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.
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.
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.
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.
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