Methodology Development

Applications in Public Health, Pre-Clinical & Clinical Studies

Methodology Development:

Yang X and Xue F. (2013). Bayesian Statistics in Translational Medicine-From Personal to Public Health. Accepted by Chinese Journal of Preventive Medicine.

Zhang X, Yang X, Yuan Z, Liu Y, Li F, Zhao J, Xue F. (2013). A gene-based method for detecting gene-gene co-association with application to genetic network construction. Accepted by PloS ONE.

Yang X, Peng B, Chen R, Zhang Q, Zhu D, Xue F, and Qi L. (2013). Compare Statistical Profiling Methods within the Framework of Hierarchical Logistic Regression Models for Health Care Providers with Binary Outcomes. Submitted to Journal of Applied Statistics.

Liu G, Belin TR, and Yang X. (2013). Bayesian Variable Selection in Binomial Regression with Missing Covariates. To be submitted to Statistics in Medicine.

Hui Li and Chunmei Liu (2012). Biomarker Identification Using Text Mining. Computational and Mathematical Methods in Medicine, vol. 2012, Article ID 135780, 4 pages, 2012. doi:10.1155/2012/135780.

Hui Li and Chunmei Liu (2012). A Dynamic Data-Driven Framework for Biological Data Using 2D Barcodes. Computational and Mathematical Methods in Medicine, vol. 2012, Article ID 892098, 5 pages, 2012. doi:10.1155/2012/892098.

Hui Li; Chunmei Liu, Legand Berge, William Southerland (2012). Identification of two post-translational modifications via tandem mass spectrometry. International Journal of Computational Biology and Drug Design, 5, 314-324(11).

Hui Li and Chunmei C Liu (2012). Peptide sequence tag generation for tandem mass spectra containing post-translational modifications. Computational Biology and Drug Design 5(3/4):325-334.

Hui Li and Chunmei Liu (2012). Predicting Protein-Protein Interactions Using Full Bayesian 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops. Workshop 8. The 3rd Integrative Data Analysis in Systems Biology (IDASB 2012) 544-550.

Peng B, Zhu D, Yang X, Huang W, Liu L, Zhou X, Yi D. (2012). An Extended Association Rule Mining Strategy for Gene Relationship Discovery from Microarray Data. Journal of Statistical Computation and Simulation, iFirst, 2012, 1-13.

Li C-S, Lin T-C, and Yang X (2012). Bayesian Analysis of Semiparametric Zero-Inflated Poisson Regression Models. Journal of Taiwan Intelligent Technologies and Applied Statistics, 10(1):1-16.

Xu H, Shen Q, Yang X, and Shoptaw S. (2011). A quasi F test for functional linear models with functional covariates and its application to longitudinal data. Statistics in Medicine, 30:2842-2853.

Hui Li, Chunmei Liu, Xumin Liu, Diakite, M. (2010); 979-984 Burge, L.;Peptide Sequence Tag-Based Blind Identification-based SVM ModelMachine Learning and Applications (ICMLA), 2010 Ninth International Conference in Washington, DC.

Yang, X., Li, J., and Shoptaw, S. (2008). Imputation-based Strategies for Clinical Trial Longitudinal Data with Nonignorable Missing Values. Statistics in Medicine Jul 10;27(15):2826-49.

Yang, X. and Nie, K. (2007). Hypothesis Testing in Functional Linear Regression Models with Neyman's Truncation and Wavelet Thresholding for Longitudinal Data. Statistics in Medicine Volume 27, Issue 6, Pages 845 - 863.

Yang, X., Nie, K., Belin, T., Liu, J., and Shoptaw, S. (2007). Markov Transition Models for Binary Repeated Measures with Ignorable and Nonignorable Missing Values. Statistical Methods in Medical Research 16(4): 347-364.

Li, J., Yang, X., and Wu, Y. (2007). A Random-Effects Markov Transition Model for Poisson-distributed Repeated Measures with Nonignorable Missing Values. Statistics in Medicine 30:26(12), 2519-2532.

Yang, X., Shen, Q., Xu, H., and Shoptaw, S. (2006). Functional Regression Analysis using an F Test for Longitudinal Data with Large Numbers of Repeated Measures. Statistics in Medicine 26:7, 1552-1566.

Yang, X., Belin,T.R. and Boscardin, J. (2005). Simultaneous vs. sequential handling of imputation and variable selection for linear regression models, Biometrics, 61, 498-506.

Yang, X. and Shoptaw, S. (2005). Assessing Missing Data Assumptions in Longitudinal Studies: An Example Using a Smoking Cessation Trial. Drug and Alcohol Dependence, 77(3): 213-25.

Applications in Public Health, Pre-Clinical and Clinical Studies:

Zhang Q, Zhang C, Song X, Lin H, Zhang D, Meng W, Zhang Y, Zhu Z, Tang F, Liu L, Yang X, and Xue F. (2012). A longitudinal cohort based association study between uric acid level and metabolic syndrome in han chinese urban male population. BMC Public Health 12:419.

