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For: Hou R, Denisenko E, Ong HT, Ramilowski JA, Forrest ARR. Predicting cell-to-cell communication networks using NATMI. Nat Commun 2020;11:5011. [PMID: 33024107 DOI: 10.1038/s41467-020-18873-z] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022]  Open
Number Cited by Other Article(s)
1
Wagner E, Larijani B, Kirane AR. Predictive Biomarkers for Immune Checkpoint Inhibitor Therapy in Advanced Melanomas. Surg Oncol Clin N Am 2025;34:437-451. [PMID: 40413009 DOI: 10.1016/j.soc.2025.01.006] [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: 05/27/2025]
2
Dupuis L, Debeaupuis O, Simon F, Isambert H. CausalCCC: a web server to explore intracellular causal pathways enabling cell-cell communication. Nucleic Acids Res 2025:gkaf404. [PMID: 40366019 DOI: 10.1093/nar/gkaf404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Revised: 04/26/2025] [Accepted: 05/05/2025] [Indexed: 05/15/2025]  Open
3
Duan L, Hashemi M, Ngom A, Rueda L. Ligand-receptor dynamics in heterophily-aware graph neural networks for enhanced cell type prediction from single-cell RNA-seq data. Front Mol Biosci 2025;12:1547231. [PMID: 40421418 PMCID: PMC12104675 DOI: 10.3389/fmolb.2025.1547231] [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: 12/18/2024] [Accepted: 04/07/2025] [Indexed: 05/28/2025]  Open
4
Liu Z, Yang Y, Fang H, Cen B, Fan Y, Li J, Wang L, He S. Single-cell and spatial analyses reveal the effect of VSIG4+S100A10+TAMs on the immunosuppression of glioblastoma and anti-PD-1 immunotherapy. Int J Biol Macromol 2025;308:142415. [PMID: 40127797 DOI: 10.1016/j.ijbiomac.2025.142415] [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: 08/03/2024] [Revised: 03/04/2025] [Accepted: 03/21/2025] [Indexed: 03/26/2025]
5
Jia C, Wang H, Zhao J, Xia J, Zheng C. scSDNE: A semi-supervised method for inferring cell-cell interactions based on graph embedding. PLoS Comput Biol 2025;21:e1013027. [PMID: 40333631 PMCID: PMC12072665 DOI: 10.1371/journal.pcbi.1013027] [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: 09/12/2024] [Accepted: 04/04/2025] [Indexed: 05/09/2025]  Open
6
Wu G, Liang Y, Xi Q, Zuo Y. New Insights and Implications of Cell-Cell Interactions in Developmental Biology. Int J Mol Sci 2025;26:3997. [PMID: 40362237 PMCID: PMC12072105 DOI: 10.3390/ijms26093997] [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: 03/11/2025] [Revised: 04/17/2025] [Accepted: 04/22/2025] [Indexed: 05/15/2025]  Open
7
Guo H, Zhang L, Tang H, Liu P, Hu B, Gong Y, Hou R, Wu Z. Exploring the Role of T-Cell Metabolism in Modulating Immunotherapy Efficacy for Non-Small Cell Lung Cancer Based on Clustering. J Clin Lab Anal 2025:e25020. [PMID: 40244859 DOI: 10.1002/jcla.25020] [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: 11/17/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 04/19/2025]  Open
8
Li X, Pan L, Li W, Liu B, Xiao C, Chew V, Zhang X, Long W, Ginhoux F, Loscalzo J, Buggert M, Zhang X, Sheng R, Wang Z. Deciphering immune predictors of immunotherapy response: A multiomics approach at the pan-cancer level. Cell Rep Med 2025;6:101992. [PMID: 40054456 PMCID: PMC12047473 DOI: 10.1016/j.xcrm.2025.101992] [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: 08/03/2024] [Revised: 01/15/2025] [Accepted: 02/05/2025] [Indexed: 04/18/2025]
9
