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Protocol for modeling injury-induced regeneration in retinal organoids and isolating hNRSCs for subretinal transplantation in rd10 mice.
Chen M, Zhang Y, Gao N, Pan W, Cheng C, Liu X, Li S*, Su J*, Liu H*.
STAR Protocols, 2025 Dec; 6(4). doi: 10.1016/j.xpro.2025.104232
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Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases.
Ma Y#, Yao Y#, Zhou Y#, Dai W#, Li J, Gui Y, Sun H, Zhu Z, Jiang D, Chen C, Deng C, Huang Y, Han H, Zhou J, Su J*.
Nature Aging, 2025. doi: 10.1038/s43587-025-01027-5
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Chemical reprogramming of fibroblasts into retinal pigment epithelium cells for vision restoration.
Li S#, Liu H#, Pan SH#, Zhu Z, Zhang S, Li J, Yao Y, Wang X, Gao N, Liu X, Chen M, Hu H, Pan W, Zhu Q, Cai Y, Qu J*, Gao S*, Su J*.
Nature Communications, 2025 Dec 9. doi: 10.1038/s41467-025-67104-w
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DNMT3A regulates murine megakaryocyte-biased hematopoietic stem cell fate decisions.
Waldvogel SM, Camacho V, Fan D, Guzman AG, Garcia-Martell A, Khabusheva E, Pridgen JR, De La Fuente J, Rau R, Laidman AG, Barrachina MN, Carminita E, Courson JA, Williamson MR, Hsu JI, Chen CW, Reyes J, Pradhan S, Rumbaut RE, Burns AR, Deneen B, Su J, Machlus KR, Goodell MA*.
Blood Advances, 2025, 9(9):2285-2299.
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NKX2-5/LHX1 and UHRF1 Establishing a Positive Feedback Regulatory Circuitry Drives Esophageal Squamous Cell Carcinoma through Epigenetic Dysregulation.
Li X#, Fan D#, Li Y#, Yuan J, Sun W, Zhu Q, Qi L, Wu X, Cai J, Gong T, Zhao N, Su J*, Liu Z*, Chen H*.
Advanced Science, 2025, doi: 10.1002/advs.202413508
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Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response.
Liu J#, Li Y#, Tang W#, Qian T#, Dai L#, Jia Z#, Cao H, Li C, Liu Y, Huang Y, Wu J, Ma D, Qiao G, Bao H, Chang S, Zhu D, Yang S, Wu X, Wu X, Xu H, Chen H, Shao Y, Wang X*, Liu Z*, Su J*.
Genomics, Proteomics & Bioinformatics, 2025, doi: 10.1093/gpbjnl/qzaf028
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Transcriptomic profiling of blood platelets identifies a diagnostic signature for pancreatic cancer.
Ji W#, Xiong Y#, Yang W#, Shao Z, Guo X, Jin G, Su J*, Zhou M*.
British Journal of Cancer. 2025 Jun;132(10):937-946. doi: 10.1038/s41416-025-02980-z
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Whole-exome sequencing reveals sex difference in the genetic architecture of high myopia.
Liu X#, Liang J#, Li S#, Yang Y, Zhu Q, Qiu R, Chen ZJ, Yao Y, Ren Q, Yu X, Qu J, Su J, Yuan J*, MAGIC.
Journal of Medical Genetics, 2025, 62(5):358-368.
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Identification and characterization of human retinal stem cells capable of retinal regeneration.
Liu H#, Ma Y#, Gao N#, Zhou Y, Li G, Zhu Q, Liu X, Li S, Deng C, Chen C, Yang Y, Ren Q, Hu H, Cai Y, Chen M, Xue Y, Zhang K, Qu J*, Su J*.
Science Translatitonal Medecine, 2025, 17(791):eadp6864.
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Integrating microbial GWAS and single-cell transcriptomics reveals associations between host cell populations and the gut microbiome.
Li J#, Ma Y#, Cao Y#, Zheng G, Ren Q, Chen C, Zhu Q, Zhou Y, Lu Y, Zhang Y, Deng C, Chen WH*, Su J*.
