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Rosenberger, K, Duan, R, Chen, Y, and Lin, L, Predictive P-score for treatment ranking in Bayesian network meta-analysis, BMC Medical Research Methodology (October, 2021) 21:213.

Zhou, T, Zhou, J, Hodges, J, Lin, L, Chen, Y, Cole, S, and Chu, H, Estimating the Complier Average Causal Effect in a Meta-analysis of Randomized Clinical Trials with Binary Outcomes Accounting for Noncompliance: A Generalized Linear Latent and Mixed Model Approach, American Journal of Epidemiology (September, 2021) 191(1):220-229

Xiao, M, Chen, Y, Cole, S, MacLehose RF, Richardson, DB, Chu, H. Is OR “portable” in meta-analysis? Time to consider bivariate generalized linear mixed model, Journal of Clinical Epidemiology (August, 2021) S0895-4356(21)00243-2.

Xiao, M, Chu, H, Cole, S, Chen, Y, MacLehose, R, Richardson, DB and Greenland, S. Odds ratios are far from “portable”—A call to use realistic models for effect variation in meta-analysis, Journal of Clinical Epidemiology (August, 2021) S0895-4356(21)00242-0.

Lian, X, Zhang, J, Hodges, J, Chen, Y and Chu, H. Accounting for Post-randomization Variables in Meta-analysis: A Joint Meta-Regression Approach, Biometrics (August, 2021)

Rott, K, Shi, A, Lin, L, Hodges, J, Siegel, L, Chen, Y and Chu, H. Bayesian meta-analysis using SAS PROC BGLIMM, (June, 2021) Research Synthesis Methods 12(6):692-700

ML Delle Monache, K Chi, Chen, Y, P Goatin, K Han, JM Qiu, B Piccoli. A Three-Phase Fundamental Diagram from Three-Dimensional Traffic Data, (March, 2021) Axioms 10 (1)
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Mishra, A, Dey, D, Chen, Y, and Chen, K: Generalized Co-sparse Factor Regression. Computational Statistics and Data Analysis 157, May 2021 Notes: doi: 10.1016/j.csda.2020.107127. Epub ahead of print.

Marks-Anglin, A, Luo, C, Piao, J, Gibbons, M, Schmid, C, Ning, J and Chen, Y: EMBRACE: an EM-based Bias Reduction Approach through Copas-Model Estimation for Quantifying the evidence of selective publishing in network meta-analysis. Biometrics 2021 Feb 9.

Duan, R, Ning, Y and Chen, Y: Heterogeneity-aware communication efficient distributed statistical inference Biometrika 23 Mar 2021,

Lian, X, Zhang, J, Hodges, J, Chen, Y and Chu, H. Accounting for Post-randomization Variables in Meta-analysis: A Joint Meta-Regression Approach, Biometrics 2021 Sep 29

Huang, J, Cai, Y, Du, J., Li, R., Ellenberg, S.S., Hennessy, S., Tao, C., and Chen, Y . (Sep., 2020) Monitoring vaccine safety by studying temporal variation of adverse events using vaccine adverse event reporting system. The Annals of Applied Statistics 15(1): 252-269.

Marks-Anglin, A and Chen, Y (August, 2020) A Historical Review of Publication Bias. Research Synthesis Methods Volume 11, Issue 6, November 2020, Pages 725, 742

Marks-Anglin, A and Chen, Y (July, 2020), Small-study effects: current practice and challenges for future research, Statistics and Its Interface,Volume 13 (2020), Number 4, Pages 475 – 484

Huang, J, Ning, Y, Reid, N and Chen, Y (Jan., 2020), On specification tests for composite likelihood inference, Biometrika, Volume 107, Issue 4, December 2020, Pages 907–917.

Hong, C, Salanti, G, Morton, S, Riley, R, Chu, H, Kimmel, S, and Chen, Y (September 2019) Testing small study effects in multivariate meta-analysis, Biometrics. 2020 Dec; 76(4): 1240–1250..

Bai, R, Moran, G, Antonelli, J, Chen, Y and Boland, M. (May, 2020) Spike-and-Slab Group Lassos for Grouped Regression and Sparse Generalized Additive Models. Journal of the American Statistical Association.

Chen, Y, Liang, K-Y, Tong, P, Beaty, T, Barnes, K. and Kao, L. (May, 2020) A pseudolikelihood approach for assessing genetic association in case-control studies with unmeasured population structure, Statistical Methods in Medical Research, 2020 Nov;29(11):3153-3165.

Ning, J, Cai, C, Chen, Y, Huang, X and Wang, MC. (Jan., 2020) Semiparametric Modelling and Estimation of Covariate Adjusted Dependence between Bivariate Recurrent Events, Biometrics. Volume 76, Issue 4, December 2020, Pages 1229-1239

Duan, R, Ning, Y, Wang, S, Lindsay, B, Carroll, R, and Chen, Y (Dec., 2019) A fast score test for generalized mixture models, Biometrics 21 December 2019 (This paper won 2018 ENAR Distinguished Student Paper Award)

Hong, C, Duan, R, Zeng, L, Hubbard, R, Lumley, T, Riley, R, Chu, H, Kimmel, S and Chen, Y (2019+) Galaxy plot: a new visualization tool of bivariate metaanalysis studies, American Journal of Epidemiology, Volume 189, Issue 8, August 2020, Pages 861–869.

Wang, L, Chai, X, Chen, Y, and Chen, J (August 2019) Novel Two-Phase Sampling Designs for Studying Binary Outcomes, Biometrics 2020 Mar;76(1):210-223.

