Underline = past/current group member , * = authors
contributed equally, ✉ = corresponding author
2025 -
Multi-omic deconvolution and DNA-RNA dynamics in cancer
Dai Y, Pan X, Guo S, Ji S, Cao S, Montierth MD,
Jiang Y, Shi L, Shalapour S, Echeverria GV, Yates L, Staaf J, Chang JT, Lim B,
Yuan Y, Wang W✉. Deciphering transcriptional activity of the tumor
microenvironment for robust stratification of chemotherapy response in triple-negative
breast cancer. submitted
Dai Y, Guo S, Pan Y, Castignani C, Montierth MD, Van Loo P✉,
Wang W✉. A guide to transcriptomic deconvolution in cancer. under
review
Jiang Y*, Montierth M*, Yu K* , et al., Wang W✉.
Pan-cancer subclonal mutation analysis of 7,827 tumors predicts clinical outcome.
under review[preprint][Github:CliPP]
Guo S*, Liu X*, Cheng X*, Jiang Y, Ji S, Liang Q, Koval A, Li Y,
Owen LA, Kim IK, Aparicio A, Lee S, Sood AK, Kopetz S, Shen JP, Weinstein JN, Deangelis
MM, Chen R, Wang W✉. A deconvolution framework that uses single-cell
sequencing plus a small benchmark data set for accurate analysis of cell type ratios in
complex tissue samples. Genome Res. Published in Advance January 6, 2025,
doi:10.1101/gr.279605.124 [abstract][GitHub repository: DeMixSC]
Risk prediction with machine learning and Bayesian semi-parametric
models
Liu X, Yan, H, Shi H, Montellier E, Chi E, Hainaut P, Wang
W✉. Transfer learning for survival-based
clustering of predictors with an application
to TP53 mutation annotation. Proceedings of The Inaugural Workshop on Frontiers in
Statistical Machine Learning. 2025. FSML travel award
Corredor JL*, Dodd-Eaton EB*, Woodman-Ross J, Woodson A, Nguyen NH, Peng
G, Green S, Gutierrez AM, Arun BK✉, Wang W✉. Performance of LFSPRO
TP53 germline carrier risk predictions compared to standard genetic counseling
practice on prospectively collected probands. under revision[Preprint]
Nguyen NH, Shin SJ, Dodd-Eaton EB, Ning J, Wang W✉.
Personalized Risk Prediction for Cancer Survivors: A Bayesian Semi-parametric Recurrent
Event Model with Competing Outcomes. [preprint] AOAS, under review.
Stats Up AI
Zheng et al. Statistics and AI - A Fireside Conversation. Harvard Data Science
Review. accepted.
Collaboration Papers
Duan Y, Guo S, Yan H, Wang W, Mueller P. Spatially aligned random
partition models on spatially resolved
transcriptomics data. submitted. [Preprint]
Foutunno C, Fone MN, Mester J, et al. A quantitative Bayesian-informed approach to
gene-specific variant classification: Updated Expert Panel recommendations improve
analyses of TP53 germline variants for Li-Fraumeni syndrome. Genome Medicine, under 2nd review
Lin C et al. Cholesterol metabolism regulated by CAMKK2-CREB signaling promotes
castration-resistant prostate cancer. Cell reports. accepted
Chowdhury S, Ferri-Borgogno S, Yang P, Wang W, Peng J, Mok S, Wang P.
Learning directed acyclic graphs for ligands and receptors based on spatially resolved
transcriptomic analysis of ovarian cancer. Briefings in Bioinformatics. 2025 Mar
4;26(2):bbaf085. doi: 10.1093/bib/bbaf085. [Full
text]
Ito I et al. Development and Characterization of orthotopic patient-derived xenograft
models of mucinous appendiceal adenocarcinoma. ESMO Gastrointestinal Oncology.
accepted.
Duan, Y, Guo, S, Wang, W, Mueller, P. Immune Profiling among Colorectal
Cancer Subtypes using Dependent Mixture Models. JASA Published online: 25 Feb
2025. [Abstract]
2024 -
Multi-omic deconvolution and DNA-RNA dynamics in cancer
Ji S, Zhu T, Sethia A, Wang W. Accelerated somatic mutation calling
for whole-genome and whole-exome sequencing data from heterogenous tumor samples.
