TBI Lab

Welcome!

We are an academic data science team, led by Professor Yaomin Xu, that specializes in the field of translational Bioinformatics and Biostatistics. Our goal is to bridge the gap between cutting-edge biostatistics and bioinformatics theory and their real-world clinical applications. Our team, consisting of bioinformaticians, statisticians, basic scientists, and clinical researchers, works seamlessly together to tackle the most complex and challenging data research problems with the goal of advancing precision medicine. Our team is not only a working environment, but also an educational platform where we constantly push the boundaries of biomedical data science research through team-based problem-solving using real-world data. We also manage a state-of-the-art cloud-based research data analysis platform (RAP) that ensures persistent data storage, efficient data processing, and statistical data analyses, all with top-notch cybersecurity protection, data safety, and data privacy. We are passionate about creating data science solutions that allow for efficient, reliable, and verifiable big data research, leading to consistent and groundbreaking discoveries!

Team Members

Yaomin Xu, PhD Lab PI

Assistant Professor, Biostatistics (primary), Biomedical Informatics(secondary)

Statistical and computational methods integrating patient phenome and genome data to identify mechanistic biomarkers for precision medicine; Real-world Big Data analysis and discovery, Multivariate data analysis and visualization; Unsupervised learning; Cloud-based research data analysis infrastructures.

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Shilin Zhao Co-Investigator

Research Assistant Professor, Biostatistics

Bioinformatics

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Alexander Bick, MD, PhD Co-Investigator

Assistant Professor, Genetic Medicine

Human Genomics, Clonal Hematopoiesis

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Brian Sharber Staff

System Administrator and Cloud Application Developer

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Yu Wang Staff

Staff Scientist (Biostatistics)

Genomic or transcriptomic signatures identification related to cancer immunotherapy.

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Yajing Li Staff

Biostatistician (Biostatistics)

Collaborative statistical research to study the association between mutations and phenotypes based on data from EHR and large-scale Biobanks.

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Siwei Zhang Research Assistant

PhD Student (Biostatistics)

Unsupervised machine learning (data-driven approach) for translating EHR and Biobank data to discover the disease comorbidity and patient subgroups.

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Sharon Phillips Graduate student, co-advised with Digna Velez Edwards, PhD, MS.

Associate in Biostatistics, PhD Candidate (Epidemiology)

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Alex Silver Graduate student, Advisor: Michael R. Savona, M.D..

MD/PhD candidate (Cancer Biology)

Investigation of the etiologies, prevalence, and phenotypes of clonal hematopoiesis within a linked biobank and EHR.

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Xiaopeng Sun Graduate student, co-advised with Dr. Justin Balko, PhD.

PhD candidate (Cancer Biology)

Identify peripheral biomarker that predict breast cancer chemotherapy response.

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Matt Krantz, MD Research Rotation Student

Post-doctoral Research Fellow, MS Student in Biomedical Informatics

Genetic analysis of vancomycin-induced drug reaction with eosinophilia and systemic symptoms (DRESS

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Lydia Yao Research Assistant

MS Student (Biostatistics)

Interested in genomics in deep learning methods, high dimensional spaces, and clinical trial design.

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Huiding (Eric) Chen Research Assistant

PhD student (Biostatistics)

Interested in machine learning in EHR and biobank data.

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Alumni

Kaushik Amancherla, MD Lab Alumni

Instructor in Medicine, Cardiovascular Medicine, Vanderbilt University Medical Center

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Nick Strayer, PhD Lab Alumni

Data Scientist, RStudio Inc. 

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Ya-Chen Lisa Lin, PhD Lab Alumni

Statistical Scientist - Genentech

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Svetlana Eden, PhD Lab Alumni

Research Assistant Professor, Biostatistics, Vanderbilt Univeristy Medical Center

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Tools

The TBILab Cloud

A cloud-based research data analysis platform (RAP) for tackling the growing challenges in biomedical data sciences, with its advanced cloud-based HPC environment and emphasis on teamwork among bioinformaticians, statisticians, basic scientists, and clinical researchers. It provides a range of services for data storage, efficient data processing, bioinformatics and statistical data analyses, all with robust cybersecurity protection, data safety, and data privacy

AssociationSubgraphs

An interactive visualization method to quickly and intuitively explore high-dimensional association datasets using network science-derived statistics and visualization

Manuscript Discussion Code Repo

Phewas ME

Shiny app produced in collaboration with the Vanderbilt Drug Repurposing team. It is an interactive data exploration tool for digging into PheWAS results and the subject-level data that generated those results.

