CURRICULUM VITAE
University of Pittsburgh
School of Medicine
BIOGRAPHICAL
Name: Xinghua Lu
Home Address: Birthplace: Shanghai, China
Home Phone: Citizenship: United States
Business Address: 5607 Baum Blvd Email:
Pittsburgh, PA 15206
Business Phone: 412-624-3303 Business Fax:
EDUCATION and TRAINING
GRADUATE:
Dates Attended / Name and Location of Institution / Degree and Year / Major1979 / Shandong Medical University / M.D. 1984 / Medicine
1985 / Shandong Medical University / M.S. Clinical Res., 1988 / Cardiology
1993 / University of Connecticut Health Ctr / Ph.D., 1998 / Pharmacology
2001 / University of Pittsburgh / Certificate, 2003 / Biomedical Informatics
POSTGRADUATE:
Dates Attended / Name and Location of Institution / Program Director and Discipline
1984-1985 / Resident
Shengli Central Hospital, Dongying, China / Internal Medicine
1988-1991
1998-1998
1998-2001
2001-2003 / Chief Resident
Postdoctoral Fellow
National Institute of Environmental Health Sciences
Research Associate
University of Pittsburgh
National Library of Medicine Training Fellow
University of Pittsburgh / Dept. of Emergency Medicine
Shandong Provincial Hospital
Signal Transduction Laboratory
Dept. of Pharmacology
Center for Biomedical Informatics
APPOINTMENTS and POSITIONS
ACADEMIC:
Years Inclusive Name and Location of Institution Rank/Title
1991-1993 Dept Emergency Medicine Attending Physician
Shandong Provincial Hospital, Jinan (Cardiologist)
2003 – 2008 Dept Biostat, Bioinf & Epi., Medical Assistant Professor
University of South Carolina (MUSC)
2005 – 2010 Dept Biostat, Bioinf & Epi / Biochem Director, NLM Training
MUSC Program (NLM, NIH)
2007 – 2010 Dept Biostat, Bioinf & Epi / Biochem Director, Bioinformatics
MUSC Division
2008 – 2009 Dept Biostat, Bioinf & Epi., MUSC Associate Professor
2009 – 2010 Dept Biochemistry and Molecular Associate Professor
Biology, MUSC
2009 – 2010 Dept Biochemistry and Molecular Co-Director, GAANN
Biology, MUSC Training Program in Lipidomics and Systems Biology (funded by the Department of Education, USA)
2009 – 2010 Biochemistry, MUSC Co-Director, Biostatistics
Training for Basic Biomedical
Research Program (NIGMS)
2010 - 2012 Department of Biomedical Informatics Visiting Associate Professor
University of Pittsburgh, Pittsburgh PA
2012 - Department of Biomedical Informatics Associate Professor
University of Pittsburgh, Pittsburgh PA
2010 - Co-Director, Center for Translational
Bioinformatics, University of Pittsburgh
MEMBERSHIPS in PROFESSIONAL and SCIENTIFIC SOCIETIES
· Member of Federation of American Societies for Experimental 1996-2001
Biologists (Experimental Biology and Biophysics Societies)
· Member of American Association for the Advancement of Science 1998 - 2007
· Member of International Society for Computational Biologist 2001 - present
· Member of International mathematical Statistics 2004 - 2008
· Member of American Medical Informatics Association 2003 - present
AWARDS and HONORS
· Recipient of yearly Best Student Award from Shandong Medical University. 1981-1983
· Best Teaching Award, Shandong Provincial Hospital Nursing School. 1992
· Basic Medical Science Fellowship, University of Connecticut Health Center. 1993-1998
· SmithKline Beecham Award for Outstanding Graduate Student Research at 1997
New England Pharmacologists’ Meeting. Boston, MA.
· Fogarty Fellowship Award, National Institutes of Health. 1998
· National Library of Medicine Training Fellowship 2001-2003
· Lister Hill National Center for Biomedical Communication Summer Research 2003
Participation Program Fellowship.
