Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules. - Jia Meng 001; Shou-Jiang Gao; Yufei Huang 001 (Bioinform., 2009)

An Iterated Conditional Modes solution for sparse Bayesian factor modeling of transcriptional regulatory networks. - Jia Meng 001; Jianqiu Zhang 002; Yidong Chen 002; Yufei Huang 001 (BIBM, 2010)

An iterated conditional mode solution for Bayesian factor modeling of transcriptional regulatory networks. - Jia Meng 001; Jianqiu Zhang 002; Yidong Chen 002; Yufei Huang 001 (GENSiPS, 2010)

Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model. - Jia Meng 001; Jianqiu (Michelle) Zhang; Yuan (Alan) Qi; Yidong Chen 002; Yufei Huang 001 (EURASIP J. Adv. Signal Process., 2010)

Clustering DNA methylation expressions using nonparametric beta mixture model. - Lin Zhang 015; Jia Meng 001; Hui Liu 024; Yufei Huang 001 (GENSiPS, 2011)

Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model. - Jia Meng 001; Hung-I Chen 001; Jianqiu Zhang 002; Yidong Chen 002; Yufei Huang 001 (ICASSP, 2011)

Classification of EEG recordings without perfectly time-locked events. - Jia Meng 001; Lenis Mauricio Merino; Kay Robbins; Yufei Huang 001 (SSP, 2012)

Exploiting correlated discriminant features in time frequency and space for characterization and robust classification of image RSVP events with EEG data. - Jia Meng 001; Lenis Mauricio Merino; Kay Robbins; Yufei Huang 001 (SSP, 2012)

Basis-expansion factor models for uncovering transcription factor regulatory network. - Manuel Sanchez-Castillo; Jia Meng 001; Isabel M. Tienda-Luna; Yufei Huang 001 (SSP, 2012)

Understanding MicroRNA Regulation: A computational perspective. - Dong Yue 002; Jia Meng 001; Mingzhu Lu; C. L. Philip Chen; Maozu Guo 001; Yufei Huang 001 (IEEE Signal Process. Mag., 2012)

Unveiling the dynamics in RNA epigenetic regulations. - Jia Meng 001; Xiaodong Cui; Hui Liu 024; Lin Zhang 015; Shaowu Zhang 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (BIBM, 2013)

Integration of gene expression, genome wide DNA methylation, and gene networks for clinical outcome prediction in ovarian cancer. - Lin Zhang 015; Hui Liu 024; Jia Meng 001; Xuesong Wang 001; Yidong Chen 002; Yufei Huang 001 (BIBM, 2013)

An HMM-based Exome Peak-finding package for RNA epigenome sequencing data. - Xiaodong Cui; Jia Meng 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (GENSiPS, 2013)

A Deep Learning method for classification of images RSVP events with EEG data. - Shaheen Ahmed; Lenis Mauricio Merino; Zijing Mao; Jia Meng 001; Kay Robbins; Yufei Huang 001 (GlobalSIP, 2013)

Differential analysis of rna methylation sequencing data. - Xiaodong Cui; Jia Meng 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (GlobalSIP, 2013)

A bag-of-words model for task-load prediction from EEG in complex environments. - Lenis Mauricio Merino; Jia Meng 001; Stephen M. Gordon; Brent J. Lance; Tony Johnson; Victor Paul; Kay Robbins; Jean M. Vettel; Yufei Huang 001 (ICASSP, 2013)

Exome-based analysis for RNA epigenome sequencing data. - Jia Meng 001; Xiaodong Cui; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (Bioinform., 2013)

Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test. - Lin Zhang 015; Jia Meng 001; Hui Liu 024; Xiaodong Cui; Shao-Wu Zhang 001; Yidong Chen 002; Yufei Huang 001 (GlobalSIP, 2014)

Differential analysis of RNA methylome with improved spatial resolution. - Yu-Chen Zhang; Shao-Wu Zhang 001; Lian Liu; Lin Zhang 015; Hui Liu 024; Xiaodong Cui; Yufei Huang 001; Jia Meng 001 (GlobalSIP, 2014)

Classification of Imperfectly Time-Locked Image RSVP Events with EEG Device. - Jia Meng 001; Lenis Mauricio Merino; Kay Robbins; Yufei Huang 001 (Neuroinformatics, 2014)

Sketching the distribution of transcriptomic features on RNA transcripts with Travis coordinates. - Xiaodong Cui; Zhen Wei; Lin Zhang 015; Hui Liu 024; Lei Sun; Shaowu Zhang 001; Yufei Huang 001; Jia Meng 001 (BIBM, 2015)

Modeling of replicates variances for detecting RNA methylation site in MERIP-SEQ data. - Xiaodong Cui; Jia Meng 001; Shaowu Zhang 001; Yufei Huang 001 (ChinaSIP, 2015)