Manuscript Discussion Code Repo

Network Contagion Simulation and Visualization

Interactive simulation showing the spread of contagion through a network. All simulation parameters can be tweaked in order to better understand the dynamics of contagion spread in networks

Code Repo

Publications

2023

Germline genomic and phenomic landscape of clonal hematopoiesis in 323,112 individuals

Uddin, M. M., Yu, Z., Weinstock, J. S., Nakao, T., Niroula, A., Urbut, S. M., Koyama, S., Zekavat, S. M., Paruchuri, K., Silver, A. J., Mack, T. M., Wong, M. Y., Haidermota, S. M., Bhattacharya, R., Jorshery, S. D., Raddatz, M. A., Honigberg, M. C., Hornsby, W. E., Zhang, M. J., … Natarajan, P. (2022). Germline genomic and phenomic landscape of clonal hematopoiesis in 323,112 individuals.

MedRxiv, 2022.07.29.22278015. https://doi.org/10.1101/2022.07.29.22278015 NA

A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic datasets

Vlasschaert, C., Mack, T., Heimlich, J. B., Niroula, A., Uddin, M., Weinstock, J., Sharber, B., Silver, A. J., Xu, Y., Savona, M., Gibson, C., Lanktree, M. B., Rauh, M. J., Ebert, B. L., Natarajan, P., Jaiswal, S., & Bick, A. G.

Blood NA

Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs

Strayer, N., †Zhang, S., †Yao, L., †Vessels, T., Bejan, C. A., Hsi, R. S., Shirey-Rice, J. K., Balko, J. M., Johnson, D. B., Phillips, E. J., Bick, A., Edwards, T. L., Velez Edwards, D. R., Pulley, J. M., Wells, Q. S., Savona, M. R., Cox, N. J., Roden, D. M., Ruderfer, D. M., & Xu, Y.

Bioinformatics NA

Vol: 39, #1

2022

Single-Nuclear RNA Sequencing of Endomyocardial Biopsies Identifies Persistence of Donor-Recipient Chimerism With Distinct Signatures in Severe Cardiac Allograft Vasculopathy

Amancherla, K., Qin, J., Hulke, M. L., Pfeiffer, R. D., Agrawal, V., Sheng, Q., Xu, Y., Schlendorf, K. H., Lindenfeld, J., Shah, R. v., Freedman, J. E., Tucker, N. R., & Moslehi, J.

Circulation: Heart Failure NA

Efferocytosis drives myeloid NLRP3 dependent inflammasome signaling secretion of IL-1β to promote tumor growth

Lang, C., Roy, S., Wang, Y., Graves, D., Xu, Y., Serezani, C. H., Korrer, M., & Kim, Y. J.

Frontiers in Immunology NA

Kidney Stone Prevalence Based on Self-Report and Electronic Health Records: Insight into the Prevalence of Active Medical Care for Kidney Stones

Forbes, C. M., Nimmagadda, N., Kavoussi, N. L., Xu, Y., Bejan, C. A., Miller, N. L., & Hsi, R. S.

Urology NA

Peripheral Blood Monocyte Abundance Predicts Outcomes in Patients with Breast Cancer

Axelrod, M. L., Wang, Y., Xu, Y., Sun, X., Bejan, C. A., Gonzalez-Ericsson, P. I., Nunnery, S., Bergman, R. E., Donaldson, J., Guerrero-Zotano, A. L., Massa, C., Seliger, B., Sanders, M., Mayer, I. A., & Balko, J. M.

Cancer Research Communications NA

Vol: 2, page: 286–292, #5

Patient-specific comorbidities as prognostic variables for survival in myelofibrosis

Sochacki, A. L., Bejan, C. A., Zhao, S., Patel, A., Kishtagari, A., Spaulding, T. P., Silver, A. J., Stockton, S. S., Pugh, K., Dorand, R. D., Bhatta, M. R., Strayer, N., Zhang, S., Snider, C. A., Stricker, T. P., Nazha, A., Bick, A. G., Xu, Y., & Savona, M. R.

