Faculty

Yanxun Xu

Assistant Professor

Research Interests

  • Bayesian statistics
  • cancer genomics
  • clinical trial design
  • graphical models
  • nonparametric Bayesian statistical inference for big data analysis
  • high-throughput genomic data
  • proteomics data
Education
  • Ph.D. 2013, Rice University
  • M.S. 2010, Texas Tech University
  • B.S. 2007, Beijing University of Aeronautics and stronautics
Research Areas
  • Bayesian methodology development, application of Bayesian methods to cancer genomics and clinical trial design, big data analysis for electronic health record data
Awards
  • 2016:  Mitchell Prize
  • 2015:  Hopkins inHealth Discovery Program Award
  • 2015:  2015 David P. Byar Young Investigator Travel Award
  • 2014:  1st Place Winner in the ASA Biopharmaceutical Section Student Paper
  • 2014:  Southern Regional Council on Statistics 2014 Travel Award
  • 2013:  Women in Machine Learning 2013 Travel Award
  • 2012:  GENSIPS’12 Travel Award
  • 2011:  ENAR Student Distinguished Paper Award
Journal Articles
  • Xu, Y., Thall, P., Mueller, P., Reza, M. M. (2016).  A Decision Theoretic Comparison of Treatments to Resolve Air Leaks After Lung Surgery Based on Nonparametric Modeling.  Bayesian Analysis.
  • Mueller, P., Xu, Y., Thall, P. (2016).  Clinical Trial Design as a Decision Problem.  Applied Stochastic Models in Business and Industry.
  • Xu, Y., Müller, P., Telesca, D. (2016).  Bayesian inference for latent biologic structure with determinantal point processes (DPP)..  Biometrics.  72(3).  955-64.
  • Xu, Y., Trippa, L., Müller, P., Ji, Y. (2016).  Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trials..  Statistics in biosciences.  8(1).  159-180.
  • Yuan, Y., Liu, L., Chen, H., Wang, Y., Xu, Y., Mao, H., Li , J., Mills, G. B., Shu, Y., Li , L., Liang, H. (2016).  Comprehensive Characterization of Molecular Differences in Cancer between Male and Female Patients..  Cancer cell.  29(5).  711-22.
  • Xu, Y., Müller, P., Wahed, A. S., Thall, P. F. (2016).  Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times..  Journal of the American Statistical Association.  111(515).  921-935.
  • Xu, Y., Zhu, Y., Müller, P., Mitra, R., Ji, Y. (2015).  Characterizing Cancer-Specific Networks by Integrating TCGA Data..  Cancer informatics.  13(Suppl 2).  125-31.
  • Xu, Y. (2015).  Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times.  Journal of the American Statistical Association.
  • Zhu, Y., Xu, Y., Helseth, Jr, D. L., Gulukota, K., Yang, S., Pesce, L. L., Mitra, R., Müller, P., Sengupta, S., Guo, W., Silverstein, J. C., Foster, I., Parsad, N., White, K., Ji, Y. (2015).  Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data..  Journal of the National Cancer Institute.  107(8).
  • Xu, Y., Müller, P., Yuan, Y., Gulukota, K., Ji, Y. (2015).  MAD Bayes for Tumor Heterogeneity - Feature Allocation with Exponential Family Sampling..  Journal of the American Statistical Association.  110(510).  503-514.
  • Costello, J. C., Heiser, L. M., Georgii, E., Gönen, M., Menden, M. P., Wang, N. J., Bansal, M., Hintsanen, P., Khan, S. A., Mpindi, J., Xu, Y. (2014).  A community effort to assess and improve drug sensitivity prediction algorithms.  Nature biotechnology.  32(12).  1202–1212.
  • Xu, Y., Ji, Y. (2014).  A Latent Gaussian Process Model with Application to Monitoring Clinical Trials.  arXiv preprint arXiv:1403.7853.
  • Xu, Y., Zhu, Y., Müller, P., Mitra, R., Ji, Y. (2014).  Characterizing Cancer-Specific Networks by Integrating TCGA Data.  Cancer Informatics.  13(Suppl 2).  125.
  • Han, L., Yuan, Y., Zheng, S., Yang, Y., Li, J., Edgerton, M. E., Diao, L., Xu, Y., Verhaak, R. G., Liang, H. (2014).  The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes.  Nature Communications.  5.
  • Xu, Y., Zheng, X., Yuan, Y., Estecio, M. R., Issa, J. P., Qiu, P., Ji, Y., Liang, S. (2014).  BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data..  IEEE/ACM transactions on computational biology and bioinformatics.  11(6).  1038-44.
  • Han, L., Yuan, Y., Zheng, S., Yang, Y., Li , J., Edgerton, M. E., Diao, L., Xu, Y., Verhaak, R. G., Liang, H. (2014).  The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes..  Nature communications.  5.  3963.
  • Yuan, Y., Van Allen, E. M., Omberg, L., Wagle, N., Amin-Mansour, A., Sokolov, A., Byers, L. A., Xu, Y., Hess, K. R., Diao, L., Han, L., Huang, X., Lawrence, M. S., Weinstein, J. N., Stuart, J. M., Mills, G. B., Garraway, L. A., Margolin, A. A., Getz, G., Liang, H. (2014).  Assessing the clinical utility of cancer genomic and proteomic data across tumor types..  Nature biotechnology.  32(7).  644-52.
