Xinghua Lu, MD, PhD, MS

Vicky Chen, John Paisley and  Xinghua Lu.  Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling.  BMC Genomics 2017 18(Suppl2):105. DOI: 10.1186/s12864-017-3494-z

S. Lu, C. Cai,  G. Yan,  Z. Zhou, Y. Wan, L. Chen, V. Chen, G. Cooper, L. Obeid, Y. Hannun, A. Lee and X. Lu. Signal-oriented pathway analyses reveal a signaling complex as a synthetic lethal target for p53 mutations, Cancer Research 2016, Minor revision

Lu, S., Mandava, G., Yan, G., and Lu, X (2016) An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem.  Algorithm for Molecular Biology 11:1, DOI: 10.1186/s13015-016-0073-9   PMCID: PMC4855522

Stolovitzky, G., Hill, S., Heiser, L, Lu, X, Jiang, X, et al.  (2016) Inferring causal molecular networks: empirical assessment through a community-based effort.  Nature Methods. 13, 310–318 PMID: 26901648 PMCID: PMC4854847

 

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, 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

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