Liu, YL, Huang, J, Urbanowicz, R, Chen, K, Manduchi, E, Greene, C, Scheet, P, Moore, JH., and Chen, Y. (August 2019) Embracing study heterogeneity for finding genetic interactions in large‐scale research consortia. Genetic Epidemiology, Volume 44, Issue 1, January 2020, Pages 52-66

Duan, R, Cao, M, Ning, Y, Zhu, M, Zhang, B, McDermott, A, Chu, H, Zhou, X, Moore, J, Ibrahim, J, Scharfstein, D, Chen, Y (July, 2019), Global identifiability of latent class models with applications to diagnostic test accuracy studies: a Grobner basis approach, Biometrics, Volume 76, Issue 1, March 2020, Pages 98-108

Cai, Y, Huang, J, Ning, J, Lee, ML, Rosner, B and Chen, Y (September 2019), Two-sample test for correlated data under outcome-dependent sampling with an application to self-reported weight loss data, Statistics in Medicine, Volume 38, Issue 25, 10 November 2019, Pages 4999-5009

Shen, W, Liu, S, Chen, Y and Ning, J. (December 2018) Regression analysis of longitudinal data with outcome-dependent sampling and informative censoring . Scandinavian Journal of Statistics, Volume 46, Issue 3, September 2019, Pages 831-847

Hubbard, R, Huang, J, Harton, J, Oganisian, A, Choi, G, Utidjian, L, Eneli, I, Bailey, L, Chen, Y (September 2018) A Bayesian latent class approach for EHR-based phenotyping, Statistics in Medicine, Volume 38, Issue 1, 15 January 2019, Pages 74-87

Hong, C, Riley, R and Chen, Y (March, 2018) An improved method for bivariate meta-analysis when within study correlations are unknown, Research Synthesis Methods, 9(1):73–88.

Zhang, J, Ko, CW, Nie, L, Chen, Y and Tiwari, R. (Feb, 2018) Bayesian hierarchical methods for meta-analysis combining randomized controlled and single-arm studies, Statistical Methods in Medical Research, 28 issue: 5, page(s): 12931310.5

Chen, Y, Huang, J, Ning, Y, Liang, K-Y and Lindsay, B. (March, 2018) A conditional test for composite likelihood with boundary constraints. Biometrika 105 (1), 225-232.

Huang, J, Ning, Y, Liang, K-Y and Chen, Y (2018), Composite likelihood inference under boundary conditions, Statistica Sinica, Vol. 30, No. 2 (2020), pp. 1005-1025.

Ma, X, Lian, X, Chu, H, Ibrahim, J, and Chen, Y (Jan., 2018) A Bayesian hierarchical model for network meta-analysis of diagnostic tests, Biostatistics, 2018 Jan 1;19(1):87-102

Hong, C, Ning, Y, Wei, P, Cao, Y and Chen, Y. (2017) A semiparametric model for vQTL mapping, Biometrics 73(2): 571-581.

Hong, C, Ning, Y, Wang, S, Wu, H, Carroll, RJ and Chen, Y. (2017) PLEMT: A novel pseudolikelihood based EM test for homogeneity in generalized exponential tilt mixture models, Journal of the American Statistical Association 112 (50).(This paper won 2015 JSM Biometrics section Byar Awards)

Chen, Y, Ning, J, Ning, Y, Liang, K-Y and Bandeen-Roche, K. (2017) On pseudolikelihood inference for semiparametric models with boundary problems . Biometrika, 104 (1): 165–179.

Huang, J, Liu, YL, Vitale, S, Penning, T, Whitehead, A, Vachani, A, Clapper, M, Muscat, J, Lazarus, P, Scheet, P, Moore, JH and Chen, Y (Dec., 2017), On meta- and mega-analyses for gene environment interactions, Genetic Epidemiology 41(8): 876–886.

Piao, J, Liu, YL, Chen, Y and Ning, J. (July, 2017) Copas-like selection model to correct publication bias in systematic review of diagnostic test studies, Statistical Methods in Medical Research. 18(3):495–504.

Wang, L, Chen, Y and Zhu, H (2017) Implementing Optimal Allocation in Clinical Trials with Multiple Endpoints, Journal of Statistical Planning and Inference 182, 88-99.

Ning, J, Chen, Y, and Piao, J (July, 2017) Maximum likelihood estimation and EM algorithm of Copas selection model for publication bias correction. Biostatistics, 18(3): 495–504.

Liu, Y, DeSantis, S and Chen, Y (2017) Bayesian mixed treatment comparisons meta-analysis for correlated outcomes subject to reporting bias, Journal of the Royal Statistical Society: Series C, 67(1): 127–144.

Li, X, Chen, Y, and Li, R (Feb., 2017) A frailty model for recurrent events during alternating restraint and non-restraint time periods, Statistics in Medicine, 20 February 2017.

Chen, Y, Liu, Y, Chu, H, Lee, M and Schmid, C (2017) A simple and robust method for multivariate meta-analysis of diagnostic test accuracy, Statistics in Medicine, 36(1):105-121.

Sun, H, Wang, Y, Chen, Y, Li, Y and Wang, S. (June, 2017)pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data. Bioinformatics, 33(12):1765-1772.

Liu, Y, Chen, Y and Scheet, P (2016), A meta-analytic framework for detection of genetic interactions, Genetic Epidemiology, 40 (7), 534-543.

Chen, Y, Hong, C, Ning, Y and Su, X. (Jan., 2016) Meta-analysis of studies with bivariate binary outcomes: a marginal beta-binomial model approach, Statistics in Medicine, 35(1):21–40.

Chen, Y Cai, Y, Hong, C, and Jackson, D. (2016) Inference for correlated effect sizes using multiple univariate meta-analyses, Statistics in Medicine, 35(9): 1405-1422.

Ning, J, Chen, Y, Cai, C, Huang, X and Wang, MC. (2015) On the Dependence Structure of Bivariate Recurrent Event Processes: Inference and Estimation, Biometrika 102(2): 345-358.

