Xinghua Lu, MD, PhD, MS

Research Interests: 

Dr. Lu has broad research experiences in clinical and basic biomedical sciences. His research interest concentrates on developing artificial intelligence (AI) methodologies and their application in translational medicine, particularly precision oncology. The ongoing research in his group spans a broad spectrum of translational informatics: using causal inference methods to understand cancer disease mechanisms, using probabilistic graphic models and deep learning models to studying cancer signaling pathways, using NLP technology to mine and annotate biomedical texts (publications and medical records), using AI techniques to facilitate clinical decision making.

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

Yan G, Chen V, Lu X, Lu S. A signal-based method for finding driver modules of breast cancer metastasis to the lung. Sci Rep. 2017 Aug 30; 7(1):10023. doi: 10.1038/s41598-09951-2. PMID: 28855549. PMC ID: PMC5577160.

Chen V, Paisley J, Lu X. Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling. BMC Genomics. 2017 Mar 14;18 (Suppl 2):105. doi: 10.1186/s12864-017-3494-z. PMID: 28361690. PMC ID: PMC5374647.

Huang T, Kim CK, Alvarez AA, Pangeni RP, Wan X, Song X, Shi T, Yang Y, Sastry N, Horbinski CM, Lu S, Stupp R, Kessler JA, Nishikawa R, Nakano I, Sulman EP, Lu X, James CD, Yin XM, Hu B, Cheng SY. MST4 Phosphorylation of ATG4B Regulates Autophagic Activity, Tumorigenicity, and Radioresistance in Glioblastoma. Cancer Cell. 2017 Dec 11; 32(6):840-855.e8. doi: 10.1016/j.ccell.2017.11.005. PMID: 29232556

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. 2017 Nov 13. pii: molcanres.0378.2017. doi: 10.1158/1541-7786.MCR-17-0378. [Epub ahead of print] PMID: 29133589

Young JD, Cai C, Lu X. Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma. BMC Bioinformatics. 2017 Oct 3;18(Suppl 11): 381. doi: 10.1186/s12859-017-1798-2. PMID: 28984190. PMCID: PMC5629551

Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer Res. 206 Dec 1:76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740. Epub 2016 Oct 10. PMID: 27758891. PMCID: PMC5165695.

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.

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

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. Lu X. From data towards knowledge: Revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data. PLoS One. 2013 Apr 23;8(4):e61134. doi: 10.1371/journal.pone.0061134. Print 2013. PMID: 23637789. PMCID: PMC3634064.

Lu S, Lu X. Using graph models to find transcription factor modules: the hitting set problem and an exact algorithm. Algorithms Mol Biol. 2013 Jan 16;8(1):2. doi: 10.1186/1748-7188-8-2. PMID: 23324335. PMCID: PMC3622577.

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. Sci Signal. 2013 Oct 29;6(299): rs14. doi: 10.1126/scisignal.2004515. PMID: 24170935. PMC3974757.

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

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 SLu X. A graph model and an exact algorithm for finding cooperative transcription factor modules. Proc. 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2012 Jul 31-Aug 3; 355-359.

Lu SLu, X. Integrating genome and functional genomics data to reveal perturbed signaling pathways in ovarian cancers. 2012 AMIA Jt Summits Transl Sci Proc. 2012;2012:72-8. Epub 2012 Mar 19. PMID: 22779056. PMCID: PMC3392049.

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

Feng H, Hu B, Liu KW, Li Y, Lu X, Cheng T, Yiin JJ, Lu S, Keezer S, Fenton T, Furnari FB, Hamilton RL, Vuori K, Sarkaria JN, Nagane M, Nishikawa R, Cavenee WK, Cheng SY. Activation of Rac1 by Src-dependent phosphorylation of Dock180(Y1811) mediates PDGFRα-stimulated glioma tumorigenesis in mice and humans. J Clin Invest. 2011 Dec;121(12):4670-84. doi: 10.1172/JCI58559. Epub 2011 Nov 14. PMID: 22080864. PMCID: PMC3223070.

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

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

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

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.

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

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