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Single-cell transcriptomic analysis reveals key immune cell phenotypes in the lungs of patients with asthma exacerbation
Li, Hui, Wang, Huaqi, Sokulsky, Leon, Liu, Shaoxia, Yang, Rui, Liu, Xiaojie, Zhou, Lujia, Li, Juan, Huang, Chun, Li, Fangfang, Lei, Xu, Jia, Hongxia, Cheng, Jiuling, Li, Fuguang, Yang, Ming, Zhang, Guojun
Published in Journal of allergy and clinical immunology (01.03.2021)
Published in Journal of allergy and clinical immunology (01.03.2021)
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Journal Article
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., Mahbubani, Krishnaa, Godfrey, Edmund, Davies, Susan E., Athanasiadis, Emmanouil, Saeb-Parsy, Kourosh, Tacke, Frank, Allison, Michael, Mohorianu, Irina, Vallier, Ludovic
Published in Nature (London) (06.06.2024)
Published in Nature (London) (06.06.2024)
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Journal Article
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
Vallejos, Catalina A., Marioni, John C., Richardson, Sylvia
Published in PLoS computational biology (01.06.2015)
Published in PLoS computational biology (01.06.2015)
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Journal Article
Progressive Cellular Senescence Mediates Renal Dysfunction in Ischemic Nephropathy
Kim, Seo Rin, Puranik, Amrutesh S., Jiang, Kai, Chen, Xiaojun, Zhu, Xiang-Yang, Taylor, Ian, Khodadadi-Jamayran, Alireza, Lerman, Amir, Hickson, LaTonya J., Childs, Bennett G., Textor, Stephen C., Tchkonia, Tamara, Niewold, Timothy B., Kirkland, James L., Lerman, Lilach O.
Published in Journal of the American Society of Nephrology (01.08.2021)
Published in Journal of the American Society of Nephrology (01.08.2021)
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Journal Article
Gating mass cytometry data by deep learning
Li, Huamin, Shaham, Uri, Stanton, Kelly P, Yao, Yi, Montgomery, Ruth R, Kluger, Yuval
Published in Bioinformatics (Oxford, England) (01.11.2017)
Published in Bioinformatics (Oxford, England) (01.11.2017)
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Journal Article
A single-cell compendium of human cerebrospinal fluid identifies disease-associated immune cell populations
Cantoni, Claudia, Smirnov, Roman A., Firulyova, Maria, Andhey, Prabhakar S., Bradstreet, Tara R., Esaulova, Ekaterina, Terekhova, Marina, Schwarzkopf, Elizabeth A., Abdalla, Nada M., Kleverov, Maksim, Sabatino, Joseph J., Liu, Kang, Schwab, Nicholas, Meyer zu Hörste, Gerd, Cross, Anne H., Artyomov, Maxim N., Edelson, Brian T., Wu, Gregory F.
Published in The Journal of clinical investigation (01.01.2025)
Published in The Journal of clinical investigation (01.01.2025)
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Journal Article
scCOSMIX: A Mixed‐Effects Framework for Differential Coexpression and Transcriptional Interactions Modeling in Single‐Cell RNA‐Seq
Bussing, Anderson, Marra, Giampiero, Fan, Daping, Shinohara, Russell, Tu, Danni, Ho, Yen‐Yi
Published in Statistics in medicine (01.08.2025)
Published in Statistics in medicine (01.08.2025)
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Journal Article
Single-cell multi-cohort dissection of the schizophrenia transcriptome
Ruzicka, W. Brad, Mohammadi, Shahin, Fullard, John F., Davila-Velderrain, Jose, Subburaju, Sivan, Tso, Daniel Reed, Hourihan, Makayla, Jiang, Shan, Lee, Hao-Chih, Bendl, Jaroslav, Voloudakis, Georgios, Haroutunian, Vahram, Hoffman, Gabriel E., Roussos, Panos, Kellis, Manolis, Akbarian, Schahram, Abyzov, Alexej, Ahituv, Nadav, Arasappan, Dhivya, Almagro Armenteros, Jose Juan, Beliveau, Brian J., Berretta, Sabina, Bharadwaj, Rahul A., Bhattacharya, Arjun, Bicks, Lucy, Brennand, Kristen, Capauto, Davide, Champagne, Frances A., Chatterjee, Tanima, Chatzinakos, Chris, Chen, Yuhang, Chen, H. Isaac, Cheng, Yuyan, Cheng, Lijun, Chess, Andrew, Chien, Jo-fan, Chu, Zhiyuan, Clarke, Declan, Clement, Ashley, Collado-Torres, Leonardo, Cooper, Gregory M., Crawford, Gregory E., Dai, Rujia, Daskalakis, Nikolaos P., Deep-Soboslay, Amy, Deng, Chengyu, DiPietro, Christopher P., Dracheva, Stella, Drusinsky, Shiron, Duan, Ziheng, Duong, Duc, Dursun, Cagatay, Eagles, Nicholas J., Edelstein, Jonathan, Emani, Prashant