Bioinformatics/Biomedical Sciences

Dymacek J and Guo NL*. Systems Approach to Identifying Relevant Pathways from Phenotype Information in Dose-Dependent Time Series Microarray Data. 2011 IEEE International Conference on Bioinformatics and Biomedicine, IEEE Press, 2011. p290-293. Manuscript

Putila J and Guo NL*. Association of Arsenic Exposure with Lung Cancer Incidence Rates in the United States. PLoS ONE, 2011;6(10):e25886. Manuscript

Pacurari M, Qian Y, Fu W, Schwegler-Berry D, Ding M, Castranova V, Guo NL*. Cell Permeability, Migration, and Reactive Oxygen Species Induced by Multi-Walled Carbon Nanotubes in Human Microvascular Endothelial Cells. Journal of Toxicology and Environmental Health, Part A, 2012;Jan 15;75(2):112-28. Manuscript

Wan Y, Beer DG, and Guo NL*. Signaling pathway-based identification of extensive prognostic gene signatures for lung adenocarcinoma. Lung Cancer, 2011. Oct 31. [Epub ahead of print]. PMID:22047960. Manuscript | Supplement

Jing Y, Liu LZ, Jiang Y, Zhu Y, Guo NL, Barnett J, Rojanasakul Y, Agani F, Jiang BH. Cadmium Increases HIF-1 and VEGF Expression through ROS, ERK and AKT Signaling Pathways and Induces Malignant Transformation of Human Bronchial Epithelial Cells. Toxicol Sci. 2011 Oct 9. [Epub ahead of print]. PMID:21984483. Manuscript

Guo, NL* and Wan Y. A pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival. Artificial Intelligence in Medicine, 2012. In Press. Manuscript

Pacurari M, Qian Y, Porter DW, Wolfarth M, Wan Y, Luo D, Ding M, Castranova V, Guo NL*. Multi-Walled Carbon Nanotube-Induced Gene Expression in the Mouse Lung: Association with Lung Pathology. Toxicology and Applied Pharmacology, 2011. doi:10.1016/j.taap.2011.05.012. Manuscript

Son Y-O, Hitron JA, Cheng S, Budhraja A, Zhang Z, Guo NL, Lee J-C, Shi X. The Dual Roles of c-Jun NH2-Terminal Kinase Signaling in Cr(VI)-Induced Apoptosis in JB6 Cells. Toxicological Sciences 119(2), 335–345, 2011. Manuscript

Putila J, Remick SC, Guo NL (2011) Combining Clinical, Pathological, and Demographic Factors Refines Prognosis of Lung Cancer: A Population-Based
Study. PLoS ONE 6(2): e17493. doi:10.1371/journal.pone.0017493 Manuscript.

Guo NL*, Wan Y, Bose S, Denvir J, Kashon M, Andrew M. A novel network model identified a 13-gene lung cancer prognostic signature. The International Journal of Computational Biology and Drug Design. Special Issue on ACM-BCB.  Vol. 4 No. 1 p19-39, 2011   Manuscript

Mettu R, Wan Y, Habermann JK, Ried T, Guo NL*. A 12-Gene Genomic Instability Signature Predicts Clinical Outcomes in Multiple Cancer Types. The International Journal of Biological Markers. 2010 Nov 23;25(4):219-228.. PMID: 21110303. Author Proof

Wan Y, Xiao C, Guo NL*. Network-Based Identification of Smoking-Associated Gene Signature for Lung Cancer. Proc. IEEE International Conference on Bioinformatics & Biomedicine, IEEE Press, 2010; p479-484.  Manuscript

Wan Y, Bose S, Denvir J, and Guo NL*. A Novel Network Model for Molecular Prognosis. Proc. ACM International Conference on Bioinformatics and Computational Biology. p342-345, 2010. PDF

Wan Y, Qian Y, Rathnagiriswaran S, Castranova V, and Guo NL*. A breast cancer prognostic signature predicts clinical outcomes in multiple tumor types.  Oncology Reports, 24: 489-494, 2010. PDF  

Wan W, Sabbagh E, Raese R, Qian Y, Luo D, Denvir J, Vallyathan V, Castranova V, Guo NL*. Hybrid Models Identified a 12-Gene Signature for Lung Cancer Prognosis and Chemoresponse Prediction. PLoS ONE 5(8): e12222, 2010. Manuscript, Supplement. 