Blood Advances NA

Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer

Obradovic, A., Graves, D., Korrer, M., Wang, Y., Roy, S., Naveed, A., Xu, Y., Luginbuhl, A., Curry, J., Gibson, M., Idrees, K., Hurley, P., Jiang, P., Liu, X. S., Uppaluri, R., Drake, C. G., Califano, A., & Kim, Y. J.

Clinical Cancer Research NA

Vol: 28, page: 2094–2109, #10

2021

RNA-Sequencing Reveals a Distinct Transcriptomic Signature for Giant Cell Myocarditis and Identifies Novel Druggable Targets

Amancherla, K., Qin, J., Wang, Y., Axelrod, M. L., Balko, J. M., Schlendorf, K. H., Hoffman, R. D., Xu, Y., Lindenfeld, J., & Moslehi, J.

Circulation Research NA

Vol: 129, page: 451–453, #3

PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS

Strayer, N., Shirey-Rice, J. K., Shyr, Y., Denny, J. C., Pulley, J. M., & Xu, Y.

Bioinformatics NA

Vol: 37, page: 1778–1780, #12

The Astounding Breadth of Health Disparity: Phenome-Wide Effects of Race on Disease Risk

Pulley, J. M., Jerome, R. N., Bernard, G. R., Shirey-Rice, J. K., Xu, Y., & Wilkins, C. H.

Journal of the National Medical Association NA

Vol: 113, page: 187–194, #2

2020

Opportunities and Challenges for Analyzing Cancer Data at the Inter- and Intra-Institutional Levels

Wu, J., Bryan, J., Rubinstein, S. M., Wang, L., Lenoue-Newton, M., Zuhour, R., Levy, M., Micheel, C., Xu, Y., Bhavnani, S. K., Mackey, L., & Warner, J. L.

JCO Precision Oncology NA

Vol: 4, page: 743–756

2019

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

Finotello, F., Mayer, C., Plattner, C., Laschober, G., Rieder, D., Hackl, H., Krogsdam, A., Loncova, Z., Posch, W., Wilflingseder, D., Sopper, S., Ijsselsteijn, M., Brouwer, T. P., Johnson, D., Xu, Y., Wang, Y., Sanders, M. E., Estrada, M. v., Ericsson-Gonzalez, P., … Trajanoski, Z.

Genome Medicine NA

Vol: 11, page: 34, #1

Trans-ethnic association study of blood pressure determinants in over 750,000 individuals

Giri, Ayush; Hellwege, Jacklyn N; Keaton, Jacob M; Park, Jihwan; Qiu, Chengxiang; Warren, Helen R; Torstenson, Eric S; Kovesdy, Csaba P; Sun, Yan V; Wilson, Otis D;

Nature genetics Nature Publishing Group

Vol: 51, page: 51, #1

Tumor genomic alterations in severe-combined immunodeficiency bare-lymphocyte syndrome genes are associated with high mutational burden and disproportional neo-antigen rates

Wang, Yu; Johnson, Douglas B; Lu, Steve; Diaz, Luis A; Xu, Yaomin; Balko, Justin M;

Journal for immunotherapy of cancer BioMed Central

Vol: 7, page: 123, #1

Performance of a Natural Language Processing Method to Extract Stone Composition From the Electronic Health Record

Bejan, Cosmin A; Lee, Daniel J; Xu, Yaomin; Hsi, Ryan S;

Urology Elsevier

Vol: 132, pages: 56-62

A case report of clonal EBV-like memory CD4+ T cell activation in fatal checkpoint inhibitor-induced encephalitis

Johnson, Douglas B; McDonnell, Wyatt J; Gonzalez-Ericsson, Paula I; Al-Rohil, Rami N; Mobley, Bret C; Salem, Joe-Elie; Wang, Daniel Y; Sanchez, Violeta; Wang, Yu; Chastain, Cody A;

Nature medicine Nature Publishing Group

Vol: 25, pages: 1243-1250, #8

2018

Learning Opportunities for Drug Repositioning via GWAS and PheWAS Findings

Yin, Wen; Gao, Cheng; Xu, Yaomin; Li, Bingshan; Ruderfer, Douglas M; Chen, You;

AMIA Summits on Translational Science Proceedings American Medical Informatics Association

Vol: 2018, page: 237

Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients with metastatic triple-negative breast cancer

