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Batch effects removal for microbiome data via conditional quantile regression.
Ling W, Lu J, Zhao N, Lulla A, Plantinga AM, Fu W, Zhang A, Liu H, Song H, Li Z, Chen J, Randolph TW, Koay WLA, White JR, Launer LJ, Fodor AA, Meyer KA, Wu MC. Ling W, et al. Among authors: white jr. Nat Commun. 2022 Sep 15;13(1):5418. doi: 10.1038/s41467-022-33071-9. Nat Commun. 2022. PMID: 36109499 Free PMC article.
Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic.
Tomkovich S, Dejea CM, Winglee K, Drewes JL, Chung L, Housseau F, Pope JL, Gauthier J, Sun X, Mühlbauer M, Liu X, Fathi P, Anders RA, Besharati S, Perez-Chanona E, Yang Y, Ding H, Wu X, Wu S, White JR, Gharaibeh RZ, Fodor AA, Wang H, Pardoll DM, Jobin C, Sears CL. Tomkovich S, et al. Among authors: white jr. J Clin Invest. 2019 Mar 11;129(4):1699-1712. doi: 10.1172/JCI124196. eCollection 2019 Mar 11. J Clin Invest. 2019. PMID: 30855275 Free PMC article.
Interaction between the microbiome and TP53 in human lung cancer.
Greathouse KL, White JR, Vargas AJ, Bliskovsky VV, Beck JA, von Muhlinen N, Polley EC, Bowman ED, Khan MA, Robles AI, Cooks T, Ryan BM, Padgett N, Dzutsev AH, Trinchieri G, Pineda MA, Bilke S, Meltzer PS, Hokenstad AN, Stickrod TM, Walther-Antonio MR, Earl JP, Mell JC, Krol JE, Balashov SV, Bhat AS, Ehrlich GD, Valm A, Deming C, Conlan S, Oh J, Segre JA, Harris CC. Greathouse KL, et al. Among authors: white jr. Genome Biol. 2018 Aug 24;19(1):123. doi: 10.1186/s13059-018-1501-6. Genome Biol. 2018. PMID: 30143034 Free PMC article.
Genomic characterization of malignant progression in neoplastic pancreatic cysts.
Noë M, Niknafs N, Fischer CG, Hackeng WM, Beleva Guthrie V, Hosoda W, Debeljak M, Papp E, Adleff V, White JR, Luchini C, Pea A, Scarpa A, Butturini G, Zamboni G, Castelli P, Hong SM, Yachida S, Hiraoka N, Gill AJ, Samra JS, Offerhaus GJA, Hoorens A, Verheij J, Jansen C, Adsay NV, Jiang W, Winter J, Albores-Saavedra J, Terris B, Thompson ED, Roberts NJ, Hruban RH, Karchin R, Scharpf RB, Brosens LAA, Velculescu VE, Wood LD. Noë M, et al. Among authors: white jr. Nat Commun. 2020 Aug 14;11(1):4085. doi: 10.1038/s41467-020-17917-8. Nat Commun. 2020. PMID: 32796935 Free PMC article.
A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors.
Shaikh FY, White JR, Gills JJ, Hakozaki T, Richard C, Routy B, Okuma Y, Usyk M, Pandey A, Weber JS, Ahn J, Lipson EJ, Naidoo J, Pardoll DM, Sears CL. Shaikh FY, et al. Among authors: white jr. Clin Cancer Res. 2021 May 1;27(9):2571-2583. doi: 10.1158/1078-0432.CCR-20-4834. Epub 2021 Feb 16. Clin Cancer Res. 2021. PMID: 33593881 Free PMC article.
Detection and characterization of lung cancer using cell-free DNA fragmentomes.
Mathios D, Johansen JS, Cristiano S, Medina JE, Phallen J, Larsen KR, Bruhm DC, Niknafs N, Ferreira L, Adleff V, Chiao JY, Leal A, Noe M, White JR, Arun AS, Hruban C, Annapragada AV, Jensen SØ, Ørntoft MW, Madsen AH, Carvalho B, de Wit M, Carey J, Dracopoli NC, Maddala T, Fang KC, Hartman AR, Forde PM, Anagnostou V, Brahmer JR, Fijneman RJA, Nielsen HJ, Meijer GA, Andersen CL, Mellemgaard A, Bojesen SE, Scharpf RB, Velculescu VE. Mathios D, et al. Among authors: white jr. Nat Commun. 2021 Aug 20;12(1):5060. doi: 10.1038/s41467-021-24994-w. Nat Commun. 2021. PMID: 34417454 Free PMC article.
Automated next-generation profiling of genomic alterations in human cancers.
Keefer LA, White JR, Wood DE, Gerding KMR, Valkenburg KC, Riley D, Gault C, Papp E, Vollmer CM, Greer A, Hernandez J, McGregor PM 3rd, Zingone A, Ryan BM, Deak K, McCall SJ, Datto MB, Prescott JL, Thompson JF, Cerqueira GC, Jones S, Simmons JK, McElhinny A, Dickey J, Angiuoli SV, Diaz LA Jr, Velculescu VE, Sausen M. Keefer LA, et al. Among authors: white jr. Nat Commun. 2022 May 20;13(1):2830. doi: 10.1038/s41467-022-30380-x. Nat Commun. 2022. PMID: 35595835 Free PMC article.
2,009 results