Jennifer A., Biernaskie, Jeff, Chun, Justin · 2022 · iScience
63. Single-cell transcriptomics unveils skin cell specific antifungal immune responses and IL-1Ra- IL-1R immune evasion strategies of emerging fungal pathogen Candida auris
    Balakumar, Abishek, Das, Diprasom, Datta, Abhishek, Mishra, Abtar, Bryak, Garrett, Ganesh, Shrihari M., Netea, Mihai G., Kumar, Vinod, Lionakis, Michail S., Arora, Devender et al. · 2024 · PLOS Pathogens
64. Targeting tumor–stromal interactions in triple-negative breast cancer using a human vascularized micro-tumor model
    Hachey, Stephanie J., Hatch, Christopher J., Gaebler, Daniela, Mocherla, Aneela, Nee, Kevin, Kessenbrock, Kai, Hughes, Christopher C. W. · 2024 · Breast Cancer Research
65. Uncovering Plaque-Glia Niches in Human Alzheimer’s Disease Brains Using Spatial Transcriptomics
    Avey, Denis R., Ng, Bernard, Vialle, Ricardo A., Kearns, Nicola A., de Paiva Lopes, Katia, Iatrou, Artemis, De Tissera, Sashini, Vyas, Himanshu, Saunders, Devin M., Flood, Daniel J. et al. · 2024
66. Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2
    Peng, Lei, Renauer, Paul A., Ökten, Arya, Fang, Zhenhao, Park, Jonathan J., Zhou, Xiaoyu, Lin, Qianqian, Dong, Matthew B., Filler, Renata, Xiong, Qiancheng et al. · 2022 · Cell Reports Medicine
67. Alpha cell dysfunction in type 1 diabetes is independent of a senescence program
    Brawerman, Gabriel, Ntranos, Vasilis, Thompson, Peter J. · 2022 · Frontiers in Endocrinology
68. Enhanced microglial dynamics and a paucity of tau seeding in the amyloid plaque microenvironment contribute to cognitive resilience in Alzheimer’s disease
    Jury-Garfe, Nur, Redding-Ochoa, Javier, You, Yanwen, Martínez, Pablo, Karahan, Hande, Chimal-Juárez, Enrique, Johnson, Travis S., Zhang, Jie, Resnick, Susan, Kim, Jungsu et al. · 2024 · Acta Neuropathologica
69. LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer
    Murray, Christopher W., Brady, Jennifer J., Han, Mingqi, Cai, Hongchen, Tsai, Min K., Pierce, Sarah E., Cheng, Ran, Demeter, Janos, Feldser, David M., Jackson, Peter K. et al. · 2022 · Nature Communications
70. Molecular Logic of Cellular Diversification in the Mammalian Cerebral Cortex
    Di Bella, Daniela J., Habibi, Ehsan, Yang, Sun-Ming, Stickels, Robert R., Brown, Juliana, Yadollahpour, Payman, Chen, Fei, Macosko, Evan Z., Regev, Aviv, Arlotta, Paola · 2020
71. Baricitinib attenuates the proinflammatory phase of COVID-19 driven by lung-infiltrating monocytes
    Dobosh, Brian, Zandi, Keivan, Giraldo, Diego Moncada, Goh, Shu Ling, Musall, Kathryn, Aldeco, Milagros, LeCher, Julia, Giacalone, Vincent D., Yang, Junkai, Eddins, Devon J. et al. · 2022 · Cell Reports
72. Sphingosine Kinase 1 Aggravates Liver Fibrosis by Mediating Macrophage Recruitment and Polarization
    Ding, Xin, Zhang, Xiang, Cao, Jiafan, Chen, Shiyun, Chen, Yinghua, Yuan, Kai, Chen, Bo, Yang, Guizhi, Li, Shengwen, Yang, Jundong et al. · 2024 · Cellular and Molecular Gastroenterology and Hepatology
73. T–B cell cooperation in ectopic lymphoid follicles propagates CNS autoimmunity
    Kolz, Anna, de la Rosa, Clara, Syma, Isabel J., McGrath, Sarah, Kavaka, Vladyslav, Schmitz, Rosa, Thomann, Anna S., Kerschensteiner, Martin, Beltran, Eduardo, Kawakami, Naoto et al. · 2025 · Science Immunology
74. Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains
    Gamache, Julia, Gingerich, Daniel, Shwab, E. Keats, Barrera, Julio, Garrett, Melanie E., Hume, Cordelia, Crawford, Gregory E., Ashley-Koch, Allison E., Chiba-Falek, Ornit · 2023 · Cell & Bioscience
75. scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
    Wang, Weijian, Cen, Yihui, Lu, Zezhen, Xu, Yueqing, Sun, Tianyi, Xiao, Ying, Liu, Wanlu, Li, Jingyi Jessica, Wang, Chaochen · 2024 · Genome Biology