Genome Res. 2024 May 3;. doi: 10.1101/gr.278456.123. [Epub ahead of print] [Full
text]
Risk prediction with machine learning and Bayesian
semi-parametric models
Nguyen NH, Dodd-Eaton EB, Corredor JL, Woodman-Ross J, Green S,
Gutierrez AM, Arun BK, Wang W. Validating Risk Prediction Models for Multiple
Primaries and Competing Cancer Outcomes in Families With Li-Fraumeni Syndrome Using
Clinically Ascertained Data. J Clin Oncol. 2024 Apr 3;:JCO2301926. doi:
10.1200/JCO.23.01926. [Epub ahead of print] [Full
text]
Nguyen NH, Dodd-Eaton EB, Peng G, Corredor JL, Jiao W,
Woodman-Ross J, Arun BK, Wang W✉. LFSPROShiny: an interactive
R/Shiny app for prediction and visualization of cancer risks in families with
deleterious germline TP53 mutations. JCO Clinical Cancer
Informatics. 2024 Feb 12. Volume 8. doi: 10.1200/CCI.23.00167. [Full text][Github:LFSPROShiny]
Yousef M, Yousef A, Chowdury S, Fanaeian M, Knafl M, Peterson J, Zeineddine M,
Alfaro K, Zeineddine F, Godstein D, Horstein N, Dasari A, Huey R, Johnson B, Higbie
V, Bent A, Kee B, Lee M, Morelli MP, Morris VK, Halperin D, Overman MJ, Parseghian
C, Villar E, Wolff R, Raghav KP, White MG, Uppal A, Sun R, Wang W, Kopetz SK,
Willis J, Shen JP. Molecular, Socioeconomic, and Clinical Factors Affecting Racial
and Ethnic Disparities in Colorectal Cancer Survival. JAMA Oncol. 2024 Sep
12. doi: 10.1001/jamaoncol.2024.3666. Online ahead of print. [Full
text]
Wang JR, Zafereo ME, Cabanillas ME, Wu CC, Xu L, Dai Y, Wang W, Lai
SY, Henderson Y, Erasmus L, Williams MD, Joshu C, Ray D. The association between
thyroid differentiation score and survival outcomes in papillary thyroid carcinoma.
J Clin Endocrinol Metab. 2024 Aug 1:dgae532. doi: 10.1210/clinem/dgae532.
Online ahead of print. [Full
text]
Aparicio AM, Tidwell RSS, Yadav SS, Chen JS, Zhang M, Liu J, Guo S, Pilie
PG, Yu Y, Song X, Vundavilli H, Jindal S, Zhu K, Viscuse PV, Lebenthal JM,
Hahn AW, Soundararajan R, Corn PG, Zurita AJ, Subudhi SK, Zhang J, Wang W,
Huff C, Troncoso P, Allison JP, Sharma P, Logothetis CJ. A Modular Trial of Androgen
Signaling Inhibitor Combinations Testing a Risk-Adapted Strategy in Patients with
Metastatic Castration-Resistant Prostate Cancer. Clin Cancer Res. 2024 Apr
29;. doi: 10.1158/1078-0432.CCR-23-3740. [Epub ahead of print] [Full
text]
Bahrambeigi V, Lee JJ, Branchi V, Rajapakshe KI, Xu Z, Kui N, Henry JT, Wang K,
Stephens BM, Dhebat S, Hurd MW, Sun R, Yang P, Ruppin E, Wang W,
Kopetz S, Maitra A, Guerrero PA. Transcriptomic Profiling of Plasma Extracellular
Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and
Molecular Subtype. Cancer Res. 2024 Mar 7;. doi:
10.1158/0008-5472.CAN-23-4070. [Epub ahead of print][Full
text]
2023 -
Rangel R et al. TP53 gain-of-function mutation modulates the immunosuppressive
microenvironment in non-HPV associated oral squamous cell carcinoma. Journal
for ImmunoTherapy of Cancer, 2023 Aug;11(8):e006666. doi:
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Wang JR, Zafereo ME, Wang W, Joshu C, Debashree R. Association of
polygenic score with tumor molecular subtypes in papillary thyroid carcinoma.
Journal of Clinical Endocrinology & Metabolism, 2023 Jul 15;dgad407. doi:
10.1210/clinem/dgad407. [full
text]
Cermakova K, Tao L, Dejmek M, Sala M, Montierth MD, Chan YS, Patel I,
Chambers C, Cabrera ML, Hoffman D, Parchem RJ, Wang W, Nencka R, Barbieri
E, Hodges HC. Reactivation of the G1 enhancer landscape underlies core circuitry
addiction to SWI/SNF. Nucleic Acids Research. gkad1081,
https://doi.org/10.1093/nar/gkad1081 Published: 23 November 2023. Selected by NAR as a "breakthrough article" of the journal
issue!
