Theory and Methods
Jin W+ , Ni Y, O’Halloran J, Spence AB, Rubin LH and Xu Y# , “A Bayesian Decision Framework for Optimizing Sequential Combination Antiretroviral Therapy in People with HIV.”
Annals of Applied Statistics, In Press.
Zhou F, He K, Wang K+ , Xu Y and Ni Y, “Functional Bayesian Networks for Discovering Causality from Multivariate Functional Data.”
Biometrics, In Press.
Wang K+ , Xu Y# , “Bayesian Tensor-on-Tensor Regression with Efficient Computation.”
Statistics and Its Interface, In Press.
Trippa L+ , Xu Y, “Advancing Clinical Trials with Novel Designs and Implementations.”
Statistical Science, 2023, 38(2):216-218.
Zhang Z+ , Mei H and Xu Y# , “Continuous-Time Decision Transformer for Healthcare Applications.”
Proceedings of The 26th International Conference on Artificial Intelligence and Statistics (AISTATS 2023), PMLR 206:6245-6262, 2023..
Jin W+ , Ni Y, Rubin LH, Spence AB and Xu Y# , “A Bayesian Nonparametric Approach for Inferring Drug Combination Effects on Mental Health in People with HIV.”
Biometrics, 2022,78(3): 988-1000.
(Jin W Won 2021 JSM Student Paper Award, Mental Health Statistics Section)
Li Y+ , Ni Y, Rubin LH, Spence AB and Xu Y# , “BAGEL: A Bayesian Graphical Model for Inferring Drug Effect Longitudinally on Depression in People with HIV.”
Annals of Applied Statistics, 2022,16(1): 21-39.
Kidd B, Wang K+ , Xu Y and Ni Y, “Federated Learning for Sparse Bayesian Models with Applications to Electronic Health Records and Genomics.”
Pacific Symposium on Biocomputing, 2023.
Sun X+ , Bahmani B, Vlassis N, Sun W and Xu Y# , “Data-driven discovery of interpretable causal relations for deep learning material laws with uncertainty propagation.”
Granular Matter, 2022, 24(1). DOI: 10.1007/s10035-021-01137-y.
Wang L+ m Xie F+ , Xu Y# , “Simultaneously Learning the Dimension and Parameters of a Statistical Model with Big Data.”
Statistics in Biosciences, In Press.
Hua W+ , Mei H, Zohar S, Giral M and Xu Y# , “Personalized Dynamic Treatment Regimes in Continuous Time: A Bayesian Joint Model for Optimizing Clinical Decisions with Timing.”
Bayesian Analysis, 2021.DOI: 10.1214/21-BA1276..
(Hua W Won 2021 ENAR Distinguished Student Paper Award)
Rubin LH* , Xu Y* , Norris PJ, Wang X+ , Dastgheyb R, Fitzgerald KC, Keating SM, Kaplan RC, Maki PM, Anastos K, Springer G, Benning L, Kassaye S, Gustafson D, Valcour V, Williams DW, “Early inflammatory signatures predict subsequent cognition in long-term virally suppressed women
Frontiers in Integrative Neuroscience 14 (2020): 20.
Xu Y# , Scharfstein D, Müller P, and Daniels M, “A Bayesian Nonparametric Approach for Evaluating the Causal Effect of Treatment in Randomized Trials with Semi-Competing Risks.”
Biostatistics, 2020, kxaa008.
Xu Y# , Constantine F+ , Yuan Y and Pritchett Y, “ASIED: A Bayesian Adaptive Subgroup-Identification Enrichment Design.”
Journal of Biopharmaceutical Statistics, 2020; 30(4): 623-638.
(Constantine F Won 2017 JSM Student Paper Award, Biopharmaceutical Section)
Xu Y# , Thall P, Hua W+ , and Andersson B, “Bayesian Nonparametric Survival Regression for Optimizing Precision Dosing of Intravenous Busulfan in Allogeneic Stem Cell Transplantation.”
Journal of the Royal Statistical Society: Series C, 2019; 68(3): 809-828
Müller P, Xu Y, and Thall P, “Clinical Trial Design as a Decision Problem.”
