Xu, Yanxun

Assistant Professor
Applied Mathematics And Statistics
http://www.ams.jhu.edu/~yxu70/

Whitehead Hall 100
(410) 516-7195
yanxun.xu@jhu.edu

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About

Education
  • Ph.D. 2013, RICE UNIVERSITY
  • Master of Science 2010, Texas Tech University
  • Bachelor of Science 2007, Beijing University of Aeronautics and Astronautics
Research Areas
  • Application of Bayesian methods to cancer genomics and clincial trial design
  • Bayesian methodoly of development
  • Big data analysis for electronic health record data
Awards
  • 2016:  Mitchell Prize
  • 2015:  2015 David P. Byar Young Investigator Travel Award
  • 2015:  Hopkins inHealth Discovery Program 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
Presentations
  • "Tutorial on Bayesian Nonparametrics".  Baltimore Maryland, United States of America (the).  January 16, 2018
  • "Bayesian Nonparametric Regression and Electronic Health Record Data Analysis", International Workshop on Objective Bayes Methodology O-Bayes17.  Austin Texas, United States of America (the).  December 13, 2017
  • "Bayesian Repulsive Mixture Model", 2017 Bayesian Nonparametric Inference Workshop.  Oaxaca, Mexico.  December 4, 2017
  • "A Nonparametric Bayesian Trial Design for Basket Trials".  Vienna, Austria.  August 29, 2017
  • "A Nonparametric Bayesian Trial Design for Basket Trials", AstraZeneca.  Gaithersburg Maryland, United States of America (the).  August 22, 2017
  • "ASID: A Bayesian Adaptive Subgroup-Identification Enrichment Design", 2017 Joint Statistical Meetings (JSM).  Baltimore Maryland, United States of America (the).  August 2, 2017
  • "ASID: A Bayesian Adaptive Subgroup-Identification Enrichment Design", 2017 ISBA-EAC conference.  Changchun, China.  July 6, 2017
  • "A Nonparametric Bayesian Trial Design for Basket Trials", MedImmune.  Gaithersburg Maryland, United States of America (the).  June 27, 2017
  • "A Nonparametric Bayesian Trial Design for Basket Trials", 2017 ICSA Statistics Conference.  Chicago Illinois, United States of America (the).  June 23, 2017
  • "Innovative Bridging From Modeling Tumor Heterogeneity to Clinical Trial", 2017 Midwest Biopharmaceutical Statistics Workshop.  Muncie Indiana, United States of America (the).  May 24, 2017
  • "A Nonparametric Bayesian Trial Design for Basket Trials", The 31st New England Statistics Symposium.  Mansfield Connecticut, United States of America (the).  April 21, 2017
  • "Modeling Tumor Heterogeneity and Its Applications", Johns Hopkins University HNCR Meeting.  baltimore Maryland, United States of America (the).  February 24, 2017
  • "Modeling Tumor Heterogeneity using Bayesian Methods", Virginia CommonWealth University.  Richmond, VA.  November 1, 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.  August 1, 2016
  • "Bayesian Clinical Trial Design for Basket Trial", The Fourth Military Medical School, China.  Xi’an, China.  July 1, 2016
  • "Bayesian Methods for Cancer Research", Xi'an Jiaotong University School of Medicine.  Xi'an, Shaanxi, China.  July 1, 2016
  • "Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times", 2016 ISBA World Meeting.  Sardinia, Italy.  June 1, 2016
  • "Bayesian Nonparametric Estimation for SMART Design", 2016 ICSA China Statistics Conference.  Qingdao, China.  June 1, 2016
  • "The Power of Bayesian Methods in Learning", Beijing Normal University.  Beijing, China.  June 1, 2016
  • "Bayesian Inference for Latent Biologic Structure with Determinantal Point Processes (DPP)", 2016 Eastern North American Region (ENAR) meeting.  Austin, TX.  March 1, 2016
  • "Bayesian Inference for Latent Biologic Structure with Determinantal Point Processes (DPP)", 6th IMS-ISBA Joint Meeting Bayes Comp at MCMSki V.  Lenzerheide, Switzerland.  January 1, 2016
  • "Bayesian Subgroup-Based Adaptive Designs in Sequential, Multiple Assignment, Randomized Biomarker Trials (SMART)", 2015 Joint Statistical Meetings (JSM).  Seattle, WA.  August 1, 2015
  • "Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trials", Biostatistics in bioPharm.  Shanghai, China.  July 1, 2015
  • "Bayesian Inference for Latent Biologic Structure with Determinantal Point Processes (DPP)", 2015 ICSA China Statistics Conference.  Shanghai, China.  July 1, 2015
  • "Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times", 2015 Eastern North American Region (ENAR) meeting.  Miami, FL.  March 1, 2015

