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For: Cakir B, Prete M, Huang N, van Dongen S, Pir P, Kiselev V. Comparison of visualization tools for single-cell RNAseq data. NAR Genom Bioinform 2020;2:lqaa052. [PMID: 32766548 PMCID: PMC7391988 DOI: 10.1093/nargab/lqaa052] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/17/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]  Open
Number Cited by Other Article(s)
1
Mimpen JY, Baldwin MJ, Paul C, Ramos-Mucci L, Kurjan A, Cohen CJ, Sharma S, Chevalier Florquin MSN, Hulley PA, McMaster J, Titchener A, Martin A, Costa ML, Gwilym SE, Cribbs AP, Snelling SJB. Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution. J Physiol 2025. [PMID: 40232153 DOI: 10.1113/jp287812] [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: 10/04/2024] [Accepted: 02/21/2025] [Indexed: 04/16/2025]  Open
2
Kumar S, Wu CC, Wulandari FS, Chiao CC, Ko CC, Lin HY, Ngadio JL, Rebecca C, Xuan DTM, Solomon DD, Michael M, Kristiani L, Chuang JY, Tsai MC, Wang CY. Integration of multi-omics and single-cell transcriptome reveals mitochondrial outer membrane protein-2 (MTX-2) as a prognostic biomarker and characterizes ubiquinone metabolism in lung adenocarcinoma. J Cancer 2025;16:2401-2420. [PMID: 40302794 PMCID: PMC12036103 DOI: 10.7150/jca.106902] [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: 11/13/2024] [Accepted: 03/26/2025] [Indexed: 05/02/2025]  Open
3
Qaqorh T, Takahashi Y, Sameshima K, Otani K, Yazawa I, Nishida Y, Tonai K, Fujihara Y, Honda M, Oki S, Ohkawa Y, Thorburn DR, Frazier AE, Takeda A, Ikeda Y, Sakaguchi H, Watanabe T, Fukushima N, Tsukamoto Y, Makita N, Yamaguchi O, Murayama K, Ohtake A, Okazaki Y, Kimura T, Kato H, Inoue H, Matsuoka K, Takashima S, Shintani Y. Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by spatial and single-cell transcriptomics. SCIENCE ADVANCES 2025;11:eadq1575. [PMID: 40184463 PMCID: PMC11970478 DOI: 10.1126/sciadv.adq1575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 02/28/2025] [Indexed: 04/06/2025]
4
Muncie-Vasic JM, Sinha T, Clark AP, Brower EF, Saucerman JJ, Black BL, Bruneau BG. MEF2C controls segment-specific gene regulatory networks that direct heart tube morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.11.01.621613. [PMID: 39554149 PMCID: PMC11566030 DOI: 10.1101/2024.11.01.621613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
5
Hackenberg M, Brunn N, Vogel T, Binder H. Infusing structural assumptions into dimensionality reduction for single-cell RNA sequencing data to identify small gene sets. Commun Biol 2025;8:414. [PMID: 40069486 PMCID: PMC11897155 DOI: 10.1038/s42003-025-07872-9] [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: 04/15/2024] [Accepted: 03/03/2025] [Indexed: 03/15/2025]  Open
6
Agboraw E, Haese-Hill W, Hentzschel F, Briggs E, Aghabi D, Heawood A, Harding CR, Shiels B, Crouch K, Somma D, Otto TD. paraCell: a novel software tool for the interactive analysis and visualization of standard and dual host-parasite single-cell RNA-seq data. Nucleic Acids Res 2025;53:gkaf091. [PMID: 39988320 PMCID: PMC11840555 DOI: 10.1093/nar/gkaf091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Revised: 01/21/2025] [Accepted: 02/03/2025] [Indexed: 02/25/2025]  Open
7
Stier MT, Sewell AE, Mwizerwa EL, Sim CY, Tanner SM, Nichols CM, Durai HH, Jennings EQ, Lindau P, Wilfong EM, Newcomb DC, Bastarache JA, Ware LB, Rathmell JC. Metabolic Adaptations Rewire CD4 T Cells in a Subset-Specific Manner in Human Critical Illness with and without Sepsis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.27.635146. [PMID: 39975258 PMCID: PMC11838299 DOI: 10.1101/2025.01.27.635146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
8
Frey Y, Haj M, Ziv Y, Elkon R, Shiloh Y. Broad repression of DNA repair genes in senescent cells identified by integration of transcriptomic data. Nucleic Acids Res 2025;53:gkae1257. [PMID: 39739833 PMCID: PMC11724277 DOI: 10.1093/nar/gkae1257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 11/19/2024] [Accepted: 12/06/2024] [Indexed: 01/02/2025]  Open
9