Zheng C et al. CRISPR-Cas9-based functional interrogation of unconventional
translatome reveals human cancer dependency on cryptic non-canonical open
reading frames. Nature Structural & Molecular Biology Nov 2023; 30,
1878–1892. doi:10.1038/s41594-023-01117-1. [full text]
Zheng C et al. Multiomics analyses reveal DARS1-AS1/YBX1-controlled
post-transcriptional circuits promoting glioblastoma
tumorigenesis/radioresistance. Science Advances, Aug 4;9(31):eadf3984.
doi: 10.1126/sciadv.adf3984. Epub 2023 Aug 4. [full
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Chachad D, Patel LR, Recio CV, Pourebrahim R, Whitley EM, Wang W,
Su X, Xu A, Lee DF, Lozano G. Unique transcriptional profiles underlie
osteosarcomagenesis driven by different p53 mutants. Cancer Research,
2023 May 19:CAN-22-3464. doi: 10.1158/0008-5472.CAN-22-3464. Online ahead of
print. [Abstract][Full
text]
2022 -
Multi-omic deconvolution and DNA-RNA dynamics in cancer
Ji S, Montierth M, Wang W✉. MuSE: A Novel Approach to
Mutation Calling with Sample-Specific Error Modeling. Methods Molecular
Biology. 2022; 2493:21-27. doi: 10.1007/978-1-0716-2293-3_2.[Full
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Cao S, et al., Wang W✉ Estimation of tumor cell total
mRNA expression in 15 cancer types predicts disease progression. Nature
Biotechnology Published online June 13 2022. doi
10.1038/s41587-022-01342-x. [Abstract]
Collaboration Papers
Wang JR, Montierth M, Li X, Goswami M, Zhao X, Cote G, Wang
W, Iyer P, Dadu R, Busaidy NL, Lai SY, Grosss ND, Ferrarotto R, Lu
C, Gunn GB, Williams MD, Routbort M, Zafereo ME, Cabanillas ME. Impact of
Somatic Mutations on Survival Outcomes in Anaplastic Thyroid Carcinoma
Patients. JCO Precision Oncology no. 6 (2022) e2100504. Published
online August 17, 2022. DOI: 10.1200/PO.21.00504 [abstract][full
text]
Bondaruk J et al., Wang W, McConkey D, Wei P, Kimmel M, Czerniak B.
The origin of bladder cancer from mucosal field effects. iScience
2022 Jun 7; 25(7):104551. doi: 10.1016/j.isci.2022.104551. eCollection 2022
Jul 15 [Full
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Wang Z, Baladandayuthapani V, Kaseb AO, Amin HM, Hassan MM, Wang
W, Morris JS. Bayesian Edge
Regression in Undirected Graphical Models to Characterize
Interpatient Heterogeneity in Cancer. Journal of the American Statistical
Association. Pages 533-546. Published online Jan 5 2022. [Full
text]
2021 -
Taavitsainen S et al., Wang W, Nykter M, Urbanucci A.
Single-cell ATAC and RNA sequencing reveal pre-existing and persistent
subpopulations of cells associated with relapse of prostate cancer.
Nature Communications 2021 Sep 6;12(1):5307. doi:
10.1038/s41467-021-25624-1. [Abstract]
Cao L et al. Clinical Proteomic Tumor Analysis Consortium.
Proteogenomic Characterization of
Pancreatic Ductal Adenocarcinoma. Cell 2021 Sep
16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023. [Abstract]
Dentro S*, Leshchiner I*, Haase K*, Tarabichi M*, Wintersinger J*,
Deshwar A*, Yu K*, Rubanova Y*, Mcintyre G*, et al. PCAWG
Evolution and Heterogeneity Working Group. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.
Cell, 2021 Apr 15; 184(8): 2239-2254.e39. [abstract][Full
text]
[Github:CSR] Wang is a co-last author. Selected for the MD
Anderson Wall of Science and Research Excellence webpage.
2020 -
Morris JS, Hassan MM, Zohner YE, Wang Z, Xiao L, Rashid A,
Abdel-Wahab R, Ballard KL, Wolff RA, George B, Li L, Allen G,
Weylandt M, Li D, Wang W, Raghav K, Yao J, Amin HM, Kaseb AO.
