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Investigating immune and non-immune cell interactions in head and neck tumors by single-cell RNA sequencing.
Kürten CHL, Kulkarni A, Cillo AR, Santos PM, Roble AK, Onkar S, Reeder C, Lang S, Chen X, Duvvuri U, Kim S, Liu A, Tabib T, Lafyatis R, Feng J, Gao SJ, Bruno TC, Vignali DAA, Lu X, Bao R, Vujanovic L, Ferris RL. Kürten CHL, et al. Among authors: lu x. Nat Commun. 2021 Dec 17;12(1):7338. doi: 10.1038/s41467-021-27619-4. Nat Commun. 2021. PMID: 34921143 Free PMC article.
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.
Chen X, Chen L, Kürten CHL, Jabbari F, Vujanovic L, Ding Y, Lu B, Lu K, Kulkarni A, Tabib T, Lafyatis R, Cooper GF, Ferris R, Lu X. Chen X, et al. Among authors: lu x, lu k, lu b. PLoS Comput Biol. 2022 Dec 22;18(12):e1010761. doi: 10.1371/journal.pcbi.1010761. eCollection 2022 Dec. PLoS Comput Biol. 2022. PMID: 36548438 Free PMC article.
A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways.
Huang T, Alvarez AA, Pangeni RP, Horbinski CM, Lu S, Kim SH, James CD, J Raizer J, A Kessler J, Brenann CW, Sulman EP, Finocchiaro G, Tan M, Nishikawa R, Lu X, Nakano I, Hu B, Cheng SY. Huang T, et al. Among authors: lu x, lu s. Nat Commun. 2016 Oct 4;7:12885. doi: 10.1038/ncomms12885. Nat Commun. 2016. PMID: 27698350 Free PMC article.
Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in glioma stem cells and glioblastoma.
Pangeni RP, Zhang Z, Alvarez AA, Wan X, Sastry N, Lu S, Shi T, Huang T, Lei CX, James CD, Kessler JA, Brennan CW, Nakano I, Lu X, Hu B, Zhang W, Cheng SY. Pangeni RP, et al. Among authors: lu x, lu s. Epigenetics. 2018;13(4):432-448. doi: 10.1080/15592294.2018.1469892. Epub 2018 Aug 6. Epigenetics. 2018. PMID: 29927689 Free PMC article.
Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference.
Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang QJ, Lu X. Cai C, et al. Among authors: lu x, lu kn, lu s. PLoS Comput Biol. 2019 Jul 5;15(7):e1007088. doi: 10.1371/journal.pcbi.1007088. eCollection 2019 Jul. PLoS Comput Biol. 2019. PMID: 31276486 Free PMC article.
Inferring causal molecular networks: empirical assessment through a community-based effort.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium; Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Hill SM, et al. Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22. Nat Methods. 2016. PMID: 26901648 Free PMC article.
Chitinase-3-like 1 protein complexes modulate macrophage-mediated immune suppression in glioblastoma.
Chen A, Jiang Y, Li Z, Wu L, Santiago U, Zou H, Cai C, Sharma V, Guan Y, McCarl LH, Ma J, Wu YL, Michel J, Shi Y, Konnikova L, Amankulor NM, Zinn PO, Kohanbash G, Agnihotri S, Lu S, Lu X, Sun D, Gittes GK, Wang Q, Xiao X, Yimlamai D, Pollack IF, Camacho CJ, Hu B. Chen A, et al. Among authors: lu x, lu s. J Clin Invest. 2021 Aug 16;131(16):e147552. doi: 10.1172/JCI147552. J Clin Invest. 2021. PMID: 34228644 Free PMC article.
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