Liu, Y, Chen, Y and Chu H. (2015) A unification of models for meta-analysis of diagnostic accuracy studies without a gold standard, Biometrics, 71(2):538–47.

Chen, Y, Ning, J and Cai, C. (2015) Regression analysis of longitudinal data with irregular and informative observation times, Biostatistics, 16(4): 727-739.

Ning, Y and Chen, Y. (2015) A class of pseudolikelihood ratio tests for homogeneity in exponential tilt mixture models, Scandinavian Journal of Statistics 42 (2), 504-517.

Chen, Y, Hong, C and Riley, R. (2015) An alternative pseudolikelihood method for multivariate random effects meta-analysis, Statistics in Medicine 34 (3): 361-380.

Chen, Y, Liu, Y, Ning, J, Cormier J and Chu H. (2015) A hybrid model for combining case?control and cohort studies in systematic reviews of diagnostic tests, Journal of the Royal Statistical Society: Series C, 64(3): 469-489.

Chen, Y, Liu, Y, Ning, J, Nie, L, Zhu, H and Chu H. (Dec., 2014) A composite likelihood method for bivariate analysis of sensitivity and specificity in diagnostic reviews, Statistical Methods in Medical Research. 26(2).

Chen, Y, Chu, H, Luo, S, Nie L and Chen S. (2014) Bayesian analysis on meta-analysis of case control studies accounting for within study correlation, Statistical Methods in Medical Research.. 26(2).7

Chen, Y, Luo, S, Chu, H, Su, X and Nie, L. (2014) An Empirical Bayes Method for Multivariate Meta-analysis with Application in Clinical Trials, Communications in Statistics-Theory and Methods, 43(16), 3536-3551.

Ma, X, Chen, Y, Cole, S and Chu, H. (May, 2014) A hybrid Bayesian hierarchical model combining cohort and case control studies for meta-analysis of diagnostic tests: accounting for partial verification bias, Statistical Methods in Medical Research. 25(6).

Luo, S, Chen, Y, Su, X and Chu, H. (2014) mmeta: An R package for multivariate meta-analysis. Journal of Statistical Software, 56 (11).

Chen, Y, Luo, S, Chu, H and Wei, P. (2013) Bayesian inference on risk differences: an application to multivariate meta-analysis of adverse events in clinical trials, Statistics in Biopharmaceutical Research, 5 (2): 142-155.

Nie, L, Soon, G, Qi, K, Chen, Y and Chu, HT. (2013) A note on partial covariate adjustment and design considerations in noninferiority trials when patient level data are not available, Journal of Biopharmaceutical Statistics, 23 (5), 1042-1053.

Chen, Y, Ning, Y, Hong, C and Wang, S. (2013) Semiparametric tests for identifying differentially methylated loci with case-control designs using Illumina arrays, Genetic Epidemiology, 38 (1), 42{50.

Tong P, Chen, Y, Su X and Coombes K (2013) SIBER: Systematic Identification of Bimodally Expressed Genes Using RNAseq Data. Bioinformatics, 29 (5), 605-613.

Chu, H, Nie, L, Chen, Y, Huang, Y and Sun, W. (2012) Bivariate random effects models for meta-analysis of comparative studies with binary outcomes: methods for the absolute risk difference and relative risk, Statistical Methods in Medical Research, 21 (6): 621-633.

Nie, L, Chen, Y and Chu, H. (2011) Asymptotic Variances of Maximum Likelihood Estimator for the Correlation Coecient from a BVN Distribution with One Variable Subject to Censoring , Journal of Statistical Planning and Inference, 141 (1), 392-401.

Chen, Y and Liang, KY. (2010) On the asymptotic behaviour of the pseudolike ratio test statistic with boundary problemslihood, Biometrika, 97 (3), 603-620.

Chen, A, Luo, C, Chen, Y, Shinohara, R, Shou, H. Privacy-preserving harmonization via distributed ComBat. NeuroImage, Volume 248, March 2022, 118822

Che, S, Peng, H, Sun, L, Chen, Y and He, L. Federated Multi-View Learning for Private Medical Data Integration and Analysis. ACM Transactions on intelligent systems and technology (TIST), Vol. 1, No. 1, Article 39.

Liu, XK, Chubak, J, Hubbard, R and Chen, Y. SAT: a Surrogate Assisted Two-wave case boosting sampling method, with application to EHR-based association studies. Journal of the American Medical Informatics Association, Journal of the American,  Medical Informatics Association, 28 December 2021

Schuemie, M.J., Chen, Y, Madigan, D, Suchard, M.A., Combining Cox Regressions Across a Heterogeneous Distributed Research Network Facing Small and Zero Counts. Statistical Methods in Medical Research. November 2021.

Yin, Z, Tong, J, Chen, Y, Hubbard, R, and Tang, CY. A Cost-effective Chart Review Sampling Design to Account for Phenotyping Error in EHR data. Journal of the American Medical Informatics Association, 2021 Dec 28;29(1):52-61.

Holmes, J, Beinlich, J, Boland, MR, Bowles, RH, Chen, Y, Cook, TS, Demiris, G, Draugelis, M, Fluharty, L, Gabriel, P.E., Grundmeier, R, Hanson, W, Herman, D.S., Himes, B.E., Hubbard, R.A., Kahn C.E., Kim, D., Koppel, R, Long, Q, Mirkovic, N, Morris, J.S., Mowery, D, Ritchie, M, Urbanowicz, R, and Moore, J.H., Why Is the Electronic Health Record So Challenging for Research and Clinical Care? Methods of Information in Medicine, 2021; 60(01/02); 032-048.

