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For: Jerby-Arnon L, Regev A. DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data. Nat Biotechnol 2022;40:1467-1477. [PMID: 35513526 PMCID: PMC9547813 DOI: 10.1038/s41587-022-01288-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 03/15/2022] [Indexed: 12/22/2022]
Number Cited by Other Article(s)
1
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: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 05/20/2024]
2
Pekayvaz K, Losert C, Knottenberg V, Gold C, van Blokland IV, Oelen R, Groot HE, Benjamins JW, Brambs S, Kaiser R, Gottschlich A, Hoffmann GV, Eivers L, Martinez-Navarro A, Bruns N, Stiller S, Akgöl S, Yue K, Polewka V, Escaig R, Joppich M, Janjic A, Popp O, Kobold S, Petzold T, Zimmer R, Enard W, Saar K, Mertins P, Huebner N, van der Harst P, Franke LH, van der Wijst MGP, Massberg S, Heinig M, Nicolai L, Stark K. Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes. Nat Med 2024;30:1696-1710. [PMID: 38773340 PMCID: PMC11186793 DOI: 10.1038/s41591-024-02953-4] [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: 05/02/2023] [Accepted: 03/26/2024] [Indexed: 05/23/2024]
3
Barlow GL, Schürch CM, Bhate SS, Phillips D, Young A, Dong S, Martinez HA, Kaber G, Nagy N, Ramachandran S, Meng J, Korpos E, Bluestone JA, Nolan GP, Bollyky PL. The Extra-Islet Pancreas Supports Autoimmunity in Human Type 1 Diabetes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.03.15.23287145. [PMID: 36993739 PMCID: PMC10055577 DOI: 10.1101/2023.03.15.23287145] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
4
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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024]  Open
5
Daly AC, Cambuli F, Äijö T, Lötstedt B, Marjanovic N, Kuksenko O, Smith-Erb M, Fernandez S, Domovic D, Van Wittenberghe N, Drokhlyansky E, Griffin GK, Phatnani H, Bonneau R, Regev A, Vickovic S. Tissue and cellular spatiotemporal dynamics in colon aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590125. [PMID: 38712088 PMCID: PMC11071407 DOI: 10.1101/2024.04.22.590125] [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]
6
Baghdassarian HM, Dimitrov D, Armingol E, Saez-Rodriguez J, Lewis NE. Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples. CELL REPORTS METHODS 2024;4:100758. [PMID: 38631346 PMCID: PMC11046036 DOI: 10.1016/j.crmeth.2024.100758] [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: 08/10/2023] [Revised: 12/22/2023] [Accepted: 03/22/2024] [Indexed: 04/19/2024]
7
Li R, Chen X, Yang X. Navigating the landscapes of spatial transcriptomics: How computational methods guide the way. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024;15:e1839. [PMID: 38527900 DOI: 10.1002/wrna.1839] [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: 11/23/2023] [Revised: 02/24/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024]
8
Baghdassarian HM, Lewis NE. Resource allocation in mammalian systems. Biotechnol Adv 2024;71:108305. [PMID: 38215956 PMCID: PMC11182366 DOI: 10.1016/j.biotechadv.2023.108305] [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: 08/03/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
9
Schäfer PSL, Dimitrov D, Villablanca EJ, Saez-Rodriguez J. Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system. Nat Immunol 2024;25:405-417. [PMID: 38413722 DOI: 10.1038/s41590-024-01768-2] [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: 05/31/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
10
Lin S, Zhao F, Wu Z, Yao J, Zhao Y, Yuan Z. Streamlining spatial omics data analysis with Pysodb. Nat Protoc 2024;19:831-895. [PMID: 38135744 DOI: 10.1038/s41596-023-00925-5] [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: 04/04/2023] [Accepted: 10/02/2023] [Indexed: 12/24/2023]
11
Pascual-Reguant A, Kroh S, Hauser AE. Tissue niches and immunopathology through the lens of spatial tissue profiling techniques. Eur J Immunol 2024;54:e2350484. [PMID: 37985207 DOI: 10.1002/eji.202350484] [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: 05/31/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
12
Yao S, Harder A, Darki F, Chang YW, Li A, Nikouei K, Volpe G, Lundström JN, Zeng J, Wray N, Lu Y, Sullivan PF, Leffler JH. Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.18.24301478. [PMID: 38410450 PMCID: PMC10896415 DOI: 10.1101/2024.01.18.24301478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
13
Mason K, Sathe A, Hess PR, Rong J, Wu CY, Furth E, Susztak K, Levinsohn J, Ji HP, Zhang N. Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions. Genome Biol 2024;25:14. [PMID: 38217002 PMCID: PMC10785550 DOI: 10.1186/s13059-023-03159-6] [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: 02/13/2023] [Accepted: 12/22/2023] [Indexed: 01/14/2024]  Open
14
Liang Q, Huang Y, He S, Chen K. Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity. Nat Commun 2023;14:8416. [PMID: 38110427 PMCID: PMC10728201 DOI: 10.1038/s41467-023-44206-x] [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: 06/26/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023]  Open
15
Pham D, Tan X, Balderson B, Xu J, Grice LF, Yoon S, Willis EF, Tran M, Lam PY, Raghubar A, Kalita-de Croft P, Lakhani S, Vukovic J, Ruitenberg MJ, Nguyen QH. Robust mapping of spatiotemporal trajectories and cell-cell interactions in healthy and diseased tissues. Nat Commun 2023;14:7739. [PMID: 38007580 PMCID: PMC10676408 DOI: 10.1038/s41467-023-43120-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/01/2023] [Indexed: 11/27/2023]  Open
16
