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239 results

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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: mitchell jt. 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.
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.
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: mitchell jt. Cancer Res. 2024 May 2;84(9):1517-1533. doi: 10.1158/0008-5472.CAN-23-1660. Cancer Res. 2024. PMID: 38587552 Free PMC article.
Characteristics and Predictors of Fluctuating Attention-Deficit/Hyperactivity Disorder in the Multimodal Treatment of ADHD (MTA) Study.
Sibley MH, Kennedy TM, Swanson JM, Arnold LE, Jensen PS, Hechtman LT, Molina BSG, Howard A, Greenhill L, Chronis-Tuscano A, Mitchell JT, Newcorn JH, Rohde LA, Hinshaw SP. Sibley MH, et al. Among authors: mitchell jt. J Clin Psychiatry. 2024 Oct 16;85(4):24m15395. doi: 10.4088/JCP.24m15395. J Clin Psychiatry. 2024. PMID: 39431909
SARS-CoV-2 Genotyping Highlights the Challenges in Spike Protein Drift Independent of Other Essential Proteins.
Prokop JW, Alberta S, Witteveen-Lane M, Pell S, Farag HA, Bhargava D, Vaughan RM, Frisch A, Bauss J, Bhatti H, Arora S, Subrahmanya C, Pearson D, Goodyke A, Westgate M, Cook TW, Mitchell JT, Zieba J, Sims MD, Underwood A, Hassouna H, Rajasekaran S, Tamae Kakazu MA, Chesla D, Olivero R, Caulfield AJ. Prokop JW, et al. Among authors: mitchell jt. Microorganisms. 2024 Sep 9;12(9):1863. doi: 10.3390/microorganisms12091863. Microorganisms. 2024. PMID: 39338537 Free PMC article.
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration.
Bell ATF, Mitchell JT, Kiemen AL, Lyman M, Fujikura K, Lee JW, Coyne E, Shin SM, Nagaraj S, Deshpande A, Wu PH, Sidiropoulos DN, Erbe R, Stern J, Chan R, Williams S, Chell JM, Ciotti L, Zimmerman JW, Wirtz D, Ho WJ, Zaidi N, Thompson E, Jaffee EM, Wood LD, Fertig EJ, Kagohara LT. Bell ATF, et al. Among authors: mitchell jt. Cell Syst. 2024 Aug 21;15(8):753-769.e5. doi: 10.1016/j.cels.2024.07.001. Epub 2024 Aug 7. Cell Syst. 2024. PMID: 39116880
Phosphodiesterase-5 inhibition collaborates with vaccine-based immunotherapy to reprogram myeloid cells in pancreatic ductal adenocarcinoma.
Gross NE, Zhang Z, Mitchell JT, Charmsaz S, Hernandez AG, Coyne EM, Shin SM, Vargas Carvajal DC, Sidiropoulos DN, Cho Y, Mo G, Yuan X, Cannon C, Suresh Babu J, Lyman MR, Armstrong T, Kagohara LT, Bever KM, Le DT, Jaffee EM, Fertig EJ, Ho WJ. Gross NE, et al. Among authors: mitchell jt. JCI Insight. 2024 Aug 6;9(18):e179292. doi: 10.1172/jci.insight.179292. JCI Insight. 2024. PMID: 39106104 Free PMC article.
239 results