Edmondson, M, Luo, C, Duan, R, Maltenfort, M, Chen, Z, Locke, K, Shults, J, Bian, J, Ryan, P, Forrest, C and Chen, Y. An Efficient and Accurate Distributed Learning Algorithm for Modeling Multi-Site Zero-Inflated Count Outcomes. Scientific Reports. 2021 Oct 4;11(1):19647

Li, Q, Zhang, H, Chen, Z, Guo, Y, George, TJ, Chen, Y, Wang, F, Bian, J. Validate Real-World Data-based Endpoint Measures of Cancer Treatment Outcomes. AMIA Annu Symp Proc 2021.

Hubbard, R, Xu, J, Siegel, R, Chen, Y, Eneli, I: Studying pediatric health outcomes with electronic health records using Bayesian clustering and trajectory analysis. Journal of Biomedical Informatics Dec 2020 Notes: doi: 10.1016/j.jbi.2020.103654. Online ahead of print.

Du, J, Xiang, Y, Sankaranarayanapillai, M, Zhang, M, Wang, J, Si, Y, Pham, H, Xu, H, Chen, Y, Tao, C: Extracting post-marketing adverse events from safety reports in the Vaccine Adverse Event Reporting System (VAERS) using deep learning. Journal of the American Medical Informatics Association 2021, 2021 Jul 14;28(7):1393-1400.

Luo, C, Jiang, Y, Du, J, Tong, J, Huang, J, Lo Re, V, Ellenberg, S, Poland, G, Tao, C and Chen, Y: Prediction of post-vaccination Guillain-Barre syndrome using data from a passive surveillance system. Pharmacoepidemiology and Drug Safety 2021, Volume 30, Issue 5, May 2021, Pages 602-609

Li, R, Duan, R, Zhang, X, Lumley, T, Pendergrass, S, Bauer, C, Hakonarson, H, Carrell, D, Smoller, J, Wei, W, Carroll, R, Edwards, D, Wiesner, G, Sleiman, P, Denny, J, Mosley, J, Ritchie, M, Chen, Y and Moore, J Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics Nature Communications 12(1): 168, Jan 2021 Notes: doi: 10.1038/s41467-020-20211-2

Zuo X, Chen Y, Ohno-Machado L, Xu H: How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles. Briefings in Bioinformatics 2020 Notes: https://doi.org/10.1093/bib/bbaa331.

Gonzalez-Hernandez, G, Lu, Z, Leaman, R, Weissenbacher, D, Boland, M., Chen, Y, Du, J, Fluck, J, Greene, C, Holmes, J, Kashyap, A, Nielsen, R, Ouyang, Z, Schaaf, S, Taroni, J, Tao, C, Zhang, Y, Liu, H. (Oct, 2019) PSB 2019 Workshop on Text Mining and Visualization for Precision Medicine, Pacific Symposium on Biocomputing 2019, pp. 449-454 (2018)

Du, J, Luo, C, Shegog, R, Bian, J, Cunningham, R, Boom, J, Poland, G, Chen, Y, Tao, C. (August, 2020) Use of deep learning to analyze Twitter discussions about HPV vaccine beliefs and attitudes, JAMA Network Open 2020;3(11):e2022025

Tong, J, Chen, Z, Duan, R, Lo-Ciganic, W, Lyu, T, Tao, C, Merkel, P, Kranzler, H, Bian, J, Chen, Y. (July 2020) Identifying Clinical Risk Factors of Opioid Use Disorder using a Distributed Algorithm to Combine Real-World Data from a Large Clinical Data Research Network. AMIA Annu Symp Proc. 2021 Jan 25;2020:1220-1229. eCollection 2020.

Duan, R., Chen Z., Tong, J., Luo, C., Lyu, T., Tao, C., Maraganore, D., Bian, J. and Chen, Y. (July 2020) Leverage real-world longitudinal data in large clinical research networks for Alzheimers disease and related dementia. AMIA Annu Symp Proc. 2021 Jan 25;2020:393-401. eCollection 2020.

Duan, R., Zhang, X.,Du, J., Huang, J., Tao, C and Chen, Y .(July, 2020). On the evidence consistency of pharmacovigilance outcomes between Food and Drug Administration Adverse Event Reporting System and electronic medical record data for acute mania patients. Health Informatics Journal 2020 Jun; 26(2):753-764.

Raisaro, JL, Marino, F, Troncoso-Pastoriza, J, Bernstam, E.V., Chen, Y, Gottlieb, A, Kim, M, Klann, J, Klersy, C, Malin, B, Mean, M, Prasser, F, Scudeller, L, Wong, S, Frenkel-Morgenstern, M, Xu, H, Jiang, X, Hubaux, JP. (July 2020) SCOR: A secure international informatics infrastructure to investigate COVID-19. Journal of the American Medical Informatics Association, Volume 27, Issue 11, November 2020, Pages 1721–1726.

Li, R, Tong, J, Duan, R, Chen, Y and Moore, J (June, 2020), Evaluation of phenotyping errors on polygenic risk score predictions, International Conference on Bioinformatics Models, Methods and Algorithms, ISBN 978-989-758-398-8; ISSN 2184-4305, pages 123-130.

Duan, R, Luo, C, Schuemie, M.J., Tong, J, Liang, J., Chang, H., Boland, M.R., Bian, J., Xu, H., Holmes, J., Forrest, C., Morton, S., Berlin, J.A., Moore, J.H., Mahoney, K.B. and Chen, Y. (June, 2020) Learning from local to global — an efficient distributed algorithm for modeling time to event data, Journal of the American Medical Informatics Association Volume 27, Issue 7, July 2020, Pages 1028–1036.