Troulé K, Petryszak R, Cakir B, Cranley J, Harasty A, Prete M, Tuong ZK, Teichmann SA, Garcia-Alonso L, Vento-Tormo R. CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data. Nat Protoc 2025:10.1038/s41596-024-01137-1. [PMID: 40133495 DOI: 10.1038/s41596-024-01137-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/20/2024] [Indexed: 03/27/2025]
10
Xin Y, Amanullah M, Qian C, Zhou C, Qian J. Lignature: A Comprehensive Database of Ligand Signatures to Predict Cell-Cell Communication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.22.644770. [PMID: 40196598 PMCID: PMC11974740 DOI: 10.1101/2025.03.22.644770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
11
Xue Z, Xuan H, Lau K, Su Y, Wegener M, Li K, Turner L, Adams M, Shi X, Wen H. Expression of ENL YEATS domain tumor mutations in nephrogenic or stromal lineage impairs kidney development. Nat Commun 2025;16:2531. [PMID: 40087269 PMCID: PMC11909213 DOI: 10.1038/s41467-025-57926-z] [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: 05/10/2024] [Accepted: 03/05/2025] [Indexed: 03/17/2025]  Open
12
Ge S, Sun S, Xu H, Cheng Q, Ren Z. Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective. Brief Bioinform 2025;26:bbaf136. [PMID: 40185158 PMCID: PMC11970898 DOI: 10.1093/bib/bbaf136] [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: 12/16/2024] [Revised: 02/17/2025] [Accepted: 03/05/2025] [Indexed: 04/07/2025]  Open
13
Griffiths JI, Cosgrove PA, Medina EF, Nath A, Chen J, Adler FR, Chang JT, Khan QJ, Bild AH. Cellular interactions within the immune microenvironment underpins resistance to cell cycle inhibition in breast cancers. Nat Commun 2025;16:2132. [PMID: 40032842 PMCID: PMC11876604 DOI: 10.1038/s41467-025-56279-x] [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: 04/04/2024] [Accepted: 01/13/2025] [Indexed: 03/05/2025]  Open
14
van Santvoort M, Lapuente-Santana Ó, Zopoglou M, Zackl C, Finotello F, van der Hoorn P, Eduati F. Mathematically mapping the network of cells in the tumor microenvironment. CELL REPORTS METHODS 2025;5:100985. [PMID: 39954673 PMCID: PMC11955271 DOI: 10.1016/j.crmeth.2025.100985] [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: 05/01/2023] [Revised: 05/04/2024] [Accepted: 01/24/2025] [Indexed: 02/17/2025]
15
Liu J, Ma L, Ju F, Zhao C, Yu L. SpaCcLink: exploring downstream signaling regulations with graph attention network for systematic inference of spatial cell-cell communication. BMC Biol 2025;23:44. [PMID: 39939849 PMCID: PMC11823213 DOI: 10.1186/s12915-025-02141-x] [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: 04/22/2024] [Accepted: 01/23/2025] [Indexed: 02/14/2025]  Open
16
Shanmugam V, Tokcan N, Chafamo D, Sullivan S, Borji M, Martin H, Newton G, Nadaf N, Hanbury S, Barrera I, Cable D, Weir J, Ashenberg O, Pinkus G, Rodig S, Uhler C, Macosko E, Shipp M, Louissaint A, Chen F, Golub T. Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.24.631210. [PMID: 39896575 PMCID: PMC11785141 DOI: 10.1101/2025.01.24.631210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
17
Xin Y, Jin Y, Qian C, Blackshaw S, Qian J. MetaLigand: A database for predicting non-peptide ligand mediated cell-cell communication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.14.633094. [PMID: 39868215 PMCID: PMC11761624 DOI: 10.1101/2025.01.14.633094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
18