CZI Cell Science Program, Abdulla S, Aevermann B, Assis P, Badajoz S, Bell SM, Bezzi E, Cakir B, Chaffer J, Chambers S, Cherry J, Chi T, Chien J, Dorman L, Garcia-Nieto P, Gloria N, Hastie M, Hegeman D, Hilton J, Huang T, Infeld A, Istrate AM, Jelic I, Katsuya K, Kim YJ, Liang K, Lin M, Lombardo M, Marshall B, Martin B, McDade F, Megill C, Patel N, Predeus A, Raymor B, Robatmili B, Rogers D, Rutherford E, Sadgat D, Shin A, Small C, Smith T, Sridharan P, Tarashansky A, Tavares N, Thomas H, Tolopko A, Urisko M, Yan J, Yeretssian G, Zamanian J, Mani A, Cool J, Carr A. CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data. Nucleic Acids Res 2025;53:D886-D900. [PMID: 39607691 PMCID: PMC11701654 DOI: 10.1093/nar/gkae1142] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Revised: 10/28/2024] [Accepted: 11/01/2024] [Indexed: 11/29/2024]  Open
10
Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2025;68:5-102. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
11
Chehimi SN. Dissection of Gene Expression at the Single-Cell Level: scRNA-seq. Methods Mol Biol 2025;2866:159-173. [PMID: 39546202 DOI: 10.1007/978-1-0716-4192-7_9] [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: 11/17/2024]
12
Wang K, Gong Y, Yan Z, Dang Z, Wang J, Wu M, Zhang Y. Protocol for analyzing functional gene module perturbation during the progression of diseases using a single-cell Bayesian biclustering framework. STAR Protoc 2024;5:103349. [PMID: 39352811 PMCID: PMC11472622 DOI: 10.1016/j.xpro.2024.103349] [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: 05/19/2024] [Revised: 07/26/2024] [Accepted: 09/06/2024] [Indexed: 10/04/2024]  Open
13
Zhang H, Zhang W, Zhao S, Xu G, Shen Y, Jiang F, Qin A, Cui L. easySCF: a tool for enhancing interoperability between R and Python for efficient single-cell data analysis. Bioinformatics 2024;40:btae710. [PMID: 39585309 PMCID: PMC11634540 DOI: 10.1093/bioinformatics/btae710] [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: 08/29/2024] [Revised: 11/08/2024] [Accepted: 11/22/2024] [Indexed: 11/26/2024]  Open
14
Nazaret A, Fan JL, Lavallée VP, Burdziak C, Cornish AE, Kiseliovas V, Bowman RL, Masilionis I, Chun J, Eisman SE, Wang J, Hong J, Shi L, Levine RL, Mazutis L, Blei D, Pe’er D, Azizi E. Joint representation and visualization of derailed cell states with Decipher. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.11.566719. [PMID: 38014231 PMCID: PMC10680623 DOI: 10.1101/2023.11.11.566719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
15
Seege M, Schöls E, Barquist L. s CIRCLE-An interactive visual exploration tool for single cell RNA-Seq data. NAR Genom Bioinform 2024;6:lqae084. [PMID: 39022325 PMCID: PMC11252841 DOI: 10.1093/nargab/lqae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/17/2024] [Accepted: 07/04/2024] [Indexed: 07/20/2024]  Open
16
Mimpen JY, Ramos-Mucci L, Paul C, Kurjan A, Hulley PA, Ikwuanusi CT, Cohen CJ, Gwilym SE, Baldwin MJ, Cribbs AP, Snelling SJB. Single nucleus and spatial transcriptomic profiling of healthy human hamstring tendon. FASEB J 2024;38:e23629. [PMID: 38742770 DOI: 10.1096/fj.202300601rrr] [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: 03/29/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
17
Waichman TV, Vercesi ML, Berardino AA, Beckel MS, Giacomini D, Rasetto NB, Herrero M, Di Bella DJ, Arlotta P, Schinder AF, Chernomoretz A. scX: A user-friendly tool for scRNA-seq exploration. ARXIV 2024:arXiv:2311.00012v2. [PMID: 37961742 PMCID: PMC10635291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
18
Xia L, Lee C, Li JJ. Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nat Commun 2024;15:1753. [PMID: 38409103 PMCID: PMC10897166 DOI: 10.1038/s41467-024-45891-y] [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: 04/10/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024]  Open
19
Kondoh H. Multiple Cell Lineages Give Rise to a Cell Type. Results Probl Cell Differ 2024;72:83-104. [PMID: 38509253 DOI: 10.1007/978-3-031-39027-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
20
Xia L, Lee C, Li JJ. scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537839. [PMID: 37163087 PMCID: PMC10168265 DOI: 10.1101/2023.04.21.537839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