S., Galani, Kiki, Galeev, Timur, Gandal, Michael J., Gaynor, Sophia, Gerstein, Mark, Geschwind, Daniel H., Girdhar, Kiran, Goes, Fernando S., Greenleaf, William, Grundman, Jennifer, Guo, Hanmin, Guo, Qiuyu, Gupta, Chirag, Hadas, Yoav, Hallmayer, Joachim, Han, Xikun, Hawken, Natalie, He, Chuan, Henry, Ella, Hicks, Stephanie C., Ho, Marcus, Ho, Li-Lun, Huang, Yiling, Huuki-Myers, Louise A., Hwang, Ahyeon, Hyde, Thomas M., Iatrou, Artemis, Inoue, Fumitaka, Jajoo, Aarti, Jensen, Matthew, Jiang, Lihua, Jin, Peng, Jin, Ting, Jops, Connor, Jourdon, Alexandre, Kawaguchi, Riki, Kleinman, Joel E., Kleopoulos, Steven P., Kozlenkov, Alex, Kriegstein, Arnold, Kundaje, Anshul, Kundu, Soumya, Lee, Cheyu, Lee, Donghoon, Li, Junhao
Published in Science (American Association for the Advancement of Science) (24.05.2024)
Published in Science (American Association for the Advancement of Science) (24.05.2024)
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Journal Article
Single-cell RNA sequencing reveals B cell–related molecular biomarkers for Alzheimer’s disease
Xiong, Liu-Lin, Xue, Lu-Lu, Du, Ruo-Lan, Niu, Rui-Ze, Chen, Li, Chen, Jie, Hu, Qiao, Tan, Ya-Xin, Shang, Hui-Fang, Liu, Jia, Yu, Chang-Yin, Wang, Ting-Hua
Published in Experimental & molecular medicine (01.12.2021)
Published in Experimental & molecular medicine (01.12.2021)
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Journal Article
Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates
Böttcher, Anika, Büttner, Maren, Tritschler, Sophie, Sterr, Michael, Aliluev, Alexandra, Oppenländer, Lena, Burtscher, Ingo, Sass, Steffen, Irmler, Martin, Beckers, Johannes, Ziegenhain, Christoph, Enard, Wolfgang, Schamberger, Andrea C., Verhamme, Fien M., Eickelberg, Oliver, Theis, Fabian J., Lickert, Heiko
Published in Nature cell biology (01.01.2021)
Published in Nature cell biology (01.01.2021)
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Journal Article
UPP1 Promotes Lung Adenocarcinoma Progression through Epigenetic Regulation of Glycolysis
Wang, Xuan, Wang, Zheng, Huang, Renhong, Lu, Zhouyi, Chen, Xiaofeng, Huang, Dayu
Published in Aging and disease (01.10.2022)
Published in Aging and disease (01.10.2022)
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Journal Article
Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM
Alvarez, Marcus, Rahmani, Elior, Jew, Brandon, Garske, Kristina M., Miao, Zong, Benhammou, Jihane N., Ye, Chun Jimmie, Pisegna, Joseph R., Pietiläinen, Kirsi H., Halperin, Eran, Pajukanta, Päivi
Published in Scientific reports (03.07.2020)
Published in Scientific reports (03.07.2020)
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Journal Article
Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection
Setliff, Ian, McDonnell, Wyatt J., Raju, Nagarajan, Bombardi, Robin G., Murji, Amyn A., Scheepers, Cathrine, Ziki, Rutendo, Mynhardt, Charissa, Shepherd, Bryan E., Mamchak, Alusha A., Garrett, Nigel, Karim, Salim Abdool, Mallal, Simon A., Crowe, James E., Morris, Lynn, Georgiev, Ivelin S.
Published in Cell host & microbe (13.06.2018)
Published in Cell host & microbe (13.06.2018)
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Journal Article
Simulating paired and longitudinal single-cell RNA sequencing data with rescueSim
Wynn, Elizabeth A, Mould, Kara J, Vestal, Brian E, Moore, Camille M
Published in Bioinformatics (Oxford, England) (01.08.2025)
Published in Bioinformatics (Oxford, England) (01.08.2025)
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Journal Article
Plasma membrane folding enables constant surface area-to-volume ratio in growing mammalian cells
Wu, Weida, Lam, Alice R., Suarez, Kayla, Smith, Grace N., Duquette, Sarah M., Yu, Jiaquan, Mankus, David, Bisher, Margaret, Lytton-Jean, Abigail, Manalis, Scott R., Miettinen, Teemu P.
Published in Current biology (07.04.2025)
Published in Current biology (07.04.2025)
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Journal Article
Constructing local cell-specific networks from single-cell data
Wang, Xuran, Choi, David, Roeder, Kathryn
Published in Proceedings of the National Academy of Sciences - PNAS (21.12.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (21.12.2021)
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Journal Article