  • Xu, Y., Zhu, Y., Müller, P., Mitra, R., Ji, Y. (2014).  Characterizing Cancer-Specific Networks by Integrating TCGA Data..  Cancer informatics.  13(Suppl 2).  125-31.
  • Johnson, V. E., Xu, Y., Lee, J., Yuan, Y., Mitra, R., Liang, S., Müller, P., Ji, Y., De Blasi, P., Walker, S. G., others. (2013).  Special Issue: Papers from the 2012 ISBA World Meeting.
  • Xu, Y., Lee, J., Yuan, Y., Mitra, R., Liang, S., Müller, P., Ji, Y. (2013).  Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data..  Bayesian analysis (Online).  8(4).  759-780.
  • Mitra, R., Müller, P., Liang, S., Xu, Y., Ji, Y. (2013).  Toward breaking the histone code: bayesian graphical models for histone modifications..  Circulation. Cardiovascular genetics.  6(4).  419-26.
  • Yuan, Y., Norris, C., Xu, Y., Tsui, K., Ji, Y., Liang, H. (2012).  BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.  BMC Genomics.  13(Suppl 8).  S9.
  • Yuan, Y., Xu, Y., Xu, J., Ball, R. L., Liang, H. (2012).  Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data.  Bioinformatics.  28(9).  1246–1252.
  • Xu, Y., Zhang, J., Yuan, Y., Mitra, R., Müller, P., Ji, Y. (2012).  A Bayesian Graphical Model for Integrative Analysis of TCGA Data..  IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.  2012.  135-138.
  • Xu, Y., Zheng, X., Yuan, Y., Estecio, M. R., Issa, J. P., Ji, Y., Liang, S. (2012).  A Bayesian Model for SNP Discovery Based on Next-Generation Sequencing Data..  IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics.  2012.  42-45.
  • Yuan, Y., Xu, Y., Xu, J., Ball, R. L., Liang, H. (2012).  Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data..  Bioinformatics (Oxford, England).  28(9).  1246-52.
  • Yuan, Y., Norris, C., Xu, Y., Tsui, K. W., Ji, Y., Liang, H. (2012).  BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data..  BMC genomics.  13 Suppl 8.  S9.
  • A.A, T., Xu, Y. (2011).  Quantile Versions of Holt--Winters Forecasting Algorithms.  Journal of Statistics: Advances in Theory and Applications.  5(1).  15–35.
  • Ji, Y., Xu, Y., Zhang, Q., Tsui, K. W., Yuan, Y., Norris, Jr, C., Liang, S., Liang, H. (2011).  BM-map: Bayesian mapping of multireads for next-generation sequencing data..  Biometrics.  67(4).  1215-24.
Book Chapters
  • Xu, Y., Ji, Y., Müller, P. (2015).  Biomarker-Driven Adaptive Design.  Nonparametric Bayesian Inference in Biostatistics.  Springer International Publishing.  311–326.
  • Xu, Y. (2015).  Graphical Models for Integrating Omics Data.  Integrating Omics Data: Statistical and Computational Methods.
Conference Proceedings
  • Xu, Y., Xu, Y., Saria, S. (2016).  A Non-parametric Bayesian Approach for Estimating Treatment-Response Curves from Sparse Time Series.  Proceedings of the 1st Machine Learning for Healthcare Conference.  282-300.
  • "Modeling Tumor Heterogeneity using Bayesian Methods", Virginia CommonWealth University.  Richmond, VA.  2016
  • "A Decision Theoretic Comparison of Treatments to Resolve Air Leaks After Lung Surgery Based on Non- parametric Modeling", 2016 Joint Statistical Meetings (JSM),.  Chicago, IL.  2016
  • "Bayesian Clinical Trial Design for Basket Trial", The Fourth Military Medical School, China.  Xi’an, China.  2016
  • "Bayesian Methods for Cancer Research", Xi’an Jiaotong University School of Medicine.  Xi'an, Shaanxi, China.  2016
  • "Bayesian Nonparametric Estimation for SMART Design", 2016 ICSA China Statistics Conference.  Qingdao, China.  2016
  • "Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times", 2016 ISBA World Meeting.  Sardinia, Italy.  2016
  • "The Power of Bayesian Methods in Learning", Beijing Normal University.  Beijing, China.  2016
  • "Bayesian Inference for Latent Biologic Structure with Determinantal Point Processes (DPP)", 2016 Eastern North American Region (ENAR) meeting.  Austin, TX.  2016
  • "Bayesian Inference for Latent Biologic Structure with Determinantal Point Processes (DPP)", 6th IMS-ISBA Joint Meeting Bayes Comp at MCMSki V.  Lenzerheide, Switzerland.  2016
  • "Bayesian Subgroup-Based Adaptive Designs in Sequential, Multiple Assignment, Randomized Biomarker Trials (SMART)", 2015 Joint Statistical Meetings (JSM).  Seattle, WA.  2015
  • "Bayesian Inference for Latent Biologic Structure with Determinantal Point Processes (DPP)", 2015 ICSA China Statistics Conference.  Shanghai, China.  2015
  • "Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trials", Biostatistics in bioPharm.  Shanghai, China.  2015
  • "Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times", 2015 Eastern North American Region (ENAR) meeting.  Miami, FL.  2015
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