Nature Microbiology, 2025, 10(5):1210-1226.
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Whole-genome sequencing identifies novel loci for keratoconus and facilitates risk stratification in a Han Chinese population.
Yao Y#, Li X#, Wu L#, Zhang J, Gui Y, Yu X, Zhou Y, Li X, Liu X, Xing S, An G, Du Z, Liu H, Li S, Yu X, MAGIC, Chen H*, Su J*, Chen S*.
Eye and Vision, 2025, 12(1):5.
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Single Cell Inference of Cancer Drug Response Using Pathway-Based Transformer Network.
Yao Y#, Xu Y#, Zhang Y, Gui Y, Bai Q, Zhu Z, Peng H, Zhou Y, Chen ZJ, Sun J*, Su J*.
Small Methods, 2025, doi: 10.1002/smtd.202400991 (IF: 9.1 Q1)
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Systematic dissection of pleiotropic loci and critical regulons in excitatory neurons and microglia relevant to neuropsychiatric and ocular diseases.
Ma Y#*, Jiang D#, Li J, Zheng G, Deng Y, Gou X, Gao S, Chen C, Zhou Y, Zhang Y, Deng C, Yao Y, Han Y & Su J*.
Translational Psychiatry, 2025, 15(1):24.
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Exome-wide genetic risk score (ExGRS) to predict high myopia across multi-ancestry populations.
Yuan J#, Qiu R#, Wang Y, Chen ZJ, Sun H, Dai W, Yao Y, Zhuo R, Li K, Xing S, MAGIC, Yu X, Qiao L*, Qu J*, Su J*.
Communications Medicine, 2024, 30;4(1):280.
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RIP-AV: Joint Representative Instance Pre-training with Context Aware Network for Retinal Artery/Vein Segmentation.
Dai W, Yao Y, Kong H, Chen ZJ, Wang S, Bai Q, Sun H, Yang Y, Su J*.
Medical Image Computing and Computer Assisted Intervention, 2024, 15001:764-774.
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Distinct discrepancy in breast cancer organoids recapitulation among molecular subtypes revealed by single-cell transcriptomes analysis.
Jia Z#, Xu H#, Zhang Y#, Cao H#, Deng C, Xu L, Sun Y, Li J, Huang Y, Pu P, Shang T, Wang X*, Su J*, Liu J*.
Clinical and Translational Medicine, 2024, 14(9):e70023.
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Mendelian randomization analysis reveals a causal effect of Streptococcus salivarius on diabetic retinopathy through regulating host fasting glucose.
Li J#, Zheng G#, Jiang D, Deng C, Zhang Y, Ma Y*, Su J*.
Journal of Cellular and Molecular Medicine, 2024, 28(7):e18200.
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Exome-wide Association Study Identifies KDELR3 Mutations in Extreme Myopia.
Yuan J#, Zhuang Y#, Liu X#, Zhang Y#, Li K, Chen ZJ, Li D, Chen H, Liang J, Yao Y, Yu X, Zhuo R, Zhao F, Zhou X, MAGIC, Yu X*, Qu J*, Su J*.
Nature Communications, 2024, 15(1):6703.
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Towards Stem/Progenitor Cell-Based Therapies for Retinal Degeneration.
Liu H#, Lu S#, Chen M, Gao N, Yang Y, Hu H, Ren Q, Liu X, Chen H, Zhu Q, Li S*, Su J*.
Stem Cell Reviews and Reports, 2024, 20(6):1459-1479.
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Endogenous mutant Huntingtin alters the corticogenesis via lowering Golgi recruiting ARF1 in cortical organoid.
Liu Y#, Chen X#, Ma Y#, Song C, Ma J, Chen C, Su J, Ma L* and Saiyin H*.
Molecular Psychiatry, 2024, 29(10):3024-3039.
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Multimodal analysis of cell-free DNA methylomes for ultra-early detection of esophageal squamous cell carcinoma and precancerous lesions.
Liu J#, Dai L#, Wang Q#, Li C#, Liu Z, Gong T, Xu H, Jia Z, Sun W, Wang X, Lu M, Shang T, Zhou Y, Zhao N, Cai J, Li Z, Chen H*, Su J*, Liu Z*.
