Publications

Xinghua Lu

Minata M, Audia A, Shi J, Lu S, Bernstock J, Pavlyukov MS, Das A, Kim SH, Shin YJ, Lee Y, Koo H, Snigdha K, Waghmare I, Guo X, Mohyeldin A, Gallego-Perez D, Wang J, Chen D, Cheng P, Mukheef F, Contreras M, Reyes JF, Vaillant B, Sulman EP, Cheng SY, Markert JM, Tannous BA, Lu X, Kango-Singh M, Lee LJ, Nam DH, Nakano I, Bhat KP. Phenotypic Plasticity of Invasive Edge Glioma Stem-like Cells in Response to Ionizing Radiation. Cell Rep. 2019 Feb 12;26(7):1893-1905.e7. doi: 10.1016/j.celrep.2019.01.076. PubMed PMID: 30759398.
Chen L, Lu X. Discovering functional impacts of miRNAs in cancers using a causal deep learning model. BMC Med Genomics. 2018 Dec 31;11(Suppl 6):116. doi: 10.1186/s12920-018-0432-0. PubMed PMID: 30598118; PMCID: PMC6311958.
Lu S, Fan X, Chen L, Lu X. A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways. PLoS One. 2018;13(9):e0203871. doi: 10.1371/journal.pone.0203871. PubMed PMID: 30208101; PMCID: PMC6135403.
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. Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in glioma stem cells and glioblastoma. Epigenetics. 2018;13(4):432-448. doi: 10.1080/15592294.2018.1469892. PubMed PMID: 29927689; PMCID: PMC6140806.
Sadahiro H, Kang KD, Gibson JT, Minata M, Yu H, Shi J, Chhipa R, Chen Z, Lu S, Simoni Y, Furuta T, Sabit H, Zhang S, Bastola S, Yamaguchi S, Alsheikh H, Komarova S, Wang J, Kim SH, Hambardzumyan D, Lu X, Newell EW, DasGupta B, Nakada M, Lee LJ, Nabors B, Norian LA, Nakano I. Activation of the Receptor Tyrosine Kinase AXL Regulates the Immune Microenvironment in Glioblastoma. Cancer Res. 2018 Jun 1;78(11):3002-3013. doi: 10.1158/0008-5472.CAN-17-2433. PubMed PMID: 29531161; PMCID: PMC5984695.
Huang T, Kim CK, Alvarez AA, Pangeni RP, Wan X, Song X, Shi T, Yang Y, Sastry N, Horbinski CM, Lu S, Stupp R, Kessler JA, Nishikawa R, Nakano I, Sulman EP, Lu X, James CD, Yin XM, Hu B, Cheng SY. MST4 Phosphorylation of ATG4B Regulates Autophagic Activity, Tumorigenicity, and Radioresistance in Glioblastoma. Cancer Cell. 2017 Dec 11;32(6):840-855.e8. doi: 10.1016/j.ccell.2017.11.005. PubMed PMID: 29232556; PMCID: PMC5734934.
Ding MQ, Chen L, Cooper GF, Young JD, Lu X. Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics. Mol Cancer Res. 2018 Feb;16(2):269-278. doi: 10.1158/1541-7786.MCR-17-0378. PubMed PMID: 29133589; PMCID: PMC5821274.
Young JD, Cai C, Lu X. Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma. BMC Bioinformatics. 2017 Oct 3;18(Suppl 11):381. doi: 10.1186/s12859-017-1798-2. PubMed PMID: 28984190; PMCID: PMC5629551.
Yan G, Chen V, Lu X, Lu S. A signal-based method for finding driver modules of breast cancer metastasis to the lung. Sci Rep. 2017 Aug 30;7(1):10023. doi: 10.1038/s41598-017-09951-2. PubMed PMID: 28855549; PMCID: PMC5577160.
Chen V, Paisley J, Lu X. Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling. BMC Genomics. 2017 Mar 14;18(Suppl 2):105. doi: 10.1186/s12864-017-3494-z. PubMed PMID: 28361690; PMCID: PMC5374647.
Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer Res. 2016 Dec 1;76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740. PubMed PMID: 27758891; PMCID: PMC5165695.
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. A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways. Nat Commun. 2016 Oct 4;712885. doi: 10.1038/ncomms12885. PubMed PMID: 27698350; PMCID: PMC5059456.
Lu S, Mandava G, Yan G, Lu X. An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem. Algorithms Mol Biol. 2016;1111. doi: 10.1186/s13015-016-0073-9. PubMed PMID: 27148394; PMCID: PMC4855522.
Chen L, Cai C, Chen V, Lu X. Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model. BMC Bioinformatics. 2016 Jan 11;17 Suppl 19. doi: 10.1186/s12859-015-0852-1. PubMed PMID: 26818848; PMCID: PMC4895523.
Lu S, Lu KN, Cheng SY, Hu B, Ma X, Nystrom N, Lu X. Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets. PLoS Comput Biol. 2015 Aug;11(8):e1004257. doi: 10.1371/journal.pcbi.1004257. PubMed PMID: 26317392; PMCID: PMC4552843.
Ogoe HA, Visweswaran S, Lu X, Gopalakrishnan V. Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data. BMC Bioinformatics. 2015 Jul 23;16226. doi: 10.1186/s12859-015-0643-8. PubMed PMID: 26202217; PMCID: PMC4512094.
Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, Center for Causal Discovery team.. The center for causal discovery of biomedical knowledge from big data. J Am Med Inform Assoc. 2015 Nov;22(6):1132-6. doi: 10.1093/jamia/ocv059. PubMed PMID: 26138794; PMCID: PMC5009908.
Chen L, Cai C, Chen V, Lu X. Trans-species learning of cellular signaling systems with bimodal deep belief networks. Bioinformatics. 2015 Sep 15;31(18):3008-15. doi: 10.1093/bioinformatics/btv315. PubMed PMID: 25995230; PMCID: PMC4668779.

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