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For: McDavid A, Finak G, Chattopadyay PK, Dominguez M, Lamoreaux L, Ma SS, Roederer M, Gottardo R. Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. ACTA ACUST UNITED AC 2012;29:461-7. [PMID: 23267174 PMCID: PMC3570210 DOI: 10.1093/bioinformatics/bts714] [Citation(s) in RCA: 272] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Number Cited by Other Article(s)
1
Wei YH, Lin F. Barcodes based on nucleic acid sequences: Applications and challenges (Review). Mol Med Rep 2025;32:187. [PMID: 40314098 PMCID: PMC12076290 DOI: 10.3892/mmr.2025.13552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 03/04/2025] [Indexed: 05/03/2025]  Open
2
Bavais J, Chevallier J, Spinelli L, van de Pavert S, Puthier D. SciGeneX: enhancing transcriptional analysis through gene module detection in single-cell and spatial transcriptomics data. NAR Genom Bioinform 2025;7:lqaf043. [PMID: 40248490 PMCID: PMC12004220 DOI: 10.1093/nargab/lqaf043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 03/19/2025] [Accepted: 04/09/2025] [Indexed: 04/19/2025]  Open
3
Weidling I, Preiss CN, Chancellor SE, Srivastava G, Gibilisco L, Lin G, Brennan MS, Lee J, Roth LM, Morozova O, Nam KN, Patel NR, Liu Q, Thomas JK, Reinhardt P, Wilkens R, Ehrnhoefer DE, Striebinger A, Barghorn S, Xanthopoulos C, Weil MT, Biesinger S, Cik M, Romanul N, Yanamandra K, Welker AM, Wu J, Gasparini L, Stöhr J, Langlois X, Manos JD. hiPSC-neurons recapitulate the subtype-specific cell intrinsic nature of susceptibility to neurodegenerative disease-relevant aggregation. Acta Neuropathol Commun 2025;13:108. [PMID: 40390134 PMCID: PMC12087151 DOI: 10.1186/s40478-025-02000-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Accepted: 04/05/2025] [Indexed: 05/21/2025]  Open
4
Arya A, Tripathi P, Dubey N, Aier I, Kumar Varadwaj P. Navigating single-cell RNA-sequencing: protocols, tools, databases, and applications. Genomics Inform 2025;23:13. [PMID: 40382658 DOI: 10.1186/s44342-025-00044-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Accepted: 04/07/2025] [Indexed: 05/20/2025]  Open
5
Yu G, Li J, Zhang H, Zi H, Liu M, An Q, Qiu T, Li P, Song J, Liu P, Quan K, Li S, Liu Y, Zhu W, Du J. Single-cell analysis reveals the implication of vascular endothelial cell-intrinsic ANGPT2 in human intracranial aneurysm. Cardiovasc Res 2025;121:658-673. [PMID: 39187926 DOI: 10.1093/cvr/cvae186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/04/2024] [Accepted: 06/13/2024] [Indexed: 08/28/2024]  Open
6
Leibovich N, Goyal S. Limitations and optimizations of cellular lineages tracking. PLoS Comput Biol 2025;21:e1012880. [PMID: 40228207 PMCID: PMC11996212 DOI: 10.1371/journal.pcbi.1012880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 02/14/2025] [Indexed: 04/16/2025]  Open
7
Liu M, Zheng S, Li H, Budowle B, Wang L, Lou Z, Ge J. High resolution tissue and cell type identification via single cell transcriptomic profiling. PLoS One 2025;20:e0318151. [PMID: 40138334 PMCID: PMC11940611 DOI: 10.1371/journal.pone.0318151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Accepted: 01/11/2025] [Indexed: 03/29/2025]  Open
8
Shen Y, Jiang K, Tan D, Zhu M, Qiu Y, Huang P, Zou W, Deng J, Wang Z, Xiong Y, Hong D. uN2CpolyG-mediated p65 nuclear sequestration suppresses the NF-κB-NLRP3 pathway in neuronal intranuclear inclusion disease. Cell Commun Signal 2025;23:68. [PMID: 39920690 PMCID: PMC11806584 DOI: 10.1186/s12964-025-02079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 02/01/2025] [Indexed: 02/09/2025]  Open
9
Park CJ, Oh JE, Lin P, Zhou S, Bunnell M, Bikorimana E, Spinella MJ, Lim HJ, Ko CJ. A Dynamic Shift in Estrogen Receptor Expression During Granulosa Cell Differentiation in the Ovary. Endocrinology 2025;166:bqaf006. [PMID: 39834231 PMCID: PMC12054734 DOI: 10.1210/endocr/bqaf006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 12/29/2024] [Accepted: 01/18/2025] [Indexed: 01/22/2025]
