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Selected Publications

* (co-)first author, # (co-)corresponding author

2018
Su J*#, Huang Y*, Cui X, Zhang X, Wang X, Xin Y, Lin Xue, Chen K, Lv J, Xu J, Goodell MA# and Li W#: Homebox oncogene activation by pan-cancer DNA hypermethylation. Genome Biology 2018, 19:108.

Park H*, Ji P*, Kim S, Xia Z, Rodriguez B, Chen K, Su J, Masamha C, Wagner E#, Li W#: 3ʹ-UTR Shortening Represses Tumor Suppressors in trans by Disrupting ceRNA CrosstalkNature Genetics 2018, 50: 783-789.

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#: Whole-exome sequencing reveals known and novel variants in a cohort of intracranial vertebral-basilar artery dissection (IVAD)Journal of Human Genetics 2018, doi: https://doi.org/10.1038/s10038-018-0496-x. 


An K*, Du F*, Meng H*, Li G, Zhang M, Liu Z, Zhao Z, Zhang Z, Yu D, Wang D, Yang C, Ma W, Yuan L, Zhou M, Duan L, Jin L, Li H, Zhang Y, Su J#, Qiao J#, Su Y#: Transgenerational analysis of H3K4me3 and H3K27me3 by ChIP-seq links epigenetic inheritance to metabolism. Journal of Genetics and Genomics 2018, 45(3): 169-172.

Zhou M*, Hu L*, Zhang Z, Wu N, Sun J#Su J#Recurrence-associated long non-coding RNA signature for determining the risk of recurrence in patients with colon cancerMolecular Therapy-Nucleic Acids 2018: P518-529, doi: 10.1016/j.omtn.2018.06.007.

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#DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cellsGenome Biology 2018, 19:88.


Zhou M*, Zhao H*, Wang X, Sun J#, Su J#: Analysis of long noncoding RNAs highlights region-specific altered expression patterns and diagnostic roles in Alzheimer's disease. Briefings in Bioinformatics 2018, doi: 10.1093/bib/bby021.

Zhou M*, Zhang Z*, Zhao H, Bao S, Sun J#: A novel lncRNA-focus expression signature for survival prediction in endometrial carcinoma. BMC Cancer 2018, 18:39.

Zhou M*, Zhang Z*, Zhao H, Bao S, Cheng L, Sun J#: An Immune-Related Six-lncRNA Signature to Improve Prognosis Prediction of Glioblastoma Multiforme. Molecular Neurobiology 2018, 55:3684-3697.

Cheng L*, Jiang Y*, Ju H, Sun J, Peng J, Zhou M#, Hu Y#: InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk. BMC Genomics 2018, 19:919.

Cheng L*, Hu Y*, Sun J, Zhou M#, Jiang Q#: DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function. Bioinformatics 2018, 34(11): 1953-1956.


2014-2017
Huang Y* Su J*, Lei Y, Brunetti L, Gundry MC, Zhang X, Jeong M, Li W#, Goodell MA#: DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A. Genome Biology 2017 18:176. 

Lei Y*, Zhang X*, Su J*, Jeong M, Gundry MC, Huang YH, Zhou Y, Li W#, Goodell MA#: Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein. Nature Communications 2017, 8:16026.

Lin X*, Su J, Chen K, Rodrigues B#, Li W#: Sparse conserved under-methylated CpGs are associated with high-order chromatin structure. Genome Biology 2017.18:163

Zhang X*, Su J* , Jeong M*, Ko M, Huang Y, Park HJ, Guzman A, Lei Y, Huang YH, Rao A, Li W#, Goodell MA#: DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells. Nature Genetics 2016, doi:10.1038/ng.3610.

Wei Y*, Zhang S*, Sahng S*, Zhang B, Li S, Wang X, Wang F, Su J, Wu Q, Liu H#, Zhang Y#: SEA: a super-enhancer archive. Nucleic Acids Research 2016. 44(D1): p. D172-9.


Liu H*, Liu X*, Zhang S*, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J, Wu Q#, Zhang Y#: 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. Nucleic Acids Research 2016. 44(1): p. 75-94.

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#: Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor suppressor genes. Nature Genetics 2015, 1149-1157.

Wei Y*, Su J*, Liu H*, Lv J, Wang F, Yan H, Wen Y, Liu H, Wu Q#, Zhang Y#: MetaImprint: an information repository of mammalian imprinted genes. Development 2014, 141(12):2516-2523.


Zhou M*, Zhao H*, Xu W, Bao S, Cheng L#, Sun J#: Discovery and validation of immune-associated long non-coding RNA biomarkers associated with clinically molecular subtype and prognosis in diffuse large B cell lymphoma. Molecular Cancer 2017, 16:16.

Hu Y*, Zhou M*, Shi H, Ju H, Jiang Q#, Cheng L#: Measuring disease similarity and predicting disease-related ncRNAs by a novel method. BMC Medical Genomics 2017, 10:71.

Zhou M*, Zhong L*, Xu W*, Sun Y, Zhang Z, Zhao H, Yang L#, Sun J#: Discovery of potential prognostic long non-coding RNA biomarkers for predicting the risk of tumor recurrence of breast cancer patients. Scientific Reports 2016, 6:31038.