Applied stochastic models in business and industry 33.3 (2017): 296-301.
Müller P, Xu Y, and Jara A, “A short tutorial on Bayesian Nonparametrics”.
Journal of Statistical Research, 2016; 48-50(2): 1-19.
Xu Y, Xu Y, and Saria S, “A Non-parametric Bayesian Approach for Estimating Treatment-Response Curves from Sparse Time Series”.
Proceedings of the 1st Machine Learning for Healthcare Conference. 2016, 282-300.
Xu Y, Müller P, Wahed A and Thall P, “Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times (with discussion)”.
Journal of the American Statistical Association 111.515 (2016): 921-950.
(Winner of the 2015 David P. Byar Young Investigator Travel Award Sponsored by ASA Biometrics Section)
Xu Y, Müller P, Wahed A and Thall P, “Rejoinder: Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times”
Journal of the American Statistical Association, 2016, 111(515), 949-950.
Zhu Y* , Xu Y* , Helseth D* , Gulukota K, Yang S, Pesce L, Mitra R, Müller P, Sengupta S, Guo W, Silverstein J, Foster I, Parsad N, White K and Ji Y, “Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data.”
JNCI: Journal of the National Cancer Institute 107.8 (2015)
Xu Y, Müller P, Yuan Y, Gulukota K and Ji Y, “MAD Bayes for Tumor Heterogeneity Feature Allocation with Exponential Family Sampling.”
Journal of the American Statistical Association 110.510 (2015): 503-514
Xu Y, Lee J, Yuan Y, Mitra R, Liang S, Müller P and Ji Y, “Nonparametric Bayesian Bi-Clustering for ChIP-Seq Count Data.”
Bayesian Analysis, 2013, 8(2): 1-22.
Ji Y, Xu Y, Zhang Q, Tsui K-W, Yuan Y, Liang S and Liang H, “BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data”.
Biometrics 67.4 (2011): 1215-1224.
(Winner of the 2011 ENAR Distinguished Student Paper Award)
Xu Y, Trippa L, Müller P and Ji Y,” Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trial.”
Statistics in Biosciences 8.1 (2016): 159-180.
(1st Place Winner of the 2014 JSM Biopharmaceutical Section Student Paper)
Xu Y, Zheng X, Yuan Y, Estecio M, Issa J-P, Ji Y and Liang S, “BM-SNP: A Bayesian Model for SNP Calling using High Throughput Sequencing Data”.
IEEE/ACM Transactions on computational biology and bioinformatics 11.6 (2014): 1038-1044.
Xu Y, Zhu Y, Müller P, Mitra R, and Ji Y, “Characterizing Cancer-Specific Networks by Integrating TCGA Data”.
Cancer informatics 13 (2014): CIN-S13776
Xu Y, Zhang J, Yuan Y, Mitra R, Müller P and Ji Y, “A Bayesian Graphical Model for Integrative Analysis of TCGA Data”.
Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2012.
Mitra R, Müller P, Liang S, Xu Y and Ji Y, “Towards the Discovery of the Histone Code - A Bayesian Graphical Model for Histone Modifications”.
Circulation: Cardiovascular Genetics, 2013; 6: 419-426.
Xu Y, Zheng X, Yuan Y, Estecio M, Issa J-P, Ji Y and Liang S, “A Bayesian Model for SNP Discovery Based on Next-Generation Sequencing Data”.
Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2012.
Trindade A.A. and Xu Y, “Quantile Versions of Holt-Winters Forecasting Algorithms”.
Journal of Statistics: Advances in Theory and Applications 5.1 (2011): 15-35.
[Psychiatry] Lusi Zhang, Paulo Lizano, Xu Y, Leah H. Rubin, Adam M. Lee, Rebekka Lencer, James L. Reilly, Richard S.E. Keefe, Sarah K. Keedy, Godfrey D. Pearlson, Brett A. Clementz, Matcheri S. Keshavan, Elliot S. Gershon, Carol A. Tamminga, John A. Sweeney, S. Kristian Hill, and Jeffrey R. Bishop, “Peripheral inflammation is associated with impairments of inhibitory behavioral control and visual sensorimotor function in psychotic disorders.”