10
Song D, Chen S, Lee C, Li K, Ge X, Li JJ. Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.21.550107. [PMID: 37546812 PMCID: PMC10401959 DOI: 10.1101/2023.07.21.550107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
11
Yang Y, Zhao A, Wang T, Tang Q, Qi S, Shi X, Wang F, Gao Y. Identification of driving genes of recurrent miscarriage based on transcriptome sequencing and immunoinfiltration analysis. Int Immunopharmacol 2024;143:113095. [PMID: 39395380 DOI: 10.1016/j.intimp.2024.113095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 09/01/2024] [Accepted: 09/03/2024] [Indexed: 10/14/2024]
12
Ma J, Chu TK, Polo-Prieto M, Park YH, Li Y, Chen R, Mardon G, Frankfort BJ, Tran NM. Sample multiplexing for retinal single-cell RNA sequencing. iScience 2024;27:111250. [PMID: 39569377 PMCID: PMC11576387 DOI: 10.1016/j.isci.2024.111250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 08/09/2024] [Accepted: 10/22/2024] [Indexed: 11/22/2024]  Open
13
Vasileva E, Arata C, Luo Y, Burgos R, Crump JG, Amatruda JF. Origin of Ewing sarcoma by embryonic reprogramming of neural crest to mesoderm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.27.620438. [PMID: 39554045 PMCID: PMC11565755 DOI: 10.1101/2024.10.27.620438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
14
Yang X, Zhao Y, Liu W, Gao Z, Wang C, Wang C, Li S, Zhang X. Single-cell transcriptomics reveals neural stem cell trans-differentiation and cell subpopulations in whole heart decellularized extracellular matrix. BIOPHYSICS REPORTS 2024;10:241-253. [PMID: 39281200 PMCID: PMC11399890 DOI: 10.52601/bpr.2024.240011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/16/2024] [Indexed: 09/18/2024]  Open
15
Wen Z, Ablimit A. Aquaporin 1 aggravates lipopolysaccharide-induced macrophage polarization and pyroptosis. Sci Rep 2024;14:18569. [PMID: 39127771 PMCID: PMC11316789 DOI: 10.1038/s41598-024-68899-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]  Open
16
Fu X, Guo X, Xu H, Li Y, Jin B, Zhang X, Shu C, Fan Y, Yu Y, Tian Y, Tian J, Shu J. Varied cellular abnormalities in thin vs. normal endometrium in recurrent implantation failure by single-cell transcriptomics. Reprod Biol Endocrinol 2024;22:90. [PMID: 39085925 PMCID: PMC11293141 DOI: 10.1186/s12958-024-01263-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]  Open
17
Dunsmore G, Guo W, Li Z, Bejarano DA, Pai R, Yang K, Kwok I, Tan L, Ng M, De La Calle Fabregat C, Yatim A, Bougouin A, Mulder K, Thomas J, Villar J, Bied M, Kloeckner B, Dutertre CA, Gessain G, Chakarov S, Liu Z, Scoazec JY, Lennon-Dumenil AM, Marichal T, Sautès-Fridman C, Fridman WH, Sharma A, Su B, Schlitzer A, Ng LG, Blériot C, Ginhoux F. Timing and location dictate monocyte fate and their transition to tumor-associated macrophages. Sci Immunol 2024;9:eadk3981. [PMID: 39058763 DOI: 10.1126/sciimmunol.adk3981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 07/03/2024] [Indexed: 07/28/2024]
18
Fan Z, Karakone M, Nagarajan S, Nagy N, Mildenberger W, Petrova E, Hinte LC, Bijnen M, Häne P, Nelius E, Chen J, Ferapontova I, von Meyenn F, Trepiccione F, Berber M, Ribas DP, Eichmann A, Zennaro MC, Takeda N, Fischer JW, Spyroglou A, Reincke M, Beuschlein F, Loffing J, Greter M, Stockmann C. Macrophages preserve endothelial cell specialization in the adrenal gland to modulate aldosterone secretion and blood pressure. Cell Rep 2024;43:114395. [PMID: 38941187 DOI: 10.1016/j.celrep.2024.114395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/22/2024] [Accepted: 06/07/2024] [Indexed: 06/30/2024]  Open
19
Hegde S, Giotti B, Soong BY, Halasz L, Berichel JL, Magen A, Kloeckner B, Mattiuz R, Park MD, Marks A, Belabed M, Hamon P, Chin T, Troncoso L, Lee JJ, Ahimovic D, Bale M, Chung G, D'souza D, Angeliadis K, Dawson T, Kim-Schulze S, Flores RM, Kaufman AJ, Ginhoux F, Josefowicz SZ, Ma S, Tsankov AM, Marron TU, Brown BD, Merad M. Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600383. [PMID: 38979166 PMCID: PMC11230224 DOI: 10.1101/2024.06.24.600383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