Ramirez Flores RO, Lanzer JD, Dimitrov D, Velten B, Saez-Rodriguez J. Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease. eLife 2023;12:e93161. [PMID: 37991480 PMCID: PMC10718529 DOI: 10.7554/elife.93161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]  Open
17
Dong M, Wang B, Wei J, de O Fonseca AH, Perry CJ, Frey A, Ouerghi F, Foxman EF, Ishizuka JJ, Dhodapkar RM, van Dijk D. Causal identification of single-cell experimental perturbation effects with CINEMA-OT. Nat Methods 2023;20:1769-1779. [PMID: 37919419 PMCID: PMC10630139 DOI: 10.1038/s41592-023-02040-5] [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: 11/14/2022] [Accepted: 09/08/2023] [Indexed: 11/04/2023]
18
Walker BL, Nie Q. NeST: nested hierarchical structure identification in spatial transcriptomic data. Nat Commun 2023;14:6554. [PMID: 37848426 PMCID: PMC10582109 DOI: 10.1038/s41467-023-42343-x] [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: 06/13/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]  Open
19
Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [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: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
20
Cheng M, Jiang Y, Xu J, Mentis AFA, Wang S, Zheng H, Sahu SK, Liu L, Xu X. Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges. J Genet Genomics 2023;50:625-640. [PMID: 36990426 DOI: 10.1016/j.jgg.2023.03.011] [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: 10/05/2022] [Revised: 03/11/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
21
Bailin SS, Kropski JA, Gangula RD, Hannah L, Simmons JD, Mashayekhi M, Ye F, Fan R, Mallal S, Warren CM, Kalams SA, Gabriel CL, Wanjalla CN, Koethe JR. Changes in subcutaneous white adipose tissue cellular composition and molecular programs underlie glucose intolerance in persons with HIV. Front Immunol 2023;14:1152003. [PMID: 37711619 PMCID: PMC10499182 DOI: 10.3389/fimmu.2023.1152003] [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: 01/27/2023] [Accepted: 08/07/2023] [Indexed: 09/16/2023]  Open
22
Grody EI, Abraham A, Shukla V, Goyal Y. Toward a systems-level probing of tumor clonality. iScience 2023;26:106574. [PMID: 37192968 PMCID: PMC10182304 DOI: 10.1016/j.isci.2023.106574] [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: 05/18/2023]  Open
23
Murdaugh RL, Anastas JN. Applying single cell multi-omic analyses to understand treatment resistance in pediatric high grade glioma. Front Pharmacol 2023;14:1002296. [PMID: 37205910 PMCID: PMC10191214 DOI: 10.3389/fphar.2023.1002296] [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: 07/25/2022] [Accepted: 04/20/2023] [Indexed: 05/21/2023]  Open
24
Baghdassarian H, Dimitrov D, Armingol E, Saez-Rodriguez J, Lewis NE. Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538731. [PMID: 37162916 PMCID: PMC10168343 DOI: 10.1101/2023.04.28.538731] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
25
Benhar I, Ding J, Yan W, Whitney IE, Jacobi A, Sud M, Burgin G, Shekhar K, Tran NM, Wang C, He Z, Sanes JR, Regev A. Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury. Nat Immunol 2023;24:700-713. [PMID: 36807640 DOI: 10.1038/s41590-023-01437-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/13/2023] [Indexed: 02/22/2023]
26
Comiter C, Vaishnav ED, Ciampricotti M, Li B, Yang Y, Rodig SJ, Turner M, Pfaff KL, Jané-Valbuena J, Slyper M, Waldman J, Vigneau S, Wu J, Blosser TR, Segerstolpe Å, Abravanel D, Wagle N, Zhuang X, Rudin CM, Klughammer J, Rozenblatt-Rosen O, Kobayash-Kirschvink KJ, Shu J, Regev A. Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533680. [PMID: 36993643 PMCID: PMC10055250 DOI: 10.1101/2023.03.21.533680] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
27
Spatial RNA sequencing methods show high resolution of single cell in cancer metastasis and the formation of tumor microenvironment. Biosci Rep 2023;43:232194. [PMID: 36459212 PMCID: PMC9950536 DOI: 10.1042/bsr20221680] [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: 08/04/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/03/2022]  Open
28
Tsoumakidou M. The advent of immune stimulating CAFs in cancer. Nat Rev Cancer 2023;23:258-269. [PMID: 36807417 DOI: 10.1038/s41568-023-00549-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2023] [Indexed: 02/19/2023]
29
Danan CH, Katada K, Parham LR, Hamilton KE. Spatial transcriptomics add a new dimension to our understanding of the gut. Am J Physiol Gastrointest Liver Physiol 2023;324:G91-G98. [PMID: 36472345 PMCID: PMC9870576 DOI: 10.1152/ajpgi.00191.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 01/19/2023]
30
Haghverdi L, Ludwig LS. Single-cell multi-omics and lineage tracing to dissect cell fate decision-making. Stem Cell Reports 2023;18:13-25. [PMID: 36630900 PMCID: PMC9860164 DOI: 10.1016/j.stemcr.2022.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023]  Open
31
Ospina O, Soupir A, Fridley BL. A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data. Methods Mol Biol 2023;2629:115-140. [PMID: 36929076 DOI: 10.1007/978-1-0716-2986-4_7] [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: 03/18/2023]
32
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nat Genet 2023;55:78-88. [PMID: 36624346 PMCID: PMC9840703 DOI: 10.1038/s41588-022-01256-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/01/2022] [Indexed: 01/11/2023]
33
Rood JE, Maartens A, Hupalowska A, Teichmann SA, Regev A. Impact of the Human Cell Atlas on medicine. Nat Med 2022;28:2486-2496. [PMID: 36482102 DOI: 10.1038/s41591-022-02104-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/24/2022] [Indexed: 12/13/2022]
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