Nuovo J, Yang X, and Zeng H (2012). A Paradigm Shift in the Management of the Epidemic of Type 2 Diabetes. Accepted by Academic Journal of the Second Military Medical University, 33(3): 324-327.

Nordahl CW, Scholz R, Yang X, Buonocore M, Simon T, Rogers S, Amaral DA (2012). Increased rate of amygdala growth in children aged 2 to 4 years with autism spectrum disorders: a longitudinal study. Archives of General Psychiatry (impact score 12.26), 69(1):53-61.

Summers L, Clingerman KJ, and Yang X (2012). Validation of a body condition scoring system for Rhesus macaques. Accepted by Journal of the American Association for Laboratory Animal Science. 51(1):88-93.

Garcia L, Gold E, Wang L, Yang X, Mao M, Schwartz A. (2012). The Relation of Acculturation to Obesity, Overweight, Pre-Diabetes and Diabetes Among US Mexican-American Women and Me. Ethnicity & Disease, 22(1):58-64.

Hui Li, Chunmei Liu and William Southerland (2012) Blind Identification of Post-translational Modifications via Dynamic Time Warping Model Computational Intelligence in Bioinformatics and Computational Biology page 192-198 San Diego, May 9-12, 2012

Hui Li, Chunmei Liu Xumin Liu. (2012) Collaboration Visualization on Large Dataset for Protein-Protein Interaction Network Computational Intelligence in Bioinformatics and Computational Biology page 177-184 San Diego, May 9-12, 2012

Hui Li and Chunmei Liu (2012) Spatial Index and Visualization of Protein Structure. 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops. Workshop 8. The 3rd Integrative Data Analysis in Systems Biology (IDASB 2012), 540-544.

Hui Li, Jean-Claude Tounkara, and Chunmei Liu (2012). Prediction of protein-protein docking sites based on a cloud-computing pipeline. International Journal of Machine Learning and Computing, IJMLC 2012 Vol.2(6): 798-801

Hui Li, Chunmei Liu and Xumin Liu (2012). Collaboration visualization on large dataset for protein-protein interaction network. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) 2012 IEEE Symposium: 177-183

Hui Li, Chunmei Liu, and Legand Burge (2012). Predicting Protein-Protein Interactions Based on PPI Networks, IJMLC. 2012. V2. 239 794-797.

Tseng WH, Yang X, Wang H, Martinez SR, Chen SL, Mayers FJ, Bold RJ, Canter RJ. (2011). Nomogram to predict risk of 30-day mortality for patients with disseminated malignancy undergoing surgical intervention. Annals of Surgery, 2011 Aug; 254(2):333-8.

Zeng H, Yang X, Tang W, Wang H, Tang X, Zeng S, Jeschke S, Wang Y. (2011). Local Residents’ Awareness and Health Personnel’s Capacity on Schistosomiasis Control in the Three Gorges Dam Reservoir Area: a Cross-Sectional Study. Acta Tropica , 120(3):238-44.

Jarco M, Mendoza S, Mason W, Yang X, Bales K. (2011) Intransal Vasopressin Affects Pair-Bonding and Peripheral Gene Expression in Male Callicebus Cupreus. Genes, Brian and Behavior 10(3):375-383.

Luciw PA, Oslund KL, Yang X, Adamson L, Ravindran R, Canfield DR, Tarara R, Hirst L, Christensen M, Lerche NW, Offenstein H, Lewinsohn D, Ventimiglia F, Brignolo L, Wisner ER, HydeDM (2011). Stereologic Analysis of Bacterial Load and Lung Lesions in Nonhuman Primates (Rhesus Macaques) Experimentally Infected with Mycobacterium tuberculosis. American Journal of Physiology: Lung Cellular and Molecular Physiology. 301(5):L 731-738.

Stamova B, Green PG, Tian Y, Hertz-Picciotto I, Pessah IN, Hansen R, Yang X, Teng J, Gregg JP, Ashwood P, Van de Water J, and Sharp FR. (2011). Correlations between Gene Expression and Mercury Levels in Blood of Boys with and without Autism. Neurotoxicity Research, 19(1):31-48.

White, J.A., Yang, X., Todd, P.A., and Lerche, W. (2011). Longitudinal Patterns of Viremia and Oral Shedding of Rhesus Rhadinovirous and Retroperitoneal Fibromatosis Herpesviruses in Age Structured Captive Breeding Populations of Rhesus Macaques (Macaca mullatta). Comparative Medicine, 61(1):60-70.

Romano PS, Marcin JP, Dai J, Yang X, Kravitz R, Rocke D, Dharmar M, Li Z. (2011). Impact of Public Reporting of Coronary Artery Bypass Graft (CABG) Surgery Performance Data on Market Share Mortality, and Patient Selection. Medical Care, 49(12):1118-25.

Tian Y, Green PG, Stamova B, Hertz-Picciotto I, Pessah IN, Hansen R, Yang X, Gregg JP, Ashwood P, Jickling G, Van de Water J, and Sharp FR. (2011). Correlations of Gene Expression with Blood Lead Levels in Children with Autism Compared to Typically Developing Controls. Accepted by Neurotoxicity Research. 19(1):1-13.