· International Society for Computation Biology travel award for PSB 2004 2004
· The Third International Charleston Ceramide Conference travel award 2005
· Outstanding Paper Award, 2009 American Medical Informatics Association Summit on Translational Bioinformatics 2009
· Invited Speaker, The 175 Anniversary of National Library of Medicine Conference 2011
· 2nd Place Award, The Sage Bionetworks-DREAM Breast Cancer Prognosis
Challenge (BCC) 2012
· 1st Place Award, SBV IMPROVER Trans-species Network Challenge 2013
PUBLICATIONS
Refereed Journal Articles
1. Lu, X., Fein, A., Feinstein, M.B. and O’Rourke, F.A., (1999) Antisense knock out of the Inositol 1,3,4,5-tetrakisphosphate receptor GAP1IP4BP in the human erythroleukemia cell line leads to the appearance of intermediate conductance K(Ca) channels that hyperpolarize the membrane and enhance calcium influx. J. Gen. Physiol. 113:81-9 (IF: 5.1)
2. Signore, A., O’Rourke, F., Lu, X., Feinstein, and Yeh, H. (1999) Immunohistochemical localization of the InsP4 Receptor GTPase-Activating Protein GAP1IP4BP in the rat brain. J. Neurosci. Res. 55:321-328. (IF: 2.3)
3. Laplante JM, O'rourke F, Lu, X, Fein A, Olsen A, Feinstein MB (2000) Cloning of human Ca2+ homoeostasis endoplasmic reticulum protein (CHERP): regulated expression of antisense cDNA depletes CHERP, inhibits intracellular Ca2+ mobilization and decreases cell proliferation. Biochem. J. 348:189-99 (IF: 3.4)
4. Zhang, T., Gealy, R., Lu, X., Takimoto, K., and Levitan, ES., (2000) TRH regulates Kv1.5 gene expression though a Gq-mediated PLC-independent pathway. Mol. Cell Endocrinol. 25;165(1-2):33-39. (IF: 3.6)
5. Ng, K., Lu, X., Levitan, ES.. (2002) Physical mobilization of secretory vesicles facilitates neuropeptide release by nerve growth factor-differentiated PC12 cells. J Physiol (London) 542 (Pt2) 395-402 (4.6)
6. Ng, Y.K., Lu, X. (equal contributing author), Walkins, S.C., Ellis-Davies, G.C. and Levitan, E.S., (2002) Nerve growth factor-induced differentiation changes the cellular organization of regulated peptide release by PC12 cells. J. Neurosci. 22(10):3890-7 (IF: 8,23)
7. Lu, X., Ellis-Davies, G.C.R., and Levitan E.S.(2003) Calcium requirements do not delimit the releasable neuropeptide pool. Cell Calcium 33(4):267-271 (4.5)
8. Ng, Y.K., Lu, X., Gulacsi, A., Han, W., Saxton, M.J. and Levitan, E.S. (2003) Unexpected mobility variation among individual secretory vesicles produces an apparent refractory neuropeptide pool. Biophysical J. 84(6):4127-34
9. Lu, X., Zhai, C., Gopalakrishnan, V., and Buchanan, B.G. (2004) Automatic annotation of protein motif function with Gene Ontology terms. BMC Bioinformatics 5:122
10. Tao, T., Zhai, C., Lu, X. and Fang, H. (2004) A study of statistical methods for predicting function of protein motifs. Applied Bioinformatics, 3:115-124
11. Cowart, L.A., Okamoto, Y., Lu, X. and Hannun, Y.A. (2006) Distinct roles for de novo versus hydrolytic pathways of sphingolipid biosynthesis in Saccharomyces cerevisiae. Biochemical J. 393(3):733.
12. Zheng, B., McLean, DC., and Lu, X. (2006) Identifying biological concepts from a protein-related corpus with a probabilistic topic model. BMC Bioinformatics 7:58
13. Chen, Y.A., Chou, C.C., Lu, X., Slate, E.H., Peck, K., Xu, W., Voit, E.O., and Almeida, J.S. A (2006) Multivariate prediction model for microarray cross-hybridization. BMC Bioinformatics 7:101 (highly accessed paper)
14. Lu, X., Zheng, B., Velivelli, A. and Zhai, C (2006) Enhancing text categorization with semantic-enriched representation and training data augmentation. J Am Med Inform Assoc, 13(5):526-35
15. Chen, Y., Zheng, B., Robbins, DH., Lewin, DN., Mikhitarian, K, Graham, A., Rumpp, L, Glenn, T, Gillanders, WE, Cole, DJ, Lu, X, Hoffman, BJ. and Michael Mitas (2007) Accurate discrimination of pancreatic ductal adenocarcinoma and chronic focal pancreatitis using multi-marker expression data and samples obtained by minimally invasive fine needle aspiration. International Journal of Cancer, 120(7):1511
16. Zheng, B., and Lu, X. (2007) Novel metrics for evaluating the functional coherence of protein groups via protein-semantic-network. Genome Biology 8:R153[doi:10.1186/gb-2007-8-7-r153]
17. Jin, B., Muller, B., Zhai, CX, and Lu, X (2008) Multi-label literature classification based on the Gene Ontology graph. BMC Bioinformatics 9:525
18. Kozel, FA., Johnson, KA., Grenesko, EL., Laken, SJ., Kose, S, Lu, X., Pollina, D., Ryan, A and George, MS (2009) Functional MRI detection of deception after committing a mock sabotage crime. J. Forensic Sciences, 54(1):220-31. PMID: 19067772
19. Jin, B., Strasburger, A., Laken, SJ., Kozel, FA., Johnson, KA., George, MS., and Lu, X. (2009) Feature selection for fMRI-based deception detection. BMC Bioinformatics 10 (Suppl 9):S15 (Outstanding Paper Award at the AMIA Summit on Translational Bioinformatics) PMID: 19761569
20. 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
21. 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.