Schizophrenia Research, 2023, 255: 69-78.
[HIV] Rubin LH, Maki PM, Dastgheyb RM, Steigman PJ, Burke-Miller J, Xu Y, Jin W+ , Sosanya O, Gustafson D, Merenstein D, Milam J, Weber KM, Springer G, Cook JA, and Brian T. Garibaldi. “Trauma across the lifespan and multisystem morbidity in women with HIV.”
Psychosomatic Medicine, 2023, 85(4): 341-350.
[COVID] Ashraf Fawzy, Tianshi David Wu, Kunbo Wang+ , Matthew L. Robinson, Jad Farha, Amanda Bradke, Sherita H. Golden, Xu Y, and Brian T. Garibaldi. “Racial discrepancy in pulse oximetry and delayed identification of treatment eligibility among COVID-19 patients.”
The Journal of the American Medical Association (JAMA) Internal Medicine, 2022;182(7):730-738.
[HIV] Williams DW, Flores BR, Xu Y, Wang Y+ , Yu D+ , Peters BA, Adedimeji A, Wilson TE, Merenstein D, Tien PC, Cohen MH, Weber KM, Adimora AA, Ofotokun I, Fischl M, Turan J, Turan B, Laumet G, Landay AL, Dastgheyb RM, Gange SJ, Weiser SD, Rubin LH. “T-cell activation state differentially contributes to neuropsychiatric complications in women with HIV.”
Brain, Behavior, & Immunity - Health, 2022, 25: 100498.
[Psychiatry] Lusi Zhang, Paulo Lizano, Bin Guo, Xu Y, Leah H. Rubin, Scot Kristian Hill, Ney Alliey-Rodriguez, Adam M. Lee, Baolin Wu, Sarah K. Keedy, Carol A. Tamminga, Godfrey D. Pearlson, Brett A. Clementz, Matcheri S. Keshavan, Elliot S. Gershon, John A. Sweeney, and Jeffrey R. Bishop, Inflammation subtypes in psychosis and their relationships with genetic risk for psychiatric and cardiometabolic disorders.
Brain, Behavior, & Immunity - Health, 2022.
[COVID] Brian T. Garibaldi, Kunbo Wang+ , Matthew L. Robinson, Joshua Betz, Caleb Alexander, Kathleen M. Andersen, Corey S. Joseph, Hemalkumar B. Mehta, Kimberly Korwek, Kenneth E. Sands, Arielle M. Fisher, Robert Bollinger, and Xu Y. Real-world Effectiveness of Remdesivir in Adults Hospitalized With COVID-19: A Retrospective, Multicenter Comparative Effectiveness Study.
Clinical Infectious Disease, 2022, 75 (1), 516-524.
[Psychiatry] Dung Hoang, Xu Y, Olivia Lutz, Deepthi Bannai, Victor Zeng, Jeffrey R. Bishop, Matcheri Ke- shavana, and Paulo Lizanoa. Inflammatory Subtypes in Antipsychotic-Naive First-Episode Schizophre- nia are Associated with Altered Brain Morphology and Topological Organization.
Brain, Behavior, & Immunity, 2022, 100:297-308.
[HIV] Rubin LH, O’Halloran JA, Williams DW, Li Y+ , Fitzgerald KC, Dastgheyb R, Damron AL, Maki PM, Spence AB, Sharma A, Gustafson DR, Milam J, Weber KM, Adimora AA, Ofotokun I, Fischl MA, Konkle-Parker D, and Xu Y# , Integrase inhibitors are associated with neuropsychiatric symptoms in women with HIV. Journal of Neuroimmune Pharmacology, 2021.
[COVID] Michael S Burnim, Kunbo Wang+ , William Checkley, Eric Nolley, Xu Y and Brian T Garibaldi. The Effectiveness of High-Flow Nasal Cannula in Coronavirus Disease 2019 Pneumonia.
Critical Care Medicine, 2022, 50(3):e253-e262.
