Xinghua Lu, MD, PhD, MS

Learning Latent Causal Structures with a Redundant Input Neural Network

Young JD, Andrews B, Cooper GF, Lu X. Learning Latent Causal Structures with a Redundant Input Neural Network. arXiv:2003.13135v1 29 Mar 2020.

Pharmacologic Suppression of B7-H4 Glycosylation Restores Antitumor Immunity in Immune-Cold Breast Cancers

Song X, Zhou Z, Li H, Xue Y, Lu X, Bahar I, Kepp O, Hung M-C, Kromer G, Wan Y. Pharmacologic Suppression of B7-H4 Glycosylation Restores Antitumor Immunity in Immune-Cold Breast Cancers. Cancer Discovery December 2020. doi:10.1158/2159-8290.CD-20-0402

elF4E S209 phosphorylation licenses Myc- and stress-driven oncogenesis

Ruan H, Li X, Xu X, Leibowitz BJ, Tong J, Chen L, Ao l, Xing W, Luo J, Yu Y, Schoen RE, Sonenberg N, Lu X, Zhang L, Yu J.  elF4E S209 phosphorylation licenses Myc- and stress-driven oncogenesis. Elife. 2020 Nov 2;e60151. Doi: 10.7554/eLife.60151. PMID: 33135632

Predicting Drug Sensitivity of Cancer Cells Lines via Collaborative Filtering with Contextual Attention.

Yifeng Tao, Shuangxia Ren, Michael Q. Ding, Russell Schwartz, Xinghua Lu. Predicting Drug Sensitivity of Cancer Cells Lines via Collaborative Filtering with Contextual Attention.  Proceedings of Machine Learning Research. 2020. 1-A7

Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inferenc

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 JQ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLOS Comput Biol, 2019 Jul 15(7):e1007088. doi: 10.1371/journal.pcbi.1007088. [Epub ahead of print] PMID: 31276486; PMCID: PMC6650088.

Integrating data and knowledge to identify functional modules of genes: a multilayer approach

Liang L, Chen V, Zhu K, Fan X, Lu X, Lu S. Integrating data and knowledge to identify functional modules of genes: a multilayer approach. BMC Bioinformatics. 2019 May 2;20(1):225. doi: 10.1186/s12859-019-2800-y. PubMed PMID: 31046665. 

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.

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. 2018 Feb;16(2):269-278. doi: 10.1158/1541-7786.MCR-17-0378. Epub 2017 Nov 13. PMID: 29133589. PMCID: PMC5821274.

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