Comprehensive Integration of Single-Cell Data

Cited by (497)

Items 201–300 of 497

1. The multiple myeloma microenvironment is defined by an inflammatory stromal cell landscape
   de Jong, Madelon M. E., Kellermayer, Zoltán, Papazian, Natalie, Tahri, Sabrin, Hofste op Bruinink, Davine, Hoogenboezem, Remco, Sanders, Mathijs A., van de Woestijne, Pieter C., Bos, P. Koen, Khandanpour, Cyrus et al. · 2021 · Nature Immunology
2. Functional inference of gene regulation using single-cell multi-omics
   Kartha, Vinay K., Duarte, Fabiana M., Hu, Yan, Ma, Sai, Chew, Jennifer G., Lareau, Caleb A., Earl, Andrew, Burkett, Zach D., Kohlway, Andrew S., Lebofsky, Ronald et al. · 2022 · Cell Genomics
3. Distinct Airway Epithelial Stem Cells Hide among Club Cells but Mobilize to Promote Alveolar Regeneration
   Kathiriya, Jaymin J., Brumwell, Alexis N., Jackson, Julia R., Tang, Xiaodan, Chapman, Harold A. · 2020 · Cell Stem Cell
4. A subset of Kupffer cells regulates metabolism through the expression of CD36
   Blériot, Camille, Barreby, Emelie, Dunsmore, Garett, Ballaire, Raphaelle, Chakarov, Svetoslav, Ficht, Xenia, De Simone, Giorgia, Andreata, Francesco, Fumagalli, Valeria, Guo, Wei et al. · 2021 · Immunity
5. A curated database reveals trends in single-cell transcriptomics
   Svensson, Valentine, da Veiga Beltrame, Eduardo, Pachter, Lior · 2020 · Database
6. Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data
   Xi, Nan Miles, Li, Jingyi Jessica · 2021 · Cell Systems
7. Single-cell transcriptomic analysis of the adult mouse spinal cord reveals molecular diversity of autonomic and skeletal motor neurons
   Blum, Jacob A., Klemm, Sandy, Shadrach, Jennifer L., Guttenplan, Kevin A., Nakayama, Lisa, Kathiria, Arwa, Hoang, Phuong T., Gautier, Olivia, Kaltschmidt, Julia A., Greenleaf, William J. et al. · 2021 · Nature Neuroscience
8. A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
   Joglekar, Anoushka, Prjibelski, Andrey, Mahfouz, Ahmed, Collier, Paul, Lin, Susan, Schlusche, Anna Katharina, Marrocco, Jordan, Williams, Stephen R., Haase, Bettina, Hayes, Ashley et al. · 2021 · Nature Communications
9. Decoding molecular and cellular heterogeneity of mouse nucleus accumbens
   Chen, Renchao, Blosser, Timothy R., Djekidel, Mohamed N., Hao, Junjie, Bhattacherjee, Aritra, Chen, Wenqiang, Tuesta, Luis M., Zhuang, Xiaowei, Zhang, Yi · 2021 · Nature Neuroscience
10. Complement activation induces excessive T cell cytotoxicity in severe COVID-19
    Georg, Philipp, Astaburuaga-García, Rosario, Bonaguro, Lorenzo, Brumhard, Sophia, Michalick, Laura, Lippert, Lena J., Kostevc, Tomislav, Gäbel, Christiane, Schneider, Maria, Streitz, Mathias et al. · 2022 · Cell
11. Slide-tags enables single-nucleus barcoding for multimodal spatial genomics
    Russell, Andrew J. C., Weir, Jackson A., Nadaf, Naeem M., Shabet, Matthew, Kumar, Vipin, Kambhampati, Sandeep, Raichur, Ruth, Marrero, Giovanni J., Liu, Sophia, Balderrama, Karol S. et al. · 2024 · Nature
12. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection
    Alsoussi, Wafaa B, Turner, Jackson S, Case, James B, Zhao, Haiyan, Schmitz, Aaron J, Zhou, Julian Q, Chen, Rita E, Lei, Tingting, Rizk, Amena A, McIntire, Katherine M et al. · 2020 · The Journal of Immunology
13. The spatiotemporal program of zonal liver regeneration following acute injury