[COVID] Mary Boulanger, Emily Molina, Kunbo Wang+ , Thomas Kickler, Xu Y and Brian T. Garibaldi, “Peripheral Plasma Cells Associated with Mortality Benefit in Severe COVID-19: A Marker of Disease Resolution”.
American Journal of Medicine, 2021.
[HIV] Aparicio JM, Xu Y, Li Y+ , Colatuoni C, Dastgheyb R, Williams DW, Asahchop E, McMillian JM, Power C, Fujiwara E, Gill MJ and Rubin LH, “Plasma microRNAs are associated with domain-specific cognitive function in people with HIV”.
[COVID] Shannon Wongvibulsin, Brian T. Garibaldi, Annukka A. R. Antar, Jiyang Wen, Mei-Cheng Wang, Amita Gupta, Robert Bollinger, Xu Y, Kunbo Wang+ , Joshua F. Betz, John Muschelli, Karen Bandeen-Roche, Scott L. Zeger and Matthew L. Robinson, “Development of Severe COVID-19 Adaptive Risk Predictor (SCARP), a calculator to predict severe disease or death in hospitalized patients with COVID-19”.
Annals of Internal Medicine, 2021.
[COVID] Brian T. Garibaldi*# , Kunbo Wang*+ , Matthew Robinson, Scott L. Zeger, Karen Bandeen Roche, #
Mei-Cheng Wang, Caleb Alexander, Amita Gupta, Robert Bollinger and Xu Y# , “Comparison of Clinical Improvement of Treatment With or Without Remdesivir Among Hospitalized Patients With COVID- 19”.
The Journal of the American Medical Association (JAMA) Open Network, 2021.
[HIV] Dastgheyb R, Buchholz AS, Fitzgerald KC, Xu Y, Williams DW, Springer G, Anastos K, Gustafson DR, Spence AB, Adimora AA, Waldrop D, Vance DE, Milam J, Bolivar H, Weber KM, Haughey NJ, Maki PM, Rubin LH, “Patterns and predictors of cognitive function among virally suppressed women with HIV”.
Frontiers in Neurology, 2021.
[HIV] Vecchio AC, Williams DW, Xu Y, Yu, D+ , Saylor D, Lofgren S, O’Toole R, Boulware DR, Nakasujja N, Nakigozi G, Kisakye A, Batte J, Mayanja R, Anok A, Reynolds SJ, Quinn TC, Gray RH, Wawer MJ, Sacktor N, Rubin LH, “Sex-specific associations between cerebrospinal fluid inflammatory marker levels and cognitive function in antiretroviral treated people living with HIV in rural Uganda”.
Brain Behavior and Immunity, 2021.
[HIV] O’Halloran JA*+ , Kunbo Wang*+ , Spence AB, Williams DW, Dastgheyb R, Fitzgerald KC, Kamkwalala AR, Maki PM, Sharma A, Gustafson DR, Milam J, Weber KM, Adimora AA, Ofotokun I, Fischl MA, Konkle-Parker D, Lahiri CD, Sheth AN, Xu Y# , Rubin LH# , “Integrase strand transfer inhibitor start or switch impacts learning in women with HIV”.
Journal of Acquired Immune Deficiency Syndromes, 2021.
[HIV] Asante R Kamkwalala* , Kunbo Wang*+ , P Jane O’Halloran, Dionna W. Williams, Raha Dastgheyb, Kathryn C. Fitzgerald, Amanda B. Spence, Pauline M. Maki, Deborah R. Gustafson, Joel Milam, Anjali Sharma, Kathleen M. Weber, Adaora A. Adimora, Igho Ofotokun, Anandi N. Sheth, Cecile D. Lahiri, Margaret A. Fischl, Deborah Konkle-Parker, Xu Y# , Rubin LH# , “Starting or Switching to an Integrase Inhibitor-Based Regimen Affects PTSD Symptoms in Women with HIV”.
AIDS and Behavior, 2021; 25(1): 225-236.
