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hadge: a comprehensive pipeline for donor deconvolution in single-cell studies.
Curion F, Wu X, Heumos L, André MMG, Halle L, Ozols M, Grant-Peters M, Rich-Griffin C, Yeung HY, Dendrou CA, Schiller HB, Theis FJ. Curion F, et al. Among authors: theis fj. Genome Biol. 2024 Apr 26;25(1):109. doi: 10.1186/s13059-024-03249-z. Genome Biol. 2024. PMID: 38671451 Free PMC article.
Defining and benchmarking open problems in single-cell analysis.
Luecken MD, Gigante S, Burkhardt DB, Cannoodt R, Strobl DC, Markov NS, Zappia L, Palla G, Lewis W, Dimitrov D, Vinyard ME, Magruder DS, Andersson A, Dann E, Qin Q, Otto DJ, Klein M, Botvinnik OB, Deconinck L, Waldrant K; Open Problems Jamboree Members; Bloom JM, Pisco AO, Saez-Rodriguez J, Wulsin D, Pinello L, Saeys Y, Theis FJ, Krishnaswamy S. Luecken MD, et al. Among authors: theis fj. Res Sq [Preprint]. 2024 Apr 4:rs.3.rs-4181617. doi: 10.21203/rs.3.rs-4181617/v1. Res Sq. 2024. PMID: 38645152 Free PMC article. Preprint.
Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex.
Koupourtidou C, Schwarz V, Aliee H, Frerich S, Fischer-Sternjak J, Bocchi R, Simon-Ebert T, Bai X, Sirko S, Kirchhoff F, Dichgans M, Götz M, Theis FJ, Ninkovic J. Koupourtidou C, et al. Among authors: theis fj. Nat Commun. 2024 Apr 3;15(1):2866. doi: 10.1038/s41467-024-46625-w. Nat Commun. 2024. PMID: 38570482 Free PMC article.
SpatialData: an open and universal data framework for spatial omics.
Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B, Pollaris L, Lehner L, Vöhringer H, Kats I, Saeys Y, Saka SK, Huber W, Gerstung M, Moore J, Theis FJ, Stegle O. Marconato L, et al. Among authors: theis fj. Nat Methods. 2024 Mar 20. doi: 10.1038/s41592-024-02212-x. Online ahead of print. Nat Methods. 2024. PMID: 38509327
Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts.
Mayr CH, Sengupta A, Asgharpour S, Ansari M, Pestoni JC, Ogar P, Angelidis I, Liontos A, Rodriguez-Castillo JA, Lang NJ, Strunz M, Porras-Gonzalez D, Gerckens M, De Sadeleer LJ, Oehrle B, Viteri-Alvarez V, Fernandez IE, Tallquist M, Irmler M, Beckers J, Eickelberg O, Stoleriu GM, Behr J, Kneidinger N, Wuyts WA, Wasnick RM, Yildirim AÖ, Ahlbrecht K, Morty RE, Samakovlis C, Theis FJ, Burgstaller G, Schiller HB. Mayr CH, et al. Among authors: theis fj. Eur Respir J. 2024 Feb 8;63(2):2301326. doi: 10.1183/13993003.01326-2023. Print 2024 Feb. Eur Respir J. 2024. PMID: 38212077 Free PMC article.
Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma.
Kirschenbaum D, Xie K, Ingelfinger F, Katzenelenbogen Y, Abadie K, Look T, Sheban F, Phan TS, Li B, Zwicky P, Yofe I, David E, Mazuz K, Hou J, Chen Y, Shaim H, Shanley M, Becker S, Qian J, Colonna M, Ginhoux F, Rezvani K, Theis FJ, Yosef N, Weiss T, Weiner A, Amit I. Kirschenbaum D, et al. Among authors: theis fj. Cell. 2024 Jan 4;187(1):149-165.e23. doi: 10.1016/j.cell.2023.11.032. Epub 2023 Dec 21. Cell. 2024. PMID: 38134933
Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis.
Lang NJ, Gote-Schniering J, Porras-Gonzalez D, Yang L, De Sadeleer LJ, Jentzsch RC, Shitov VA, Zhou S, Ansari M, Agami A, Mayr CH, Hooshiar Kashani B, Chen Y, Heumos L, Pestoni JC, Molnar ES, Geeraerts E, Anquetil V, Saniere L, Wögrath M, Gerckens M, Lehmann M, Yildirim AÖ, Hatz R, Kneidinger N, Behr J, Wuyts WA, Stoleriu MG, Luecken MD, Theis FJ, Burgstaller G, Schiller HB. Lang NJ, et al. Among authors: theis fj. Sci Transl Med. 2023 Dec 6;15(725):eadh0908. doi: 10.1126/scitranslmed.adh0908. Epub 2023 Dec 6. Sci Transl Med. 2023. PMID: 38055803
Modeling fragment counts improves single-cell ATAC-seq analysis.
Martens LD, Fischer DS, Yépez VA, Theis FJ, Gagneur J. Martens LD, et al. Among authors: theis fj. Nat Methods. 2024 Jan;21(1):28-31. doi: 10.1038/s41592-023-02112-6. Epub 2023 Dec 4. Nat Methods. 2024. PMID: 38049697 Free PMC article.
Early life adversity shapes social subordination and cell type-specific transcriptomic patterning in the ventral hippocampus.
Kos A, Lopez JP, Bordes J, de Donno C, Dine J, Brivio E, Karamihalev S, Luecken MD, Almeida-Correa S, Gasperoni S, Dick A, Miranda L, Büttner M, Stoffel R, Flachskamm C, Theis FJ, Schmidt MV, Chen A. Kos A, et al. Among authors: theis fj. Sci Adv. 2023 Dec;9(48):eadj3793. doi: 10.1126/sciadv.adj3793. Epub 2023 Dec 1. Sci Adv. 2023. PMID: 38039370 Free PMC article.
328 results