Xinghua Lu, MD, PhD, MS

A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways

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. September 2018; 13(9). https://doi.org/10.1371/journal.pone.0203871. 

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. 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. Epub 2018 Aug 6. PMID: 29927689.

Activation of the receptor tyrosine kinase AXL mediates the immune microenvironment in glioblastoma

Sadahiro H, Kang K, Gibson J, 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 S, Hambardzumyan D, Lu X, Newell E, Dasgupta B, Nakada M, Lee L, Nabors B, Norian L, Nakano I. Activation of the receptor tyrosine kinase AXL mediates the immune microenvironment in glioblastoma.  2018 Jun 1;78(11):3002-3013. doi: 10.1158/0008-5472.CAN-17-2433. Epub 2018 Mar 12. PMID: 29531161.

A signal-based method for finding driver modules of breast cancer metastasis to the lung

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/s41598-09951-2. PMID: 28855549. PMC ID: PMC5577160.

Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen

Watters RJ, Hartmaier RJ, Osmanbeyoglu HU, Gillihan RM, Rae JM, Liao L, Chen K, Li W, Lu X, Oesterreich S. Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen. Mol Cell Endocrinol. 2017 Jun 15; 448:21-27. doi: 10.1016/j.mce.2017.03.005. Epub 2017 Mar 7. PMID: 28286232. 

Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling

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. PMID: 28361690. PMC ID: PMC5374647.

MST4 Phosphorylation of ATG4B Regulates Autophagic Activity, Tumorigenicity, and Radioresistance in Glioblastoma

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. PMID: 29232556. 

Precision Oncology Beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics

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. 2017 Nov 13. pii: molcanres.0378.2017. doi: 10.1158/1541-7786.MCR-17-0378. [Epub ahead of print] PMID: 29133589

Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma

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. PMID: 28984190. PMCID: PMC5629551. 

Signal-oriented pathway analyses reveal a signaling complex as a synthetic lethal target for p53 mutations

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. 206 Dec 1:76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740. Epub 2016 Oct 10. PMID: 27758891. PMCID: PMC5165695.

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