    Ben-Moshe, Shani, Veg, Tamar, Manco, Rita, Dan, Stav, Papinutti, Delfina, Lifshitz, Aviezer, Kolodziejczyk, Aleksandra A., Bahar Halpern, Keren, Elinav, Eran, Itzkovitz, Shalev · 2022 · Cell Stem Cell
14. Mutations in BRCA1 and BRCA2 differentially affect the tumor microenvironment and response to checkpoint blockade immunotherapy
    Samstein, Robert M., Krishna, Chirag, Ma, Xiaoxiao, Pei, Xin, Lee, Ken-Wing, Makarov, Vladimir, Kuo, Fengshen, Chung, Jonathan, Srivastava, Raghvendra M., Purohit, Tanaya A. et al. · 2020 · Nature Cancer
15. Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens
    Morris, John A., Caragine, Christina, Daniloski, Zharko, Domingo, Júlia, Barry, Timothy, Lu, Lu, Davis, Kyrie, Ziosi, Marcello, Glinos, Dafni A., Hao, Stephanie et al. · 2023 · Science
16. Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data
    Lause, Jan, Berens, Philipp, Kobak, Dmitry · 2021 · Genome Biology
17. TGFβ-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts
    Grauel, Angelo L., Nguyen, Beverly, Ruddy, David, Laszewski, Tyler, Schwartz, Stephanie, Chang, Jonathan, Chen, Julie, Piquet, Michelle, Pelletier, Marc, Yan, Zheng et al. · 2020 · Nature Communications
18. Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics
    Cheemarla, Nagarjuna R., Watkins, Timothy A., Mihaylova, Valia T., Wang, Bao, Zhao, Dejian, Wang, Guilin, Landry, Marie L., Foxman, Ellen F. · 2021 · Journal of Experimental Medicine
19. Deep learning enables genetic analysis of the human thoracic aorta
    Pirruccello, James P., Chaffin, Mark D., Chou, Elizabeth L., Fleming, Stephen J., Lin, Honghuang, Nekoui, Mahan, Khurshid, Shaan, Friedman, Samuel F., Bick, Alexander G., Arduini, Alessandro et al. · 2022 · Nature Genetics
20. Baricitinib treatment resolves lower-airway macrophage inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques
    Hoang, Timothy N., Pino, Maria, Boddapati, Arun K., Viox, Elise G., Starke, Carly E., Upadhyay, Amit A., Gumber, Sanjeev, Nekorchuk, Michael, Busman-Sahay, Kathleen, Strongin, Zachary et al. · 2021 · Cell
21. Single-cell RNA sequencing identifies senescent cerebromicrovascular endothelial cells in the aged mouse brain
    Kiss, Tamas, Nyúl-Tóth, Ádám, Balasubramanian, Priya, Tarantini, Stefano, Ahire, Chetan, DelFavero, Jordan, Yabluchanskiy, Andriy, Csipo, Tamas, Farkas, Eszter, Wiley, Graham et al. · 2020 · GeroScience
22. Senescent alveolar macrophages promote early-stage lung tumorigenesis
    Prieto, Luis I., Sturmlechner, Ines, Graves, Sara I., Zhang, Cheng, Goplen, Nick P., Yi, Eunhee S., Sun, Jie, Li, Hu, Baker, Darren J. · 2023 · Cancer Cell
23. Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing
    Li, Carman Man-Chung, Shapiro, Hana, Tsiobikas, Christina, Selfors, Laura M., Chen, Huidong, Rosenbluth, Jennifer, Moore, Kaitlin, Gupta, Kushali P., Gray, G. Kenneth, Oren, Yaara et al. · 2020 · Cell Reports
24. Comparative transcriptomics reveals human-specific cortical features
    Jorstad, Nikolas L., Song, Janet H. T., Exposito-Alonso, David, Suresh, Hamsini, Castro-Pacheco, Nathan, Krienen, Fenna M., Yanny, Anna Marie, Close, Jennie, Gelfand, Emily, Long, Brian et al. · 2023 · Science
25. Computational methods for single-cell omics across modalities
    Efremova, Mirjana, Teichmann, Sarah A. · 2020 · Nature Methods
26. Early Alzheimer’s disease pathology in human cortex involves transient cell states
