Selected Publications
Unbiased characterization of atrial fibrillation phenotypic architecture
provides insight to genetic liability and clinically relevant outcomes
Davogustto G ., Zhao S ., Li Y ., Farber-Eger E ., Lowery B ., Shaffer L
., Mosley J ., Shoemaker M ., Xu Y ., Roden D ., Wells Q .
Toward personalized skin cancer care: multiple skin cancer development
in five cohorts
Wheless L ., Liao K ., Zheng S ., Li Y ., Yao L ., Xu Y ., Madden C .,
Ike J ., Smith I ., Mosley D ., Grossarth S ., Hartman R ., Wilson O .,
Hung A ., Wehner M .
Overcome the Limitation of Phenome-Wide Association Studies (PheWAS):
Extension of PheWAS to Efficient and Robust Large-Scale ICD Codes
Analysis
Lin Y ., Zhang S ., Vessels T ., Bastarache L ., Bejan C ., Hsie R .,
Philips E ., Ruderfer D ., Pulley J ., Edwards T ., Wells Q ., Warner J
., Denny J ., Roden D ., Kang H ., Xu Y .
Interoperability of phenome-wide multimorbidity patterns: a comparative
study of two large-scale EHR systems
Strayer N ., Vessels T ., Choi K ., Zhang S ., Li Y ., Han L ., Sharber
B ., Hsi R ., Bejan C ., Bick A ., Balko J ., Johnson D ., Wheless L .,
Wells Q ., Philips E ., Pulley J ., Self W ., Chen Q ., Hartert T .,
Wilkins C ., Savona M ., Shyr Y ., Roden D ., Smoller J ., Ruderfer D .,
Xu Y .
The association of infant urinary adrenal steroids with the risk of
childhood asthma development
Turi K ., Li Y ., Xu Y ., Gebretsadik T ., Rosas-Salazar C ., Wiggins D
., McKennan C ., Newcomb D ., Gern J ., Hartert T .
Annals of Allergy, Asthma & Immunology
(2024)
Clonal Hematopoiesis and Inflammation in the VasculaturE (CHIVE): a
prospective, longitudinal cohort and biorepository
Shannon M ., Heimlich J ., Olson S ., Debevec A ., Copeland Z .,
Kishtagari A ., Vlasschaert C ., Snider C ., Silver A ., Brown D .,
Spaulding T ., Bhatta M ., Pugh K ., Stockton S ., Ulloa J ., Xu Y .,
Baljevic M ., Moslehi J ., Jahangir E ., Ferrell P ., Slosky D ., Bick A
., Savona M .
Ablation of IFNγ in myeloid cells suppresses liver inflammation and
fibrogenesis in mice with hepatic small heterodimer partner (SHP)
deletion
Zhu L ., Litts B ., Wang Y ., Rein J ., Atzrodt C ., Chinnarasu S ., An
J ., Thorson A ., Xu Y ., Stafford J .
Molecular Metabolism
(2024)
Polygenic risk score for ulcerative colitis predicts immune checkpoint
inhibitor-mediated colitis
Middha P ., Thummalapalli R ., Betti M ., Yao L ., Quandt Z .,
Balaratnam K ., Bejan C ., Cardenas E ., Falcon C ., Faleck D ., Leighl
N ., Bradbury P ., Shepherd F ., Sacher A ., Eng L ., Gubens M .,
Huntsman S ., Johnson D ., Kachuri L ., Khan K ., Li M ., Lovly C .,
Murray M ., Patel D ., Werking K ., Xu Y ., Zhan L ., Balko J ., Liu G
., Aldrich M ., Schoenfeld A ., Ziv E ., NA NA .
Nature Communications
(2024)
Solid Organ Transplant Recipients Exhibit More TET2-Mutant Clonal
Hematopoiesis of Indeterminate Potential Not Driven by Increased
Transplantation Risk
Silver A ., Vlasschaert C ., Mack T ., Sharber B ., Xu Y ., Bick A .,
Pinson C ., Savona M .
Clinical Cancer Research
(2024)
PheMIME: An Interactive Web App and Knowledge Base for Phenome-Wide,
Multi-Institutional Multimorbidity Analysis
Zhang S ., Strayer N ., Vessels T ., Choi K ., Wang G ., Li Y ., Bejan C
., Hsi R ., Bick A ., Velez Edwards D ., Savona M ., Philips E ., Pulley
J ., Self W ., Hopkins W ., Roden D ., Smoller J ., Ruderfer D ., Xu Y .
