xxvwang@ucdavis

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PUBLICATIONS

  • Statistics Methodology Interest: Bayesian Analysis; Data Integration; High-Dimensional Clustering; Statistical Learning and AI Machine Learning; Deep Learning
  • Bioinformatics Research Interest: Multi-Omics Data Integration; Long-Read RNA Sequencing; Metabolome; Microbiome; CyToF; Statistical Genomics and Genetics
  • Disease Domain Experience: Cancer; Atopic dermatitis and psoriasis; Alzheimer’s disease; Necrotizing enterocolitis (NEC); Pediatric inflammatory bowel disease (IBD); Sepsis; Preterm labor

PEER-REVIEWED ARTICLES

  • Methodological and Major Papers
    • Wenjia Wang, Weihong Gu, Ron Schweitzer, Omry Koren, Soliman Khatib, George C. Tseng, Liza Konnikova. (2024) “In utero human intestine contains maternally derived bacterial metabolites”. Microbiome. Major Revision.
    • Peng Liu, Yuchen Pan, Hung-Ching Chang, Wenjia Wang,Yusi Fang, Xiangning Xue, Jian Zou, Jessica M. Toothaker, Oluwabunmi Olaloye, Eduardo Gonzalez Santiago, Black McCourt, Vanessa Mitsialis, Pietro Presicce, Suhas G. Kallapur, Scott B. Snapper, Jia-Jun Liu, George C. Tseng, Liza Konnikova, Silvia Liu. (2024) “Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating”. Briefings in Bioinformatics. Major Revision.
    • Wenjia Wang, Yuzhen Li, Sungjin Ko, Ning Feng, Manling Zhang, Jia-Jun Liu, Songyang Zheng, Baoguo Ren, Yan P. Yu, Jian-Hua Luo, George C. Tseng, and Silvia Liu. (2024) “IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data”. Genome Biology. Under review. (Bash tool, code and data available on GitHub)
    • Yujia Li^, Peng Liu^, Wenjia Wang^, Wei Zong, Yusi Fang, Zhao Ren, Lu Tang, George C. Tseng. (2024) “Outcome-guided disease subtyping by generative model and weighted joint likelihood in transcriptomic applications”. The Annals of Applied Statistics. 18:1947-1964. (R package, code and data available on GitHub) (^equal contribution)
    • Wenjia Wang, Yusi Fang, Chung Chang, George C. Tseng. (2024) "Accurate and ultra-efficient p-value calculation for higher criticism tests". Journal of Computational and Graphical Statistics. 33:2, 463-476. (The paper received 2023 ASA Statistical Computing and Graphics Student Paper Award) (R package, code and data available on GitHub)
  • Collaboration Papers
    • Lixin Zhang, Yusi Fang, Ibrahim Uygun, Danyang Li, Mary Strange, Syed K Zaidi, Wenjia Wang, Julia Knight, Mackenzy Radolec, Esther Elishaev, Joan F Brozick, Allison Edwards, George Tseng, Sandra Cascio, Ronald Buckanovich, Robert P Edwards, Anda M Vlad. (2024) “Novel murine cell lines with defined mutations model different histological subtypes of epithelial ovarian cancer”. Disease Models & Mechanisms. Major revision.
    • Silas A. Buck, Sophie A. Rubin, Tenzin Kunkhyen, Christoph D. Treiber, Xiangning Xue, Lief E. Fenno, Samuel J. Mabry, Varun R. Sundar, Zilu Yang, Divia Shah, Kyle D. Ketchesin, Darius D. Becker-Krail, Iaroslavna Vasylieva, Megan C. Smith, Florian J. Weisel, Wang Wenjia, M. Quincy Erickson-Oberg, Emma I. O’Leary, Eshan Aravind, Charu Ramakrishnan, Yoon Seok Kim, Yanying Wu, Matthias Quick, Jonathan A. Coleman, William A. MacDonald, Rania Elbakri, Briana R. De Miranda, Michael J. Palladino, Brian D. McCabe, Kenneth N. Fish, Marianne L. Seney, Stephen Rayport, Susana Mingote, Karl Deisseroth, Thomas S. Hnasko, Rajeshwar Awatramani, Alan M. Watson, Scott Waddell, Claire E. J. Cheetham, Ryan W. Logan, Zachary Freyberg. (2024) “Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration”. Neuron. Under review.
    • Lauren Smith, Eduardo Gonzalez Santiago,Chino Eke, Weihong Gu, Wenjia Wang, Dhana Llivichuzhca-Loja, Tessa Kehoe, Kerri St Denis, Madison Strine, Sarah Taylor, George Tseng, Liza Konnikova. (2024) “Human milk supports robust intestinal organoid growth, differentiation, and homeostatic cytokine production”. Gastro Hep Advances. Accepted.
    • Yuan Gui, Yanbao Yu, Wenjia Wang, Yuanyuan Wang, Hanyue Lu1, Sarah Mozdzierz, Eskander, Kirollos, Yi-Han Lin, Hanwen Li, Xiaojun Tian, Silvia Liu, Dong Zhou. (2024) “Proteomes characterization of liver-kidney comorbidity after microbial sepsis”. The FASEB Journal. 38(7):e23597.
    • Silvia Liu, Caroline Obert, Yan-Ping Yu, Junhua Zhao, Baoguo Ren, Kelly Brease, Benjamin Krajacich, Wenjia Wang, Kyle Metcalfe, Mat Smith, Tuval Ben-Yehezkel, Jianhua Luo. (2024) "Utility analyses of AVITI sequencing chemistry". BMC Genomics. 25, 778.
    • Silvia Liu, Yan-ping Yu, Bao-guo Ren, Tuval Ben-Yehezkel, Caroline Obert, Mat Smith, Wenjia Wang, Alina Ostrowska, Alejandro Soto-Gutierrez, Jian-Hua Luo. (2024) "Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells". eLife. 12: RP87607.

