Publications

Methodological Publications

Mediation analysis

HMBART: Liu, Chen, Xu Qin+, Victor B Talisa, and Wang, Jiebiao+. Heterogeneous causal mediation analysis with Bayesian additive regression trees. Biometrics, accepted, 2026. (ASA Health Policy Statistics Section Student Paper Award, 2025)

Fan Yang, Kevin J Gleason, Wang, Jiebiao, Jubao Duan, Xin He, Brandon L Pierce, and Lin S Chen. Cross-condition mediation analysis for identifying replicable trans-associations mediated by cis-gene expression. Bioinformatics, volume 37, pages 2513–2520, 2021.

Fan Yang, Wang, Jiebiao, Brandon L Pierce, and Lin S Chen. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Research, volume 27, pages 1859–1871, 2017.

Cellular deconvolution and single-cell / tissue omics

BLEND: Huang, Penghui, Cai, Manqi, Chris McKennan, and Wang, Jiebiao+. Probabilistic cellular deconvolution with individualized single-cell reference integration. Genome Biology, volume 26, article 328, 2025.

MOFUN-CCC: Yue, Molin, Cai, Manqi, Chong Zhao, Jinling Liu, Shikun Tao, Hao Hu, Yongrui Chen, Hanxi Huang, Juan C Celedon, Wang, Jiebiao+, and Wei Chen+. A multi-omics intermediate fusion network for digital white blood cell count prediction. Genomics, Proteomics & Bioinformatics, accepted, 2025.

EMixed: Cai, Manqi, Zhao, Kangyi, Huang, Penghui, Juan C Celedon, Chris McKennan, Wei Chen, and Wang, Jiebiao+. Probabilistic multi-omics cellular deconvolution of bulk omics data. Journal of Data Science, volume 23, pages 592–606, 2025.

HiDecon: Huang, Penghui, Cai, Manqi, Xinghua Lu, Chris McKennan, and Wang, Jiebiao+. Accurate estimation of rare cell type fractions from tissue omics data via hierarchical deconvolution. Annals of Applied Statistics, volume 18, pages 1178–1194, 2024. (ICSA Research Poster Award; NESS Student Research Award, 2023)

scMD: Cai, Manqi, Jingtian Zhou, Chris McKennan, and Wang, Jiebiao+. scMD facilitates cell type deconvolution using single-cell DNA methylation references. Communications Biology, volume 7, article 1, 2024. (Editors’ Highlight)

Xuesi Zhou, Cai, Manqi, Yue, Molin, Juan C Celedon, Wang, Jiebiao, Ying Ding, Wei Chen, and Yan Li. Molecular group and correlation guided structural learning for multi-phenotype prediction. Briefings in Bioinformatics, volume 25, article bbae585, 2024.

Pramod Bharadwaj Chandrashekar, Sayali Alatkar, Wang, Jiebiao, Gabriel E Hoffman, Chenfeng He, Ting Jin, Saniya Khullar, Jaroslav Bendl, John F Fullard, Panos Roussos, and Daifeng Wang. DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype–phenotype prediction. Genome Medicine, volume 15, article 88, 2023.

EnsDeconv: Cai, Manqi, Yue, Molin, Tianmeng Chen, Jinling Liu, Erick Forno, Xinghua Lu, Timothy Billiar, Juan C Celedon, Chris McKennan, Wei Chen, and Wang, Jiebiao+. Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution. Bioinformatics, volume 38, pages 3004–3010, 2022.

bMIND: Wang, Jiebiao+, Kathryn Roeder+, and Bernie Devlin+. Bayesian estimation of cell-type-specific gene expression with prior derived from single-cell data. Genome Research, volume 31, pages 1807–1818, 2021.

Yingying Qiu, Wang, Jiebiao, Jing Lei, and Kathryn Roeder. Identification of cell-type-specific marker genes from co-expression patterns in tissue samples. Bioinformatics, volume 37, pages 3228–3234, 2021.

Tian, Jinjin, Wang, Jiebiao, and Kathryn Roeder. ESCO: single cell expression simulation incorporating gene co-expression. Bioinformatics, volume 37, pages 2374–2381, 2021.

Siwei Chen*, Wang, Jiebiao*, Ercument Cicek, Kathryn Roeder, Haiyuan Yu, and Bernie Devlin. De novo missense variants disrupting protein–protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. Molecular Autism, volume 11, article 76, 2020.

MIND: Wang, Jiebiao, Bernie Devlin, and Kathryn Roeder. Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression. Bioinformatics, volume 36, pages 782–788, 2020. (Platform talk, ASHG 2018)

Other statistical genomics

F Kyle Satterstrom*, Jack A Kosmicki*, Wang, Jiebiao*, et al. Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism. Cell, volume 180, pages 568–584.e23, 2020.

mvMISE: Wang, Jiebiao, Pei Wang, Donald Hedeker, and Lin S Chen. Using multivariate mixed-effects selection models for analyzing batch-processed proteomics data with non-ignorable missingness. Biostatistics, volume 20, pages 648–665, 2019.

Robert D Gibbons, Kwan Hur, John V Lavigne, Wang, Jiebiao, and J John Mann. Medications and suicide: high-dimensional empirical Bayes screening (iDEAS). Harvard Data Science Review, 2019.

ofGEM: Wang, Jiebiao, Qianying Liu, Brandon L Pierce, Dezheng Huo, Olufunmilayo I Olopade, Habibul Ahsan, and Lin S Chen. A meta-analysis approach with filtering for identifying gene-level gene–environment interactions. Genetic Epidemiology, volume 42, pages 434–446, 2018.