Cost-effective and scalable clonal hematopoiesis assay provides insight
into clonal dynamics
Mack T ., Vlasschaert C ., von Beck K ., Silver A ., Heimlich J .,
Poisner H ., Condon H ., Ulloa J ., Sochacki A ., Spaulding T .,
Kishtagari A ., Bejan C ., Xu Y ., Savona M ., Jones A ., Bick A .
A practical approach to curate clonal hematopoiesis of indeterminate
potential in human genetic datasets
Vlasschaert C ., Mack T ., Heimlich J ., Niroula A ., Uddin M .,
Weinstock J ., Sharber B ., Silver A ., Xu Y ., Savona M ., Gibson C .,
Lanktree M ., Rauh M ., Ebert B ., Natarajan P ., Jaiswal S ., Bick A .
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 ., Pfeiffer R ., Agrawal V ., Sheng Q
., Xu Y ., Schlendorf K ., Lindenfeld J ., Shah R ., Freedman J .,
Tucker N ., Moslehi J .
Circulation: Heart Failure (2023)
Kidney Stone Prevalence Based on Self-Report and Electronic Health
Records: Insight into the Prevalence of Active Medical Care for Kidney
Stones
Forbes C ., Nimmagadda N ., Kavoussi N ., Xu Y ., Bejan C ., Miller N .,
Hsi R .
Patient-specific comorbidities as prognostic variables for survival
in myelofibrosis
Sochacki A ., Bejan C ., Zhao S ., Patel A ., Kishtagari A ., Spaulding
T ., Silver A ., Stockton S ., Pugh K ., Dorand R ., Bhatta M ., Strayer
N ., Zhang S ., Snider C ., Stricker T ., Nazha A ., Bick A ., Xu Y .,
Savona M .
Germline genomic and phenomic landscape of clonal hematopoiesis in
323,112 individuals
Uddin M ., Yu Z ., Weinstock J ., Nakao T ., Niroula A ., Urbut S .,
Koyama S ., Zekavat S ., Paruchuri K ., Silver A ., Mack T ., Wong M .,
Haidermota S ., Bhattacharya R ., Jorshery S ., Raddatz M ., Honigberg M
., Hornsby W ., Zhang M ., Sankaran V ., Griffin G ., Gibson C ., Kresge
H ., Ellinor P ., Cho K ., Sun Y ., Wilson P ., Pyarajan S ., Genovese G
., Xu Y ., Savona M ., Reiner A ., Jaiswal S ., Ebert B ., Bick A .,
Natarajan P ., NA NA .
Interactive network-based clustering and investigation of multimorbidity
association matrices with associationSubgraphs
Strayer N ., Zhang S ., Yao L ., Vessels T ., Bejan C ., Hsi R .,
Shirey-Rice J ., Balko J ., Johnson D ., Phillips E ., Bick A ., Edwards
T ., Velez Edwards D ., Pulley J ., Wells Q ., Savona M ., Cox N .,
Roden D ., Ruderfer D ., Xu Y .
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 ., Korrer M
., Kim Y .
Frontiers in Immunology
(2022)
Peripheral Blood Monocyte Abundance Predicts Outcomes in Patients with
Breast Cancer
Axelrod M ., Wang Y ., Xu Y ., Sun X ., Bejan C ., Gonzalez-Ericsson P
., Nunnery S ., Bergman R ., Donaldson J ., Guerrero-Zotano A ., Massa C
., Seliger B ., Sanders M ., Mayer I ., Balko J .
Cancer Research Communications (2022)
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 ., Uppaluri R ., Drake C ., Califano A ., Kim Y .
Clinical Cancer Research
(2022)
RNA-Sequencing Reveals a Distinct Transcriptomic Signature for Giant
Cell Myocarditis and Identifies Novel Druggable Targets
Amancherla K ., Qin J ., Wang Y ., Axelrod M ., Balko J ., Schlendorf K
., Hoffman R ., Xu Y ., Lindenfeld J ., Moslehi J .
Circulation Research
(2021)
The Astounding Breadth of Health Disparity: Phenome-Wide Effects of Race
on Disease Risk
Pulley J ., Jerome R ., Bernard G ., Shirey-Rice J ., Xu Y ., Wilkins C
.
Journal of the National Medical Association
(2021)
PheWAS-ME: a web-app for interactive exploration of multimorbidity
patterns in PheWAS
Strayer N ., Shirey-Rice J ., Shyr Y ., Denny J ., Pulley J ., Xu Y .
Opportunities and Challenges for Analyzing Cancer Data at the Inter- and
Intra-Institutional Levels
Wu J ., Bryan J ., Rubinstein S ., Wang L ., Lenoue-Newton M ., Zuhour R
., Levy M ., Micheel C ., Xu Y ., Bhavnani S ., Mackey L ., Warner J .