ARTICLES UNDER PREPARATION

  • Wenjia Wang, Yusi Fang, Chung Chang, and George C. Tseng. (2024) “Combining p-values: historical development, recent advances and future opportunities”. (ready for submission)
  • Balamurugan Ramatchandirin, Wenjia Wang, Marie Amalie Balamurugan, Yasemin Alnahaas, Suneetha Desiraju, Arjun Subrramanya, Juanitaa George Raj, Zainab D Lawal, Megan Ferris, Liza Konnikova, George C. Tseng, Krishnan MohanKumar. (2024) “Immune landscape in liver of neonatal mice with phlebotomy-induced anemia”. (ready for submission)
  • Wenjia Wang, George C. Tseng. (2024) “A Byesian outcome-guided clustering framework via consensus clustering for molecular disease subtyping”. (under preparation)
  • Wenjia Wang, George C. Tseng. (2024) “Bayesian consensus clustering for integration of metabolomics and microbiomics data”. (under preparation)
  • Sarah Wang, Wenjia Wang, George C. Tseng. (2024) “Efficient p-value calculation for adaptive rank truncated p-value combination tests”. (under preparation)
  • Danyang Li, Wenjia Wang, Wei Zong, George C. Tseng (2024). “Multivariate guided disease subtyping for high-dimensional omics data”. (under preparation)
  • Hung-Ching Chang, Wenjia Wang, George C. Tseng. (2024) “The CCombP R package for p-value combination tests”. (under preparation)
  • Hung-Ching Chang, Wenjia Wang, Danyang Li, Sarah Wang, Yuxin Shi, Ria Sia, Jian Zou, George C. Tseng. (2024) “Evaluation of copy number variation inference methods for tumor subclone identification using single-cell RNA-sequencing data”. (under preparation)
  • Jiajun Liu, Wenjia Wang, Dong Zhouu, Paul Monga, Silvia Liu (2024). “Meta-analytic framework for robust biomarker and cell subtype identification on single-cell and spatial transcriptomics data”. (under preparation)

JOURNAL PEER REVIEW

  • The Journal of Emerging Investigators (2022-2024)
  • PLOS Digital Health (2022)

OPEN-SOURCE SOFTWARE

  • HCp - Package Website. An R package that includes functions of different methods for p-value computation of Higher Criticism test.
  • ogClust - Package Website. An R package that implements two outcome-guided clustering methods for disease subtyping: the generative model and the weighted joint likelihood model.
  • IFDlong - Tool Website. A unified software performing long-read RNA-seq alignment, isoform/fusion annotation, and isoform/fusion quantification.