Chew HK, Somlo G, Mack PC, Giltlitz B, Gandour-Edwards R, Christensen S, Linden H, Yang X, Davies AM (2011). Phase I study of continuous and intermittent schedules of lapatinib in combination with vinorelbine in solid tumors. Annals of Oncology, Published Online on July 21.

Hui Li, Chunmei Liu, Mugizi Robert Rwebangira, Legand Burge, William M. Southerland (2011):Rapid identification of multi-PTMs peptide sequence tags with a graph search approach. BIBM Workshops 2011: 247-250

Hui Li, L. Scott, C. Liu, M. Rwebangira, L. Burge, and W. (2011) Curriculum Vitae “Peptide Sequence Tag Based Blind Identification of Post-Translational Modification with Graph Search Approach”, The 7th International Symposium on Bioinformatics Research and Applications 16. (ISBRA 2011), May 2011.

C. Liu, Hui Li (2010), A Heuristic Algorithm for Finding the Longest Pathways in a Biochemical Network Model. Machine Learning and Applications (ICMLA) 2010:515-521

Parker JP, Hoegh H, Li Z, Danielsen B, Yang X, Yeo KK, Romano P, Rocke D, Marcin JP, Mahendra G, Amsterdam E, White E, Kravitz R, Steimle A. (2009). The California Report on Coronary Artery Bypass Graft Surgery: 2005-2006 Hospital and Surgeon Data.

Chin AI, Raffo WR, Yang X, Madison JR. (2009). Evolution of hemodialysis access resistance: a longitudinal 5-year model using functional principal components analysis. International Journal of Artificial Organs, 32(12):864-71.

Siddiqui AR, Lee K, Bennett D, Yang X, Brown KH, Bhutta ZA, Gold EB. (2009) Kitchen Carbon Monoxide and PM2.5 Concentrations by Cooking Fuel in a Village of Semi-Rural Pakistan. Indoor Air 19(1):75-82.

White J, Todd P, Yee J, Kalman-Bowlus A, Yang X, Wong S, Barry P, Lerche N. (2009). Prevalence of viremia and oral shedding of two gamma-2-herpesviruses, rhesus rhadinovirus (RRV) and retroperitoneal fibromatosis herpesvirus (RFHV), in large age-structured breeding groups of rhesus macaques (Macaca mulatta). Comparative Medicine, 59(4):383-90.

Shoptaw S, Reback CJ, Larkins S, Wang PC, Rotheram-Fuller E, Dang J, Yang X (2008). Outcomes using two tailored behavioral treatments for substance abuse in urban gay and bisexual men. J Substance Abuse Treat. 2008 Oct:35(3): 285-93

Siddiqui AR, Gold EB, Yang X, Lee K, Brown KH, and Bhutta ZA. (2008). Prenatal Exposure to Wood Fuel Smoke and Low Birth Weight. Environmental Health Perspectives Volume 116:4, 543-549.

Shoptaw S, Huber A, Peck J, Yang X, Liu J, Jeff Dang, Roll J, Shapiro B, Rotheram-Fuller E, Ling W. (2006). Randomized, placebo-controlled trial of sertraline and contingency management for the treatment of methamphetamine dependence. Drug and Alcohol Dependence. 85(1):12-8.

Heinzerling KG, Shoptaw S, Peck JA, Yang X, Liu J, Roll J, Ling W. (2006). Randomized, placebo-controlled trial of baclofen and gabapentin for the treatment of methamphetamine dependence. Drug Alcohol Depend, 85(3):177-84.

Peck, J.A., Reback, C.J., Yang, X., Rotheram-Fuller, E., Shoptaw, S. (2005). Sustained Reductions in Drug Use and Depression Symptoms from Treatment for Drug Abuse in Methamphetamine-Dependent Gay and Bisexual Men. Journal of Urban Health 82:100-108.

Shoptaw, S., Reback, C.J., Peck, J.A., Yang, X., et al. (2005). Behavioral treatment approaches for methamphetamine dependence and HIV-related sexual risk behaviors among urban gay and bisexual men. Drug and Alcohol Dependence, 78, 125-134.

Shoptaw, S., Majewska, M.D., Wilkins, J., Twitchell, G., Yang, X., & Ling, W. (2004). Participants receiving dehydroepiandrosterone during treatment for cocaine dependence show high rates of cocaine use in a placebo-controlled pilot study. Experimental and Clinical Psychopharmacology,12(2), 126-135.

Shoptaw,S., Yang, X., Rotheram-Fuller, E.J., Hsieh, Y-C.M., Kintaudi, P.C., Charuvastra, V.C., & Ling, W. (2003). Randomized Placebo-Controlled Trial of Baclofen for Cocaine Dependence: Preliminary Effects for Individuals with Chronic Patterns of Cocaine Use. Journal of Clinical Psychiatry, 64, 1440-1448.

Shoptow, S., Rotheram-Fuller, E., Yang, X., Frosch, D., Nahom, D., Jarvik, M.E., Rawson, R. A., Ling, W. (2002). Smoking Cessation in Methadone Maintenance. Addictions, 97 (10), 1317-1328.