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Year Number of Results
2017 1
2018 11
2019 18
2020 19
2021 15
2022 15
2023 23
2024 3

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85 results

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Page 1
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. 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.
Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade.
Shu DH, Ho WJ, Kagohara LT, Girgis A, Shin SM, Danilova L, Lee JW, Sidiropoulos DN, Mitchell S, Munjal K, Howe K, Bendinelli KJ, Qi H, Mo G, Montagne J, Leatherman JM, Lopez-Vidal TY, Zhu Q, Huff AL, Yuan X, Hernandez A, Coyne EM, Zaidi N, Zabransky DJ, Engle LL, Ogurtsova A, Baretti M, Laheru D, Durham JN, Wang H, Anders R, Jaffee EM, Fertig EJ, Yarchoan M. Shu DH, et al. bioRxiv [Preprint]. 2023 Oct 26:2023.10.16.562104. doi: 10.1101/2023.10.16.562104. bioRxiv. 2023. PMID: 37904980 Free PMC article. Preprint.
TP53 structure-function relationships in metastatic castrate-sensitive prostate cancer and the impact of APR-246 treatment.
Hoang T, Sutera P, Nguyen T, Chang J, Jagtap S, Song Y, Shetty AC, Chowdhury DD, Chan A, Carrieri FA, Hathout L, Ennis R, Jabbour SK, Parikh R, Molitoris J, Song DY, DeWeese T, Marchionni L, Ren L, Sawant A, Simone N, Lafargue A, Van Der Eecken K, Bunz F, Ost P, Tran PT, Deek MP. Hoang T, et al. Prostate. 2024 Jan;84(1):87-99. doi: 10.1002/pros.24629. Epub 2023 Oct 9. Prostate. 2024. PMID: 37812042
Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.
Johnson JAI, Stein-O'Brien GL, Booth M, Heiland R, Kurtoglu F, Bergman DR, Bucher E, Deshpande A, Forjaz A, Getz M, Godet I, Lyman M, Metzcar J, Mitchell J, Raddatz A, Rocha H, Solorzano J, Sundus A, Wang Y, Gilkes D, Kagohara LT, Kiemen AL, Thompson ED, Wirtz D, Wu PH, Zaidi N, Zheng L, Zimmerman JW, Jaffee EM, Hwan Chang Y, Coussens LM, Gray JW, Heiser LM, Fertig EJ, Macklin P. Johnson JAI, et al. bioRxiv [Preprint]. 2023 Nov 5:2023.09.17.557982. doi: 10.1101/2023.09.17.557982. bioRxiv. 2023. PMID: 37745323 Free PMC article. Preprint.
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. 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.
Identification of a Predictive Genomic Biomarker for Prostate-directed Therapy in Synchronous Low-volume Metastatic Castration-sensitive Prostate Cancer.
Sutera P, Shetty AC, Song Y, Hodges T, Hoang T, Rana Z, Pienta K, Feng F, Song DY, DeWeese T, Gillessen S, Sweeney C, James N, Attard G, Deek M, Tran PT. Sutera P, et al. Eur Urol Oncol. 2024 Apr;7(2):241-247. doi: 10.1016/j.euo.2023.07.014. Epub 2023 Aug 8. Eur Urol Oncol. 2024. PMID: 37558543 Free article.
85 results