Wing Hong Wong

Most-cited papers

SMAD4–dependent barrier constrains prostate cancer growth and metastatic progression
Z. Ding, Chang-Jiun Wu, Gerald C. Chu, Yong-Hong Xiao +24 more
2011Nature510 citations Open access
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Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks
Joo-Seop Park, Wen-Xiu Ma, Lori L O'Brien, Eunah Chung +6 more
2012Developmental Cell259 citations Open access
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CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming
Yanxia Liu, Chen Yu, Timothy P. Daley, Fangyuan Wang +12 more
2018Cell Stem Cell186 citations Open access
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scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning
Yingxin Lin, Tung-Yu Wu, Sheng Wan, J. Yang +2 more
2022Nature Biotechnology159 citations Open access
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Density estimation using deep generative neural networks
Qiao Liu, Jiaze Xu, Rui Jiang, Wing Hong Wong
2021Proceedings of the National Academy of Sciences of the United States of America122 citations Open access
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Nested Epistasis Enhancer Networks for Robust Genome Regulation
Xue-Qiu Lin, Yanxia Liu, Shuai Liu, Xiang Zhu +13 more
2022Science98 citations Open access
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Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer
M. Stackpole, Wei-Hua Zeng, Shuo Li, Chun-Chi Liu +36 more
2022Nature Communications88 citations Open access
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Deterministic evolution and stringent selection during preneoplasia
Kasper Karlsson, M. Przybilla, E. Kotler, Aziz Khan +14 more
2023bioRxiv82 citations Open access
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Simultaneous deep generative modeling and clustering of single cell genomic data
Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hong Wong
2020Nature Machine Intelligence79 citations Open access
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Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring
Shuo Li, Wei-Hua Zeng, X. Ni, Qiao Liu +18 more
2023Proceedings of the National Academy of Sciences of the United States of America68 citations Open access
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Dynamic chromatin regulatory landscape of human CAR T cell exhaustion
D. Gennert, Rachel C. Lynn, Jeffrey M. Granja, Evan W. Weber +9 more
2021Proceedings of the National Academy of Sciences of the United States of America62 citations Open access
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DDUNet: Dense Dense U-Net with Applications in Image Denoising
Fan Jia, Wing Hong Wong, T. Zeng
20212021 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)60 citations
Semantic Scholar
Using CisGenome to Analyze ChIP-chip and ChIP-seq Data
H. Ji, Hui Jiang, Wen-Xiu Ma, Wing Hong Wong
2011Current Protocols in Bioinformatics49 citations Open access
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EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics
Zijing Gao, Qiao Liu, Wan-Wen Zeng, Rui Jiang +1 more
2024Genome Biology42 citations Open access
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Sc-compReg enables the comparison of gene regulatory networks between conditions using single-cell data
Z. Duren, Wenhui Sophia Lu, Joseph G. Arthur, Preyas Shah +6 more
2021Nature Communications36 citations Open access
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Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
Z. Duren, Feng-tzu Chang, Fnu Naqing, Jingxue Xin +2 more
2022Genome Biology34 citations Open access
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Modeling regulatory network topology improves genome-wide analyses of complex human traits
Xiang Zhu, Z. Duren, Wing Hong Wong
2020Nature Communications32 citations Open access
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HiChIPdb: a comprehensive database of HiChIP regulatory interactions
Wan-Wen Zeng, Qiao Liu, Qi-Jin Yin, Rui Jiang +1 more
2022Nucleic Acids Res.30 citations Open access
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Challenges and recommendations for epigenomics in precision health
Ava C. Carter, Howard Y. Chang, George Church, Ashley Dombkowski +17 more
2017Nature Biotechnology26 citations Open access
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Feature Consistency Training With JPEG Compressed Images
Sheng Wan, Tung-Yu Wu, Heng-Wei Hsu, Wing Hong Wong +1 more
2020IEEE transactions on circuits and systems for video technology (Print)18 citations Open access
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Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis
Shuo Li, Z. Noor, Wei-Hua Zeng, M. Stackpole +10 more
2021Nature Communications17 citations Open access
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NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks
Zheng Wei, Kui Hua, Lei Wei, Shining Ma +5 more
2023Proceedings of the National Academy of Sciences of the United States of America16 citations Open access
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hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context
Zhanying Feng, Z. Duren, Zi-Yi Xiong, Sijia Wang +3 more
2021Communications Biology16 citations Open access
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An encoding generative modeling approach to dimension reduction and covariate adjustment in causal inference with observational studies
Qiao Liu, Zhong-Ren Chen, Wing Hong Wong
2024Proceedings of the National Academy of Sciences of the United States of America15 citations Open access
Semantic Scholar
EpiGePT: a Pretrained Transformer model for epigenomics
Zijing Gao, Qiao Liu, Wan-Wen Zeng, Rui Jiang +1 more
2023bioRxiv13 citations Open access
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Leveraging cell-type-specific regulatory networks to interpret genetic variants in abdominal aortic aneurysm
Shining Ma, Xi Chen, Xiang Zhu, Philip S. Tsao +1 more
2021Proceedings of the National Academy of Sciences of the United States of America12 citations Open access
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Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
Ye Henry Li, Dangna Li, N. Samusik, Xiaowei Wang +3 more
2017bioRxiv11 citations Open access
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An AI-powered Bayesian Generative Modeling Approach for Causal Inference in Observational Studies
Qiao Liu, Wing Hong Wong
2025Journal of the American Statistical Association7 citations Open access
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Mutations in human DNA methyltransferase DNMT1 induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment.