Nature Communications, 2024, 15(1):3700.
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Histone 3 lysine 9 acetylation-specific reprogramming regulates esophageal squamous cell carcinoma progression and metastasis.
Chen Z#, Li C#, Zhou Y#, Li P, Cao G, Qiao Y, Yao Y* and Su J*.
Cancer Gene Therapy, 2024, 31(4):612-626.
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Augmentation of scleral glycolysis promotes myopia through histone lactylation.
Lin X#, Lei Y#, Pan M#, Hu C#, Xie B#, Wu W, Su J, Li Y, Tan Y, Wei X, Xue Z, Xu R, Di M, Deng H, Liu S, Yang X, Qu J, Chen W*, Zhou X*, Zhao F*.
Cell Metabolism, 2024, 36(3):511-525.e7.
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Protocol for detecting rare and common genetic associations in whole-exome sequencing studies using MAGICpipeline.
Yuan J#, Li K#, Peng H, Zhang Y, Yao Y, Myopia Associated Genetics and Intervention Consortium, Qu J, Su J*.
STAR Protocols, 2024, 5(1):102806.
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DeepGraFT: A novel semantic segmentation auxiliary ROI-based deep learning framework for effective fundus tessellation classification.
Yao Y#, Yang J#, Sun H, Kong H, Wang S, Xu K, Dai W, Jiang S, Bai Q, Xing S, Yuan J, Liu X, Lu F, Chen Z*, Qu J*, Su J*.
Computers in Biology and Medicine, 2024, 169:107881.
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scDMV: A Zero-one Inflated Beta Mixture Model for DNA Methylation Variability with scBS-Seq Data.
Zhou Y#, Zhang Y, Peng M#, Zhang Y, Li C, Shu L, Hu Y*, Su J*, Xu J*.
Bioinformatics, 2023, 40(1):btad772.
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Whole-Exome Sequencing Among School-Aged Children With High Myopia.
Yu X#, Yuan J#, Chen ZJ, Li K, Yao Y, Xing S, Xue Z, Zhang Y, Peng H, An G, Yu X, Qu J*, Su J*; Myopia Associated Genetics and Intervention Consortiums.
JAMA Network Open, 2023, 6(12):e2345821.
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Progenitor-like exhausted SPRY1+CD8+ T cells potentiate responsiveness to neoadjuvant PD-1 blockade in esophageal squamous cell carcinoma.
Liu Z#, Zhang Y#, Ma N#, Yang Y#, Ma Y#, Wang F, Wang Y, Wei J, Chen H, Tartarone A, Velotta JB, Dayyani F, Gabriel E, Wakefield CJ, Kidane B, Carbonelli C, Long L*, Liu Z*, Su J*, Li Z*.
Cancer Cell, 2023, S1535-6108(23)00327-6.
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Integration of human organoids single-cell transcriptomic profiles and human genetics repurposes critical cell type-specific drug targets for severe COVID-19.
Ma Y#, Zhou Y#, Jiang D#, Dai W#, Li J, Deng C, Chen C, Zheng G, Zhang Y, Qiu F, Sun H, Xing S, Han H, Qu J, Wu N, Yao Y*, Su J*.
Cell Proliferation, 2023, 57(3):e13558.
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Network characterization linc1393 in the maintenance of pluripotency provides the principles for lncRNA targets prediction.
Hou W#, Zong M#, Zhao Q#, Yang X, Zhang J, Liu S, Li X, Chen L, Tang C, Wang X, Dong Z, Gao M*, Su J* and Kong Q*.
iScience, 2023, 26(8):107469.
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DNA damage repair profiling of esophageal squamous cell carcinoma uncovers clinically relevant molecular subtypes with distinct prognoses and therapeutic vulnerabilities.
Zhao N#, Zhang Z#, Wang Q#, Li L#, Wei Z, Chen H*, Zhou M*, Liu Z*, Su J*.
eBioMedicine, 2023, 96:104801.