Zhou M*, Xu W*, Yue X*, Zhao H, Wang Z, Shi H, Cheng L, Sun J#: Relapse-related long non-coding RNA signature to improve prognosis prediction of lung adenocarcinoma. Oncotarget 2016, 7:29720-29738.

Zhou M*, Wang X, Shi H, Cheng L, Wang Z, Zhao H, Yang L, Sun J#: Characterization of long non-coding RNA-associated ceRNA network to reveal potential prognostic lncRNA biomarkers in human ovarian cancer. Oncotarget 2016, 7:12598-12611.

Zhou M*, Sun Y*, Sun Y*, Xu W, Zhang Z, Zhao H, Zhong Z#, Sun J#: Comprehensive analysis of lncRNA expression profiles reveals a novel lncRNA signature to discriminate nonequivalent outcomes in patients with ovarian cancer. Oncotarget 2016, 7:32433-32448.

Sun J*, Cheng L*, Shi H*, Zhang Z, Zhao H, Wang Z#, Zhou M#: A potential panel of six-long non-coding RNA signature to improve survival prediction of diffuse large-B-cell lymphoma. Scientific Reports 2016, 6:27842.

Cheng L*, Sun J*, Xu W, Dong L, Hu Y#, Zhou M#: OAHG: an integrated resource for annotating human genes with multi-level ontologies. Scientific Reports 2016, 6:34820.

Zhou M*, Zhao H*, Wang Z*, Cheng L, Yang L, Shi H, Yang H, Sun J#: Identification and validation of potential prognostic lncRNA biomarkers for predicting survival in patients with multiple myeloma. Journal of Experimental Clinical Cancer Research 2015, 34:102.

Zhou M*, Guo M*, He D*, Wang X, Cui Y, Yang H, Hao D#, Sun J#: A potential signature of eight long non-coding RNAs predicts survival in patients with non-small cell lung cancer. Journal of Translational Medicine 2015, 13:231.

Sun J*, Shi H*, Wang Z, Zhang C, Liu L, Wang L, He W, Hao D#, Liu S#, Zhou M#: Inferring novel lncRNA-disease associations based on a random walk model of a lncRNA functional similarity network. Molecular Biosystems 2014, 10:2074-2081.

Lu J, Wu D, Li C*, Zhou M#, Hao D#: Correlation between gene expression and mutator phenotype predicts homologous recombination deficiency and outcome in ovarian cancer. Journal of Molecular Medicine (Berlin, Germany) 2014, 92:1159-1168.


Hao D*#, Wang G, Yin Z, Li C, Cui Y, Zhou M#: Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome. European Journal of Human Genetics 2014, 22:1260-1267.

Hao D*#, Li C, Zhang S, Lu J, Jiang Y, Wang S, Zhou M#: Network-based analysis of genotype-phenotype correlations between different inheritance modes. Bioinformatics 2014, 30:3223-3231.


2009-2013
Su J*, Yan H*, Wei Y, Liu H, Wang F, Lv J, Wu Q#, Zhang Y#: CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Research 2013, 41(1):e4.

Lv J*, Liu H*, Huang Z*, Su J, He H, Xiu Y, Zhang Y#, Wu Q#: Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Research 2013, 41(22):10044-10061.

Lv J*, Liu H*, Su J*, Wu X, Li B, Xiao X, Wang F, Wu Q#, Zhang Y#: DiseaseMeth: a human disease methylation database. Nucleic Acids Research 2012, 40(Database issue):D1030-1035.

Su J*#, Shao X, Liu H, Liu S, Wu Q, Zhang Y#: Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts. Genomics 2012, 99(1):10-171.

Su J*, Qi Y, Liu S, Wu X, Lv J, Liu H, Zhang R, Zhang Y#: Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network. Molecular Biology Reports 2012, 39(2):1701-1712.

Liu H*, Su J*, Li J, Liu H, Lv J, Li B, Qiao H#, Zhang Y#: Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. BMC Systems Biology 2011, 5:158.

Zhang Y*#, Liu H*, Lv J*, Xiao X, Zhu J, Liu X, Su J, Li X, Wu Q, Wang F, Cui Y: QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Research 2011, 39(9):e58.

Zhang Y*#, Lv J*, Liu H*, Zhu J, Su J, Wu Q, Qi Y, Wang F, Li X#: HHMD: the human histone modification database. Nucleic Acids Research 2010, 38(Database issue):D149-154.

Su J*, Zhang Y*#, Lv J*, Liu H, Tang X, Wang F, Qi Y, Feng Y, Li X#: CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes. Nucleic Acids Research 2010, 38(1):e6.

Sun J*, Gao B*, Zhou M*#, Wang ZZ, Zhang F, Deng JE, Li X#: Comparative genomic analysis reveals evolutionary characteristics and patterns of microRNA clusters in vertebrates. Gene 2013, 512:383-391.

Zhou M*, Wang Q, Sun J, Li X#, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He T, Zheng Y: In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach. Genomics 2009, 94:125-131.
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