Gong Z, Wu T, Zhao Y, Guo J, Zhang Y, Li B, Li Y. Intercellular Tunneling Nanotubes as Natural Biophotonic Conveyors. ACS NANO 2025;19:1036-1043. [PMID: 39630614 DOI: 10.1021/acsnano.4c12681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
19
Jin S, Plikus MV, Nie Q. CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics. Nat Protoc 2025;20:180-219. [PMID: 39289562 DOI: 10.1038/s41596-024-01045-4] [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: 07/31/2023] [Accepted: 06/27/2024] [Indexed: 09/19/2024]
20
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]
21
Qiu X, Zhu DY, Lu Y, Yao J, Jing Z, Min KH, Cheng M, Pan H, Zuo L, King S, Fang Q, Zheng H, Wang M, Wang S, Zhang Q, Yu S, Liao S, Liu C, Wu X, Lai Y, Hao S, Zhang Z, Wu L, Zhang Y, Li M, Tu Z, Lin J, Yang Z, Li Y, Gu Y, Ellison D, Chen A, Liu L, Weissman JS, Ma J, Xu X, Liu S, Bai Y. Spatiotemporal modeling of molecular holograms. Cell 2024;187:7351-7373.e61. [PMID: 39532097 DOI: 10.1016/j.cell.2024.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/29/2024] [Accepted: 10/08/2024] [Indexed: 11/16/2024]
22
Lee D, Vicari JM, Porras C, Spencer C, Pjanic M, Wang X, Kinrot S, Weiler P, Kosoy R, Bendl J, Prashant NM, Psychogyiou K, Malakates P, Hennigan E, Monteiro Fortes J, Zheng S, Therrien K, Mathur D, Kleopoulos SP, Shao Z, Argyriou S, Alvia M, Casey C, Hong A, Beaumont KG, Sebra R, Kellner CP, Bennett DA, Yuan GC, Voloudakis G, Theis FJ, Haroutunian V, Hoffman GE, Fullard JF, Roussos P. Plasticity of Human Microglia and Brain Perivascular Macrophages in Aging and Alzheimer's Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.25.23297558. [PMID: 39677435 PMCID: PMC11643149 DOI: 10.1101/2023.10.25.23297558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
23
Agrawal A, Thomann S, Basu S, Grün D. NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis. Nat Commun 2024;15:10628. [PMID: 39639035 PMCID: PMC11621405 DOI: 10.1038/s41467-024-54973-w] [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: 08/17/2024] [Accepted: 11/22/2024] [Indexed: 12/07/2024]  Open
24
Wang X, Almet AA, Nie Q. Detecting global and local hierarchical structures in cell-cell communication using CrossChat. Nat Commun 2024;15:10542. [PMID: 39627184 PMCID: PMC11615294 DOI: 10.1038/s41467-024-54821-x] [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: 05/01/2024] [Accepted: 11/20/2024] [Indexed: 12/06/2024]  Open
25
Gu Y, Feng Z, Xu X, Jin L. Identification of a novel immune-related gene signature by single-cell and bulk sequencing for the prediction of the immune landscape and prognosis of breast cancer. Cancer Cell Int 2024;24:393. [PMID: 39627792 PMCID: PMC11613745 DOI: 10.1186/s12935-024-03589-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 11/26/2024] [Indexed: 12/08/2024]  Open
26
Zhao D, Song Z, Shen L, Xia T, Ouyang Q, Zhang H, He X, Kang K. Single-cell transcriptomics and tissue metabolomics uncover mechanisms underlying wooden breast disease in broilers. Poult Sci 2024;103:104433. [PMID: 39489032 PMCID: PMC11566330 DOI: 10.1016/j.psj.2024.104433] [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: 08/13/2024] [Revised: 09/26/2024] [Accepted: 10/12/2024] [Indexed: 11/05/2024]  Open
27