Moore, J, Barnett, I, Boland, M, Chen, Y, Demiris, G, Gonzalez-Hernandez, G, Herman, D, Himes, B, Hubbard, R, Kim, D, Morris, J, Mowery, D, Ritchie, M, Shen, L, Urbanowicz, R, and Holmes, J. (May, 2020) Ideas for how informaticians can get involved with COVID-19 research. BioData Mining 13, Article number: 3 (2020)

Li, R, Chen, Y, Ritchie, M and Moore, J. (March, 2020) Electronic health records and polygenic risk scores for predicting disease risk. Nature Reviews Genetics 21, pages493–502 (2020)

Hubbard, R, Tong, J, Duan, R and Chen, Y. (Dec, 2019) Reducing Bias Due to Outcome Misclassification for Epidemiologic Studies Using EHR-derived Probabilistic Phenotypes. Epidemiology, 31(4), pp.542-550.

Tong, J, Duan, R, Li, R, Scheuemie, M, Moore, J and Chen, Y. (Oct, 2019) Robust-ODAL: Learning from heterogeneous health systems without sharing patient-level data. In Pacific Symposium on Biocomputing (Vol. 25, pp. 695-706).

Duan, R, Boland, MB, Liu, ZX, Liu, Y, Chang, H, Xu, H, Chu, H, Schmid, C, Forrest, C, Holmes, J, Schuemie, M, Berlin, J.A. and Chen, Y. (Oct, 2019) Learning from Electronic Health Records Across Multiple Sites: A Communication-efficient and Privacy-preserving Distributed Algorithm. Journal of the American Medical Informatics Association, Volume 27, Issue 3, March 2020, Pages 376–385.

Tong, J, Huang, J, Wang, X, Moore, J, Hubbard, R and Chen, Y. (Sep. 2019) An augmented estimation procedure for EHR-based association studies accounting for differential misclassification. Journal of the American Medical Informatics Association,  Volume 27, Issue 2, February 2020, Pages 244–253.

Jia, Y, Zhu, C, Du, J, Xiang, Y, Chen, Y, Wang, W and Tao, C. (Aug. 2019) Investigating Safety Profiles of Human Papillomavirus Vaccine Across Group Differences using VAERS Data and MedDRA, PeerJ 7:e7490 https://doi.org/10.7717/peerj.7490.

Maltenfort, M, Chen, Y and Forrest, C. (Aug. 2019) Prediction of 30-day pediatric unplanned hospitalizations using the Johns Hopkins Adjusted Clinical Groups Risk Adjustment, Plos One 2019 Aug 15;14(8):e0221233.

Huang, J, Chen, Y, Landis, R and Mahoney, K. (July, 2019) Patient portal: how does it change our health behaviors and outcomes? – a retrospective, observational cohort study at Penn Medicine, Journal of Medical Internet Research [co-first author] 2019;21(10):e13146

Huang, J, Zhang, X, Tong, J, Du, J, Duan, R, Liu, Y, Moore, J, Tao, C and Chen, Y. (July, 2019) Comparing drug safety of Hepatitis C therapies using post-market data. BMC Medical Informatics and Decision Making 19(4), pp1-12.

Li, R, Duan, R, Kember, R, Regeneron Genetic Center, Rader, D, Damrauer, S, Moore, J and Chen, Y. (July, 2019) A regression framework to uncover pleiotropy in large-scale electronic health record data. Journal of the American Medical Informatics Association Volume 26, Issue 10, October 2019, Pages 1083–1090

Du, J, Cunningham, RM, Xiang, Y, Li, F, Jia, Y, Boom, JA, Myneni, S, Bian, J, Luo, C, Chen, Y and Tao, C. (April 2019) Leveraging deep learning to understand health beliefs about the Human Papillomavirus Vaccine from social media. Nature Partner Journal (NPJ) Digital Medicine. 2, Article number: 27 (2019).

Li, R, Chen, Y and Moore, J (April 2019). Integration of genetic and clinical information to improve imputation of data missing from electronic health records. Journal of the American Medical Informatics Association, Volume 26, Issue 10, October 2019, Pages 1056–1063.

Duan, R, Boland, M, Moore, J and Chen, Y (2019). ODAL: A one-shot distributed algorithm to perform logistic regressions on electronic health records data from multiple clinical sites. Pacific Symposium on Biocomputing 2019 ; 24: 30–41.

Amith, M, Zhu, A, Cunningham, R, Lin, R, Savas, L, Shay, L, Chen, Y, Gong, Y, Boom, J, Roberts, K and Tao, C. (Feb, 2019) Early Usability Assessment of a Conversational Agent for HPV Vaccination, Information Technology and Communications in Health (ITCH) 2019;257:17-23

Huang, J, Zhang, X, Du, J, Duan, R, Yang, L, Moore, JH, Chen, Y, Tao, C (Feb 2019), Comparing adverse effects of Hepatitis C drugs using FAERS data, IEEE BIBM 2018 Proceedings.

Chen, Y, Wang, J, Chubak, J, Hubbard, R (2018) Inflation of type I error rates due to differential misclassification in EHR-derived outcomes: Empirical illustration using breast cancer recurrence, Pharmacoepidemiology & Drug Safety 28(2):264-268

Moore, J, Olson, RS, Chen, Y, and Sipper, M. (2019) Automated discovery of test statistics using genetic programming, Genetic Programming and Evolvable Machines 20, Issue 1, pp 127–137.

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Lin, R, Amith, M, Liang, C, Duan, R, Chen, Y and Tao, C. (July, 2018) Visualized Emotion Ontology: A Model For Representing Visual Cues of Emotions, BMC Medical Informatics and Decision Making 18(Suppl 2): 64

Cao, M, Chen, Y, Fujimoto, K and Schweinberger, M. (2018) A two-stage working model strategy for network analysis under Hierarchical Exponential Random Graph Models, 2018 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) August 2018, Pages 290–298.