K. Davis, Ping-Ping Qu, Shining Ma, Ling Lin +10 more
2023Human Molecular Genetics6 citations Open access
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scJoint: transfer learning for data integration of single-cell RNA-seq and ATAC-seq
Yingxin Lin, Tung-Yu Wu, Sheng Wan, J. Yang +2 more
2021bioRxiv6 citations Open access
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Roundtrip: A Deep Generative Neural Density Estimator
Qiao Liu, Jiaze Xu, Rui Jiang, Wing Hong Wong
2020arXiv.org6 citations
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Toward the simultaneous detection of multiple diseases with a highly cost-effective cell-free DNA methylome test
Wei-Hua Zeng, Chun-Chi Liu, Shuo Li, Yonggang Zhou +50 more
2026Proceedings of the National Academy of Sciences of the United States of America5 citations Open access
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Improving polygenic prediction from whole-genome sequencing data by leveraging predicted epigenomic features
Wan-Wen Zeng, Han-Min Guo, Qiao Liu, Wing Hong Wong
2025Proceedings of the National Academy of Sciences of the United States of America5 citations Open access
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Heritability enrichment in context-specific regulatory networks improves phenotype-relevant tissue identification
Zhanying Feng, Z. Duren, Jingxue Xin, Qiuyue Yuan +4 more
2022bioRxiv5 citations Open access
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Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling
Xi Xi, Haochen Li, Shengquan Chen, Ting-Ting Lv +5 more
2022iScience4 citations Open access
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Human stem cells with in vivo high plasticity generated by cell–cell communication
Shao-Wei Li, Xi Chen, Jingxue Xin, Bo-Wen Liu +3 more
2025Proceedings of the National Academy of Sciences of the United States of America2 citations Open access
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Author Correction: Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
Z. Duren, F. Chang, Fnu Naqing, Jingxue Xin +2 more
2022Genome Biology2 citations Open access
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MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting
Meng Zou, Z. Duren, Qiuyue Yuan, Henry Li +3 more
2021Briefings Bioinform.2 citations Open access
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One-dimensional phase retrieval: regularization, box relaxation and uniqueness
Wing Hong Wong, Y. Lou, S. Marchesini, T. Zeng
2019Inverse Problems2 citations Open access
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Haplotype-resolved and integrated genome analysis of ENCODE cell line HepG2
Bo Zhou, Steve S. Ho, S. Greer, N. Spies +15 more
20182 citations
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A 7.11mJ/Gb/query data-driven machine learning processor (D2MLP) for big data analysis and applications
Chang-Hung Tsai, Tung-Yu Wu, Shu-Yu Hsu, Chia-Ching Chu +6 more
20142014 Symposium on VLSI Circuits Digest of Technical Papers2 citations
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Generative steering to adapt proteins beyond native biological contexts
Xiao-Wei Zhang, Wenhui Sophia Lu, B. Viggiano, Kevin Reynolds +12 more
2026bioRxiv1 citations Open access
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scTIE: data integration and inference of gene regulation using single-cell temporal multimodal data
Yingxin Lin, Tung-Yu Wu, Xi Chen, Sheng Wan +5 more
2023bioRxiv1 citations Open access
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Datasets: density estimation using deep generative neural network
Qiao Liu, Jiaze Xu, Ruituo Jiang, Wing Hong Wong
20201 citations
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Phase Retrieval for Binary Signals: Box Relaxation and Uniqueness
Wing Hong Wong, Y. Lou, T. Zeng
2019arXiv.org1 citations
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Author Correction: Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis
Shuo Li, Z. Noor, Wei-Hua Zeng, M. Stackpole +10 more
2026Nature Communications0 citations Open access
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Prioritizing disease-related rare variants by integrating gene expression data
Han-Min Guo, A. E. Urban, Wing Hong Wong
2024PLoS Genetics0 citations Open access
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EpiGePT : a Pretrained Transformer model for epigenomics 1
Zijing Gao, Qiao Liu, Wan-Wen Zeng, Wing Hong Wong +1 more
20230 citations
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T18. DETECTION OF COMPLEX STRUCTURAL GENOME VARIANTS USING ARC-SV AND THEIR ENRICHMENT INSIDE GENES OF NEURODEVELOPMENTAL PATHWAYS
Christopher R. Hughes, Bo Zhou, Joseph G. Arthur, Taeyoung Kim +4 more
2022European Neuropsychopharmacology0 citations
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Interpreting ruminant specific conserved non-coding elements by developmental gene regulatory network
Xiangyu Pan, Zhao-Xia Ma, Xinqi Sun, Hui Li +8 more
2021bioRxiv0 citations Open access
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