    Gazestani, Vahid, Kamath, Tushar, Nadaf, Naeem M., Dougalis, Antonios, Burris, S.J., Rooney, Brendan, Junkkari, Antti, Vanderburg, Charles, Pelkonen, Anssi, Gomez-Budia, Mireia et al. · 2023 · Cell
27. Diverse human astrocyte and microglial transcriptional responses to Alzheimer’s pathology
    Smith, Amy M., Davey, Karen, Tsartsalis, Stergios, Khozoie, Combiz, Fancy, Nurun, Tang, See Swee, Liaptsi, Eirini, Weinert, Maria, McGarry, Aisling, Muirhead, Robert C. J. et al. · 2022 · Acta Neuropathologica
28. Atlas of the aging mouse brain reveals white matter as vulnerable foci
    Hahn, Oliver, Foltz, Aulden G., Atkins, Micaiah, Kedir, Blen, Moran-Losada, Patricia, Guldner, Ian H., Munson, Christy, Kern, Fabian, Pálovics, Róbert, Lu, Nannan et al. · 2023 · Cell
29. SpaGE: Spatial Gene Enhancement using scRNA-seq
    Abdelaal, Tamim, Mourragui, Soufiane, Mahfouz, Ahmed, Reinders, Marcel J T · 2020 · Nucleic Acids Research
30. Normalizing and denoising protein expression data from droplet-based single cell profiling
    Mulè, Matthew P., Martins, Andrew J., Tsang, John S. · 2022 · Nature Communications
31. A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers
    Hanada, Ken-ichi, Zhao, Chihao, Gil-Hoyos, Raul, Gartner, Jared J., Chow-Parmer, Christopher, Lowery, Frank J., Krishna, Sri, Prickett, Todd D., Kivitz, Scott, Parkhurst, Maria R. et al. · 2022 · Cancer Cell
32. Systematic comparison of sequencing-based spatial transcriptomic methods
    You, Yue, Fu, Yuting, Li, Lanxiang, Zhang, Zhongmin, Jia, Shikai, Lu, Shihong, Ren, Wenle, Liu, Yifang, Xu, Yang, Liu, Xiaojing et al. · 2024 · Nature Methods
33. Transformer for one stop interpretable cell type annotation
    Chen, Jiawei, Xu, Hao, Tao, Wanyu, Chen, Zhaoxiong, Zhao, Yuxuan, Han, Jing-Dong J. · 2023 · Nature Communications
34. A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma
    Pozniak, Joanna, Pedri, Dennis, Landeloos, Ewout, Van Herck, Yannick, Antoranz, Asier, Vanwynsberghe, Lukas, Nowosad, Ada, Roda, Niccolò, Makhzami, Samira, Bervoets, Greet et al. · 2024 · Cell
35. Modeling Sporadic Alzheimer's Disease in Human Brain Organoids under Serum Exposure
    Chen, Xianwei, Sun, Guoqiang, Tian, E, Zhang, Mingzi, Davtyan, Hayk, Beach, Thomas G., Reiman, Eric M., Blurton‐Jones, Mathew, Holtzman, David M., Shi, Yanhong · 2021 · Advanced Science
36. CNS fibroblasts form a fibrotic scar in response to immune cell infiltration.
    Dorrier, Cayce E., Aran, Dvir, Haenelt, Ezekiel A., Sheehy, Ryan N., Hoi, Kimberly K., Pintarić, Lucija, Chen, Yanan, Lizama, Carlos O., Cautivo, Kelly M., Weiner, Geoffrey A. et al. · 2021 · Nature Neuroscience
37. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression
    Wu, Steven J., Furlan, Scott N., Mihalas, Anca B., Kaya-Okur, Hatice S., Feroze, Abdullah H., Emerson, Samuel N., Zheng, Ye, Carson, Kalee, Cimino, Patrick J., Keene, C. Dirk et al. · 2021 · Nature Biotechnology
38. Transcriptional Programs of Circuit Assembly in the Drosophila Visual System
    Kurmangaliyev, Yerbol Z., Yoo, Juyoun, Valdes-Aleman, Javier, Sanfilippo, Piero, Zipursky, S. Lawrence · 2020 · Neuron
39. Temporal modelling using single-cell transcriptomics
    Ding, Jun, Sharon, Nadav, Bar-Joseph, Ziv · 2022 · Nature Reviews Genetics
40. Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis
    Avagyan, S., Henninger, J. E., Mannherz, W. P., Mistry, M., Yoon, J., Yang, S., Weber, M. C., Moore, J. L., Zon, L. I. · 2021 · Science
41. A genetic map of the mouse dorsal vagal complex and its role in obesity
    Ludwig, Mette Q., Cheng, Wenwen, Gordian, Desiree, Lee, Julie, Paulsen, Sarah J., Hansen, Stine N., Egerod, Kristoffer L., Barkholt, Pernille, Rhodes, Christopher J., Secher, Anna et al. · 2021 · Nature Metabolism
42. Tumor microbiome links cellular programs and immunity in pancreatic cancer
    Ghaddar, Bassel, Biswas, Antara, Harris, Chris, Omary, M. Bishr, Carpizo, Darren R., Blaser, Martin J., De, Subhajyoti · 2022 · Cancer Cell
43. Neuronal ApoE upregulates MHC-I expression to drive selective neurodegeneration in Alzheimer’s disease
    Zalocusky, Kelly A., Najm, Ramsey, Taubes, Alice L., Hao, Yanxia, Yoon, Seo Yeon, Koutsodendris, Nicole, Nelson, Maxine R., Rao, Antara, Bennett, David A., Bant, Jason et al. · 2021 · Nature Neuroscience
44. Expansion of Pathogenic Cardiac Macrophages in Immune Checkpoint Inhibitor Myocarditis
    Ma, Pan, Liu, Jing, Qin, Juan, Lai, Lulu, Heo, Gyu Seong, Luehmann, Hannah, Sultan, Deborah, Bredemeyer, Andrea, Bajapa, Geetika, Feng, Guoshuai et al. · 2024 · Circulation
45. Statistical and machine learning methods for spatially resolved transcriptomics data analysis
    Zeng, Zexian, Li, Yawei, Li, Yiming, Luo, Yuan · 2022 · Genome Biology
46. An atlas of gene regulatory elements in adult mouse cerebrum
    Li, Yang Eric, Preissl, Sebastian, Hou, Xiaomeng, Zhang, Ziyang, Zhang, Kai, Qiu, Yunjiang, Poirion, Olivier B., Li, Bin, Chiou, Joshua, Liu, Hanqing et al. · 2021 · Nature
47. Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells
    Delacher, Michael, Simon, Malte, Sanderink, Lieke, Hotz-Wagenblatt, Agnes, Wuttke, Marina, Schambeck, Kathrin, Schmidleithner, Lisa, Bittner, Sebastian, Pant, Asmita, Ritter, Uwe et al. · 2021 · Immunity
48. Aging-associated deficit in CCR7 is linked to worsened glymphatic function, cognition, neuroinflammation, and β-amyloid pathology
    Da Mesquita, Sandro, Herz, Jasmin, Wall, Morgan, Dykstra, Taitea, de Lima, Kalil Alves, Norris, Geoffrey T., Dabhi, Nisha, Kennedy, Tatiana, Baker, Wendy, Kipnis, Jonathan · 2021 · Science Advances
49. Pathological angiogenesis in retinopathy engages cellular senescence and is amenable to therapeutic elimination via BCL-xL inhibition
    Crespo-Garcia, Sergio, Tsuruda, Pamela R., Dejda, Agnieszka, Ryan, Rathi D., Fournier, Frederik, Chaney, Shawnta Y., Pilon, Frederique, Dogan, Taner, Cagnone, Gael, Patel, Priyanka et al. · 2021 · Cell Metabolism
50. Detection of differentially abundant cell subpopulations in scRNA-seq data
    Zhao, Jun, Jaffe, Ariel, Li, Henry, Lindenbaum, Ofir, Sefik, Esen, Jackson, Ruaidhrí, Cheng, Xiuyuan, Flavell, Richard A., Kluger, Yuval · 2021 · Proceedings of the National Academy of Sciences
51. Coordinated changes in cellular behavior ensure the lifelong maintenance of the hippocampal stem cell population
    Harris, Lachlan, Rigo, Piero, Stiehl, Thomas, Gaber, Zachary B., Austin, Sophie H.L., Masdeu, Maria del Mar, Edwards, Amelia, Urbán, Noelia, Marciniak-Czochra, Anna, Guillemot, François · 2021 · Cell Stem Cell
52. A Binary Cre Transgenic Approach Dissects Microglia and CNS Border-Associated Macrophages
    Kim, Jung-Seok, Kolesnikov, Masha, Peled-Hajaj, Shany, Scheyltjens, Isabelle, Xia, Yuan, Trzebanski, Sebastien, Haimon, Zhana, Shemer, Anat, Lubart, Alisa, Van Hove, Hannah et al. · 2021 · Immunity