Tong J, Huang J, Du J, Cai Y, Tao C, Chen Y. Identification of Rare Adverse Events with Year-varying Reporting Rates for FLU4 Vaccine in VAERS. AMIA Annu Symp Proc. 2018 Dec 5;2018:1544-1551

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Huang, J., Du, J., Duan, R., Zhang, X., Tao, C., Chen, Y. (2018) Characterization of the differential adverse event rates by race/ethnicity groups for HPV vaccine by integrating data from different sources. Frontiers in pharmacology 9:539.

Moore, J, Olson, R, Schmitt, P, Chen, Y and Manduchi, E. (2018) How computational thought experiments can improve our understanding of the genetic architecture of common human diseases, Artificial Life, isal_a_00012, pp. 23-30; 8 pages

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Duan, R, Zhang, X, Du, J, Huang, J, Tao, C, and Chen, Y (2017). Post-marketing Drug Safety Evaluation using Data Mining Based on FAERS. International Conference on Data Mining and Big Data (pp. 379-389). Springer, Cham.

Huang, J, Zhang, X, Du, J, Duan, R, Yang, L, Moore, JH, Chen, Y, Tao, C (2017), Comparing difference of adverse effects among multiple drugs using FAERS data, Stud Health Technol Inform 2017;245:1268.

Du, J, Huang, J, Duan, R, Chen, Y, Tao, C (2017),Comparing the Human Papillomavirus Vaccination Opinions Trends from Different Twitter User Groups with a Machine Learning Based System and Semiparametric Nonlinear Regression, Stud Health Technol Inform 2017;245:1218..

Cai, Y, Du, J, Huang, J, Ellenberg, S, Hennessy, S, Tao, C, and Chen, Y. (July, 2017) A Signal Detection Method for Temporal Variation of Adverse Effect with Vaccine Adverse Event Reporting System Data. BMC Medical Informatics and Decision Making, 17(Suppl 2): 76.

Duan, R, Cao, M, Wu, Y, Huang, J, Denny, J, Xu, H and Chen, Y. (2016) An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies, AMIA annual symposium proceedings, 10:1764-1773 (This paper won the first prize of \Best of Student Papers in Knowledge Discovery and Data Mining (KDDM)”Awards)

Du, J, Cai, Y, Chen, Y and Tao, C. (2016) Trivalent influenza vaccine adverse symptoms analysis based on MedDRA terminology using VAERS data in 2011, Journal of Biomedical Semantics, 7-13.

Du, J, Cai, Y, Chen, Y, He, Y, and Tao, C. (2016) Analysis of Individual Differences in Vaccine Pharmacovigilance using VAERS Data and MedDRA System Organ Classes: A Use Case Study with Trivalent Influenza Vaccine, Biomedical Informatics Insight, 2016.

Tao, C, Du, J, Cai, Y and Chen, Y. (2015) Trivalent Influenza Vaccine Adverse Event Analysis Based On MedDRA System Organ Classes Using VAERS Data, Studies in health technology and informatics, 2015. 216:1076.

Du, J, Cai Y, Chen, Y, Tao C. Adverse Event Analysis for Trivalent In Vaccine Based On MedDRA Terminology Using VAERS Data, International Workshop on Vaccine and Drug Ontology Studies (VDOS)-in conjunction with the International Conference on Biomedical Ontology (ICBO) 2015, Lisbon, July 2015.

Cao M, Chen, Y, Zhu M, Zhang J. (2015) Automated Evaluation of Medical Software Usage: Algorithm and Statistical Analyses, Studies in health technology and informatics, 2015. 216:965.

Huang, J, Chen, Y, Swartz, M and Ionita-Laza, I (2014) Family-Based Association Test for Sequence Data with Applications in the GAW 18 Simulated data, BMC Proceedings 8 (Suppl 1): S27, 2014.

Asch, D, Islam, M, Scheils, N, Chen, Y, Doshi, J, Buresh, J. and Werner, R. (May 2021) Patient and Hospital Factors Associated With Differences in Mortality Rates Among Black and White US Medicare Beneficiaries Hospitalized With COVID-19 Infection. JAMA Network Open, 2021;4(6):e2112842.

Liang, J, Liu, J, Fan, R, Chen, Z, Chen, X, Tong, J, Chen, Y, Peng, F, Jiang, Y: Plasma Homocysteine Level Is Associated with the Expanded Disability Status Scale in Neuromyelitis Optica Spectrum Disorder Neuroimmunomodulation 26(5): 258-264, Oct 2019 Notes: doi: 10.1159/000503426. Epub 2019 Oct 25.

Asch, D, Scheils, N, Islam, M, Chen, Y, Werner, R, Buresh, J and Doshi, J: Variation in US hospital mortality rates for patients admitted with COVID-19 during the first 6 months of the pandemic. JAMA Internal Medicine Dec 2020 Notes: doi:10.1001/jamainternmed.2020.8193. Epub December 22, 2020.

Fan R, Zhang Y, Xu Y, Tong J, Chen Z, Gu M, Fan W, Chen Y, Peng F, Jiang Y: Serum antinuclear antibodies associate with worse prognosis in AQP4 positive neuromyelitis optica spectrum disorder. Brain and Behaviour 11(1): e01865, Jan 2021 Notes: doi: 10.1002/brb3.1865. Epub 2020 Dec 14.