20
Tian Y, Wu L, Huang CC, Wang L. Identify Regulatory eQTLs by Multiome Sequencing in Prostate Single Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599704. [PMID: 38948854 PMCID: PMC11213234 DOI: 10.1101/2024.06.19.599704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
21
Li C, Shao X, Zhang S, Wang Y, Jin K, Yang P, Lu X, Fan X, Wang Y. scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network. Cell Rep Med 2024;5:101568. [PMID: 38754419 PMCID: PMC11228399 DOI: 10.1016/j.xcrm.2024.101568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 12/27/2023] [Accepted: 04/21/2024] [Indexed: 05/18/2024]
22
Gao Q, Ji Z, Wang L, Owzar K, Li QJ, Chan C, Xie J. SifiNet: a robust and accurate method to identify feature gene sets and annotate cells. Nucleic Acids Res 2024;52:e46. [PMID: 38647069 PMCID: PMC11109959 DOI: 10.1093/nar/gkae307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/25/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024]  Open
23
Tamiato A, Tombor LS, Fischer A, Muhly-Reinholz M, Vanicek LR, Toğru BN, Neitz J, Glaser SF, Merten M, Rodriguez Morales D, Kwon J, Klatt S, Schumacher B, Günther S, Abplanalp WT, John D, Fleming I, Wettschureck N, Dimmeler S, Luxán G. Age-Dependent RGS5 Loss in Pericytes Induces Cardiac Dysfunction and Fibrosis. Circ Res 2024;134:1240-1255. [PMID: 38563133 PMCID: PMC11081481 DOI: 10.1161/circresaha.123.324183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/11/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
24
Ma J, Chu TK, Polo Prieto M, Park Y, Li Y, Chen R, Mardon G, Frankfort BJ, Tran NM. Sample multiplexing for retinal single-cell RNA-sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.589797. [PMID: 38712294 PMCID: PMC11071429 DOI: 10.1101/2024.04.23.589797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
25
Pullin JM, McCarthy DJ. A comparison of marker gene selection methods for single-cell RNA sequencing data. Genome Biol 2024;25:56. [PMID: 38409056 PMCID: PMC10895860 DOI: 10.1186/s13059-024-03183-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/07/2024] [Indexed: 02/28/2024]  Open
26
Monnier L, Cournède PH. A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization. PLoS Comput Biol 2024;20:e1011880. [PMID: 38386700 PMCID: PMC10914288 DOI: 10.1371/journal.pcbi.1011880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 03/05/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]  Open
27
Adegoke A, Ribeiro JMC, Smith R, Karim S. Tick innate immune responses to hematophagy and Ehrlichia infection at single-cell resolution. Front Immunol 2024;14:1305976. [PMID: 38274813 PMCID: PMC10808623 DOI: 10.3389/fimmu.2023.1305976] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024]  Open
28
Feng J, Goedegebuure SP, Zeng A, Bi Y, Wang T, Payne P, Ding L, DeNardo D, Hawkins W, Fields RC, Li F. sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data. PLoS Comput Biol 2024;20:e1011785. [PMID: 38181047 PMCID: PMC10796047 DOI: 10.1371/journal.pcbi.1011785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 01/18/2024] [Accepted: 12/23/2023] [Indexed: 01/07/2024]  Open
29
Zhu J, Yang Y. Imputation for Single-cell RNA-seq Data with Non-negative Matrix Factorization and Transfer Learning. J Bioinform Comput Biol 2023;21:2350029. [PMID: 38248911 DOI: 10.1142/s0219720023500294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
30
Lu Y, Chen QM, An L. Semi-reference based cell type deconvolution with application to human metastatic cancers. NAR Genom Bioinform 2023;5:lqad109. [PMID: 38143958 PMCID: PMC10748484 DOI: 10.1093/nargab/lqad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/01/2023] [Accepted: 12/13/2023] [Indexed: 12/26/2023]  Open
31