Publications

Journal Articles
  • Xie F, Zhou M, Xu Y (2017).  BayCount: A Bayesian Decomposition Method for Inferring Tumor Heterogeneity using RNA-Seq Counts.  arXiv preprint arXiv:1702.07981.
  • M"uller P, Xu Y, Thall PF (2017).  Clinical trial design as a decision problem.  Applied Stochastic Models in Business and Industry.
  • Xie F, Xu Y (2017).  Bayesian Repulsive Gaussian Mixture Model.  arXiv preprint arXiv:1703.09061.
  • M"uller P, Xu Y, Jara A (2017).  A Short Tutorial on Bayesian Nonparametrics.  Journal of Statistical Research.  48--50.
  • Thall PF, Mueller P, Xu Y, Guindani M (2017).  Bayesian nonparametric statistics: A new toolkit for discovery in cancer research.  Pharmaceutical statistics.  16.  414--423.
  • Xu Y, Thall PF, M"uller P, Reza MJ, others (2017).  A Decision-Theoretic Comparison of Treatments to Resolve Air Leaks After Lung Surgery Based on Nonparametric Modeling.  Bayesian Analysis.  International Society for Bayesian Analysis.  12.  639--652.
  • Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yang Y, Martincorena I, Creighton C, Weinstein JN, Xu Y, others (2017).  Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers.  bioRxiv.  Cold Spring Harbor Labs Journals.  161356.
  • Xie F, Xu Y (2017).  Adaptive Bayesian nonparametric regression using kernel mixture of polynomials with application to partial linear model.  arXiv preprint arXiv:1710.08017.
  • Xie F, Jin W, Xu Y (2017).  A Theoretical Framework for Bayesian Nonparametric Regression: Orthonormal Random Series and Rates of Contraction.  arXiv preprint arXiv:1712.05731.
  • Xu Y, Thall PF, M"uller P, Reza MJ, others (2017).  A Decision-Theoretic Comparison of Treatments to Resolve Air Leaks After Lung Surgery Based on Nonparametric Modeling.  Bayesian Analysis.  International Society for Bayesian Analysis.  12.  639--652.
  • 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 GB, 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, Mueller P, Thall P (2016).  Clinical Trial Design as a Decision Problem.  Applied Stochastic Models in Business and Industry.
  • Yuan Y, Liu L, Chen H, Wang Y, Xu Y, Mao H, Li J, Mills GB, Shu Y, Li L, others (2016).  Comprehensive Characterization of Molecular Differences in Cancer between Male and Female Patients.  Cancer Cell.  Cell Press.  29.  711--722.
  • Xu Y, M"uller P, Telesca D (2016).  Bayesian inference for latent biologic structure with determinantal point processes (DPP).  Biometrics.  72.  955--964.
  • Xu Y, M"uller P, Wahed AS, Thall PF (2016).  Bayesian nonparametric estimation for dynamic treatment regimes with sequential transition times.  Journal of the American Statistical Association.  Taylor & Francis.  111.  921--950.
  • Xu Y, Mueller P, Mitra R, Berry D (2016).  A Nonparametric Bayesian Basket Trial Design.  arXiv preprint arXiv:1612.02705.
  • Xu Y, Müller P, Wahed AS, Thall PF (2016).  Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times..  Journal of the American Statistical Association.  111(515).  921-935.
  • Xu Y, Trippa L, M"uller P, Ji Y (2016).  Subgroup-based adaptive (suba) designs for multi-arm biomarker trials.  Statistics in biosciences.  Springer US.  8.  159--180.
  • 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.
  • Zhu Y, Xu Y, Helseth, Jr DL, Gulukota K, Yang S, Pesce LL, Mitra R, Müller P, Sengupta S, Guo W, Silverstein JC, 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.
  • XU Y, ZHU Y, JI Y (2015).  A Bayesian Graphical Model for Integrative Analysis of TCGA Data: BayesGraph for TCGA Integration.  Integrating Omics Data.  Cambridge University Press.  205.
  • Xu Y, M"uller 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.  Taylor & Francis.  110.  503--514.
  • Zhu Y, Xu Y, Helseth DL, Gulukota K, Yang S, Pesce LL, Mitra R, M"uller P, Sengupta S, Guo W, others (2015).  Zodiac: a comprehensive depiction of genetic interactions in cancer by integrating TCGA data.  JNCI: Journal of the National Cancer Institute.  Oxford University Press.  107.
  • Xu Y, Zheng X, Yuan Y, Estecio MR, Issa JP, 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 ME, Diao L, Xu Y, Verhaak RG, 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 EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, Han L, Huang X, Lawrence MS, Weinstein JN, Stuart JM, Mills GB, Garraway LA, Margolin AA, 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, M"uller P, Mitra R, Ji Y (2014).  Characterizing cancer-specific networks by integrating TCGA data.  Cancer informatics.  SAGE Publications Sage UK: London, England.  13.  CIN--S13776.
  • Xu Y, Zheng X, Yuan Y, Estecio MR, Issa J, 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.  IEEE.  11.  1038--1044.
  • Han L, Yuan Y, Zheng S, Yang Y, Li J, Edgerton ME, Diao L, Xu Y, Verhaak RG, Liang H (2014).  The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes.  Nature communications.  Nature Publishing Group.  5.  3963.
  • Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, others (2014).  Assessing the clinical utility of cancer genomic and proteomic data across tumor types.  Nature biotechnology.  Nature Publishing Group.  32.  644--652.
  • Costello JC, Heiser LM, Georgii E, G"onen M, Menden MP, Wang NJ, Bansal M, Hintsanen P, Khan SA, Mpindi J, others (2014).  A community effort to assess and improve drug sensitivity prediction algorithms.  Nature biotechnology.  Nature Publishing Group.  32.  1202--1212.
  • Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Hintsanen P, Khan SA, 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.
  • Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, others (2014).  各種腫瘍のがんゲノムおよびプロテオームデータの臨床的有用性評価.  Nature Biotechnology.  Nature Research.  32.  644--652.
  • 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.
  • 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 ME, Diao L, Xu Y, Verhaak RG, Liang H (2014).  The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes.  Nature Communications.  5.
  • 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.
  • Mitra R, M"uller P, Liang S, Xu Y, Ji Y (2013).  Computational and Systems Biology Computational and Systems Biology.
  • Johnson VE, Xu Y, Lee J, Yuan Y, Mitra R, Liang S, Müller P, Ji Y, De Blasi P, Walker SG, others (2013).  Special Issue: Papers from the 2012 ISBA World Meeting.
  • Xu Y, Lee J, Yuan Y, Mitra R, Liang S, M"uller P, Ji Y, others (2013).  Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data.  Bayesian Analysis.  International Society for Bayesian Analysis.  8.  759--780.
  • Johnson VE, Xu Y, Lee J, Yuan Y, Mitra R, Liang S, M"uller P, Ji Y, De Blasi P, Walker SG, others (2013).  Special Issue: Papers from the 2012 ISBA World Meeting.
  • Mitra R, M"uller P, Liang S, Xu Y, Ji Y (2013).  Toward Breaking the Histone Code Bayesian Graphical Models for Histone Modifications.  Circulation: Cardiovascular Genetics.  Lippincott Williams & Wilkins.  6.  419--426.
  • 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 MR, Issa JP, 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 RL, 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, Ji Y, Liang H (2012).  BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.  BMC genomics.  BioMed Central.  13.  S9.
  • Yuan Y, Norris C, Xu Y, Tsui KW, 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 RL, Liang H (2012).  Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data.  Bioinformatics.  Oxford Univ Press.  28.  1246--1252.
  • Yuan Y, Xu Y, Xu J, Ball RL, Liang H (2012).  Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data.  Bioinformatics.  28(9).  1246-1252.
  • 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.
  • Ji Y, Xu Y, Zhang Q, Tsui KW, 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.
  • A.A T, Xu Y (2011).  Quantile Versions of Holt---Winters Forecasting Algorithms.  Journal of Statistics: Advances in Theory and Applications.  5.  15--35.
  • Ji Y, Xu Y, Zhang Q, Tsui K, Yuan Y, Norris Jr C, Liang S, Liang H (2011).  BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data.  Biometrics.  Wiley Online Library.  67.  1215--1224.
  • 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.
  • Lee J, Ji Y, Xu Y, Johns Hopkins U  A Bayesian Feature Allocation Model for Tumor Heterogeneity Peter M"uller.
  • Xu Y (2015).  Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times.  Journal of the American Statistical Association.
  • Xu Y, Thall P, Mueller P, Reza MM (2016).  A Decision Theoretic Comparison of Treatments to Resolve Air Leaks After Lung Surgery Based on Nonparametric Modeling.  Bayesian Analysis.
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, Ji Y, M"uller 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 Bayesian Nonparametric Approach for Estimating Individualized Treatment-Response Curves.  Machine Learning for Healthcare Conference.  282--300.
  • Xu Y, Saria S, Xu Y (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.
  • Xu Y, Xu Y, Saria S (2016).  A Bayesian Nonparametric Approach for Estimating Individualized Treatment-Response Curves.  Machine Learning for Healthcare Conference.  282--300.
  • 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.
  • Xu Y, Zheng X, Yuan Y, Estecio MR, Issa J, Ji Y, Liang S (2012).  A Bayesian model for SNP discovery based on next-generation sequencing data.  Genomic Signal Processing and Statistics,(GENSIPS), 2012 IEEE International Workshop on.  IEEE.  42--45.
  • Xu Y, Zhang J, Yuan Y, Mitra R, M"uller P, Ji Y (2012).  A Bayesian graphical model for integrative analysis of TCGA data.  Genomic Signal Processing and Statistics,(GENSIPS), 2012 IEEE International Workshop on.  IEEE.  135--138.
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