Liu, J, Luo, C, Li, M, Wang, Y, Xu, X, Yang, L, Qin, B, Chen, Y, Jiang, Y, Peng, F. (November, 2020) Predictors of post-infectious inflammatory response syndrome in HIV-negative immunocompetent cryptococcal meningitis. Journal of Neurology, Neurosurgery & Psychiatry

Falcone, M†, Luo, C†, Chen, Y, Birtwell, D, Cheatle, M, Duan, R, Gabriel, P, He, L, Ko, E, Mirkovic, N, Mowery, D, Ochroch, A, Paulson, C, Schriver, E, Schnoll, R, Bekelman, J, Lerman, C. (August, 2020) Risk of persistent opioid use following major surgery in matched samples of patients with and without cancer. Cancer Epidemiology, Biomarkers & Prevention

Pham Nguyen T, Chen, Y, Thibault, D, Leonard, C, Hennessy, S and Willis, A. Impact of hospitalization and medication switching on future adherence to oral anticoagulants in high-risk atrial fibrillation patients, (July, 2020) Pharmacotherapy

Paydary, K, Banwell, E, Tong, J, Chen, Y and Cuker, A. Diagnostic Accuracy of the PLASMIC score in Patients with Suspected Thrombotic Thrombocytopenic Purpura: A Systematic Review and Meta-Analysis, (June, 2020) Transfusion.

Chen, Z., Huang, J., Fan, R., Weng, R., Shinohara, R., Landis, R., Chen, Y and Jiang, Y. (Nov., 2019) Urinalysis in patients with neuromyelitis optica spectrum disorder, European Journal of Neurology, 2020 Apr;27(4):619-625

Chiasakul, T, Jesus, E, Tong, J, Chen, Y, Crowther, M, Garcia, D, Chai-Adisaksopha, C, Messe, S and Cuker A. (Sep., 2019) Inherited Thrombophilia and the Risk of Arterial Ischemic Stroke: A Systematic Review and Meta-Analysis, Journal of the American Heart Association  2019;8:e012877

Singh, J, Kallan, M, Chen, Y, Parks, M, Ibrahim, S. (accepted in Aug, 2019) Association of Race/Ethnicity with Hospital discharge disposition after Elective Total Knee Arthroplasty, JAMA Network Open 2019 Oct; 2(10): e1914259.

Lin, L, Chu, H, Murad, M, Hong, C, Qu, Z, Cole, S, and Chen, Y. (Aug. 2018) Empirical Comparison of publication bias tests in meta-analysis, Journal of General Internal Medicine 33(8):1260-1267.

Wang, L, Rouse, B, Marks-Anglin, A, Duan, R, Shi, Q, Quach, K, Chen, Y Schmid, CH, Li, T. (June, 2019) Rapid network meta-analysis using data from Food and Drug Administration approval packages is feasible but with limitations. Journal of Clinical Epidemiology. 114:84–94.

Agarwal, R, Bartsch, SM, Kelly, BJ, Prewitt, M, Liu, YL, Chen, Y, and Umscheid, CA. (April, 2018) Newer glycopeptide antibiotics for treatment of complicated skin and soft tissue infections: systematic review, network meta-analysis and cost analysis, Clinical Microbiology and Infection, 24(4):361–368.

Lake, E, Jordan, J, Duan, R, and Chen, Y (May, 2019) A Meta-Analysis of the Associations Between the Nurse Work Environment in Hospitals and 4 Sets of Outcomes, Medical Care 59(5) 353-360.12

Chiasakul, T, Jesus, E, Tong, J, Chen, Y, Crowther, M, Garcia, D, Chai-Adisaksopha, C, Messe, S and Cuker A. (Nov. 2018) Inherited Thrombophilia and The Risk of Arterial Ischemic Stroke: A Systematic Review and Meta-Analysis, American Society of Hematology Annual meetings 132 no. Suppl 1-2518.

Ashana, D, Umscheid, C, Stephens-Shields, A, Kohn, R, Madden, V, Harhay, M, Chen, Y, Kerlin, M. (Aug. 2019) Determining the association between end-of-life care resources and patient outcomes in Pennsylvania intensive care units, Critical Care Medicine.

Chen, X, Fan, R, Peng, F, Liu, J, Huang, J, Liang, J, Chen, Z, Chen, Y and Jiang, Y. (June, 2019) Blood pressure and body fat percent in women with NMOSD, Brain and Behavior.

Liu, L, Liang, J, Liu, Q, Luo, C, Liu, J, Fan, R, Chen, Z, Chen, Y, Peng, F, Jiang, Y. (May, 2019) Elevated plasma homocysteine levels in anti-N-methyl-D-aspartate receptor encephalitis. Frontiers in Neurology. 10:464.

Gluck, C, Qiu, C, Han, S, Palmer, M, Park, J, Ko, Y, Hanson, R, Huang, J, Chen, Y, Park, A, Mantzaris, I, Verma, A, Li, H, and Susztak, K. (June, 2019) Kidney cytosine methylation changes can improve renal function decline estimation in patients with diabetic kidney disease, Nature Communications 10, Article number: 2461 (2019)

Umscheid, C, Jonathan, W, Matthew, G, Jenna G, Tessa, C, Liu, YL, Chen, Y, and Jennifer, M. (June 2019) National Survey of Hospitalists Experiences with Incidental Pulmonary Nodules. Journal of Hospital Medicine 14(6):353-356

Leas, B, Kahwati, L, Liu, Y, Chen, Y, D’Anci, K, and Umscheid, C, (2018) Using Qualitative Comparative Analysis (QCA) to Assess Interventions for Improving Asthma Care, Academy Health Research Meeting.

Jiang, Y, Weng, R, Zhang, Y, Fan, R, Liu, Y, Chen, Z, Peng, F, Chen, Y, and Chen, X, (April, 2018) The performance of rapid plasma reagin (RPR) titer in HIV-negative general paresis after neurosyphilis therapy, BMC Infectious Diseases 18(1):144

Qiu, C, Hanson, R, Fufaa, G, Kobes, S, Gluck, C, Huang, J, Chen, Y, Nelson, R, Knowler, W, Susztak, K, (June, 2018) Cytosine methylation changes and prediction of Renal Function decline in American Indians, Kidney International 93, 14171431.