Sun T, Grassam-Rowe A, Pu Z, Li Y, Ren H, An Y, Guo X, Hu W, Liu Y, Zheng Y, Liu Z, Kou K, Ou X, Chen T, Fan X, Liu Y, Tu S, He Y, Ren Y, Chen A, Shang Z, Xia Z, Miquerol L, Smart N, Zhang H, Tan X, Shou W, Lei M. Dbh+ catecholaminergic cardiomyocytes contribute to the structure and function of the cardiac conduction system in murine heart. Nat Commun 2023;14:7801. [PMID: 38016975 PMCID: PMC10684617 DOI: 10.1038/s41467-023-42658-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 10/18/2023] [Indexed: 11/30/2023]  Open
32
Tzaferis C, Karatzas E, Baltoumas FA, Pavlopoulos GA, Kollias G, Konstantopoulos D. SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data. Comput Struct Biotechnol J 2023;21:5382-5393. [PMID: 38022693 PMCID: PMC10651449 DOI: 10.1016/j.csbj.2023.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]  Open
33
Mooring M, Yeung GA, Luukkonen P, Liu S, Akbar MW, Zhang GJ, Balogun O, Yu X, Mo R, Nejak-Bowen K, Poyurovsky MV, Booth CJ, Konnikova L, Shulman GI, Yimlamai D. Hepatocyte CYR61 polarizes profibrotic macrophages to orchestrate NASH fibrosis. Sci Transl Med 2023;15:eade3157. [PMID: 37756381 PMCID: PMC10874639 DOI: 10.1126/scitranslmed.ade3157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
34
Wang T, Zhao H, Xu Y, Wang Y, Shang X, Peng J, Xiao B. scMultiGAN: cell-specific imputation for single-cell transcriptomes with multiple deep generative adversarial networks. Brief Bioinform 2023;24:bbad384. [PMID: 37903416 PMCID: PMC11020228 DOI: 10.1093/bib/bbad384] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/13/2023] [Accepted: 10/03/2023] [Indexed: 11/01/2023]  Open
35
Causer A, Tan X, Lu X, Moseley P, Teoh SM, Molotkov N, McGrath M, Kim T, Simpson PT, Perry C, Frazer IH, Panizza B, Ladwa R, Nguyen Q, Gonzalez-Cruz JL. Deep spatial-omics analysis of Head & Neck carcinomas provides alternative therapeutic targets and rationale for treatment failure. NPJ Precis Oncol 2023;7:89. [PMID: 37704757 PMCID: PMC10499928 DOI: 10.1038/s41698-023-00444-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]  Open
36
He T, Guo W, Yang G, Su H, Dou A, Chen L, Ma T, Su J, Liu M, Su B, Qi W, Li H, Mao W, Wang X, Li X, Yang Y, Song Y, Cao G. A Single-Cell Atlas of an Early Mongolian Sheep Embryo. Vet Sci 2023;10:543. [PMID: 37756065 PMCID: PMC10536297 DOI: 10.3390/vetsci10090543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/25/2023] [Accepted: 08/22/2023] [Indexed: 09/28/2023]  Open
37
Song D, Li K, Ge X, Li JJ. ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping. RESEARCH SQUARE 2023:rs.3.rs-3211191. [PMID: 37577698 PMCID: PMC10418557 DOI: 10.21203/rs.3.rs-3211191/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
38
Xing L, Wang L, Liu S, Sun L, Wessel GM, Yang H. Single-Cell Transcriptome and Pigment Biochemistry Analysis Reveals the Potential for the High Nutritional and Medicinal Value of Purple Sea Cucumbers. Int J Mol Sci 2023;24:12213. [PMID: 37569587 PMCID: PMC10419132 DOI: 10.3390/ijms241512213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023]  Open
39
Park CJ, Minabe S, Hess RA, Lin PCP, Zhou S, Bashir ST, Barakat R, Gal A, Ko CJ. Single neonatal estrogen implant sterilizes female animals by decreasing hypothalamic KISS1 expression. Sci Rep 2023;13:9627. [PMID: 37316510 DOI: 10.1038/s41598-023-36727-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]  Open
40
Diwanji R, O'Brien NA, Choi JE, Nguyen B, Laszewski T, Grauel AL, Yan Z, Xu X, Wu J, Ruddy DA, Piquet M, Pelletier MR, Savchenko A, Charette L, Rodrik-Outmezguine V, Baum J, Millholland JM, Wong CC, Martin AM, Dranoff G, Pruteanu-Malinici I, Cremasco V, Sabatos-Peyton C, Jayaraman P. Targeting the IL1β Pathway for Cancer Immunotherapy Remodels the Tumor Microenvironment and Enhances Antitumor Immune Responses. Cancer Immunol Res 2023;11:777-791. [PMID: 37040466 DOI: 10.1158/2326-6066.cir-22-0290] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 12/14/2022] [Accepted: 04/07/2023] [Indexed: 04/13/2023]
