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Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones.
Denisenko E, de Kock L, Tan A, Beasley AB, Beilin M, Jones ME, Hou R, Muirí DÓ, Bilic S, Mohan GRKA, Salfinger S, Fox S, Hmon KPW, Yeow Y, Kim Y, John R, Gilderman TS, Killingbeck E, Gray ES, Cohen PA, Yu Y, Forrest ARR. Denisenko E, et al. Among authors: kim y. Nat Commun. 2024 Apr 3;15(1):2860. doi: 10.1038/s41467-024-47271-y. Nat Commun. 2024. PMID: 38570491 Free PMC article.
High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging.
He S, Bhatt R, Brown C, Brown EA, Buhr DL, Chantranuvatana K, Danaher P, Dunaway D, Garrison RG, Geiss G, Gregory MT, Hoang ML, Khafizov R, Killingbeck EE, Kim D, Kim TK, Kim Y, Klock A, Korukonda M, Kutchma A, Lewis ZR, Liang Y, Nelson JS, Ong GT, Perillo EP, Phan JC, Phan-Everson T, Piazza E, Rane T, Reitz Z, Rhodes M, Rosenbloom A, Ross D, Sato H, Wardhani AW, Williams-Wietzikoski CA, Wu L, Beechem JM. He S, et al. Among authors: kim d, kim tk, kim y. Nat Biotechnol. 2022 Dec;40(12):1794-1806. doi: 10.1038/s41587-022-01483-z. Epub 2022 Oct 6. Nat Biotechnol. 2022. PMID: 36203011
Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease.
Garrido-Trigo A, Corraliza AM, Veny M, Dotti I, Melón-Ardanaz E, Rill A, Crowell HL, Corbí Á, Gudiño V, Esteller M, Álvarez-Teubel I, Aguilar D, Masamunt MC, Killingbeck E, Kim Y, Leon M, Visvanathan S, Marchese D, Caratù G, Martin-Cardona A, Esteve M, Ordás I, Panés J, Ricart E, Mereu E, Heyn H, Salas A. Garrido-Trigo A, et al. Among authors: kim y. Nat Commun. 2023 Jul 26;14(1):4506. doi: 10.1038/s41467-023-40156-6. Nat Commun. 2023. PMID: 37495570 Free PMC article.
Author Correction: Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease.
Garrido-Trigo A, Corraliza AM, Veny M, Dotti I, Melón-Ardanaz E, Rill A, Crowell HL, Corbí Á, Gudiño V, Esteller M, Álvarez-Teubel I, Aguilar D, Masamunt MC, Killingbeck E, Kim Y, Leon M, Visvanathan S, Marchese D, Caratù G, Martin-Cardona A, Esteve M, Ordás I, Panés J, Ricart E, Mereu E, Heyn H, Salas A. Garrido-Trigo A, et al. Among authors: kim y. Nat Commun. 2024 Jan 29;15(1):857. doi: 10.1038/s41467-024-45212-3. Nat Commun. 2024. PMID: 38287036 Free PMC article. No abstract available.
In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection.
Tan CW, Chen J, Liu N, Bhuva DD, Blick T, Monkman J, Cooper C, Kharbanda M, Feher K, Phipson B, Killingbeck EE, Pan L, Kim Y, Liang Y, Nam A, Leon M, Souza-Fonseca-Guimaraes P, Nagashima S, Camargo Martins AP, Machado-Souza C, de Noronha L, Tang B, Short K, Fraser J, Belz GT, Souza-Fonseca-Guimaraes F, Kulasinghe A, Davis MJ. Tan CW, et al. Among authors: kim y. EBioMedicine. 2024 Mar;101:105016. doi: 10.1016/j.ebiom.2024.105016. Epub 2024 Feb 19. EBioMedicine. 2024. PMID: 38377798 Free PMC article.
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.
Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR Jr, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Butler D, et al. Among authors: kim y. Nat Commun. 2021 Mar 12;12(1):1660. doi: 10.1038/s41467-021-21361-7. Nat Commun. 2021. PMID: 33712587 Free PMC article.
The spatial landscape of lung pathology during COVID-19 progression.
Rendeiro AF, Ravichandran H, Bram Y, Chandar V, Kim J, Meydan C, Park J, Foox J, Hether T, Warren S, Kim Y, Reeves J, Salvatore S, Mason CE, Swanson EC, Borczuk AC, Elemento O, Schwartz RE. Rendeiro AF, et al. Among authors: kim j, kim y. Nature. 2021 May;593(7860):564-569. doi: 10.1038/s41586-021-03475-6. Epub 2021 Mar 29. Nature. 2021. PMID: 33780969 Free PMC article.
An information theoretic approach to detecting spatially varying genes.
Jones DC, Danaher P, Kim Y, Beechem JM, Gottardo R, Newell EW. Jones DC, et al. Among authors: kim y. Cell Rep Methods. 2023 Jun 16;3(6):100507. doi: 10.1016/j.crmeth.2023.100507. eCollection 2023 Jun 26. Cell Rep Methods. 2023. PMID: 37426750 Free PMC article.
Spatially resolved analysis of pancreatic cancer identifies therapy-associated remodeling of the tumor microenvironment.
Shiau C, Cao J, Gong D, Gregory MT, Caldwell NJ, Yin X, Cho JW, Wang PL, Su J, Wang S, Reeves JW, Kim TK, Kim Y, Guo JA, Lester NA, Bae JW, Zhao R, Schurman N, Barth JL, Ganci ML, Weissleder R, Jacks T, Qadan M, Hong TS, Wo JY, Roberts H, Beechem JM, Castillo CF, Mino-Kenudson M, Ting DT, Hemberg M, Hwang WL. Shiau C, et al. Among authors: kim tk, kim y. Nat Genet. 2024 Nov;56(11):2466-2478. doi: 10.1038/s41588-024-01890-9. Epub 2024 Sep 3. Nat Genet. 2024. PMID: 39227743
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