Jie Lyu

Publications

• YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer
• Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data.
• DevMouse, the mouse developmental methylome database and analysis tools.
• DiseaseMeth: a human disease methylation database.
• 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.
• QDMR: a quantitative method for identification of differentially methylated regions by entropy.
• HHMD: the human histone modification database.
• Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.
• Identification and Epigenetic Analysis of a Maternally Imprinted Gene Qpct.
• Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network.
• Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure.
• CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.
• Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation
• Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer.
• The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation
• DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features
• A Click Chemistry Approach Reveals the Chromatin-Dependent Histone H3K36 Deacylase Nature of SIRT7.
• ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia.
• Homeobox oncogene activation by pan-cancer DNA hypermethylation.
• DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database.
• Computational identification of putative lincRNAs in mouse embryonic stem cell.
• ChIP-seq Data Plays an Important Role in a Cytosine-Based DNA Methylation Prediction Model
• Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network.
• Long intergenic non-coding RNA detection benefited from integrative modeling of (Epi)genomic data
• Rice protein improves adiposity, body weight and reduces lipids level in rats through modification of triglyceride metabolism.
• Covalent Modifications of Histone H3K9 Promote Binding of CHD3.
• MiR-1188 at the imprinted Dlk1-Dio3 domain acts as a tumor suppressor in hepatoma cells.
• Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types.
• Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development.
• Identification and characterization of long intergenic non-coding RNAs related to mouse liver development.
• MetaImprint: an information repository of mammalian imprinted genes.
• Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features.
• Z curve theory-based analysis of the dynamic nature of nucleosome positioning in Saccharomyces cerevisiae.
• CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data.
• Detecting novel hypermethylated genes in breast cancer benefiting from feature selection.
• A comprehensive atlas of epigenetic regulators reveals tissue-specific epigenetic regulation patterns
• Gene function and cell surface protein association analysis based on single-cell multiomics data
• DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database
• Homeobox oncogene activation by pan-cancer DNA hypermethylation
• A Click Chemistry Approach Reveals the Chromatin-Dependent Histone H3K36 Deacylase Nature of SIRT7
• Covalent Modifications of Histone H3K9 Promote Binding of CHD3
• EPRIM: An approach of identifying cancer immune-related epigenetic regulators
• Identifying SARS-CoV-2 infected cells with scVDN.
• SCTC: inference of developmental potential from single-cell transcriptional complexity