41
Du J, Wang Y, Chen W, Xu M, Zhou R, Shou H, Chen J. High-resolution anatomical and spatial transcriptome analyses reveal two types of meristematic cell pools within the secondary vascular tissue of poplar stem. MOLECULAR PLANT 2023;16:809-828. [PMID: 36895162 DOI: 10.1016/j.molp.2023.03.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 02/12/2023] [Accepted: 03/06/2023] [Indexed: 05/04/2023]
42
Jia J, Zhao Y, Wang JH, Kuang YQ. Isolating peripheral blood mononuclear cells from HIV-infected patients for single-cell RNA sequencing and integration analysis. STAR Protoc 2023;4:102222. [PMID: 37060557 PMCID: PMC10140154 DOI: 10.1016/j.xpro.2023.102222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/21/2023] [Accepted: 03/15/2023] [Indexed: 04/16/2023]  Open
43
Wei Y, Hong Y, Yang L, Wang J, Zhao T, Zheng X, Kang L, Chen J, Han L, Long C, Shen L, Wu S, Wei G. Single-cell transcriptomic dissection of the toxic impact of di(2-ethylhexyl) phthalate on immature testicular development at the neonatal stage. Food Chem Toxicol 2023;176:113780. [PMID: 37059381 DOI: 10.1016/j.fct.2023.113780] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
44
Magenheim J, Maestro MA, Sharon N, Herrera PL, Murtaugh LC, Kopp J, Sander M, Gu G, Melton DA, Ferrer J, Dor Y. Matters arising: Insufficient evidence that pancreatic β cells are derived from adult ductal Neurog3-expressing progenitors. Cell Stem Cell 2023;30:488-497.e3. [PMID: 37028408 DOI: 10.1016/j.stem.2023.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/29/2022] [Accepted: 03/01/2023] [Indexed: 04/08/2023]
45
Nguyen HCT, Baik B, Yoon S, Park T, Nam D. Benchmarking integration of single-cell differential expression. Nat Commun 2023;14:1570. [PMID: 36944632 PMCID: PMC10030080 DOI: 10.1038/s41467-023-37126-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 03/03/2023] [Indexed: 03/23/2023]  Open
46
Wang X, Liu Q, Li J, Zhou L, Wang T, Zhao N. Dynamic cellular and molecular characteristics of spermatogenesis in the viviparous marine teleost Sebastes schlegelii†. Biol Reprod 2023;108:338-352. [PMID: 36401879 DOI: 10.1093/biolre/ioac203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 07/13/2022] [Accepted: 11/02/2022] [Indexed: 11/21/2022]  Open
47
Danielli SG, Porpiglia E, De Micheli AJ, Navarro N, Zellinger MJ, Bechtold I, Kisele S, Volken L, Marques JG, Kasper S, Bode PK, Henssen AG, Gürgen D, Delattre O, Surdez D, Roma J, Bühlmann P, Blau HM, Wachtel M, Schäfer BW. Single-cell profiling of alveolar rhabdomyosarcoma reveals RAS pathway inhibitors as cell-fate hijackers with therapeutic relevance. SCIENCE ADVANCES 2023;9:eade9238. [PMID: 36753540 PMCID: PMC9908029 DOI: 10.1126/sciadv.ade9238] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
48
Dousti Mousavi N, Yang J, Aldirawi H. Variable Selection for Sparse Data with Applications to Vaginal Microbiome and Gene Expression Data. Genes (Basel) 2023;14:403. [PMID: 36833330 PMCID: PMC9956208 DOI: 10.3390/genes14020403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023]  Open
49
Piekna-Przybylska D, Na D, Zhang J, Baker C, Ashton JM, White PM. Single cell RNA sequencing analysis of mouse cochlear supporting cell transcriptomes with activated ERBB2 receptor indicates a cell-specific response that promotes CD44 activation. Front Cell Neurosci 2023;16:1096872. [PMID: 36687526 PMCID: PMC9853549 DOI: 10.3389/fncel.2022.1096872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023]  Open
50
Cheema AS, Duan K, Dalod M, Vu Manh TP. Harnessing Single-Cell RNA Sequencing to Identify Dendritic Cell Types, Characterize Their Biological States, and Infer Their Activation Trajectory. Methods Mol Biol 2023;2618:319-373. [PMID: 36905526 DOI: 10.1007/978-1-0716-2938-3_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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