Huang, J, Huang, J, Chen, Y and Ying, G (Feb., 2018), Evaluation of Approaches to Analyzing Continuous Correlated Eye Data When Sample Size Is Small, Ophthalmic Epidemiology 25(1): 45–54.

Chahoud, J, Semaan, A, Chen, Y, Cao, M, Rieber, A, Rady, P and Tyring, S. (2016) The Association between Beta-genus Human Papillomavirus and Cutaneous Squamous Cell Carcinoma in Immunocompetent Individuals: a Meta-analysis, JAMA Dermatology, 152(12):1354-1364.

Lu, G, Changb, J, Liu, Z, Chen, Y, Li, M, and Zhu, J. (2016) Phospholipase C Beta 1: A Candidate Signature Gene for Proneural Subtype High-Grade Glioma, Molecular Neurobiology 53:6511-6525.

Liu, L, Xu, H, Wang, W, Wu, C, Chen, Y, Yang, J, Cen, P, Xu, J, Liu, C, Long, J, Guha, S, Fu, D, Ni, Q, Jatoi, A, Chari, S, McCleary-Wheeler, A, Fernandez-Zapico, M, Li, M, Yu, X, (2015) A Preoperative Serum Signature of CEA+/CA125+/CA19-9 1,000 U/mL Indicates Poor Outcome to Pancreatectomy for Pancreatic Cancer, International Journal of Cancer (9), 2216-2227.

Xu, C, Wallace, M, Yang, J, Jiang, L, Zhai, Q, Zhang, Y, Hong, C, Chen, Y, Frank, T, Stauer, J, Asbun, H, Raimondo, M, Woodward, T, Li, Z, Guha, S, Zheng, L and Li, M (2014) ZIP4 is a Novel Diagnostic and Prognostic Marker in Human Pancreatic Cancer: A Systemic Comparison Between EUS-FNA and Surgical Specimens, Current Molecular Medicine, 14, 1-7.

Lin, Y, Chen, Y, Wang, Yy, Yang, Jy, Zhu, V, Liu, Y, Cui, X, Yan, W, Jiang, T, Hergenroeder, G, Fletcher, S, Levine, J, Kim, D, Tandon, N, Zhu, J and Li, M, (2013) ZIP4 is a novel molecular marker for glioma, Neuro-Oncology, 15 (8), 1008-1016. PMID: 21191590.

Zhang Y, Yang, J, Cui, X, Chen, Y, Zhu, V, Hagan, J, Wang, H, Yu, X, Hodges, S, Fang, J, Chiao, P, Logsdon, C, Fisher, W, Brunicardi, F, Chen, C, Yao, Q, Fernandez-Zapico, M, and Li, M, (2013), A Novel epigenetic CREB-miR 373 Axis Mediates ZIP4-Induced Pancreatic Cancer Growth, EMBO Molecular Medicine, 5 (9), 1322-1334.

Lin Y, Zhang G, Zhang J, Gao G, Li M, Chen, Y, Wang J, Li G, Song S, Wang Y and Jiang T, (2013) A panel of four cytokines predicts the prognosis of patients with malignant gliomas, Journal of Neuro-Oncology, 114 (2), 199-208.

Go, VF, Frangakis, C, Minh, N, Latkin, C, Ha, T, Mo, T, Sripaipan, T, Davis, W, Zelaya, C, Chen, Y, Celentano, D and Quan, V, (2013) Effects of an HIV peer prevention intervention on sexual and injecting risk behaviors among injecting drug 10 users and their risk partners in Thai Nguyen, Vietnam: a randomized controlled trial, Social Science & Medicine, 96 154-164.

Nestadt, G,Wang, Y, Grados, MA, Riddle, MA, Greenberg, BD, Knowles, JA, Fyer, AJ, McCracken, JT, Rauch, SL, Murphy, DL, Rasmussen, SA, Cullen, B, Piacentini, J, Geller, D, Pauls, D, Bienvenu, OJ, Chen, Y, Liang, KY, Goes, FS, Maher, B, Pulver, AE, Shugart, YY, Valle, D, Samuels, JF and Chang, YC (2011) Homeobox genes in obsessive-compulsive disorder, American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 159 (1), 53-60.

Blom, RM, Samuels, JF, Grados, MA, Chen, Y, Bienvenu, OJ, Riddle, MA, Liang, KY, Brandt, J and Nestadt, G (2011), Cognitive functioning in compulsive hoarding, Journal of Anxiety Disorders, 25 (8), 1139-1144.

Frangakis, CE, Geschwind J, Kim, D, Chen, Y, Koteish, A, Hong, K, Liapi, E, Georgiades, CS. (2010). Chemoembolization decreases drop-o risk of hepatocellular carcinoma patients on the liver transplant list, Cardiovascular and interventional radiology, 34 (6), 1254-1261.

Wible, BC, Rilling, WS, Drescher, P, Hieb, RA, Saeian, K, Frangakis, CE, Chen, Y, Eastwood, D., Kim, HS. (2010). Longitudinal Quality of Life Assessment of Patients with Hepatocellular Carcinoma After Primary Transarterial Chemoembolization, Journal of Vascular and Interventional Radiology, 21(7), 1024-1030.

Buijs, M, Vossen, JA, Frangakis, CE, Hong, K, Georgiades, C, Chen, Y, Liapi, E, and Geschwind, JF. (2008). Nonresectable Hepatocellular Carcinoma: Long-term Toxicity in Patients Treated with Transarterial Chemoembolization Single-Center Experience. Radiology, 249, 346-354.