22. 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, 26 (12): i79-i87 (Supplement issue for the Proceedings for the Intelligent Systems in Molecular Biology (ISMB) 2010, 19% acceptance)
23. 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 which presents major advance in the field; invited presentation at the Gordon Research Conference 2010)
24. Jin, B. and Lu, X (2010). Identifying informative subsets of the Gene Ontology with information bottleneck methods. Bioinformatics 26 (19): 2445-2451
25. 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
26. 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
27. 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
28. 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)
29. 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
30. 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
31. Lu, S., Jin, B., Cowart, LA., and Lu, X (2013) From data towards knowledge: Revealing the architectureof signaling systems by unifying knowledge mining and data mining of systematic perturbation data. PLoS One 8(4): e61134
32. Chen, V and Lu, X (2013) Conceptualization of molecular findings by mining gene annotations. BMC Proceedings 7(Suppl 7):S2
33. 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
34. 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
35. 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
36. Jiang X, Cai B, Xue D, Lu X, Neapolitan RE, Cooper GF (2014). A Comparative Analysis of Methods for Predicting Clinical Outcomes Using High-Dimensional Genomic Datasets. J Am. Medical Informatics Assoc. 21:e312-e319
37. Bilal, E, et al. (2014) A crowd-sourcing approach for the construction of species-specific cell signaling networks. Bioinformatics. doi:10.1093/bioinf (This is the report of the Species Translation Challenge organized by the Systems Biology Verification Consortium (SBV). Our team won the first place in the challenge, and we are listed as participants authors)
38. Cai, C., Chen, L., Jiang, X., and Lu, X., (2014) Integrating protein phosphorylation and gene expression data to infer signaling pathways. Cancer Informatics, 13(S1):59-67
39. Chen, L., Cai, C., Chen, V., and Lu, X (2015) Trans-species learning of cellular signaling systems with bimodal deep belief networks. Bioinformatics (doi: 10.1093/bioinformatics/btv315)
40. 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 (to appear)
41. 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)
42. 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 (Accepted)
Refereed Conference Proceeding Papers
43. Tao, T., Zhai, C., Lu, X. and Fang, H. (2003) A study of statistical methods for predicting function of protein motifs. In Proceedings of Biological Language Conference 2003, Pittsburgh, PA
44. Lu, X., Hauskrecht, M. and Day, R.S. (2004) Modeling Cellular Processes with Variational Bayesian Cooperative Vector Quantizer. In Proceedings of Pacific Symposium on Biocomputing, pp533.
45. 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
46. 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
47. Jin, B., Chen, V., Chen, L., and Lu, X. (2011) Mapping annotations with textual evidence using an scLDA model. Proceedings of AMIA Annual Symposium 2011, Washington DC
48. 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.
Books, Chapters, Reviews, Non-refereed Invited Published Papers, Non-refereed Proceedings of Conference and Symposia, Unpublished Technical Reports, Monographs, Books and Book Chapters
49. Wei, C., Li, X., Zhang, Z. and Lu, X. et al Ed. (1992) Intensive Care of Critical Diseases. Yellow River Press Inc. Shandong, China
50. Lu, X., Zhai, CX., Gopalakrishnan, V., Buchanan, B.G.. (2002) Predicting functions of protein motifs by mining the knowledge base of Gene Ontology. Center for Biomedical Informatics Technical Report, University of Pittsburgh, Series Number: CBMI-02-180
51. Lu, X., Day, R.S. and Hauskrecht, M. (2002) Variational Bayesian learning of a multiple causal model – Part I: The Theory Center for Biomedical Informatics Technical Report, University of Pittsburgh, Series Number: CBMI-02-181