Xinghua Lu, MD, PhD, MS

Room 525
5607 Baum Boulevard
Pittsburgh, PA 15206
412-624-3303
412-624-5310
Admin Support: 
Research Interests: 

Dr. Lu’s research focuses on the computational methods for identifying signaling pathways underlying biological processes and diseases as well as statistical methods for acquiring knowledge from biomedical literature. He was trained in Pharmacology and works in the field of bioinformatics after NLM sponsored postdoctoral training in Biomedical Informatics. His research interest concentrates on applying latent variable models to simulate biological signaling system and text mining.

Currently, Dr. Lu is working on developing his research in translational bioinformatics and systems/computational biology and its application to specific domains relevant to human disease. He is pursuing collaboration in the area of natural language processing and text mining with the eventual goal of establishing a Center or Institute in Translational Bioinformatics.

Professor of Biomedical Informatics
Biomedical Informatics Training Program Core Faculty
University of Pittsburgh School of Medicine
Publications

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

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

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 

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

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

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

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

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

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.
 

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

Zhao, Z., Shen, B., Lu, X., and Vongsangnak, W (2013) Translational Biomedical Informatics and Computational Systems Medicine. BioMed Research International, vol. 2013, Article ID 237465, 2013. doi:10.1155/2013/237465

Montefusco, D., Chen, L, Matmati, N., Lu, S., Newcomb, B., Cooper, GF., Hannun, YA., Lu, X., (2013) Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and integromics analyses. Science Signaling 6:rs14

Pages

Selected Publications: 

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

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

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

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

Zhao, Z., Shen, B., Lu, X., and Vongsangnak, W (2013) Translational Biomedical Informatics and Computational Systems Medicine. BioMed Research International, vol. 2013, Article ID 237465, 2013. doi:10.1155/2013/237465

Montefusco, D., Chen, L, Matmati, N., Lu, S., Newcomb, B., Cooper, GF., Hannun, YA., Lu, X., (2013) Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and integromics analyses. Science Signaling 6:rs14

Osmanbeyoglu, H, Lu, K., Oesterreich, S, Day, RS, Benos, PV, Coronnello, C., and, Lu, X (2013) Estrogen represses gene expression through chromatin reconfiguration. Nucleic Acid Research 41(17): 8061-8071

Chen, V and Lu, X (2013) Conceptualization of molecular findings by mining gene annotations. BMC Proceedings 7(Suppl 7):S2

Mowrey, D., Cheng, M., Liu, L., Willenbring, D., Lu, X., Wymore, T., Xu, Y., and Tang, P.. (2013) Asymmetric ligand binding facilitates conformational transitions in pentameric ligand-gated ion channels. J Am Chem Soc. 135(6):2172-80. PMCID: PMC3582375

Lu, S., and Lu, X (2013) Using graph model to find transcription factor modules: the hitting set problem and an exact algorithm. Algorithms for Molecular Biology 8:2 PMCID: PMC3622577

Qin, T., Tsoi, LC., Sims KJ, Lu, X and Zheng, WJ (2012) Signaling network prediction using the ontology fingerprint enhanced Bayesian networks. BMC Systems Biology 6 (Suppl 3) : S3 (co-corresponding author)

Richards, A., Schwacke, J., Rohrer, B., Cowart, LA. and Lu, X (2012) Revealing functionally coherent gene subset using spectral clustering and information integration approaches. BMC Systems Biology 6 (Suppl 3) : S7

Osmanbeyoglu, H, Hartmaier, R., Oesterreich, S., and Lu, X. (2012) Improving ChIP-seq peak-calling for functional indirect co-regulator binding by integrating multiple sources of biological information. BMC Genomics 13(Suppl 1):S1

Feng, H, Hu, B, Liu, KW, Lu, X, Yiin, JJ, Lu, S, Keezer, S, Fenton, T, Furnari, FB, Hamilton, RL, Vuori, K, Nagane, M, Nishikawa, R, Cavenee, WK and Cheng, SY (2012) Aberrant Activation of Rac1 by Src-dependent Phosphorylation of Dock180Y1811 Mediates PDGFRα-stimulated Glioma Growth and Invasion. Journal of Clinical Investigation 121(12):4670–4684

Lu, S. and Lu, X (2012) Integrating genome and functional genomics data to reveal perturbed signaling pathways in ovarian cancers. Proceedings of AMIA Summit on Translational Bioinformatics, San Francisco.

Jin, B., Chen, V., Chen, L., and Lu, X. (2011) Mapping annotations with textual evidence using an scLDA model. Proceedings of AMIA Annual Symposium, Washington DC

Lu, S and Lu, X (2011). A graph model and an exact algorithm for finding cooperative transcription factor modules. Proceedings of ACM Bioinformatics and Computational Biology 2011

Jin, B. and Lu, X (2010). Identifying informative subsets of the Gene Ontology with information bottleneck methods. Bioinformatics 26 (19): 2445-2451

Cowart, LA., Shotwell, M., Worley, ML.,  Richards, AJ, Montefusco, DJ, Hannun YA, and Lu, X. (2010) Revealing a signaling role of PHS1P in yeast using integrative systems approaches.  Molecular Systems Biology 6:349 PMID: 20160710(Selected for presentation at the Highlight Track of ISMB 2010 as a major advance in the field)

Richards*, AJ, Muller, B., Shotwell, M, Cowart, LA, Rohrer, B, and Lu, X (2010) Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.  Bioinformatics, supplement issue for the Proceedings for the Intelligent Systems in Molecular Biology (ISMB) 2010 (19% acceptance) PMID: 20529941

Zheng*, B. and Lu, X (2009) Application of semantic modeling in bioinformatics domain.  In: Data Management in Semantic Web, Ed. Jin, H. and Lv, Z,.  Nova Science Publishers, Inc.

Jin*, B and Lu, X (2009) Enhancing GO-graph-based multi-label classification using semantic-rich GO terms.   Proceedings of the Annual Meeting of the ISMB BioLINK Workshop 2009

Muller*, B., Richards, AJ., Jin, B., Lu, X. (2009) GOGrapher; A Python library for GO graph representation and analysis.  BMC Research Notes 2:122 PMID:19583843

^