Zhou L, Song J, Li Z, Hu Y, Guo W. THGB: predicting ligand-receptor interactions by combining tree boosting and histogram-based gradient boosting. Sci Rep 2024;14:29604. [PMID: 39609487 PMCID: PMC11604971 DOI: 10.1038/s41598-024-78954-7] [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: 07/16/2024] [Accepted: 11/05/2024] [Indexed: 11/30/2024]  Open
28
Zhang T, Zhang X, Wu Z, Ren J, Zhao Z, Zhang H, Wang G, Wang T. VGAE-CCI: variational graph autoencoder-based construction of 3D spatial cell-cell communication network. Brief Bioinform 2024;26:bbae619. [PMID: 39581873 PMCID: PMC11586124 DOI: 10.1093/bib/bbae619] [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: 08/23/2024] [Revised: 10/04/2024] [Accepted: 11/12/2024] [Indexed: 11/26/2024]  Open
29
Xia H, Ji B, Qiao D, Peng S. CellMsg: graph convolutional networks for ligand-receptor-mediated cell-cell communication analysis. Brief Bioinform 2024;26:bbae716. [PMID: 39800874 PMCID: PMC11725396 DOI: 10.1093/bib/bbae716] [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: 09/09/2024] [Revised: 12/04/2024] [Accepted: 12/27/2024] [Indexed: 01/16/2025]  Open
30
Ji B, Wang X, Wang X, Xu L, Peng S. scDCA: deciphering the dominant cell communication assembly of downstream functional events from single-cell RNA-seq data. Brief Bioinform 2024;26:bbae663. [PMID: 39694816 DOI: 10.1093/bib/bbae663] [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: 10/21/2024] [Revised: 11/24/2024] [Accepted: 12/04/2024] [Indexed: 12/20/2024]  Open
31
Dalla E, Papanicolaou M, Park MD, Barth N, Hou R, Segura-Villalobos D, Valencia Salazar L, Sun D, Forrest ARR, Casanova-Acebes M, Entenberg D, Merad M, Aguirre-Ghiso JA. Lung-resident alveolar macrophages regulate the timing of breast cancer metastasis. Cell 2024;187:6631-6648.e20. [PMID: 39378878 PMCID: PMC11568918 DOI: 10.1016/j.cell.2024.09.016] [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: 05/09/2023] [Revised: 06/13/2024] [Accepted: 09/11/2024] [Indexed: 10/10/2024]
32
Henderson DJ, Alqahtani A, Chaudhry B, Cook A, Eley L, Houyel L, Hughes M, Keavney B, de la Pompa JL, Sled J, Spielmann N, Teboul L, Zaffran S, Mill P, Liu KJ. Beyond genomic studies of congenital heart defects through systematic modelling and phenotyping. Dis Model Mech 2024;17:dmm050913. [PMID: 39575509 PMCID: PMC11603121 DOI: 10.1242/dmm.050913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 10/29/2024] [Indexed: 12/01/2024]  Open
33
Fu C, Qiu D, Zhou M, Ni S, Jin X. Characterization of ligand-receptor pair in acute myeloid leukemia: a scoring model for prognosis, therapeutic response, and T cell dysfunction. Front Oncol 2024;14:1473048. [PMID: 39484036 PMCID: PMC11525004 DOI: 10.3389/fonc.2024.1473048] [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: 07/30/2024] [Accepted: 09/20/2024] [Indexed: 11/03/2024]  Open
34
Zhu J, Wang Y, Chang WY, Malewska A, Napolitano F, Gahan JC, Unni N, Zhao M, Yuan R, Wu F, Yue L, Guo L, Zhao Z, Chen DZ, Hannan R, Zhang S, Xiao G, Mu P, Hanker AB, Strand D, Arteaga CL, Desai N, Wang X, Xie Y, Wang T. Mapping cellular interactions from spatially resolved transcriptomics data. Nat Methods 2024;21:1830-1842. [PMID: 39227721 DOI: 10.1038/s41592-024-02408-1] [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: 01/24/2024] [Accepted: 08/02/2024] [Indexed: 09/05/2024]
35
