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Refereed Journal Articles



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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 Gq-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




  1. 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

  2. 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

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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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)

  9. 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

  10. 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)

  11. 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)


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