Yong Qian; Alan Ducatman; Rebecca Ward; Steve Leonard; Valerie Bukowski; Nancy Lan Guo; Xianglin Shi; Val Vallyathan;Vincent Castranova. Perfluorooctane Sulfonate (PFOS) Induces Reactive Oxygen Species (ROS) Production in Human Microvascular Endothelial Cells: Role in Endothelial Permeability. Journal of Toxicology and Environmental Health,Part A, 73:819–836, 2010 Manuscript

Shruti Rathnagiriswaran, Ying-Wooi Wan, Jame Abraham, Vincent Castranova, Yong Qian, and Nancy L. Guo*.  A Population-based gene signature is predictive of breast cancer survival and chemoresponse.  Int. J. Oncology, 2010 Mar;36(3):607-16 Manuscript, Appendix

Nancy L. Guo*, Kursad Tosun, and Kimberly Horn. Impact and interactions between smoking and traditional prognostic factors in lung cancer progression. Lung Cancer, March 2009 Manuscript

Apopa PL, Qian Y*, Shao R, Guo NL, Schwegler-Berry D, Pacurari M, Porter D, Shi X, Vallyathan V, Castranova V, Flynn DC*.  Iron oxide  anoparticles induce human microvascular endothelial cell permeability through reactive oxygen species production and microtubule remodeling. Particle and Fibre Toxicology, 6(1): 1743-8977(2009) Manuscript

Habermann JK, Doering J, Hautaniemi S, Roblick UJ, Bündgen NK, Nicorici D, Kronenwett U, Rathnagiriswaran S, Mettu RK, Ma Y, Krüger S, Bruch HP, Auer G, Guo NL*, Ried T*.  The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome. Int. J. Cancer, 124(7): 1552–1564 (2009) Manuscript

Hua Yao, Lan Guo, Bing-Hua Jiang, Jia Luo, and Xianglin Shi. Oxidative Stress and Chromium (VI) Carcinogenesis. Journal of Environmental Pathology, Taxicology, and Oncology. 27(2):77-88 (2008) Manuscript

Nancy L. Guo, Ying-Wooi Wan, Kursad Tosun, Hong Lin, Zola Msiska, Daniel C. Flynn, Scot C. Remick, Val Vallyathan,  Afshin Dowlati,  Xianglin Shi,  Vincent Castranova,  David G. Beer,  and Yong Qian, Confirmation of Gene Expression-Based Prediction of Survival in Non-Small Cell Lung Cancer. Clinical Cancer Research, 14(24): 8213-8220 (2008) Manuscript Supplementary

Yan Ma, Zhenyu Ding, Yong Qian, Ying-wooi Wan, Kursad Tosun, Xianglin Shi,Vincent Castranova, E. James Harner, and Nancy L Guo*. An Integrative Genomic and Proteomic Approach to Chemosensitivity Prediction. Int. J. Oncology, 34(1):107-115 (2008) Manuscript   Appendix Supplementary

Guo L*, Abraham J, Flynn D.C, Castranova V, Shi X and Qian Y.Individualized Survival and Treatment Response Predictions in Breast Cancer Patients: Involvements of Phospho-EGFR and Phospho-Her2/Neu Proteins. The Open Clinical Cancer Journal, 2008, Volume 2,pp.18-31 Manuscript

Ma Y, Qian Y, Wei L, Abraham J, Shi X, Castranova V, Harner J, Flynn D.C. and Guo L*. Population-Based Molecular Prognosis of Breast Cancer by Transcriptional Profiling. Clinical Cancer Research, 13(7):2014-22, 2007. [Cover sidebar] Manuscript Supplementary