21
Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol 2023;20:597-614. [PMID: 37258747 PMCID: PMC10527367 DOI: 10.1038/s41575-023-00784-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2023] [Indexed: 06/02/2023]
22
Daniels RR, Taylor RS, Robledo D, Macqueen DJ. Single cell genomics as a transformative approach for aquaculture research and innovation. REVIEWS IN AQUACULTURE 2023;15:1618-1637. [PMID: 38505116 PMCID: PMC10946576 DOI: 10.1111/raq.12806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/21/2024]
23
Lim J, Chin V, Fairfax K, Moutinho C, Suan D, Ji H, Powell JE. Transitioning single-cell genomics into the clinic. Nat Rev Genet 2023:10.1038/s41576-023-00613-w. [PMID: 37258725 DOI: 10.1038/s41576-023-00613-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
24
Patil AR, Kumar G, Zhou H, Warren L. scViewer: An Interactive Single-Cell Gene Expression Visualization Tool. Cells 2023;12:1489. [PMID: 37296611 PMCID: PMC10253102 DOI: 10.3390/cells12111489] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/09/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]  Open
25
Li K, Sun YH, Ouyang Z, Negi S, Gao Z, Zhu J, Wang W, Chen Y, Piya S, Hu W, Zavodszky MI, Yalamanchili H, Cao S, Gehrke A, Sheehan M, Huh D, Casey F, Zhang X, Zhang B. scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing. BMC Genomics 2023;24:228. [PMID: 37131143 PMCID: PMC10155351 DOI: 10.1186/s12864-023-09332-2] [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: 01/17/2023] [Accepted: 04/25/2023] [Indexed: 05/04/2023]  Open
26
Choi Y, Li R, Quon G. siVAE: interpretable deep generative models for single-cell transcriptomes. Genome Biol 2023;24:29. [PMID: 36803416 PMCID: PMC9940350 DOI: 10.1186/s13059-023-02850-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 01/06/2023] [Indexed: 02/22/2023]  Open
27
Cheng F, Keller MS, Qu H, Gehlenborg N, Wang Q. Polyphony: an Interactive Transfer Learning Framework for Single-Cell Data Analysis. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2023;29:591-601. [PMID: 36155452 PMCID: PMC10039961 DOI: 10.1109/tvcg.2022.3209408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
28
Chuwdhury GS, Ng IOL, Ho DWH. scAnalyzeR: A Comprehensive Software Package With Graphical User Interface for Single-Cell RNA Sequencing Analysis and its Application on Liver Cancer. Technol Cancer Res Treat 2022;21:15330338221142729. [PMID: 36476060 PMCID: PMC9742707 DOI: 10.1177/15330338221142729] [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] [Indexed: 12/13/2022]  Open
29
Prieto C, Barrios D, Villaverde A. SingleCAnalyzer: Interactive Analysis of Single Cell RNA-Seq Data on the Cloud. FRONTIERS IN BIOINFORMATICS 2022;2:793309. [PMID: 36304292 PMCID: PMC9580930 DOI: 10.3389/fbinf.2022.793309] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/09/2022] [Indexed: 12/13/2022]  Open
30
Cai G, Yu X, Youn C, Zhou J, Xiao F. SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data. Database (Oxford) 2022;2022:6520818. [PMID: 35134150 PMCID: PMC9246089 DOI: 10.1093/database/baab086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/01/2021] [Accepted: 12/27/2021] [Indexed: 01/07/2023]
31
Elorbany R, Popp JM, Rhodes K, Strober BJ, Barr K, Qi G, Gilad Y, Battle A. Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation. PLoS Genet 2022;18:e1009666. [PMID: 35061661 PMCID: PMC8809621 DOI: 10.1371/journal.pgen.1009666] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 02/02/2022] [Accepted: 12/21/2021] [Indexed: 12/13/2022]  Open
32
Medini H, Zirman A, Mishmar D. Immune system cells from COVID-19 patients display compromised mitochondrial-nuclear expression co-regulation and rewiring toward glycolysis. iScience 2021;24:103471. [PMID: 34812416 PMCID: PMC8599136 DOI: 10.1016/j.isci.2021.103471] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/15/2021] [Accepted: 11/14/2021] [Indexed: 01/06/2023]  Open
33
Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M. UCSC Cell Browser: visualize your single-cell data. Bioinformatics 2021;37:4578-4580. [PMID: 34244710 PMCID: PMC8652023 DOI: 10.1093/bioinformatics/btab503] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023]  Open
34
Stephenson M, Nip KM, HafezQorani S, Gagalova KK, Yang C, Warren RL, Birol I. RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes. NAR Genom Bioinform 2021;3:lqab105. [PMID: 34859209 PMCID: PMC8633890 DOI: 10.1093/nargab/lqab105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/21/2021] [Accepted: 11/26/2021] [Indexed: 11/12/2022]  Open
35
Legetth O, Rodhe J, Lang S, Dhapola P, Wallergård M, Soneji S. CellexalVR: A virtual reality platform to visualize and analyze single-cell omics data. iScience 2021;24:103251. [PMID: 34849461 PMCID: PMC8609247 DOI: 10.1016/j.isci.2021.103251] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/15/2021] [Accepted: 10/07/2021] [Indexed: 12/20/2022]  Open
36
Roma S, Carpen L, Raveane A, Bertolini F. The Dual Role of Innate Lymphoid and Natural Killer Cells in Cancer. from Phenotype to Single-Cell Transcriptomics, Functions and Clinical Uses. Cancers (Basel) 2021;13:cancers13205042. [PMID: 34680190 PMCID: PMC8533946 DOI: 10.3390/cancers13205042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023]  Open
37
Wang W, Wang L, She J, Zhu J. Examining heterogeneity of stromal cells in tumor microenvironment based on pan-cancer single-cell RNA sequencing data. Cancer Biol Med 2021;19:j.issn.2095-3941.2020.0762. [PMID: 34398535 PMCID: PMC8763007 DOI: 10.20892/j.issn.2095-3941.2020.0762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/05/2021] [Indexed: 11/28/2022]  Open
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Djekidel MN, Rosikiewicz W, Peng JC, Kanneganti TD, Hui Y, Jin H, Hedges D, Schreiner P, Fan Y, Wu G, Xu B. CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.05.14.444026. [PMID: 34075382 PMCID: PMC8168395 DOI: 10.1101/2021.05.14.444026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Orvis J, Gottfried B, Kancherla J, Adkins RS, Song Y, Dror AA, Olley D, Rose K, Chrysostomou E, Kelly MC, Milon B, Matern MS, Azaiez H, Herb B, Colantuoni C, Carter RL, Ament SA, Kelley MW, White O, Bravo HC, Mahurkar A, Hertzano R. gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration. Nat Methods 2021;18:843-844. [PMID: 34172972 PMCID: PMC8996439 DOI: 10.1038/s41592-021-01200-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Kim HK, Ha TW, Lee MR. Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming. Int J Mol Sci 2021;22:ijms22115988. [PMID: 34206025 PMCID: PMC8198005 DOI: 10.3390/ijms22115988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022]  Open
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Marín-Sedeño E, de Morentin XM, Pérez-Pomares JM, Gómez-Cabrero D, Ruiz-Villalba A. Understanding the Adult Mammalian Heart at Single-Cell RNA-Seq Resolution. Front Cell Dev Biol 2021;9:645276. [PMID: 34055776 PMCID: PMC8149764 DOI: 10.3389/fcell.2021.645276] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/09/2021] [Indexed: 12/24/2022]  Open
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Wolfien M, David R, Galow AM. Single-Cell RNA Sequencing Procedures and Data Analysis. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
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Guruprasad P, Lee YG, Kim KH, Ruella M. The current landscape of single-cell transcriptomics for cancer immunotherapy. J Exp Med 2021;218:e20201574. [PMID: 33601414 PMCID: PMC7754680 DOI: 10.1084/jem.20201574] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 12/28/2022]  Open
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Linderman GC. Dimensionality Reduction of Single-Cell RNA-Seq Data. Methods Mol Biol 2021;2284:331-342. [PMID: 33835451 DOI: 10.1007/978-1-0716-1307-8_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Ferrero R, Rainer P, Deplancke B. Toward a Consensus View of Mammalian Adipocyte Stem and Progenitor Cell Heterogeneity. Trends Cell Biol 2020;30:937-950. [PMID: 33148396 DOI: 10.1016/j.tcb.2020.09.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 12/31/2022]
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