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Deep annotation of long noncoding RNAs by assembling RNA-seq and small RNA-seq data.
Zhang J#, Hou W#, Zhao Q#, Xiao S, Linghu H, Zhang L, Du J, Cui H, Yang X, Ling S*, Su J* and Kong Q*.
Journal of Biological Chemistry, 2023, 299(9):105130.
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Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data.
Ma Y#, Deng C#, Zhou Y#, Zhang Y, Qiu F, Jiang D, Zheng G, Li J, Shuai J, Zhang Y*, Yang J*, Su J*.
Cell Genomics, 2023, 3(9):100383.
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Liquid biopsies for cancer: From bench to clinic.
Chen Z#, Li C#, Zhou Y, Yao Y, Liu J, Wu M*, Su J*.
MedComm, 2023, 4(4):e329.
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The transcriptional landscape and diagnostic potential of long non-coding RNAs in esophageal squamous cell carcinoma.
Zhou M#, Bao S#, Gong T#, Wang Q#, Sun J, Li J, Lu M, Sun W, Su J*, Chen H* & Liu Z*.
Nature Communications, 2023, 14(1):3799.
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Association of mitochondrial DNA variation with high myopia in a Han Chinese population.
Xing S, Jiang S, Wang S, Lin P, Sun H, Peng H, Yang J, Kong H, Wang S, Bai Q, Qiu R, Dai W, Yuan J, Ma Y, MAGIC, Yu X, Yao Y* & Su J*.
Molecular Genetics and Genomics, 2023, 298(5):1059-1071.
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Sequencing of 19,219 exomes identifies a low-frequency variant in FKBP5 promoter predisposing to high myopia in a Han Chinese population.
Su J#*, Yuan J#, Xu L#, Xing S#, Sun M#, Yao Y, Ma Y, Chen F, Jiang L, Li K, Yu X, Xue Z, Zhang Y, Fan D, Zhang J, Liu H, Liu X, Zhang G, Wang H, Zhou M, Lyu F, An G, Yu X, MAGIC, Xue Y*, Yang J* and Qu J*.
Cell Reports, 2023, 42(5):112510.
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Partial erosion on under-methylated regions and chromatin reprogramming contribute to oncogene activation in IDH mutant gliomas.
Wang X#, Dai L#, Liu Y, Li C, Fan D, Zhou Y, Li P, Kong Q, Su J*.
Epigenetics & Chromatin. 2023, 16(1):13.
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Single-cell RNA sequencing reveals new subtypes of lens superficial tissue in humans.
Zhu MC#, Hu W#, Lin L#, Yang QW, Zhang L, Xu JL, Xu YT, Liu JS, Zhang MD, Tong XY, Zhu KY, Feng K, Feng Y*, Su JZ*, Huang XF*, Li J*.
Cell Proliferation, 2023, e13477.
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Roles of non-coding RNAs in eye development and diseases.
Shi X#, Xue Z#, Ye K, Yuan J, Zhang Y, Qu J, Su J*.
Wiley Interdiscip Rev RNA, 2023, e1785.
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Modeling and analyzing single-cell multimodal data with deep parametric inference.
Hu H#, Feng Z, Lin H, Zhao J, Zhang Y, Xu F, Cheng L, Chen F, Ma Y, Su J, Zhao Q*, Shuai J*.
Briefings in Bioinformatics, 2023, 24(1):bbad005.
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Mutant NPM1 hijacks transcriptional hub to maintain pathogenic gene programs in acute myeloid leukemia.
Wang XQD#, Fan D#, Han Q#, Liu Y#, Miao H, Wang X, Li Q, Chen D, Gore H, Himadewi P, Pfeifer GP, Cierpicki T, Grembecka J, Su J, Chong S*, Wan L*, Zhang X*.
Cancer Discovery, 2022, CD-22-0424.
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Genome-wide characterization of RNA editing highlights roles of high editing events of glutamatergic synapse during mouse retinal development.
Li C#, Shi X#, Yang J, Li K, Dai L, Zhang Y, Zhou M*, Su J*.
Computational and Structural Biotechnology Journal, 2022, 20:2648-2656.