MeT-DB: a database of transcriptome methylation in mammalian cells. - Hui Liu 024; Mario A. Flores; Jia Meng 001; Lin Zhang 015; Xinyu Zhao; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (Nucleic Acids Res., 2015)

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data. - Xiaodong Cui; Jia Meng 001; Shaowu Zhang 001; Yidong Chen 002; Yufei Huang 001 (Bioinform., 2016)

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks. - Song-Yao Zhang; Shao-Wu Zhang 001; Lian Liu; Jia Meng 001; Yufei Huang 001 (PLoS Comput. Biol., 2016)

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model. - Lian Liu; Shao-Wu Zhang 001; Yufei Huang 001; Jia Meng 001 (BMC Bioinform., 2017)

Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. - Lin Zhang 015; Hui Liu 024; Yufei Huang 001; Xuesong Wang 001; Yidong Chen 002; Jia Meng 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

A Machine Learning Approach for Uncovering N6-methyladenosine-Disease Association. - Songyao Zhang; Shaowu Zhang 001; Xiaonan Fan 001; Jia Meng 001; Yidong Chen 002; Yufei Huang 001 (BCB, 2018)

trumpet: transcriptome-guided quality assessment of m6A-seq data. - Teng Zhang; Shao-Wu Zhang 001; Lin Zhang 015; Jia Meng 001 (BMC Bioinform., 2018)

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. - Hui Liu 024; Huaizhi Wang; Zhen Wei; Songyao Zhang; Gang Hua 002; Shao-Wu Zhang 001; Lin Zhang 015; Shou-Jiang Gao; Jia Meng 001; Xing Chen 001; Yufei Huang 001 (Nucleic Acids Res., 2018)

MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data. - Xiaodong Cui; Lin Zhang 015; Jia Meng 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Detection of m6A RNA Methylation in Nanopore Sequencing Data Using Support Vector Machine. - Shen Jia; Haochen Luo; Qiheng Gao; Jiaqi Guo; Jionglong Su; Jia Meng 001; Xiangyu Wu (CISP-BMEI, 2019)

RNA methylation and diseases: experimental results, databases, Web servers and computational models. - Xing Chen 001; Ya-Zhou Sun; Hui Liu 024; Lin Zhang 015; Jian-Qiang Li 001; Jia Meng 001 (Briefings Bioinform., 2019)

FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes. - Song-Yao Zhang; Shao-Wu Zhang 001; Xiao-Nan Fan 001; Teng Zhang; Jia Meng 001; Yufei Huang 001 (Bioinform., 2019)

m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network. - Xiangyu Wu; Zhen Wei; Kunqi Chen; Qing Zhang; Jionglong Su; Hui Liu 024; Lin Zhang 015; Jia Meng 001 (BMC Bioinform., 2019)

Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. - Song-Yao Zhang; Shaowu Zhang 001; Xiaonan Fan 001; Jia Meng 001; Yidong Chen 002; Shou-Jiang Gao; Yufei Huang 001 (PLoS Comput. Biol., 2019)

An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features. - Jinge Wu; Lihan Zhang; Yuanzhe Wang; Jia Meng 001; Jionglong Su; Yue Wang 060 (BIBE, 2020)

Gibbs Sampling Based Banoian Biclustering of Gene Expression Data. - Daoyuan Chen; Qinyi Liu; Jia Meng 001; Jionglong Su (CISP-BMEI, 2020)

ISGm1A: Integration of Sequence Features and Genomic Features to Improve the Prediction of Human m1A RNA Methylation Sites. - Lian Liu; Xiujuan Lei; Jia Meng 001; Zhen Wei (IEEE Access, 2020)

m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. - Bowen Song; Yujiao Tang; Kunqi Chen; Zhen Wei; Rong Rong; Zhiliang Lu; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001 (Bioinform., 2020)

REW-ISA: unveiling local functional blocks in epi-transcriptome profiling data via an RNA expression-weighted iterative signature algorithm. - Lin Zhang 015; Shutao Chen; Jingyi Zhu; Jia Meng 001; Hui Liu 024 (BMC Bioinform., 2020)

Prediction of m6A Reader Substrate Sites Using Deep Convolutional and Recurrent Neural Network. - Yuxuan Wu; Yuxin Zhang; Ruoqi Wang; Jia Meng 001; Kunqi Chen; Yiyou Song; Daiyun Huang (BIBE, 2021)

Computational Prediction of N6-methyladenosine (m6A) RNA Methylation in SARS-CoV-2 Viral Transcripts. - Qingru Xu; Xiangyu Wu; Jia Meng 001 (BIBE, 2021)

A Meta-analysis: Evaluating the Effect of METTL3/METTL14 on m6A Level Based on Knockdown Samples. - Yuxin Zhang; Yuxuan Wu; Di Zhen; Kunqi Chen; Jia Meng 001 (BIBE, 2021)

