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A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade.
Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. Jerby-Arnon L, et al. Among authors: liu d. Cell. 2018 Nov 1;175(4):984-997.e24. doi: 10.1016/j.cell.2018.09.006. Cell. 2018. PMID: 30388455 Free PMC article.
Evolution of delayed resistance to immunotherapy in a melanoma responder.
Liu D, Lin JR, Robitschek EJ, Kasumova GG, Heyde A, Shi A, Kraya A, Zhang G, Moll T, Frederick DT, Chen YA, Wang S, Schapiro D, Ho LL, Bi K, Sahu A, Mei S, Miao B, Sharova T, Alvarez-Breckenridge C, Stocking JH, Kim T, Fadden R, Lawrence D, Hoang MP, Cahill DP, Malehmir M, Nowak MA, Brastianos PK, Lian CG, Ruppin E, Izar B, Herlyn M, Van Allen EM, Nathanson K, Flaherty KT, Sullivan RJ, Kellis M, Sorger PK, Boland GM. Liu D, et al. Nat Med. 2021 Jun;27(6):985-992. doi: 10.1038/s41591-021-01331-8. Epub 2021 May 3. Nat Med. 2021. PMID: 33941922 Free PMC article.
MITI minimum information guidelines for highly multiplexed tissue images.
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA; Human Tumor Atlas Network; Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. Schapiro D, et al. Nat Methods. 2022 Mar;19(3):262-267. doi: 10.1038/s41592-022-01415-4. Nat Methods. 2022. PMID: 35277708 Free PMC article.
Influence of melanoma type on incidence and downstream implications of cutaneous immune-related adverse events in the setting of immune checkpoint inhibitor therapy.
Nguyen N, Wan G, Ugwu-Dike P, Alexander NA, Raval N, Zhang S, Jairath R, Phillipps J, Leung B, Roster K, Seo J, Lu C, Tang K, Choi MS, DeSimone MS, Theodosakis N, Amadife M, Cox N, Le TK, Liu F, Chen W, Bai X, Boland G, Liu D, Hurlbert MS, LeBoeuf N, Reynolds KL, Yu KH, Tsao H, Asgari M, Gusev A, Kwatra SG, Semenov YR. Nguyen N, et al. Among authors: liu f, liu d. J Am Acad Dermatol. 2023 Jun;88(6):1308-1316. doi: 10.1016/j.jaad.2023.02.014. Epub 2023 Feb 22. J Am Acad Dermatol. 2023. PMID: 36828138 Free PMC article.
SpatialCells: Automated Profiling of Tumor Microenvironments with Spatially Resolved Multiplexed Single-Cell Data.
Wan G, Maliga Z, Yan B, Vallius T, Shi Y, Khattab S, Chang C, Nirmal AJ, Yu KH, Liu D, Lian CG, DeSimone MS, Sorger PK, Semenov YR. Wan G, et al. Among authors: liu d. bioRxiv [Preprint]. 2023 Nov 14:2023.11.10.566378. doi: 10.1101/2023.11.10.566378. bioRxiv. 2023. Update in: Brief Bioinform. 2024 Mar 27;25(3):bbae189. doi: 10.1093/bib/bbae189. PMID: 38014067 Free PMC article. Updated. Preprint.
Identification of cancer driver genes based on nucleotide context.
Dietlein F, Weghorn D, Taylor-Weiner A, Richters A, Reardon B, Liu D, Lander ES, Van Allen EM, Sunyaev SR. Dietlein F, et al. Among authors: liu d. Nat Genet. 2020 Feb;52(2):208-218. doi: 10.1038/s41588-019-0572-y. Epub 2020 Feb 3. Nat Genet. 2020. PMID: 32015527 Free PMC article.
Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade.
Sehgal K, Portell A, Ivanova EV, Lizotte PH, Mahadevan NR, Greene JR, Vajdi A, Gurjao C, Teceno T, Taus LJ, Thai TC, Kitajima S, Liu D, Tani T, Noureddine M, Lau CJ, Kirschmeier PT, Liu D, Giannakis M, Jenkins RW, Gokhale PC, Goldoni S, Pinzon-Ortiz M, Hastings WD, Hammerman PS, Miret JJ, Paweletz CP, Barbie DA. Sehgal K, et al. Among authors: liu d. J Clin Invest. 2021 Jan 19;131(2):e135038. doi: 10.1172/JCI135038. J Clin Invest. 2021. PMID: 33151910 Free PMC article.
The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine.
Garofalo A, Sholl L, Reardon B, Taylor-Weiner A, Amin-Mansour A, Miao D, Liu D, Oliver N, MacConaill L, Ducar M, Rojas-Rudilla V, Giannakis M, Ghazani A, Gray S, Janne P, Garber J, Joffe S, Lindeman N, Wagle N, Garraway LA, Van Allen EM. Garofalo A, et al. Among authors: liu d. Genome Med. 2016 Jul 26;8(1):79. doi: 10.1186/s13073-016-0333-9. Genome Med. 2016. PMID: 27460824 Free PMC article.
Mechanisms of Resistance to Immune Checkpoint Blockade.
Liu D, Jenkins RW, Sullivan RJ. Liu D, et al. Am J Clin Dermatol. 2019 Feb;20(1):41-54. doi: 10.1007/s40257-018-0389-y. Am J Clin Dermatol. 2019. PMID: 30259383 Free PMC article. Review.
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