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Genome-wide association meta-analysis of 88,250 individuals highlights pleiotropic mechanisms of five ocular diseases in UK Biobank.
Xue Z#, Yuan J#, Chen F#, Yao Y, Xing S, Yu X, Li K, Wang C, Bao J, Qu J, Su J*, Chen H*.
eBioMedicine, 2022, 82:104161.
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Multi-omic characterization of genome-wide abnormal DNA methylation reveals diagnostic and prognostic markers for esophageal squamous-cell carcinoma.
Xi Y#, Lin Y#, Guo W#, Wang X, Zhao H, Miao C, Liu W, Liu Y, Liu T, Luo Y, Fan W, Lin A, Chen Y, Sun Y, Ma Y, Niu X, Zhong C, Tan W, Zhou M, Su J*, Wu C* and Lin D*.
Signal Transduction and Targeted Therapy, 2022, 7(1):53.
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DrABC: deep learning accurately predicts germline pathogenic mutation status in breast cancer patients based on phenotype data.
Liu J#, Zhao H#, Zheng Y#, Dong L#, Zhao S#, Huang Y, Huang S, Qian T, Zou J, Liu S, Li J, Yan Z, Li Y, Zhang S, Huang X, Wang W, Li Y, Wang J, Ming Y, Li X, Xing Z, Qin L, Zhao Z, Jia Z, Li J, Liu G, Zhang M, Feng K, Wu J, Zhang J, Yang Y, Wu Z, Liu Z, Ying J, Wang X, Su J*, Wang X* and Wu N*.
Genome Medicine, 2022, 14(1):21.
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Integrating single cell sequencing data with GWAS summary statistics reveals genetics-influenced CD16+ monocytes and memory CD8+T cells involved in severe COVID-19.
Ma Y#, Qiu F#, Deng C#, Li J#, Huang Y#, Wu Z, Zhou Y, Zhang Y, Xiong Y, Yao Y, Zhong Y, Qu J, Su J*.
Genome Medicine, 2022, 14(1):16.
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Cell-free DNA 5-hydroxymethylcytosine profiles of long non-coding RNA genes enable early detection and progression monitoring of human cancers.
Zhou M#, Hou P#, Yan C#, Chen L, Li K, Wang Y, Zhao J, Su J* & Sun J*.
Clinical Epigenetics, 2021, 13(1):197.
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The genetic source tracking of human urinary exosomes.
Zhu Q#, Cheng L#, Deng C#, Huang L, Li J, Wang Y, Li M, Yang Q, Dong X, Su J, Lee LP*, and Liu F*.
Proceedings of the National Academy of Sciences, 2021, 118(43):e2108876118.
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PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria.
Dai W#, Li J#, Li Q, Cai J, Su J*, Stubenrauch C*, and Wang J*.
Nucleic Acids Research, 2021, 50(D1):D848-D857.
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Design, methodology, and baseline of whole city-million scale children and adolescents myopia survey (CAMS) in Wenzhou, China.
Xu L#, Zhuang Y#, Zhang G#, Ma Y#, Yuan J#, Tu C, Li MM, Wang W, Zhang Y, Lu X, Li J, Liu X, Xue Z, Zhou M, Sun J, Bao J, Li M, Lu F*, Wang H*, Su J*, Qu J*.
Eye and Vision, 2021, 8(1):31.
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Loss of grand histone H3 lysine 27 trimethylation domains mediated transcriptional activation in esophageal squamous cell carcinoma.
Yuan J#, Jiang Q#, Gong T#, Fan D#, Zhang J, Chen F, Zhu X, Wang X, Qiao Y, Chen H*, Liu Z* and Su J*.
npj Genomic Medicine, 2021, 6(1):65.
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MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction.
Zhao KL, Liu J, Zhou XG, Su JZ*, Zhang Y* and Zhang GJ*.
Bioinformatics, 2021, btab484.
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Oncogenic enhancers drive esophageal squamous cell carcinogenesis and metastasis.
Ye B#, Fan D#, Xiong W#, Lin J, Yuan J, Jiang Q, Zhao Y, Li M, Liu J, Lv Y, Wang X, Li Z*, Su J*, Qiao Y*.