76. Systematic analysis of cellular cross-talk reveals a role for SEMA6D-TREM2 regulating microglial function in Alzheimer’s disease
    D’Oliveira Albanus, Ricardo, Finan, Gina M., Brase, Logan, Sweeney, Nicholas, Kim, Tae Yeon, Chen, Shuo, Ryoo, Yeonsu, Park, Joseph, Guo, Qi, Iyer, Abhirami K. et al. · 2025 · Science Translational Medicine
77. Primary cilia-mediated regulation of microglial secretion in Alzheimer’s disease
    Yeo, Seungeun, Jang, Jaemyung, Jung, Hyun Jin, Lee, Hyeyoung, Choe, Youngshik · 2023 · Frontiers in Molecular Biosciences
78. A Review on Genomics Data Analysis using Machine Learning
    Aggarwal, Ashwani Kumar · 2023 · WSEAS TRANSACTIONS ON BIOLOGY AND BIOMEDICINE
79. StabMap: Mosaic single cell data integration using non-overlapping features
    Ghazanfar, Shila, Guibentif, Carolina, Marioni, John C. · 2022
80. Ancestral developmental potentials in early bony fish contributed to vertebrate water-to-land transition
    Bi, Xu-Peng, 深圳华大基因，广东 深圳518083，中国, BGI-Shenzhen, Shenzhen, Guangdong 518083, China, Zhang, Guo-Jie, 中国科学院动物进化与遗传前沿交叉卓越创新中心，云南 昆明 650223，中国, 中国科学院昆明动物研究所遗传资源与进化国家重点实验室，云南 昆明 650223，中国, Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China, Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark · 2021 · Zoological Research
81. Therapeutic Idol reduction ameliorates amyloidosis and improves cognitive function in APP/PS1 mice
    Gao, Jie, Littman, Russell, Diamante, Graciel, Xiao, Xu, Ahn, In Sook, Yang, Xia, Cole, Tracy A., Tontonoz, Peter · 2020 · Molecular and Cellular Biology
82. Cspg4 high microglia contribute to microgliosis during neurodegeneration
    Liu, Ya-jing, Ding, Yu, Yin, Yan-qing, Xiao, Hui, Hu, Gang, Zhou, Jia-wei · 2023 · Proceedings of the National Academy of Sciences
83. Single-cell multiomic analysis identifies a HOX-PBX gene network regulating the survival of lymphangioleiomyomatosis cells
    Olatoke, Tasnim, Wagner, Andrew, Astrinidis, Aristotelis, Zhang, Erik Y., Guo, Minzhe, Zhang, Alan G., Mattam, Ushodaya, Kopras, Elizabeth J., Gupta, Nishant, Smith, Eric P. et al. · 2023 · Science Advances
84. The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration
    Rao, Anupama, Lyu, Baken, Jahan, Ishrat, Lubertozzi, Anna, Zhou, Gao, Tedeschi, Frank, Jankowsky, Eckhard, Kang, Junsu, Carstens, Bryan, Poss, Kenneth D. et al. · 2023 · Development
85. Genetic Mapping of Monocyte Fate Decisions Following Myocardial Infarction
    Koenig, Andrew L, Kadyrov, Farid F, Amrute, Junedh M, Yang, Steven, Weinheimer, Carla J, Nigro, Jessica M, Kovacs, Attila, Smith, Gabriella, Lavine, Kory J · 2023
86. SenPred: a single-cell RNA sequencing-based machine learning pipeline to classify deeply senescent dermal fibroblast cells for the detection of an in vivo senescent cell burden
    2025
87. Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex
    Risgaard, Ryan D., Hanthanan Arachchilage, Kalpana, Knaack, Sara A., Hosseini, Masoumeh, Chen, Rachel J., Kumarage, Pubudu, Schmidt, Danielle K., Huang, Xiang, Sheng, Jie, Wang, Carlos J. et al. · 2026 · Science
88. Single-cell analyses reveal metastasis mechanism and microenvironment remodeling of lymph node in intrahepatic cholangiocarcinoma
    Li, Zhe, Ma, Lijie, Chen, Mengdi, Chen, Xing, Sha, Meng, Hang, Hualian · 2025 · JHEP Reports
89. Identification of Repurposable Drugs and Adverse Drug Reactions for Various Courses of COVID-19 Based on Single-Cell RNA Sequencing Data
    Wang, Zhihan, Guo, Kai, Gao, Pan, Pu, Qinqin, Wu, Min, Li, Changlong, Hur, Junguk · 2020 · arXiv
90. Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment
    Snabel, Rebecca R., Cofiño-Fabrés, Carla, Baltissen, Marijke, Schwach, Verena, Passier, Robert, Veenstra, Gert Jan C. · 2025 · Stem Cell Reports
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