Xinghua Lu, MD, PhD, MS

Lu, S., Lu, KN, Cheng, S., Ma, X., Nystrom, N., Lu, X. (2015) Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets.  PLoS Computational Biology 11(8):e1004257 PMID: 26317392  PMCID: PMC4552843

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

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. Journal of the American Medical Informatics Association 2015 Jul 2. pii: ocv059. doi: 10.1093/jamia/ocv059. [Epub ahead of print]  PMID: 26138794

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

Hatice Ulku Osmanbeyoglu, Kevin N. Lu, Steffi Oesterreich, Roger S. Day, Panayiotis V. Benos, Claudia Coronnello and Xinghua Lu. Estrogen represses gene expression through reconfiguring chromatin structures. Nucleic Acids Research, 2013, 1–11. doi:10.1093/nar/gkt586.
 

Lu, S., Jin, B., Cowart, LA., and Lu, X (2013) From data towards knowledge: Revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data. PLoS One 8(4): e61134  PMID: 23637789 PMCID: PMC3634064

Montefusco DJ, Chen L, Matmati N, Lu S, Newcomb B, Cooper GF, Hannun YA, Lu X. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses.  Science Signaling 6(299), rs14. [DOI: 10.1126/scisignal.2004515] (2013)  PMID: 24170935 PMC3974757

David J. Montefusco, Lujia Chen, Nabil Matmati, Songjian Lu, Benjamin Newcomb, Gregory F. Cooper, Yusuf A. Hannun, and Xinghua Lu.  Science Signaling, 6(299): p. rs14 [DOI: 10.1126/scisignal.2004515] http://stke.sciencemag.org/cgi/content/full/sigtrans;6/299/rs14

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