Nature Communications, 2021, 12(1):4457.
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EyeDiseases: an integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases.
Yuan J#, Chen F#, Fan D#, Jiang Q, Xue Z, Zhang J, Yu X, Li K, Qu J* and Su J*.
NAR Genomics and Bioinformatics, 2021, 3(2):lqab050.
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Integrative genomics analysis reveals a 21q22.11 locus contributing to susceptibility of COVID-19.
Ma Y#, Huang Y#, Zhao S, Yao Y, Zhang Y, Qu J, Wu N*, Su J*.
Human Molecular Genetics, 2021, 30(13):1247-1258.
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COVID-19 quarantine reveals behavioral changes effect on myopia progression.
Xu L#, Ma Y#, Yuan J#, Zhang Y#, Wang H#, Zhang G, Tu C, Lu X, Li J, Xiong Y, Chen F, Liu X, Xue Z, Zhou M, Li W, Wu N, Bao J, Chen H, Lu F*, Su J*, Qu J*.
Ophthalmology, 2021, S0161-6420(21)00257-8.
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Genome-wide cell-free DNA methylation analyses improve accuracy of non-invasive diagnostic imaging for early-stage breast cancer.
Liu J#, Zhao H#, Huang Y#, Xu S#, Zhou Y, Zhang W, Li J, Ming Y, Wang X, Zhao S, Li K, Dong X, Ma Y, Qian T, Chen X, Xing Z, Zhang Y, Chen H, Liu Z, Pang D, Zhou M, Wu Z, Wang X, Wang X*, Wu N* and Su J*.
Molecular Cancer, 2021, 20(1):36.
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Perturbations of genes essential for Müllerian duct and Wölffian duct development in Mayer-Rokitansky-Küster-Hauser syndrome.
Chen N#, Zhao S#, Jolly A#, Wang L#, Pan H#, Yuan J, Chen S, Koch A, Ma C, Tian W, Jia Z, Kang J, Zhao L, Qin C, X Fan, Rall R, Coban Z, Chen Z, Jhangiani S, Liang Z, Niu Y, Li X, Yan Z, Wu Y, Dong S, Song C, Qiu G, Zhang S, Liu P, Posey J, Zhang F, Luo G, Wu H, Su J, Zhang J, Chen E, Rouskas K, Glentis S, Bacopoulou F, Deligeoroglou E, Chrousos G, Lyonnet S, Polak M, Rosenberg K, Dingeldein I, Bonilla X, Borel C, Gibbs R, Dietrich J, Dimas A, Antonarakis S, Brucker S, Lupski J, Wu N*, Zhu L*.
The American Journal of Human Genetics, 2021, S0002-9297(20)30450-X.
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Genomic instability-derived plasma extracellular vesicle-microRNA signature as a minimally invasive predictor of risk and unfavorable prognosis in breast cancer.
Bao S#, Hu T#, Liu J#, Su J, Sun J, Ming Y, Li J, Wu N*, Chen H* and Zhou M*.
Journal of Nanobiotechnology, 2021, 19(1):22.
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Machine learning-based integrative analysis of methylome and transcriptome identifies novel prognostic DNA methylation signature in uveal melanoma.
Hou P, Bao S, Fan D, Yan C, Su J, Qu J*, Zhou M*.
Briefings in Bioinformatics, 2021, 22(4):bbaa371.
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Cellular heterogeneity–adjusted clonal methylation (CHALM) provides better prediction of gene expression.
Xu J#, Shi J#, Cui X, Cui Y, Li J, Goel A, Chen X, Issa J*, Su J*, Li W*.
Nature Communications, 2021, 12(1):400.
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Human Embryonic Stem Cell-Derived Organoid Retinoblastoma Reveals a Cancerous Origin.
Liu H#, Zhang Y#, Zhang Y, Li Y, Hua Z, Han F, Jin S, Zhang C, Wu K, Lv J, Yu F, Lin Q, Chen C, Zhang Y, Lu F, Qu J, Su J*, Jin Z*.