53. Technological advances in cancer immunity: from immunogenomics to single‐cell analysis and artificial intelligence
    Xu, Ying, Su, Guan-Hua, Ma, Ding, Xiao, Yi, Shao, Zhi-Ming, Jiang, Yi-Zhou · 2021 · Signal Transduction and Targeted Therapy
54. ELAVL4, splicing, and glutamatergic dysfunction precede neuron loss in MAPT mutation cerebral organoids
    Bowles, Kathryn R., Silva, M. Catarina, Whitney, Kristen, Bertucci, Taylor, Berlind, Joshua E., Lai, Jesse D., Garza, Jacob C., Boles, Nathan C., Mahali, Sidhartha, Strang, Kevin H. et al. · 2021 · Cell
55. Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways
    Stewart, Alexander, Ng, Joseph Chi-Fung, Wallis, Gillian, Tsioligka, Vasiliki, Fraternali, Franca, Dunn-Walters, Deborah K. · 2021 · Frontiers in Immunology
56. SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 ⁺ T cell responses
    Agerer, Benedikt, Koblischke, Maximilian, Gudipati, Venugopal, Montaño-Gutierrez, Luis Fernando, Smyth, Mark, Popa, Alexandra, Genger, Jakob-Wendelin, Endler, Lukas, Florian, David M., Mühlgrabner, Vanessa et al. · 2021 · Science Immunology
57. Single-cell antigen-specific landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL
    Bai, Zhiliang, Woodhouse, Steven, Zhao, Ziran, Arya, Rahul, Govek, Kiya, Kim, Dongjoo, Lundh, Stefan, Baysoy, Alev, Sun, Hongxing, Deng, Yanxiang et al. · 2022 · Science Advances
58. Transcriptional and spatial resolution of cell types in the mammalian habenula
    Hashikawa, Yoshiko, Hashikawa, Koichi, Rossi, Mark A., Basiri, Marcus L., Liu, Yuejia, Johnston, Nathan L., Ahmad, Omar R., Stuber, Garret D. · 2020 · Neuron
59. Targeting p21Cip1 highly expressing cells in adipose tissue alleviates insulin resistance in obesity
    Wang, Lichao, Wang, Binsheng, Gasek, Nathan S., Zhou, Yueying, Cohn, Rachel L., Martin, Dominique E., Zuo, Wulin, Flynn, William F., Guo, Chun, Jellison, Evan R. et al. · 2022 · Cell Metabolism
60. Decoding gene regulation in the fly brain
    Janssens, Jasper, Aibar, Sara, Taskiran, Ibrahim Ihsan, Ismail, Joy N., Spanier, Katina I., Bravo González-Blas, Carmen, Quan, Xiao Jiang, Papasokrati, Dafni, Hulselmans, Gert, Makhzami, Samira et al. · 2021
61. Decoding gene regulation in the fly brain
    Janssens, Jasper, Aibar, Sara, Taskiran, Ibrahim Ihsan, Ismail, Joy N., Gomez, Alicia Estacio, Aughey, Gabriel, Spanier, Katina I., De Rop, Florian V., González-Blas, Carmen Bravo, Dionne, Marc et al. · 2022 · Nature
62. Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation
    Machado, Léo, Geara, Perla, Camps, Jordi, Dos Santos, Matthieu, Teixeira-Clerc, Fatima, Van Herck, Jens, Varet, Hugo, Legendre, Rachel, Pawlotsky, Jean-Michel, Sampaolesi, Maurilio et al. · 2021 · Cell Stem Cell
63. Unsupervised removal of systematic background noise from droplet-based single-cell experiments using <tt>CellBender</tt>
    Fleming, Stephen J., Chaffin, Mark D., Arduini, Alessandro, Akkad, Amer-Denis, Banks, Eric, Marioni, John C., Philippakis, Anthony A., Ellinor, Patrick T., Babadi, Mehrtash · 2019
64. Absence of microglia promotes diverse pathologies and early lethality in Alzheimer’s disease mice
    Kiani Shabestari, Sepideh, Morabito, Samuel, Danhash, Emma Pascal, McQuade, Amanda, Sanchez, Jessica Ramirez, Miyoshi, Emily, Chadarevian, Jean Paul, Claes, Christel, Coburn, Morgan Alexandra, Hasselmann, Jonathan et al. · 2022 · Cell Reports