Deconvolution-based Circulating Biomarker Aberration Score Enhances
Hepatocellular Carcinoma Staging. Hepatology. Published
online 2020/9/15. [abstract][Full text]
Haider H*, Tyekucheva S, Prandi D, Fox NS, Ahn J, Xu AW,
Pantazi A, Park PJ, Laird PW, Sander C, Wang W*, Demichelis
F*, Loda M*, Boutros PC*, TCGA Research Network. Systematic
assessment of tumour purity and its clinical implications. JCO
Precision Oncology. No. 4 (2020) 995-1005. Published online
September 4, 2020. [abstract][Full
text]. *co-senior author
Gao F*, Pan X*, Dodd EB, Vera Recio C,
Bojadzieva J, Mai PL, Johnson VE, Zelley K, Kim E. Nichols KE,
Garber JE, Savage SA, Strong LC, Wang W✉. A
pedigree-based prediction model identifies carriers of deleterious
de novo mutations in families with Li-Fraumeni syndrome.
Genome Research. 2020 Aug 18. doi: 10.1101/gr.249599.119.
Online ahead of print. [Abstract][Full
Text] *authors contributed equally
Amir Nikooienejad, Wenyi Wang, Valen Johnson. Bayesian
Variable Selection For Survival Data Using Inverse Moment Priors.
Annals of Applied Statistics. Volume 14, Number 2 (2020),
809-828. [Abstract][preprint]
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.
Pan-cancer analysis of whole genomes. Nature. 2020
Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb
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T, Lyu R, HipSci Consortium, Wang W, Gaffney DJ, Simons BD,
Stegle O, Teichmann SA. Cardelino: computational integration of
somatic clonal substructure and single-cell transcriptomes
Nature Methods 2020 Apr;17(4):414-421. doi:
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Wu CC, Beird H, Livingston JL, Advani S, Cao S, Reuben A,
Ingram D, Ju Z, Wang WL, Leung CH, Zheng Y, Mitra A, Lin H, RoszikJ,
Wang W, Patel S, Benjamin R, Gordon M, Hwu P, Gorlick R,
Lazar A, Daw N, Lewis V, and Futreal PA. Immuno-genomic landscape of
osteosarcoma. Nature Communications 2020 Feb 21;11(1):1008.
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evaluating tumor subclonal reconstruction. Nature
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2019 -
Seung Jun Shin, Elissa Dodd, Gang Peng,
Jasmina Bojadzieva, Jingxiao Chen, Chris Amos, Phuong L.
Mai, Sharon A. Savage, Mandy L. Ballinger, David M. Thomas, Ying
Yuan, Louise C. Strong, Wenyi Wang✉. Penetrance of
Different Cancer Types in Families with Li-Fraumeni Syndrome: A
Validation Study Using Multicenter Cohorts. Cancer
Research. 2020 Jan 15;80(2):354-360. doi:
10.1158/0008-5472.CAN-19-0728. Epub 2019 Nov 12. [Abstract][Software:
LFSPRO2.0.0] for risk assessment of specific cancer
type.
Seung Jun Shin, Elissa B. Dodd, Fan Gao,
Jasmina Bojadzieva, Jingxiao Chen, Xianhua Kong, Chris
Amos, Jing Ning, Louise C. Strong, Wenyi Wang✉.
Penetrance Estimates Over Time to First and Second Primary
Cancer Diagnosis in Families with Li-Fraumeni Syndrome: A Single
Institution Perspective. Cancer Research. 2020 Jan
15;80(2):347-353. doi: 10.1158/0008-5472.CAN-19-0725. Epub 2019
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Carniti C, Heavican T, Pellegrinelli A, Pruneri G, Butler A,
Bhosle S, Chiappella A, Rocco AD, Zinzani PL, Zaja F, Piva R,
Inghirami G, Wang W, Palomero T, Iqbal J, Neri A,
Campbell PJ, Corradini P. Integration of Transcriptional and
Mutational Data improves the Stratification of Peripheral T-Cell
Lymphoma. American Journal of Hematology March 4 2019
doi: 10.1002/ajh.25450.
Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz
F; PCAWG Evolution and Heterogeneity Working Group, Spellman
PT, Morris QD, Lingjaerde OC, Wedge DC, Van Loo P. Neutral
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Shin SJ, Li J, Ning J, Bodjadzieva J, Strong
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the penetrance estimation of multiple primary cancers in
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Wang Z, Morris JS, Cao S, Ahn J, Liu
R, Tyekucheva S, Li B, Lu W, Tang X, Wistuba II,
Bowden M, Mucci L, Loda M, Parmigiani G, Holmes CC, Wang
W✉ .Transcriptome Deconvolution of
Heterogeneous Tumor Samples with Immune Infiltration.
iScience. 2018 Nov 30;9:451-460. doi:
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text][Software:DeMixT]
Shin SJ, Ying Yuan✉, Louise C. Strong, Jasmina
Bojadzieva, Wang W✉ . Bayesian Semiparametric
Estimation of Cancer-specic
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Li J, Fu C, Speed TP, Wang W✉ , Symmans
WF✉. Accurate RNA Sequencing From Formalin-Fixed Cancer
Tissue To Represent High Quality Transcriptome From Frozen
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PO in 2018
2017 -
Peng G, Bojadzieva J, Ballinger ML, Thomas DM,
Strong LC, Wang W✉ . Estimating TP53
Mutation Carrier Probability in Families with
Li-Fraumeni Syndrome Using LFSPRO. Cancer
Epidemiology, Biomarker and Prevention Jan 2017.
DOI: 10.1158/1055-9965.EPI-16-0695. [Abstract][Full
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Ahn J, Morita S, Wang W✉ and Yuan
Y✉. Bayesian shared-parameter models for
longitudinal dyadic data with informative missing data
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2016 -
Fan Y, Xi L, Hughes DST, Zhang J, Zhang J,
Futreal PA, Wheeler DA and Wang W✉. MuSE:
accounting for tumor heterogeneity using a
sample-specific error model improves sensitivity and
specificity in mutation calling from sequencing
data. Genome Biology. 2016. 17:178
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Nikooienejad A, Wang W✉ , Johnson
VE✉. Bayesian Variable Selection for Binary
Outcomes in High
Dimensional Genomic Studies Using Non-Local Priors.
Bioinformatics Jan 6, 2016. doi:
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J, Asselin-Labat ML, Smyth GK, Ritchie ME. RNA-seq
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2015 -
Lefterova MI*, Shen P*, Odegaard JI*, Fung E,
Chiang T, Peng G, Davis RW, Wang W,
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I, Scharfe C. Next-generation molecular testing
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The Cancer Genome Atlas Research Network. The
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C, Yamaguchi TN, Bare JC, P'ng C, Waggott D,
Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation
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Margolin AA, Stuart JM, Boutros PC. Combining
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2014 -
Peng G, Fan Y, Wang W✉
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2013 -
Ahn J, Liu S, Wang W✉ and
Yuan Y✉. Bayesian latent-class mixed-effect
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69(4):914-24, 2013 Dec [Abstract]
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. DeMix: Deconvolution for Mixed Cancer
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Bioinformatics 2013 doi:
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Davis RW and Scharfe C. Multiplex target capture
with double-stranded DNA probes. Genome
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Peng G, Fan Y, Palculict TB, Shen
P, Ruteshouser EC, Chi A,
Davis RW, Huff V, Scharfe C, Wang W✉
. Rare variant detection
using family-based sequencing analysis.
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The Cancer Genome Atlas Research Network. The
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Srivastava S, Wang W, Manyem G,
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2012 -
Zhang N, Xu Y, O'Hely M, Speed TP,
Scharfe C and Wang W✉ . SRMA: an R
package for resequencing array data
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Hua Y, Gorshkov K, Yang Y, Wang W, Zhang
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Rubio JP, Wilkins EJ, Kostchet K, Cowie TC,
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2011 -
Shen P*, Wang W*, Krishnakumar S, Chi AK,
Palm C,
Enns GM, Davis RW, Speed TP, Mindrinos M, Scharfe C.
High quality DNA sequence capture of 524 disease
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2010 -
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Wang W, Shen P, Thyagarajan S, Lin S,
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Wang W, Niendorf KB, Patel D, Blackford
A, Marroni F, Sober AJ, Parmigiani G and Tsao H.
Estimating CDKN2A Carrier Probability and
Personalizing Cancer Risk Assessments in
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2008 -
Wang W, Carvalho B, Miller N, Pevsner J,
Chakaravarti A and Irizarry RA. Estimating
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2007 -
Wang W, Chen S, Brune KA, Hruban RH,
Parmigiani G and Klein AP. PancPRO: risk
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2007;25:1417-22. [Abstract]
Nicodemus KK, Wang Wand Shugart YY.
Stability of Variable Importance Scores and
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using Statistical Learning Tools on Single
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