Hough RF, Alvira CM, Bastarache JA, Erzurum SC, Kuebler WM, Schmidt EP, Shimoda LA, Abman SH, Alvarez DF, Belvitch P, Bhattacharya J, Birukov KG, Chan SY, Cornfield DN, Dudek SM, Garcia JGN, Harrington EO, Hsia CCW, Islam MN, Jonigk DD, Kalinichenko VV, Kolb TM, Lee JY, Mammoto A, Mehta D, Rounds S, Schupp JC, Shaver CM, Suresh K, Tambe DT, Ventetuolo CE, Yoder MC, Stevens T, Damarla M. Studying the Pulmonary Endothelium in Health and Disease: An Official American Thoracic Society Workshop Report. Am J Respir Cell Mol Biol 2024;71:388-406. [PMID: 39189891 PMCID: PMC11450313 DOI: 10.1165/rcmb.2024-0330st] [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: 07/16/2024] [Indexed: 08/28/2024]  Open
36
Xu Y, Lau P, Chen X, Zhao S, He Y, Jiang Z, Chen X, Zhang G, Liu H. Integrated multiomics revealed adenosine signaling predict immunotherapy response and regulate tumor ecosystem of melanoma. Hum Genomics 2024;18:101. [PMID: 39278925 PMCID: PMC11404024 DOI: 10.1186/s40246-024-00651-3] [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: 03/22/2024] [Accepted: 07/28/2024] [Indexed: 09/18/2024]  Open
37
Ding Q, Yang W, Xue G, Liu H, Cai Y, Que J, Jin X, Luo M, Pang F, Yang Y, Lin Y, Liu Y, Sun H, Tan R, Wang P, Xu Z, Jiang Q. Dimension reduction, cell clustering, and cell-cell communication inference for single-cell transcriptomics with DcjComm. Genome Biol 2024;25:241. [PMID: 39252099 PMCID: PMC11382422 DOI: 10.1186/s13059-024-03385-6] [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: 01/09/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024]  Open
38
Su J, Song Y, Zhu Z, Huang X, Fan J, Qiao J, Mao F. Cell-cell communication: new insights and clinical implications. Signal Transduct Target Ther 2024;9:196. [PMID: 39107318 PMCID: PMC11382761 DOI: 10.1038/s41392-024-01888-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: 12/29/2023] [Revised: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 09/11/2024]  Open
39
Zang X, Gu S, Wang W, Shi J, Gan J, Hu Q, Zhou C, Ding Y, He Y, Jiang L, Gu T, Xu Z, Huang S, Yang H, Meng F, Li Z, Cai G, Hong L, Wu Z. Dynamic intrauterine crosstalk promotes porcine embryo implantation during early pregnancy. SCIENCE CHINA. LIFE SCIENCES 2024;67:1676-1696. [PMID: 38748354 DOI: 10.1007/s11427-023-2557-x] [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: 01/18/2024] [Accepted: 02/21/2024] [Indexed: 08/09/2024]
40
Mathys H, Boix CA, Akay LA, Xia Z, Davila-Velderrain J, Ng AP, Jiang X, Abdelhady G, Galani K, Mantero J, Band N, James BT, Babu S, Galiana-Melendez F, Louderback K, Prokopenko D, Tanzi RE, Bennett DA, Tsai LH, Kellis M. Single-cell multiregion dissection of Alzheimer's disease. Nature 2024;632:858-868. [PMID: 39048816 PMCID: PMC11338834 DOI: 10.1038/s41586-024-07606-7] [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: 06/20/2022] [Accepted: 05/24/2024] [Indexed: 07/27/2024]
41
Li W, Wang H, Zhao J, Xia J, Sun X. scHyper: reconstructing cell-cell communication through hypergraph neural networks. Brief Bioinform 2024;25:bbae436. [PMID: 39276328 PMCID: PMC11401449 DOI: 10.1093/bib/bbae436] [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: 05/26/2024] [Revised: 07/14/2024] [Accepted: 08/07/2024] [Indexed: 09/16/2024]  Open
42
Sudhakar M, Vignesh H, Natarajan KN. Crosstalk between tumor and microenvironment: Insights from spatial transcriptomics. Adv Cancer Res 2024;163:187-222. [PMID: 39271263 DOI: 10.1016/bs.acr.2024.06.009] [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: 09/15/2024]