JCO Precision Oncology
(2020)
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 ., Johnson D ., Xu Y ., Wang Y ., Sanders
M ., Estrada M ., Ericsson-Gonzalez P ., Charoentong P ., Balko J ., de
Miranda N ., Trajanoski Z .
Performance of a Natural Language Processing Method to Extract Stone
Composition From the Electronic Health Record
Bejan C ., Lee D ., Xu Y ., Hsi R .
A case report of clonal EBV-like memory CD4+ T cell activation in fatal
checkpoint inhibitor-induced encephalitis
Johnson D ., McDonnell W ., Gonzalez-Ericsson P ., Al-Rohil R ., Mobley
B ., Salem J ., Wang D ., Sanchez V ., Wang Y ., Chastain C ., Barker K
., Liang Y ., Warren S ., Beechem J ., Menzies A ., Tio M ., Long G .,
Cohen J ., Guidon A ., O’Hare M ., Chandra S ., Chowdhary A .,
Lebrun-Vignes B ., Goldinger S ., Rushing E ., Buchbinder E ., Mallal S
., Shi C ., Xu Y ., Moslehi J ., Sanders M ., Sosman J ., Balko J .
Trans-ethnic association study of blood pressure determinants in over
750,000 individuals
Giri A ., NA NA ., Hellwege J ., Keaton J ., Park J ., Qiu C ., Warren H
., Torstenson E ., Kovesdy C ., Sun Y ., Wilson O ., Robinson-Cohen C .,
Roumie C ., Chung C ., Birdwell K ., Damrauer S ., DuVall S ., Klarin D
., Cho K ., Wang Y ., Evangelou E ., Cabrera C ., Wain L ., Shrestha R
., Mautz B ., Akwo E ., Sargurupremraj M ., Debette S ., Boehnke M .,
Scott L ., Luan J ., Zhao J ., Willems S ., Thériault S ., Shah N .,
Oldmeadow C ., Almgren P ., Li-Gao R ., Verweij N ., Boutin T ., Mangino
M ., Ntalla I ., Feofanova E ., Surendran P ., Cook J ., Karthikeyan S
., Lahrouchi N ., Liu C ., Sepúlveda N ., Richardson T ., Kraja A .,
Amouyel P ., Farrall M ., Poulter N ., Laakso M ., Zeggini E ., Sever P
., Scott R ., Langenberg C ., Wareham N ., Conen D ., Palmer C ., Attia
J ., Chasman D ., Ridker P ., Melander O ., Mook-Kanamori D ., Harst P
., Cucca F ., Schlessinger D ., Hayward C ., Spector T ., Jarvelin M .,
Hennig B ., Timpson N ., Wei W ., Smith J ., Xu Y ., Matheny M ., Siew E
., Lindgren C ., Herzig K ., Dedoussis G ., Denny J ., Psaty B ., Howson
J ., Munroe P ., Newton-Cheh C ., Caulfield M ., Elliott P ., Gaziano J
., Concato J ., Wilson P ., Tsao P ., Velez Edwards D ., Susztak K .,
O’Donnell C ., Hung A ., Edwards T ., NA NA ., NA NA ., NA NA .
Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients
with metastatic triple-negative breast cancer
Stover D ., Gil Del Alcazar C ., Brock J ., Guo H ., Overmoyer B .,
Balko J ., Xu Q ., Bardia A ., Tolaney S ., Gelman R ., Lloyd M ., Wang
Y ., Xu Y ., Michor F ., Wang V ., Winer E ., Polyak K ., Lin N .
Multiple tumor suppressors regulate a HIF-dependent negative feedback
loop via ISGF3 in human clear cell renal cancer
Liao L ., Liu Z ., Langbein L ., Cai W ., Cho E ., Na J ., Niu X .,
Jiang W ., Zhong Z ., Cai W ., Jagannathan G ., Dulaimi E ., Testa J .,
Uzzo R ., Wang Y ., Stark G ., Sun J ., Peiper S ., Xu Y ., Yan Q .,
Yang H .
Tumor-specific MHC-II expression drives a unique pattern of resistance
to immunotherapy via LAG-3/FCRL6 engagement
Johnson D ., Nixon M ., Wang Y ., Wang D ., Castellanos E ., Estrada M
., Ericsson-Gonzalez P ., Cote C ., Salgado R ., Sanchez V ., Dean P .,
Opalenik S ., Schreeder D ., Rimm D ., Kim J ., Bordeaux J ., Loi S .,
Horn L ., Sanders M ., Ferrell P ., Xu Y ., Sosman J ., Davis R ., Balko
J .