Proceedings of the National Academy Sciences, 2020, 117(52):33628-33638.
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DORGE: Discovery of Oncogenes and Tumor SuppressoR Genes Using Genetic and Epigenetic Features.
Lyu J#, Li J#, Su J, Peng F, Chen Y, Ge X, Li Wei*.
Science Advance, 2020, 6(46):eaba6784.
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Benchmarking algorithms for pathway activity transformation of single-cell RNA-seq data.
Zhang Y#, Ma Y#, Huang Y, Zhang Y, Jiang Q, Zhou M, Su J*.
Computational and Structural Biotechnology Journal, 2020, 18:2953-2961.
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Co-expression of Mitochondrial Genes and ACE2 in Cornea Involved in COVID-19.
Yuan J#, Fan D#, Xue Z, Qu J*, Su J*.
Investigative Ophthalmology & Visual Science, 2020, 61(12):13.
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Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity.
Zhang X#, Jeong M#, Huang X#, Wang X, Wang X, Zhou W, Shamim M, Gore H, Himadewi P, Liu Y, Bochkov I, Reyes J, Doty M, Huang Y, Jung H, Heikamp E, Aiden A, Li W, Su J, Aiden E*, Goodell M*.
Molecular Cell, 2020, 78(3):506-521.e6.
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scTPA: a web tool for single-cell transcriptome analysis of pathway activation signatures.
Zhang Y#, Zhang Y#, Hu J#, Zhang J, Guo F, Zhou M, Zhang G*, Yu F*, Su J*.
Bioinformatics, 2020, 36(14):4217-4219.
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CFEA: a cell-free epigenome atlas in human diseases.
Yu F#, Li K#, Li S#, Liu J, Zhang Y, Zhou M, Zhao H, Chen H, Wu N, Liu Z*, Su J*.
Nucleic acids research, 2020, 48(D1): D40-D44.
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Identification of tumor immune infiltration-associated lncRNAs for improving prognosis and immunotherapy response of patients with non-small cell lung cancer.
Sun J#, Zhang Z#, Bao S#, Yan C, Hou P, Wu N, Su J, Xu L*, Zhou M*.
Journal for ImmunoTherapy of Cancer, 2020, 8(1):e000110.
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Computational recognition of lncRNA signature of tumor-infiltrating B lymphocytes with potential implications in prognosis and immunotherapy of bladder cancer.
Zhou M#，Zhang Z#, Bao S#, Hou P, Yan C, Su J*, Sun J*.
Briefings in Bioinformatics, 2020, 22(3):bbaa047.
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Dnmt3a loss and Idh2 neomorphic mutations mutually potentiate malignant hematopoiesis.
Zhang X#*, Wang X#,Xue Q#, David W#, Su J*, Nagireddy P, Zhou T, Qu Y, Jeong M, Guzman A, Rosas C, Huang Y, Sreekuma A, Li W, Goodell M.
Blood, 2020, 135 (11): 845–856.
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Computational identification of mutator-derived lncRNA signatures of genome instability for improving the clinical outcome of cancers: a case study in breast cancer.
Bao S#, Zhao H, Yuan J, Fan D, Zhang Z, Su J*, Zhou M*.
Briefings in Bioinformatics, 2020, 21(5):1742-1755.
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Homebox oncogene activation by pan-cancer DNA hypermethylation.
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Genome Biology, 2018, 19(1):108.
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3ʹ-UTR Shortening Represses Tumor Suppressors in trans by Disrupting ceRNA Crosstalk.
Park H#, Ji P#, Kim S, Xia Z, Rodriguez B, Chen K, Su J, Masamha C, Wagner E*, Li W*.
Nature Genetics, 2018, 50(6):783-789.
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Whole-exome sequencing reveals known and novel variants in a cohort of intracranial vertebral-basilar artery dissection (IVAD).
Wang K#, Zhao S#, Zhang Q, Yuan J, Liu J, Ding X, Song X, Lin J, Du R, Zhou Y, Michihiko S, Chen W, Yuan B, Liu J, Yan Z, Liu B, Zhang Y, Li X, Niu Y, Long B, Shen Y, Zhang S, Kuniya A, Su J, Wu Z, Wu N*, Liu P*, Yang X*.