43
Zhang Y, Yang Y, Ren L, Zhan M, Sun T, Zou Q, Zhang Y. Predicting intercellular communication based on metabolite-related ligand-receptor interactions with MRCLinkdb. BMC Biol 2024;22:152. [PMID: 38978014 PMCID: PMC11232326 DOI: 10.1186/s12915-024-01950-w] [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: 03/16/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]  Open
44
Wang Y, Shen Z, Mo S, Zhang H, Chen J, Zhu C, Lv S, Zhang D, Huang X, Gu Y, Yu X, Ding X, Zhang X. Crosstalk among proximal tubular cells, macrophages, and fibroblasts in acute kidney injury: single-cell profiling from the perspective of ferroptosis. Hum Cell 2024;37:1039-1055. [PMID: 38753279 PMCID: PMC11194220 DOI: 10.1007/s13577-024-01072-z] [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: 10/20/2023] [Accepted: 04/27/2024] [Indexed: 06/24/2024]
45
Sarkar H, Chitra U, Gold J, Raphael BJ. A count-based model for delineating cell-cell interactions in spatial transcriptomics data. Bioinformatics 2024;40:i481-i489. [PMID: 38940134 PMCID: PMC11211854 DOI: 10.1093/bioinformatics/btae219] [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] [Indexed: 06/29/2024]  Open
46
Zuo C, Xia J, Chen L. Dissecting tumor microenvironment from spatially resolved transcriptomics data by heterogeneous graph learning. Nat Commun 2024;15:5057. [PMID: 38871687 DOI: 10.1038/s41467-024-49171-7] [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: 06/10/2023] [Accepted: 05/22/2024] [Indexed: 06/15/2024]  Open
47
Armingol E, Baghdassarian HM, Lewis NE. The diversification of methods for studying cell-cell interactions and communication. Nat Rev Genet 2024;25:381-400. [PMID: 38238518 PMCID: PMC11139546 DOI: 10.1038/s41576-023-00685-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 05/20/2024]
48
Deng X, Mo Y, Zhu X. Deciphering Müller cell heterogeneity signatures in diabetic retinopathy across species: an integrative single-cell analysis. Eur J Med Res 2024;29:265. [PMID: 38698486 PMCID: PMC11067085 DOI: 10.1186/s40001-024-01847-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: 01/13/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024]  Open
49
Ho NCW, Yap JYY, Zhao Z, Wang Y, Fernando K, Li CH, Kwang XL, Quah HS, Arcinas C, Iyer NG, Fong ELS. Bioengineered Hydrogels Recapitulate Fibroblast Heterogeneity in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2307129. [PMID: 38493497 PMCID: PMC11132030 DOI: 10.1002/advs.202307129] [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: 09/27/2023] [Revised: 01/30/2024] [Indexed: 03/19/2024]
50
Hashimoto M, Kojima Y, Sakamoto T, Ozato Y, Nakano Y, Abe T, Hosoda K, Saito H, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Hata T, Nagayama S, Kagawa K, Goto Y, Utou M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Takahashi K, Niida A, Hirose H, Hayashi S, Koseki J, Fukuchi S, Murakami K, Yoshizumi T, Kadomatsu K, Tobo T, Oda Y, Uemura M, Eguchi H, Doki Y, Mori M, Oshima M, Shibata T, Suzuki Y, Shimamura T, Mimori K. Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis. EBioMedicine 2024;103:105102. [PMID: 38614865 PMCID: PMC11121171 DOI: 10.1016/j.ebiom.2024.105102] [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: 10/18/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024]  Open
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