65. Cobolt: integrative analysis of multimodal single-cell sequencing data
    Gong, Boying, Zhou, Yun, Purdom, Elizabeth · 2021 · Genome Biology
66. FGF21 Signals to Glutamatergic Neurons in the Ventromedial Hypothalamus to Suppress Carbohydrate Intake
    Jensen-Cody, Sharon O., Flippo, Kyle H., Claflin, Kristin E., Yavuz, Yavuz, Sapouckey, Sarah A., Walters, Grant C., Usachev, Yuriy M., Atasoy, Deniz, Gillum, Matthew P., Potthoff, Matthew J. · 2020 · Cell Metabolism
67. Single-cell RNA sequencing of human liver reveals hepatic stellate cell heterogeneity
    Payen, Valéry L., Lavergne, Arnaud, Alevra Sarika, Niki, Colonval, Megan, Karim, Latifa, Deckers, Manon, Najimi, Mustapha, Coppieters, Wouter, Charloteaux, Benoît, Sokal, Etienne M. et al. · 2021 · JHEP Reports
68. Evaluation of Cell Type Annotation R Packages on Single-Cell RNA-Seq Data
    Huang, Qianhui, Liu, Yu, Du, Yuheng, Garmire, Lana X. · 2021 · Genomics, Proteomics &amp; Bioinformatics
69. Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord
    Alkaslasi, Mor R., Piccus, Zoe E., Hareendran, Sangeetha, Silberberg, Hanna, Chen, Li, Zhang, Yajun, Petros, Timothy J., Le Pichon, Claire E. · 2021 · Nature Communications
70. Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
    Khrameeva, Ekaterina, Kurochkin, Ilia, Han, Dingding, Guijarro, Patricia, Kanton, Sabina, Santel, Malgorzata, Qian, Zhengzong, Rong, Shen, Mazin, Pavel, Sabirov, Marat et al. · 2020 · Genome Research
71. Schizophrenia is defined by cell-specific neuropathology and multiple neurodevelopmental mechanisms in patient-derived cerebral organoids
    Notaras, Michael, Lodhi, Aiman, Dündar, Friederike, Collier, Paul, Sayles, Nicole M., Tilgner, Hagen, Greening, David, Colak, Dilek · 2022 · Molecular Psychiatry
72. 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
73. AD-linked R47H- <i>TREM2</i> mutation induces disease-enhancing microglial states via AKT hyperactivation
    Sayed, Faten A., Kodama, Lay, Fan, Li, Carling, Gillian K., Udeochu, Joe C., Le, David, Li, Qingyun, Zhou, Lu, Wong, Man Ying, Horowitz, Rose et al. · 2021 · Science Translational Medicine
74. Intratumor microbiome features reveal antitumor potentials of intrahepatic cholangiocarcinoma
    Chai, Xiaoqiang, Wang, Jie, Li, Huanping, Gao, Chao, Li, Shuangqi, Wei, Chuanyuan, Huang, Jianhang, Tian, Yingming, Yuan, Jian, Lu, Jiacheng et al. · 2023 · Gut Microbes
75. Profiling B cell immunodominance after SARS-CoV-2 infection reveals antibody evolution to non-neutralizing viral targets
    Dugan, Haley L., Stamper, Christopher T., Li, Lei, Changrob, Siriruk, Asby, Nicholas W., Halfmann, Peter J., Zheng, Nai-Ying, Huang, Min, Shaw, Dustin G., Cobb, Mari S. et al. · 2021 · Immunity
76. Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation
    Baek, Seungbyn, Lee, Insuk · 2020 · Computational and Structural Biotechnology Journal
77. A human multi-lineage hepatic organoid model for liver fibrosis
    Guan, Yuan, Enejder, Annika, Wang, Meiyue, Fang, Zhuoqing, Cui, Lu, Chen, Shih-Yu, Wang, Jingxiao, Tan, Yalun, Wu, Manhong, Chen, Xinyu et al. · 2021 · Nature Communications
78. The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells
    Melani, Rafael D., Gerbasi, Vincent R., Anderson, Lissa C., Sikora, Jacek W., Toby, Timothy K., Hutton, Josiah E., Butcher, David S., Negrão, Fernanda, Seckler, Henrique S., Srzentić, Kristina et al. · 2022 · Science
79. Single-cell transcriptomic landscape of human blood cells
    Xie, Xiaowei, Liu, Mengyao, Zhang, Yawen, Wang, Bingrui, Zhu, Caiying, Wang, Chenchen, Li, Qing, Huo, Yingying, Guo, Jiaojiao, Xu, Changlu et al. · 2021 · National Science Review
80. Multimodal chromatin profiling using nanobody-based single-cell CUT&amp;Tag
    Bartosovic, Marek, Castelo-Branco, Gonçalo · 2023 · Nature Biotechnology
81. Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations
    Mattei, Daniele, Ivanov, Andranik, van Oostrum, Marc, Pantelyushin, Stanislav, Richetto, Juliet, Mueller, Flavia, Beffinger, Michal Matheus, Schellhammer, Linda, vom Berg, Johannes, Wollscheid, Bernd et al. · 2020
82. DSCAM/PAK1 pathway suppression reverses neurogenesis deficits in iPSC-derived cerebral organoids from patients with Down syndrome
    Tang, Xiao-Yan, Xu, Lei, Wang, Jingshen, Hong, Yuan, Wang, Yuanyuan, Zhu, Qian, Wang, Da, Zhang, Xin-Yue, Liu, Chun-Yue, Fang, Kai-Heng et al. · 2021 · Journal of Clinical Investigation
83. Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes
    Zaitsev, Aleksandr, Chelushkin, Maksim, Dyikanov, Daniiar, Cheremushkin, Ilya, Shpak, Boris, Nomie, Krystle, Zyrin, Vladimir, Nuzhdina, Ekaterina, Lozinsky, Yaroslav, Zotova, Anastasia et al. · 2022 · Cancer Cell
84. 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
85. Integrating spatial and single-cell transcriptomics to characterize the molecular and cellular architecture of the ischemic mouse brain
    Han, Bing, Zhou, Shunheng, Zhang, Yuan, Chen, Sina, Xi, Wen, Liu, Chenchen, Zhou, Xu, Yuan, Mengqin, Yu, Xiaoyu, Li, Lu et al. · 2024 · Science Translational Medicine
86. NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells
    Chen, Amy F., Parks, Benjamin, Kathiria, Arwa S., Ober-Reynolds, Benjamin, Goronzy, Jorg J., Greenleaf, William J. · 2022 · Nature Methods
87. Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming.
    Liuyang, Shijia, Wang, Guan, Wang, Yanglu, He, Huanjing, Lyu, Yulin, Cheng, Lin, Yang, Zhihan, Guan, Jingyang, Fu, Yao, Zhu, Jialiang et al. · 2023 · Cell Stem Cell
88. TGFβ2 and TGFβ3 isoforms drive fibrotic disease pathogenesis
    Sun, Tianhe, Huang, Zhiyu, Liang, Wei-Ching, Yin, Jianping, Lin, Wei Yu, Wu, Jia, Vernes, Jean-Michel, Lutman, Jeff, Caplazi, Patrick, Jeet, Surinder et al. · 2021 · Science Translational Medicine
89. Kupffer-cell-derived IL-6 is repurposed for hepatocyte dedifferentiation via activating progenitor genes from injury-specific enhancers
    Li, Lu, Cui, Lei, Lin, Ping, Liu, Zhaoyuan, Bao, Shujie, Ma, Xiaolong, Nan, Haitao, Zhu, Wencheng, Cen, Jin, Mao, Yunuo et al. · 2023 · Cell Stem Cell
90. An <i>in vitro</i> vascularized micro-tumor model of human colorectal cancer recapitulates <i>in vivo</i> responses to standard-of-care therapy
    Hachey, Stephanie J., Movsesyan, Silva, Nguyen, Quy H., Burton-Sojo, Giselle, Tankazyan, Ani, Wu, Jie, Hoang, Tuyen, Zhao, Da, Wang, Shuxiong, Hatch, Michaela M. et al. · 2021 · Lab on a Chip
91. Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets
    Caglayan, Emre, Liu, Yuxiang, Konopka, Genevieve · 2022 · Neuron
92. Acute ischemia induces spatially and transcriptionally distinct microglial subclusters
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