Phenome-wide scanning identifies multiple diseases and disease severity
phenotypes associated with HLA variants
Karnes J ., Bastarache L ., Shaffer C ., Gaudieri S ., Xu Y ., Glazer A
., Mosley J ., Zhao S ., Raychaudhuri S ., Mallal S ., Ye Z ., Mayer J
., Brilliant M ., Hebbring S ., Roden D ., Phillips E ., Denny J .
Science Translational Medicine (2017)
Genome-wide analysis of DNA methylation and gene expression defines
molecular characteristics of Crohn’s disease-associated fibrosis
Sadler T ., Bhasin J ., Xu Y ., Barnholz-Sloan J ., Chen Y ., Ting A .,
Stylianou E .
Clinical Epigenetics
(2016)
Targeted Next Generation Sequencing Identifies Markers of Response to
PD-1 Blockade
Johnson D ., Frampton G ., Rioth M ., Yusko E ., Xu Y ., Guo X ., Ennis
R ., Fabrizio D ., Chalmers Z ., Greenbowe J ., Ali S ., Balasubramanian
S ., Sun J ., He Y ., Frederick D ., Puzanov I ., Balko J ., Cates J .,
Ross J ., Sanders C ., Robins H ., Shyr Y ., Miller V ., Stephens P .,
Sullivan R ., Sosman J ., Lovly C .
Cancer Immunology Research (2016)
Fulminant Myocarditis with Combination Immune Checkpoint Blockade
Johnson D ., Balko J ., Compton M ., Chalkias S ., Gorham J ., Xu Y .,
Hicks M ., Puzanov I ., Alexander M ., Bloomer T ., Becker J ., Slosky D
., Phillips E ., Pilkinton M ., Craig-Owens L ., Kola N ., Plautz G .,
Reshef D ., Deutsch J ., Deering R ., Olenchock B ., Lichtman A ., Roden
D ., Seidman C ., Koralnik I ., Seidman J ., Hoffman R ., Taube J .,
Diaz L ., Anders R ., Sosman J ., Moslehi J .
New England Journal of Medicine (2016)
In-depth genomic data analyses revealed complex transcriptional and
epigenetic dysregulations of BRAF V600E in melanoma
Guo X ., Xu Y ., Zhao Z .
Methylome-wide Sequencing Detects DNA Hypermethylation Distinguishing
Indolent from Aggressive Prostate Cancer
Bhasin J ., Lee B ., Matkin L ., Taylor M ., Hu B ., Xu Y .,
Magi-Galluzzi C ., Klein E ., Ting A .
Snowball: resampling combined with distance-based regression to discover
transcriptional consequences of a driver mutation
Xu Y ., Guo X ., Sun J ., Zhao Z .
Exhaled Breath Analysis with a Colorimetric Sensor Array for the
Identification and Characterization of Lung Cancer
Mazzone P ., Wang X ., Xu Y ., Mekhail T ., Beukemann M ., Na J .,
Kemling J ., Suslick K ., Sasidhar M .
Journal of Thoracic Oncology (2012)
Unique DNA methylome profiles in CpG island methylator phenotype colon
cancers
Xu Y ., Hu B ., Choi A ., Gopalan B ., Lee B ., Kalady M ., Church J .,
Ting A .
Natural selection on EPAS1 ( HIF2α ) associated with low
hemoglobin concentration in Tibetan highlanders
Beall C ., Cavalleri G ., Deng L ., Elston R ., Gao Y ., Knight J ., Li
C ., Li J ., Liang Y ., McCormack M ., Montgomery H ., Pan H ., Robbins
P ., Shianna K ., Tam S ., Tsering N ., Veeramah K ., Wang W ., Wangdui
P ., Weale M ., Xu Y ., Xu Z ., Yang L ., Zaman M ., Zeng C ., Zhang L
., Zhang X ., Zhaxi P ., Zheng Y .
Proceedings of the National Academy of Sciences
(2010)
Breast-Cancer Stromal Cells withTP53Mutations and Nodal
Metastases
Patocs A ., Zhang L ., Xu Y ., Weber F ., Caldes T ., Mutter G .,
Platzer P ., Eng C .
New England Journal of Medicine (2007)
Microenvironmental Genomic Alterations and Clinicopathological Behavior
in Head and Neck Squamous Cell Carcinoma
Weber F ., Xu Y ., Zhang L ., Patocs A ., Shen L ., Platzer P ., Eng C .