Lin S Chen, Wang, Jiebiao, Xianlong Wang, and Pei Wang. A mixed-effects model for incomplete data from labeling-based quantitative proteomics experiments. Annals of Applied Statistics, volume 11, pages 114–138, 2017.

MixRF: Wang, Jiebiao, Eric R Gamazon, Brandon L Pierce, Barbara E Stranger, Hae Kyung Im, Robert D Gibbons, Nancy J Cox, Dan L Nicolae, and Lin S Chen. Imputing gene expression in uncollected tissues within and beyond GTEx. American Journal of Human Genetics, volume 98, pages 697–708, 2016.

Collaborative Publications

Hai-Wei Liang, Nathaniel Snyder, Wang, Jiebiao, et al. An assessment of measurement error when using maternal urinary phthalates as proxies for placental tissue levels in the estimation of the association of prenatal phthalates and infant anogenital distance. Journal of Exposure Science and Environmental Epidemiology, accepted.

Tingyan He, Junfeng Wang, Marion C Tumba, …, Wang, Jiebiao, …, Qing Zhou. Multicenter international cohort study of HA20 reveals novel genetic architecture and phenotypic evolution. Journal of Allergy and Clinical Immunology, accepted.

Emily K Schworer, Matthew D Zammit, Wang, Jiebiao, et al. Amyloid chronicity and tau PET timeline to symptomatic Alzheimer’s disease in Down syndrome. Lancet Neurology, volume 23, pages 1214–1224, 2024.

Jung-Min Pyun, Young Ho Park, Wang, Jiebiao, et al. Transcriptional risk scores in Alzheimer’s disease: from pathology to cognition. Alzheimer’s & Dementia, volume 20, pages 243–252, 2024.

Jung-Min Pyun, Young Ho Park, Wang, Jiebiao, et al. Aberrant GAP43 gene expression is Alzheimer disease pathology-specific. Annals of Neurology, volume 93, pages 1047–1048, 2023.

Hai-Wei Liang, Nathaniel Snyder, Wang, Jiebiao, et al. A study on the association of placental and maternal urinary phthalate metabolites. Journal of Exposure Science and Environmental Epidemiology, volume 33, pages 264–272, 2023.

William H Cuddleston, Xuanjia Fan, Laura Sloofman, et al., Wang, Jiebiao, et al. Spatiotemporal and genetic regulation of A-to-I editing throughout human brain development. Cell Reports, volume 41, article 111585, 2022.

Zhenhua Xu, Xinyu Wang, Lei Fan, et al., Wang, Jiebiao, et al. Integrative analysis of spatial transcriptome with single-cell transcriptome and single-cell epigenome in mouse lungs after immunization. iScience, volume 25, article 104900, 2022.

Brandon C McKinney, Lora L McClain, Christina M Hensler, et al., Wang, Jiebiao, Ying Ding, and Robert A Sweet. Schizophrenia-associated differential DNA methylation in brain is distributed across the genome and annotated to MAD1L1. Translational Psychiatry, volume 12, article 340, 2022.

Nicholas F Fitz, Wang, Jiebiao, M Ilyas Kamboh, Radosveta Koldamova, and Iliya Lefterov. Small nucleolar RNAs in plasma extracellular vesicles and their discriminatory power as diagnostic biomarkers of Alzheimer’s disease. Neurobiology of Disease, volume 159, article 105481, 2021.

Marianne L Seney, Sam-Moon Kim, Jill R Glausier, et al., Wang, Jiebiao, et al. Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder. Biological Psychiatry, volume 90, pages 550–562, 2021.

Cheryl A King, David Brent, Jacqueline Grupp-Phelan, et al., Wang, Jiebiao, and Robert Gibbons. Prospective development and validation of the computerized adaptive screen for suicidal youth. JAMA Psychiatry, volume 78, pages 540–549, 2021.

Sean C Piantadosi, Lora L McClain, Lambertus Klei, Wang, Jiebiao, et al. Transcriptome alterations are enriched for synapse-associated genes in the striatum of subjects with obsessive-compulsive disorder. Translational Psychiatry, volume 11, article 171, 2021.

Jason J Pitt, Markus Riester, Yonglan Zheng, et al., Wang, Jiebiao, et al. Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features. Nature Communications, volume 9, article 4181, 2018.

Siwei Chen, Robert Fragoza, Lambertus Klei, Yuan Liu, Wang, Jiebiao, Kathryn Roeder, Bernie Devlin, and Haiyuan Yu. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Nature Genetics, volume 50, pages 1032–1040, 2018.

Preprints and Submitted

Rain Katz, Ryan Cvejkus, Wang, Jiebiao, et al. Large-scale protein assay identifies novel protein biomarkers associated with arterial stiffness and vascular calcification measures. International Journal of Hypertension, under review.

Shuangjia Xue, Mehdi Nouraie, Wang, Jiebiao, et al. Oxidative stress pathway genotypes interact with environmental pollutant levels to influence gene expression and lung function. eBioMedicine, under review.

Sigan Hartley, Liu, Chen, Wang, Jiebiao, et al. Trajectory of cognitive decline in relation to PET and plasma biomarkers in Down syndrome-associated Alzheimer disease. Lancet Neurology, under review.