Journal of Human Genetics, 2018, 63(11):1119-1128.
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DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells.
Gu T#, Lin X#, Cullen SM#, Luo M, Jeong M, Estecio M, Shen J, Hardikar S, Sun D, Su J, Rux D, Guzman A, Lee M, Qi L, Chen J, Kyba M, Huang Y, Chen T, Li W*, Goodell MA*.
Genome Biology, 2018, 19(1):88.
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DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A.
Huang Y# Su J#, Lei Y, Brunetti L, Gundry MC, Zhang X, Jeong M, Li W*, Goodell MA*.
Genome Biology, 2017 18(1):176.
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Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein.
Lei Y#, Zhang X#, Su J#, Jeong M, Gundry MC, Huang YH, Zhou Y, Li W*, Goodell MA*.
Nature Communications, 2017, 8:16026.
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Sparse conserved under-methylated CpGs are associated with high-order chromatin structure.
Lin X#, Su J, Chen K, Rodrigues B*, Li W*.
Genome Biology, 2017.18(1):163.
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DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells.
Zhang X#, Su J#, Jeong M#, Ko M, Huang Y, Park HJ, Guzman A, Lei Y, Huang YH, Rao A, Li W*, Goodell MA*.
Nature Genetics, 2016, 48(9):1014-23.
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Wei Y#, Zhang S#, Sahng S#, Zhang B, Li S, Wang X, Wang F, Su J, Wu Q, Liu H*, Zhang Y*.
Nucleic Acids Research, 2016, 44(D1):D172-9.
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Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.
Liu H#, Liu X#, Zhang S#, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J, Wu Q*, Zhang Y*.
Nucleic Acids Research, 2016, 44(1):75-94.
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Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor suppressor genes.
Chen K# Chen Z#, Wu D, Zhang L, Lin X, Su J, Rodriguez B, Xi Y, Xia Z, Chen X, Shi X, Wang Q*, Li W*.
Nature Genetics, 2015, 47(10):1149-57.
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MetaImprint: an information repository of mammalian imprinted genes.
Wei Y#, Su J, Liu H, Lv J, Wang F, Yan H, Wen Y, Liu H, Wu Q*, Zhang Y*.
Development, 2014, 141(12):2516-2523.
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CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data.
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Nucleic Acids Research, 2013, 41(1):e4.
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Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features.
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Nucleic Acids Research, 2013, 41(22):10044-10061.
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DiseaseMeth: a human disease methylation database.
Lv J#, Liu H#, Su J#, Wu X, Li B, Xiao X, Wang F, Wu Q*, Zhang Y*.
Nucleic Acids Research, 2012, 40(Database issue):D1030-1035.
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Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts.
Su J#*, Shao X, Liu H, Liu S, Wu Q, Zhang Y*.
Genomics, 2012, 99(1):10-171.
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Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network.
Su J#, Qi Y, Liu S, Wu X, Lv J, Liu H, Zhang R, Zhang Y*.
Molecular Biology Reports, 2012, 39(2):1701-1712.
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Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network.
Liu H#, Su J#, Li J, Liu H, Lv J, Li B, Qiao H*, Zhang Y*.
BMC Systems Biology, 2011, 5:158.
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QDMR: a quantitative method for identification of differentially methylated regions by entropy.
Zhang Y#*, Liu H#, Lv J#, Xiao X, Zhu J, Liu X, Su J, Li X, Wu Q, Wang F, Cui Y.
Nucleic Acids Research, 2011, 39(9):e58.
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HHMD: the human histone modification database.
Zhang Y#*, Lv J#, Liu H#, Zhu J, Su J, Wu Q, Qi Y, Wang F, Li X*.
Nucleic Acids Research, 2010, 38(Database issue):D149-154.
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CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.
Su J#, Zhang Y#*, Lv J#, Liu H, Tang X, Wang F, Qi Y, Feng Y, Li X*.
Nucleic Acids Research, 2010, 38(1):e6.