Stover, Daniel G; Del Alcazar, Carlos R Gil; Brock, Jane; Guo, Hao; Overmoyer, Beth; Balko, Justin; Xu, Qiong; Bardia, Aditya; Tolaney, Sara M; Gelman, Rebecca;

NPJ Breast Cancer Nature Publishing Group

Vol: 4, page: 10, #1

Multiple tumor suppressors regulate a HIF-dependent negative feedback loop via ISGF3 in human clear cell renal cancer

Liao, Lili; Liu, Zongzhi Z; Langbein, Lauren; Cai, Weijia; Cho, Eun-Ah; Na, Jie; Niu, Xiaohua; Jiang, Wei; Zhong, Zhijiu; Cai, Wesley L;

eLife eLife Sciences Publications Limited

Vol: 7, page: e37925

Tumor-specific MHC-II expression drives a unique pattern of resistance to immunotherapy via LAG-3/FCRL6 engagement

Johnson, Douglas B; Nixon, Mellissa J; Wang, Yu; Wang, Daniel Y; Castellanos, Emily; Estrada, Monica V; Ericsson-Gonzalez, Paula I; Cote, Candace H; Salgado, Roberto; Sanchez, Violeta;

JCI insight American Society for Clinical Investigation

Vol: 3, #24

2017

Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants

Karnes, Jason H; Bastarache, Lisa; Shaffer, Christian M; Gaudieri, Silvana; Xu, Yaomin; Glazer, Andrew M; Mosley, Jonathan D; Zhao, Shilin; Raychaudhuri, Soumya; Mallal, Simon;

Science translational medicine American Association for the Advancement of Science

Vol: 9, page: eaai8708, #389

Advanced molecular characterization of severe autoimmune toxicities associated with checkpoint inhibitor therapies.

Balko, Justin M; Wang, Daniel Y; Wang, Yu; Al-Rohil, Rami; Compton, Margaret; Sosman, Jeffery A; Puzanov, Igor; Mobley, Bret; Hoffman13, Robert D; Xu, Yaomin;

Cancer Research American Association for Cancer Research

2016

Genome-wide analysis of DNA methylation and gene expression defines molecular characteristics of Crohn’s disease-associated fibrosis

Sadler, Tammy; Bhasin, Jeffrey M; Xu, Yaomin; Barnholz-Sloan, Jill; Chen, Yanwen; Ting, Angela H; Stylianou, Eleni;

Clinical epigenetics BioMed Central

Vol: 8, page: 30, #1

Targeted next generation sequencing identifies markers of response to PD-1 blockade

Johnson, Douglas B; Frampton, Garrett M; Rioth, Matthew J; Yusko, Erik; Xu, Yaomin; Guo, Xingyi; Ennis, Riley C; Fabrizio, David; Chalmers, Zachary R; Greenbowe, Joel;

Cancer immunology research American Association for Cancer Research

Vol: 4, pages: 959-967, #11

Fulminant myocarditis with combination immune checkpoint blockade

Johnson, Douglas B; Balko, Justin M; Compton, Margaret L; Chalkias, Spyridon; Gorham, Joshua; Xu, Yaomin; Hicks, Mellissa; Puzanov, Igor; Alexander, Matthew R; Bloomer, Tyler L;

New England Journal of Medicine Massachusetts Medical Society

Vol: 375, pages: 1749-1755, #18

2015

In-depth genomic data analyses revealed complex transcriptional and epigenetic dysregulations of BRAF V600E in melanoma

Guo, Xingyi; Xu, Yaomin; Zhao, Zhongming;

Molecular cancer BioMed Central

Vol: 14, page: 60, #1

Methylome-wide sequencing detects DNA hypermethylation distinguishing indolent from aggressive prostate cancer

Bhasin, Jeffrey M; Lee, Byron H; Matkin, Lars; Taylor, Margaret G; Hu, Bo; Xu, Yaomin; Magi-Galluzzi, Cristina; Klein, Eric A; Ting, Angela H;

Cell reports Elsevier

Vol: 13, pages: 2135-2146, #10

2014

Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation

Xu, Yaomin; Guo, Xingyi; Sun, Jiayang; Zhao, Zhongming;

Bioinformatics Oxford University Press

Vol: 31, pages: 84-93, #1

2013

Screening for SNPs with Allele-Specific Methylation Based on Next-Generation Sequencing Data