[COVID] Elisa H. Ignatius*+ , Kunbo Wang*+ , Andrew Karaba, Matthew Robinson, Robin K. Avery, Paul Blair, Natasha Chida, Tania Jain, Brent G. Petty, Zishan Siddiqui, Michael T. Melia, Paul G. Auwaerter, Xu Y# , Brian T. Garibaldi# , “Tocilizumab for the treatment of COVID-19 among hospitalized patients: A matched retrospective cohort analysis”.
Open Forum Infectious Diseases, 2021; 8(1): ofaa598
[HIV] Lahiri CD, Xu Y, Kunbo Wang*+ , Alvarez JA, Sheth AN, O’Halloran J, Spence AB, Tien P, Gustafson DR, Milam J, Fischl MA, Konkle-Parker D, Adimora AA, Sharma A, Weber KM, Ofotokun I, Rubin LH, “Weight and body mass index change after switching to integrase inhibitors or tenofovir alafenamide among women living with HIV”.
AIDS Research and Human Retroviruses, 2020.
[Psychiatry] Paulo Lizano, Olivia Lutz, Xu Y# , Leah H Rubin, Lyle Paskowitz*+ , Adam Lee, Seenae Eum, Sarah Keedy, Scot Hill, James Reilly, Baolin Wu, Carol Tamminga, Brett Clementz, Godfrey Pearlson, Elliot Gershon, Matcheri Keshavan, John Sweeney, and Jeffrey Bishop, “Multivariate Relationships Between Peripheral Inflammatory Marker Subtypes and Cognitive and Brain Structural Measures in Psychosis”.
Molecular Psychiatry, 2020.
[HIV] Fitzgerald K, Maki P, Xu Y# , Jin W*+ , Dastgheyb R, Williams D, Springer G, Anastos K, GustafsonD, Jiang X, Villacres M, Adimora A, Waldrop-Valverde D, Vance D, Bolivar H, Valcour V, and Rubin L, “Factors predicting detrimental change in declarative memory among women with HIV: a study of heterogeneity in cognition”.
Frontiers in Psychology, 2020.
[HIV] Asante R Kamkwalala* , Xuzhi Wang*+ , Pauline M Maki, Dionna W Williams, Victor G Valcour,
Alexandra Damron, Phyllis C Tien, KathleenMWeber, Mardge H Cohen, Erin E Sundermann, Vanessa
J Meyer, Deborah M Little, Xu Y# , Rubin LH# , “Higher peripheral monocyte activation markers are
associated with smaller frontal and temporal cortical volumes in women with HIV”.
JAIDS Journal of Acquired Immune Deficiency Syndromes, 2020; 84(1): 54-59.
[HIV] Rubin LH* , Li Y*+ , Fitzgerald KC, Dastgheyb R, Spence AB, Maki PM, Sharma A, Gustafson DR, Milam J, Weber KM, Adimora AA, Haughey NJ, Ofotokun I, Fichl MA, Konkle-Parker D, Xu Y# , Williams DW# , “Associations between antiretrovirals and cognitive function in women living with HIV”.
Journal of Neuroimmune Pharmacology (2020): 1-12.
[HIV] Williams DW* , Li Y*+ , Dastgheyb, Fitzgerald KC, Maki PM, Spence AB, Gustafson DR, Milam J, Sharma A, Adimora AA, Ofotokun I, Fischl MA, Konkle-Parker D, Weber KM, Xu Y# , Rubin LH# , “Associations between antiretroviral drugs on depressive symptomatology in homogenous subgroups of women with HIV”.
Journal of Neuroimmune Pharmacology (2020): 1-14.
[Cancer] “The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (including Xu Y), Pan-cancer analysis of whole genomes”.
Nature, 2020; 578(7793):82-93.
[Cancer] Yuan Y, Ju Y, Kim Y, Li J, Weinstein J, ,Xu Y, and et.al, “Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers”.
Nature genetics, 2020; 52(3): 342-352.
