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For: Fleck JS, Camp JG, Treutlein B. What is a cell type? Science 2023;381:733-734. [PMID: 37590360 DOI: 10.1126/science.adf6162] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Number Cited by Other Article(s)
1
Emili E, Pérez-Posada A, Vanni V, Salamanca-Díaz D, Ródriguez-Fernández D, Christodoulou MD, Solana J. Allometry of cell types in planarians by single-cell transcriptomics. SCIENCE ADVANCES 2025;11:eadm7042. [PMID: 40333969 PMCID: PMC12057665 DOI: 10.1126/sciadv.adm7042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/02/2025] [Indexed: 05/09/2025]
2
Chen AD, Kroehling L, Ennis C, Denis GV, Monti S. A highly resolved integrated transcriptomic atlas of human breast cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.13.643025. [PMID: 40161579 PMCID: PMC11952505 DOI: 10.1101/2025.03.13.643025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
3
Jansma A, Yao Y, Wolfe J, Del Debbio L, Beentjes SV, Ponting CP, Khamseh A. High order expression dependencies finely resolve cryptic states and subtypes in single cell data. Mol Syst Biol 2025;21:173-207. [PMID: 39748128 PMCID: PMC11790937 DOI: 10.1038/s44320-024-00074-1] [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: 01/09/2024] [Revised: 10/24/2024] [Accepted: 10/31/2024] [Indexed: 01/04/2025]  Open
4
Hrovatin K, Sikkema L, Shitov VA, Heimberg G, Shulman M, Oliver AJ, Mueller MF, Ibarra IL, Wang H, Ramírez-Suástegui C, He P, Schaar AC, Teichmann SA, Theis FJ, Luecken MD. Considerations for building and using integrated single-cell atlases. Nat Methods 2025;22:41-57. [PMID: 39672979 DOI: 10.1038/s41592-024-02532-y] [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: 10/31/2023] [Accepted: 10/22/2024] [Indexed: 12/15/2024]
5
Proks M, Salehin N, Brickman JM. Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing. Nat Methods 2025;22:207-216. [PMID: 39543284 PMCID: PMC11725497 DOI: 10.1038/s41592-024-02511-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 10/15/2024] [Indexed: 11/17/2024]
6
Dong M, Agrawal K, Fan R, Sefik E, Flavell RA, Kluger Y. Scaling deep identifiable models enables zero-shot characterization of single-cell biological states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.11.566161. [PMID: 38014345 PMCID: PMC10680588 DOI: 10.1101/2023.11.11.566161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
7
Liu T, Long W, Cao Z, Wang Y, He CH, Zhang L, Strittmatter SM, Zhao H. CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis. Brief Bioinform 2024;26:bbae626. [PMID: 39592241 PMCID: PMC11596696 DOI: 10.1093/bib/bbae626] [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: 07/12/2024] [Revised: 10/07/2024] [Accepted: 11/14/2024] [Indexed: 11/28/2024]  Open
8
Li R, Qu R, Parisi F, Strino F, Lam H, Stanley JS, Cheng X, Myung P, Kluger Y. LMD: Cluster-Independent Multiscale Marker Identification in Single-cell RNA-seq Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.12.566780. [PMID: 38014159 PMCID: PMC10680591 DOI: 10.1101/2023.11.12.566780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
9
Rusnak B, Clark FK, Vadde BVL, Roeder AHK. What Is a Plant Cell Type in the Age of Single-Cell Biology? It's Complicated. Annu Rev Cell Dev Biol 2024;40:301-328. [PMID: 38724025 DOI: 10.1146/annurev-cellbio-111323-102412] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
10
Qin X, Tape CJ. Functional analysis of cell plasticity using single-cell technologies. Trends Cell Biol 2024;34:854-864. [PMID: 38355348 DOI: 10.1016/j.tcb.2024.01.006] [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: 11/02/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
11
Rood JE, Hupalowska A, Regev A. Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas. Cell 2024;187:4520-4545. [PMID: 39178831 DOI: 10.1016/j.cell.2024.07.035] [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: 05/03/2024] [Revised: 07/15/2024] [Accepted: 07/21/2024] [Indexed: 08/26/2024]
12
Szałata A, Hrovatin K, Becker S, Tejada-Lapuerta A, Cui H, Wang B, Theis FJ. Transformers in single-cell omics: a review and new perspectives. Nat Methods 2024;21:1430-1443. [PMID: 39122952 DOI: 10.1038/s41592-024-02353-z] [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: 12/19/2023] [Accepted: 06/07/2024] [Indexed: 08/12/2024]
13
del Giudice G, Serra A, Pavel A, Torres Maia M, Saarimäki LA, Fratello M, Federico A, Alenius H, Fadeel B, Greco D. A Network Toxicology Approach for Mechanistic Modelling of Nanomaterial Hazard and Adverse Outcomes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2400389. [PMID: 38923832 PMCID: PMC11348149 DOI: 10.1002/advs.202400389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/10/2024] [Indexed: 06/28/2024]
14
Rebboah E, Rezaie N, Williams BA, Weimer AK, Shi M, Yang X, Liang HY, Dionne LA, Reese F, Trout D, Jou J, Youngworth I, Reinholdt L, Morabito S, Snyder MP, Wold BJ, Mortazavi A. The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598567. [PMID: 38915583 PMCID: PMC11195270 DOI: 10.1101/2024.06.12.598567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
15
Ramirez Flores RO, Schäfer PSL, Küchenhoff L, Saez-Rodriguez J. Complementing Cell Taxonomies with a Multicellular Analysis of Tissues. Physiology (Bethesda) 2024;39:0. [PMID: 38319138 DOI: 10.1152/physiol.00001.2024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024]  Open
16
Kosik KS. Tau and the hard problem faceoff. Cytoskeleton (Hoboken) 2024;81:63-65. [PMID: 37772747 DOI: 10.1002/cm.21791] [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: 08/31/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023]
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