Hu, Bo; Ji, Yuan; Xu, Yaomin; Ting, Angela H;

Statistics in biosciences Springer-Verlag

Vol: 5, pages: 179-197, #1

2012

Exhaled breath analysis with a colorimetric sensor array for the identification and characterization of lung cancer

Mazzone, Peter J; Wang, Xiao-Feng; Xu, Yaomin; Mekhail, Tarek; Beukemann, Mary C; Na, Jie; Kemling, Jonathan W; Suslick, Kenneth S; Sasidhar, Madhu;

Journal of Thoracic Oncology Elsevier

Vol: 7, pages: 137-142, #1

Unique DNA methylome profiles in CpG island methylator phenotype colon cancers

Xu, Yaomin; Hu, Bo; Choi, Ae-Jin; Gopalan, Banu; Lee, Byron H; Kalady, Matthew F; Church, James M; Ting, Angela H;

Genome research Cold Spring Harbor Lab

Vol: 22, pages: 283-291, #2

2011

Excessive biologic response to IFNβ is associated with poor treatment response in patients with multiple sclerosis

Rudick, Richard A; Rani, MR Sandhya; Xu, Yaomin; Lee, Jar-Chi; Na, Jie; Shrock, Jennifer; Josyula, Anupama; Fisher, Elizabeth; Ransohoff, Richard M;

PLoS One Public Library of Science

Vol: 6, page: e19262, #5

2010

Natural selection on EPAS1 (HIF2α) associated with low hemoglobin concentration in Tibetan highlanders

Beall, Cynthia M; Cavalleri, Gianpiero L; Deng, Libin; Elston, Robert C; Gao, Yang; Knight, Jo; Li, Chaohua; Li, Jiang Chuan; Liang, Yu; McCormack, Mark;

Proceedings of the National Academy of Sciences National Academy of Sciences

Vol: 107, pages: 11459-11464, #25

Major differences in the responses of primary human leukocyte subsets to IFN-β

van Boxel-Dezaire, Anette HH; Zula, Joana A; Xu, Yaomin; Ransohoff, Richard M; Jacobberger, James W; Stark, George R;

The Journal of Immunology American Association of Immunologists

Vol: 185, pages: 5888-5899, #10

2007

Breast-cancer stromal cells with TP53 mutations and nodal metastases

Patocs, Attila; Zhang, Li; Xu, Yaomin; Weber, Frank; Caldes, Trinidad; Mutter, George L; Platzer, Petra; Eng, Charis;

New England Journal of Medicine Mass Medical Soc

Vol: 357, pages: 2543-2551, #25

Microenvironmental genomic alterations and clinicopathological behavior in head and neck squamous cell carcinoma

Weber, Frank; Xu, Yaomin; Zhang, Li; Patocs, Attila; Shen, Lei; Platzer, Petra; Eng, Charis;

Jama American Medical Association

Vol: 297, pages: 187-195, #2

Reduced expression of autotaxin predicts survival in uveal melanoma

Singh, Arun D; Sisley, Karen; Xu, Yaomin; Li, Jianbo; Faber, Pieter; Plummer, Sarah J; Mudhar, Hardeep S; Rennie, Ian G; Kessler, Patricia M; Casey, Graham;

British Journal of Ophthalmology BMJ Publishing Group Ltd

Vol: 91, pages: 1385-1392, #10

2006

Atherosclerosis Susceptibility Loci Identified From a Strain Intercross of Apolipoprotein E–Deficient Mice via a High-Density Genome Scan

Smith, Jonathan D; Bhasin, Jeffrey M; Baglione, Julie; Settle, Megan; Xu, Yaomin; Barnard, John;

Arteriosclerosis, thrombosis, and vascular biology Lippincott Williams & Wilkins

Vol: 26, pages: 597-603, #3

Liver failure is uncommon in adults receiving long‐term parenteral nutrition

Salvino, Richard; Ghanta, Ravi; Seidner, Douglas L; Mascha, Edward; Xu, Yaomin; Steiger, Ezra;

Journal of parenteral and enteral nutrition Sage Publications

Vol: 30, pages: 202-208, #3

Links

Lab department and center memberships:

• Vanderbilt University Medical Center
• Vanderbilt Department of Biostatistics
• Vanderbilt Department of Biomedical Informatics
• Vanderbilt-Ingram Cancer Center