Guo L*, Abraham J, Flynn D.C, Castranova V, Shi X,Qian Y. Individualized survival and treatment response predictions for breast cancers using phospho-EGFR,phospho-ER, phospho-HER2/neu, phospho-IGF-IR/In, phospho-MAPK, and phospho-p70S6K proteins.The International Journal of Biological Markers, Vol. 22 no. 1, 2007, pp. 1-11 Manuscript

Ou Y, Guo L, Zhang CQ, A New Clustering Method and Its Application to Proteomic Profiling for Colon Cancer, Proc. of IASTED on Computational and Systems Biology, pp 68-71 ACTA Press, 2006.Manuscript

Ma Y, Ding Z, Qian Y, Shi X, Castranova V, Harner, EJ, Guo L*. Predicting Cancer Drug Response by Proteomic Profiling. Clinical Cancer Research 12(15):4583-9, 2006
Manuscript Supplementary Result table(excel)

Guo L*, Ma Y, Ward R, Castranova V, Shi X, Qian Y. Constructing Molecular Classifiers for Accurate Prognosis of Lung Adenocarcinoma. Clinical Cancer Research, 12(11): 3344-3354, 2006
Manuscript Supplementary

(* - Senior Author)

Software Engineering

1. Ma Y, Guo L, Cukic B. A Statistical Framework for the Prediction of Fault-Proneness. Advances in Machine Leaning Application in Software Engineering, Idea Group Inc., 2006 Manuscript

2. Guo L, Ma Y, Cukic B, Singh H. Robust Prediction of Fault-Proneness by Random Forests. Proc. 15th IEEE International Symposium on Software Reliability Engineering (ISSRE 2004), pp.417-428, IEEE Press, 2004 (Extended paper invited by Kluwer's Empirical Software Engineering) (Acceptance rate: 25%) Manuscript

3. Guo L, Mukhopadhyay S, Cukic B. Does Your Result Checker Really Check? Proc. the International Conference on Dependable Systems and Networks (DSN 2004), pp.399-405, IEEE Press, 2004 (Acceptance rate: 15%) Manuscript

4. Boddu R, Guo L, Mukhopadhyay S, Cukic B. RETNA: From Requirements to Testing in a Natural Way. Proc. 12th IEEE International Requirements Engineering Conference (RE 2004), pp.262-271, IEEE Press, 2004 (Acceptance rate: 20%) Manuscript

5. Guo L, Cukic B, Singh H. Predicting Fault Prone Modules by the Dempster-Shafer Belief Networks. Proc. 18th IEEE International Conference on Automated Software Engineering (ASE 2003), pp.249-252, IEEE Press, 2003 (Acceptance rate: 15%) Manuscript

6. Cukic B, Gunel E, Singh H, Guo L. The Theory of Software Reliability Corroboration. IEICE Transactions on Information & Systems, Vol. E86-D, No. 10, October, 2003 Manuscript

Ph.D. Dissertation

Lan Guo,Software Quality and Reliability Prediction Using Dempster-Shafer Theory,Ph.D. Dissertation,West Virginia University, 2004 .Ph.D.Dissertation

Advisor Dr.Bojan Cukic

Book Chapters

Ma Y, Guo NL, Cukic B, A Statistical Framework for the Prediction of Fault Proneness, in Advances in Machine Learning Applications in Software Engineering, D. Zhang and J. P. Tsai (Eds), Idea Group Publishing, 2007, pp. 237-264.  Manuscript

Qian Y, Shi X, Castronova V, Guo NL*. Molecular Profiling in Breast Cancer Patients. Genomics and Pharmocogenomics in Anticancer Drug Development and Clinical Response. (Edited by Federico Innocenti), Humana Press. 2009; p287-298. ISBN:9781588296467. Manuscript