Xinghua Lu, MD, PhD, MS

Lu S, Mandava G, Yan G, and Lu X. An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem. Algorithms Mol Biol. 2016 May 4;11:11. doi: 10.1186/s13015-016-0073-9. PMID: 27148394. PMCID: PMC4855522.

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;7:12885. doi: 10.1038/ncomms12885. PMID: 27698350. PMCID: PMC5059456.

Chen, L., Cai, C., Chen, V., and Lu, X (2015) Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.  BMC Bioinformatics Suppl 1:9. doi: 10.1186/s12859-015-0852-1. 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 28; 11(8):e1004257. doi: 10.1371/journal.pcbi.1004257. eCollection 2015 Aug. PMID:26317392. PMCID: PMC4552843.

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, 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. Epub 2015 Jul 2.  PMID: 26138794. PMCID: PMC5009908.

Ogoe, HA, Visweswaran, S, Lu, X, Gopalakrishnan, V.  (2015) Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data.  BMC Bioinformatics 16:226 (designated as a Highly Accessed paper) PMID: 26202217 PMCID: PMC4512094

Lujia Chen, Chunhui Cai, Vicky Chen and Xinghua Lu.  Trans-species learning of cellular signaling systems with bimodal deep belief networks.  Bioinformatics 2015;
doi: 10.1093/bioinformatics/btv315 

Jiang X, Cai B, Xue D, Lu X, Cooper GF, Neapolitan RE. A comparative analysis of methods for predicting clinical outcomes using high-dimensional genomic datasets. Journal of the American Medical Informatics Association (2014). Oct;21(e2):e312-9. doi: 10.1136/amiajnl-2013-002358. Epub 2014 Apr 15. PMID: 24737607. PMC4173174.

Cai C, Chen L, Jiang X, Lu X. Integrating protein phosphorylation and gene expression data to infer signaling pathways. Cancer Informatics Supplement on Cancer Clinical Information Systems. 2014; 13(s1): 59-67. doi: 10.4137/CIN.S13883

Osmanbeyoglu HU, Lu KN, Oesterreich S, Day RS, Benos PV, Coronnello C, Lu X. Estrogen represses gene expression through reconfiguring chromatin structures. Nucleic Acids Research, 2013, 1–11. doi:10.1093/nar/gkt586.

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