[Cancer] Huang P, Lin CT, Li Y+ , Tammemagi M, Brock M, Atkar-Khattra S, Xu Y, Hu P, Mayo J, Schmidt
H, Gingras M, Pasian S, Stewart L, Tsai S, Seely J, Manos D, Burrowes P, Bhatia R, Tsao M, Lam
S, “Prediction of lung cancer risk at follow-up screening with low-dose CT: a training and validation
study of a deep learning method”.
The Lancet Digital Health, 2019; 1(7): e353-e362
[HIV] Rubin LH, Neigh GN, Sundermann EE, Xu Y, Scully EP, and Maki PM, “Sex differences in neurocognitive function in adults with HIV: Patterns, predictors, and mechanisms”.
Current psychiatry reports, 2019; 21(10): 94
[Cancer] Genevieve L. Stein-O’Brien, Raman Arora, Aedin C. Culhane, Alexander V. Favorov, Casey S. Greene, Loyal A. Goff, Yifeng Li, Aloune Ngom, Michael F. Ochs, Xu Y and Elana J. Fertig, “Enter the matrix: Interpreting unsupervised feature learning with matrix decomposition to discover hidden knowledge in high-throughput omics data”.
Trends in Genetics, 2018; 34(10):790-805
[Cancer] Wei L, Jin Z+ , Yang S, Xu Y, Zhu Y, and Ji Y, “TCGA-Assembler 2.0: Software Pipeline for Automatic Retrieval, Processing, and Integration of TCGA/CPTAC Data”.
Bioinformatics. 2018, 34(9):1615-1617.
Xiao F, Niu Y, Hao N, Jin Z+ , Xu Y, and Zhang H, “modSaRa: a computationally efficient R package for CNV identification”.
Bioinformatics. 2017, 33(15): 2384-2385.
[Cancer] Yuan Y, Liu L, Chen H, Wang Y, Xu Y, Mao H, Li J, Mills GB, Shu Y, Li L, Liang H, “Comprehensive characterization of molecular differences in cancer between male and female patients”.
Cancer Cell, 2016, 29(5), 711-722.
[Cancer] Yuan Y, Van Allen EM, Omberg L, Wagle N, Sokolov A, Xu Y, and et al, “Assessing the Clinical Utility of Cancer Genomic and Proteomic Data across Tumor Types”.
Nature Biotechnology. 2014, 32: 644-652.
[Cancer] Han L, Yuan Y, Zheng S, Yang Y, Li J, Edgerton M, Diao L, Xu Y, Verhaak R and Liang H, “The Pan-Cancer Analysis of Pseudogene Expression Reveals Biologically and Clinically Relevant Tumor Subtypes”.
Nature Communications. 2014, 5: 3963.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, NCI DREAM Community (including Xu Y), Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, Collins JJ, Gallahan CD, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G, “A community effort to assess and improve drug sensitivity prediction algorithms”.
Nature Biotechnology. 2014, 32(12): 1202-1212.
Yuan Y, Xu Y, Xu J and Liang H, “Predicting the lethal phenotype of the knockout mouse by integrating genomic data”.
Bioinformatics, 2012 May 1; 28(9): 1246-52.
Yuan Y, Norris C, Xu Y, Tsui KW, Ji Y and Liang H, “BM-Map: an efficient software package for accurately allocating multireads of RNA-seq data”.
BMC Genomics, 2012, 13(Suppl 8): S9.
Faraji F, Schubert A, Kagohara L, Tan M, Xu Y, Zaidi M, Fortin JP, Fakhry C, Izumchenko E, Gaykalova D, and Fertig E.
Genome-wide molecular landscapes of HPV-positive and HPV-negative head and neck squamous cell carcinoma. In: Molecular Determinants of Head and Neck Cancer, 2018
Xu Y, Zhu Y and Ji Y. Graphical models for integrating omics data. In: Integrating omics data: statistical and computational methods.
Editors: George C. Tseng, Xianghong Jasmine Zhou and Debashis Ghosh.
This book is under copyediting and production in Cambridge University Press, 2015.
Xu Y, Ji Y and Müller P
Biomarker-Driven Adaptive Design. In: Nonparametric Bayesian Methods in Biostatistics and Bioinformatics.
Editors: Mitra R and Muller P. Springer-Verlag, 2015