A Novel Application of Image-to-Image Translation: Chromosome Straightening Framework by Learning from a Single Image. - Sifan Song; Daiyun Huang; Yalun Hu; Chunxiao Yang; Jia Meng 001; Fei Ma 002; Frans Coenen; Jiaming Zhang 005; Jionglong Su (CISP-BMEI, 2021)

ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. - Bowen Song; Kunqi Chen; Yujiao Tang; Zhen Wei; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001 (Briefings Bioinform., 2021)

Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data. - Daiyun Huang; Bowen Song; Jingjue Wei; Jionglong Su; Frans Coenen; Jia Meng 001 (Bioinform., 2021)

MetaTX: deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis. - Yue Wang 060; Kunqi Chen; Zhen Wei; Frans Coenen; Jionglong Su; Jia Meng 001 (Bioinform., 2021)

A Novel Application of Image-to-Image Translation: Chromosome Straightening Framework by Learning from a Single Image. - Sifan Song; Daiyun Huang; Yalun Hu; Chunxiao Yang; Jia Meng 001; Fei Ma 002; Jiaming Zhang 005; Jionglong Su (CoRR, 2021)

RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. - Kunqi Chen; Bowen Song; Yujiao Tang; Zhen Wei; Qingru Xu; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001 (Nucleic Acids Res., 2021)

m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. - Yujiao Tang; Kunqi Chen; Bowen Song; Jiongming Ma; Xiangyu Wu; Qingru Xu; Zhen Wei; Jionglong Su; Gang Liu; Rong Rong; Zhiliang Lu; João Pedro de Magalhães; et al. (Nucleic Acids Res., 2021)

Funm6AViewer: a web server and R package for functional analysis of context-specific m6A RNA methylation. - Song-Yao Zhang; Shaowu Zhang 001; Yujiao Tang; Xiaonan Fan 001; Jia Meng 001 (Bioinform., 2021)

Stepwise Feature Fusion: Local Guides Global. - Jinfeng Wang 008; Qiming Huang; Feilong Tang; Jia Meng 001; Jionglong Su; Sifan Song (MICCAI (3), 2022)

m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. - Jiongming Ma; Bowen Song; Zhen Wei; Daiyun Huang; Yuxin Zhang; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001; Kunqi Chen (Nucleic Acids Res., 2022)

A New Convolutional Neural Network Architecture for Automatic Segmentation of Overlapping Human Chromosomes. - Sifan Song; Tianming Bai; Yanxin Zhao; Wenbo Zhang 010; Chunxiao Yang; Jia Meng 001; Fei Ma 002; Jionglong Su (Neural Process. Lett., 2022)

FBCwPlaid: A Functional Biclustering Analysis of Epi-Transcriptome Profiling Data Via a Weighted Plaid Model. - Shutao Chen; Lin Zhang 015; Lin Lu; Jia Meng 001; Hui Liu 024 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

A Robust Framework of Chromosome Straightening With Vit-Patch Gan. - Sifan Song; Jinfeng Wang 008; Fengrui Cheng; Qirui Cao; Yihan Zuo; Yongteng Lei; Ruomai Yang; Chunxiao Yang; Frans Coenen; Jia Meng 001; Kang Dang; Jionglong Su (ISBI, 2023)

RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. - Bowen Song; Xuan Wang; Zhanmin Liang; Jiongming Ma; Daiyun Huang; Yue Wang 060; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001; Gang Liu; Kunqi Chen; Zhen Wei (Nucleic Acids Res., 2023)

DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology. - Yuxin Zhang; Jie Jiang 020; Jiongming Ma; Zhen Wei; Yue Wang 060; Bowen Song; Jia Meng 001; Guifang Jia; João Pedro de Magalhães; Daniel J. Rigden; Daiyun Hang; Kunqi Chen (Nucleic Acids Res., 2023)

Multi-task adaptive pooling enabled synergetic learning of RNA modification across tissue, type and species from low-resolution epitranscriptomes. - Yiyou Song; Yue Wang 060; Xuan Wang; Daiyun Huang; Anh Nguyen; Jia Meng 001 (Briefings Bioinform., 2023)

m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues. - Bowen Song; Daiyun Huang; Yuxin Zhang; Zhen Wei; Jionglong Su; João Pedro de Magalhães; Daniel J. Rigden; Jia Meng 001; Kunqi Chen (Genom. Proteom. Bioinform., 2023)

Differentiating amino acids from nanopore sequencing. - Jiahao Zhang; Jia Meng 001; Yuxin Zhang (ICBBT, 2024)

Tissue-specific RNA methylation prediction from gene expression data using sparse regression models. - Jie Jiang 020; Bowen Song; Jia Meng 001; Jingxian Zhou (Comput. Biol. Medicine, 2024)

Multimodal zero-shot learning of previously unseen epitranscriptomes from RNA-seq data. - Yiyou Song; Bowen Song; Daiyun Huang; Anh Nguyen; Lihong Hu; Jia Meng 001; Yue Wang 060 (Briefings Bioinform., 2025)