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Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS.
Johnson JAI, Tsang AP, Mitchell JT, Zhou DL, Bowden J, Davis-Marcisak E, Sherman T, Liefeld T, Loth M, Goff LA, Zimmerman JW, Kinny-Köster B, Jaffee EM, Tamayo P, Mesirov JP, Reich M, Fertig EJ, Stein-O'Brien GL. Johnson JAI, et al. Among authors: jaffee em. Nat Protoc. 2023 Dec;18(12):3690-3731. doi: 10.1038/s41596-023-00892-x. Epub 2023 Nov 21. Nat Protoc. 2023. PMID: 37989764 Free PMC article. Review.
Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses.
Jayaraman S, Montagne JM, Nirschl TR, Marcisak E, Johnson J, Huff A, Hsiao MH, Nauroth J, Heumann T, Zarif JC, Jaffee EM, Azad N, Fertig EJ, Zaidi N, Larman HB. Jayaraman S, et al. Among authors: jaffee em. Cell Rep Methods. 2023 Oct 23;3(10):100600. doi: 10.1016/j.crmeth.2023.100600. Epub 2023 Sep 29. Cell Rep Methods. 2023. PMID: 37776855 Free PMC article.
Systems immunology spanning tumors, lymph nodes, and periphery.
Sidiropoulos DN, Ho WJ, Jaffee EM, Kagohara LT, Fertig EJ. Sidiropoulos DN, et al. Among authors: jaffee em. Cell Rep Methods. 2023 Dec 18;3(12):100670. doi: 10.1016/j.crmeth.2023.100670. Epub 2023 Dec 11. Cell Rep Methods. 2023. PMID: 38086385 Free PMC article. Review.
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces.
Deshpande A, Loth M, Sidiropoulos DN, Zhang S, Yuan L, Bell ATF, Zhu Q, Ho WJ, Santa-Maria C, Gilkes DM, Williams SR, Uytingco CR, Chew J, Hartnett A, Bent ZW, Favorov AV, Popel AS, Yarchoan M, Kiemen A, Wu PH, Fujikura K, Wirtz D, Wood LD, Zheng L, Jaffee EM, Anders RA, Danilova L, Stein-O'Brien G, Kagohara LT, Fertig EJ. Deshpande A, et al. Among authors: jaffee em. Cell Syst. 2023 Aug 16;14(8):722. doi: 10.1016/j.cels.2023.07.006. Cell Syst. 2023. PMID: 37591207 Free PMC article. No abstract available.
Molecular signature incorporating the immune microenvironment enhances thyroid cancer outcome prediction.
Xu GJ, Loberg MA, Gallant JN, Sheng Q, Chen SC, Lehmann BD, Shaddy SM, Tigue ML, Phifer CJ, Wang L, Saab-Chalhoub MW, Dehan LM, Wei Q, Chen R, Li B, Kim CY, Ferguson DC, Netterville JL, Rohde SL, Solórzano CC, Bischoff LA, Baregamian N, Shaver AC, Mehrad M, Ely KA, Byrne DW, Stricker TP, Murphy BA, Choe JH, Kagohara LT, Jaffee EM, Huang EC, Ye F, Lee E, Weiss VL. Xu GJ, et al. Among authors: jaffee em. Cell Genom. 2023 Sep 14;3(10):100409. doi: 10.1016/j.xgen.2023.100409. eCollection 2023 Oct 11. Cell Genom. 2023. PMID: 37868034 Free PMC article.
A new Neu-a syngeneic model of spontaneously metastatic HER2-positive breast cancer.
Baugh AG, Gonzalez E, Narumi VH, Kreger J, Liu Y, Rafie C, Castanon S, Jang J, Kagohara LT, Anastasiadou DP, Leatherman J, Armstrong T, Chan I, Karagiannis GS, Jaffee EM, MacLean A, Torres ETR. Baugh AG, et al. Among authors: jaffee em. Clin Exp Metastasis. 2024 May 8. doi: 10.1007/s10585-024-10289-z. Online ahead of print. Clin Exp Metastasis. 2024. PMID: 38717519
Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial-Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma.
Guinn S, Kinny-Köster B, Tandurella JA, Mitchell JT, Sidiropoulos DN, Loth M, Lyman MR, Pucsek AB, Zabransky DJ, Lee JW, Kartalia E, Ramani M, Seppälä TT, Cherry C, Suri R, Zlomke H, Patel J, He J, Wolfgang CL, Yu J, Zheng L, Ryan DP, Ting DT, Kimmelman A, Gupta A, Danilova L, Elisseeff JH, Wood LD, Stein-O'Brien G, Kagohara LT, Jaffee EM, Burkhart RA, Fertig EJ, Zimmerman JW. Guinn S, et al. Among authors: jaffee em. Cancer Res. 2024 May 2;84(9):1517-1533. doi: 10.1158/0008-5472.CAN-23-1660. Cancer Res. 2024. PMID: 38587552
Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial.
Yarchoan M, Gane EJ, Marron TU, Perales-Linares R, Yan J, Cooch N, Shu DH, Fertig EJ, Kagohara LT, Bartha G, Northcott J, Lyle J, Rochestie S, Peters J, Connor JT, Jaffee EM, Csiki I, Weiner DB, Perales-Puchalt A, Sardesai NY. Yarchoan M, et al. Among authors: jaffee em. Nat Med. 2024 Apr;30(4):1044-1053. doi: 10.1038/s41591-024-02894-y. Epub 2024 Apr 7. Nat Med. 2024. PMID: 38584166 Free PMC article. Clinical Trial.
Mesothelin CAR T Cells Secreting Anti-FAP/Anti-CD3 Molecules Efficiently Target Pancreatic Adenocarcinoma and its Stroma.
Wehrli M, Guinn S, Birocchi F, Kuo A, Sun Y, Larson RC, Almazan AJ, Scarfò I, Bouffard AA, Bailey SR, Anekal PV, Montero Llopis P, Nieman LT, Song Y, Xu KH, Berger TR, Kann MC, Leick MB, Silva H, Salas-Benito D, Kienka T, Grauwet K, Armstrong TD, Zhang R, Zhu Q, Fu J, Schmidts A, Korell F, Jan M, Choi BD, Liss AS, Boland GM, Ting DT, Burkhart RA, Jenkins RW, Zheng L, Jaffee EM, Zimmerman JW, Maus MV. Wehrli M, et al. Among authors: jaffee em. Clin Cancer Res. 2024 May 1;30(9):1859-1877. doi: 10.1158/1078-0432.CCR-23-3841. Clin Cancer Res. 2024. PMID: 38393682
269 results