List of works - Jia Meng

A nonparametric Bayesian approach for clustering bisulfate-based DNA methylation profiles.

scientific article

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data

scientific article

A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.

scientific article

An Iterative Time Windowed Signature Algorithm for Time Dependent Transcription Module Discovery

scientific article published on January 2008

Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks

scientific article published in 2011

Biclustering of time series microarray data.

scientific article

Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics

scientific article published on 13 June 2020

Characterization and robust classification of EEG signal from image RSVP events with independent time-frequency features

scientific article published on 18 September 2012

Classification of imperfectly time-locked image RSVP events with EEG device

scientific article published in April 2014

DRME: Count-based differential RNA methylation analysis at small sample size scenario

scientific article published on 3 February 2016

Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome

scientific article

Direct and efficient cellular transformation of primary rat mesenchymal precursor cells by KSHV

scientific article published on February 2012

Early remodeling of the neocortex upon episodic memory encoding.

scientific article

Enhancing Epitranscriptome Module Detection from m6A-Seq Data Using Threshold-Based Measurement Weighting Strategy.

scientific article published on 14 June 2018

Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules

scientific article published on 07 April 2009

Epigenetic priming of memory updating during reconsolidation to attenuate remote fear memories.

scientific article

Exome-based analysis for RNA epigenome sequencing data

scientific article

Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation

scientific article published in 2022

Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods

scientific article published on 02 January 2019

Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features

scientific article published on 28 April 2016

HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data

scientific article

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome.

scientific article published on 8 November 2017

MeT-DB: a database of transcriptome methylation in mammalian cells

scientific article

RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication

scientific article published in 2022

Robust inference of the context specific structure and temporal dynamics of gene regulatory network

scientific article

Spatially Enhanced Differential RNA Methylation Analysis from Affinity-Based Sequencing Data with Hidden Markov Model

scientific article published on 2 August 2015

Tet1 is critical for neuronal activity-regulated gene expression and memory extinction

scientific article

Topological Characterization of Human and Mouse m5C Epitranscriptome Revealed by Bisulfite Sequencing.

scientific article

Viral and cellular N(6)-methyladenosine and N(6),2'-O-dimethyladenosine epitranscriptomes in the KSHV life cycle.

scientific article

WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach

scientific article published on 01 April 2019

WITMSG: Large-scale Prediction of Human Intronic m6A RNA Methylation Sites from Sequence and Genomic Features

scientific article published on 01 January 2020

Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data

scientific article published in 2021

ac4CGE: Predicting N4-acetylcytidine (ac4C) RNA Modification Sites in Archaea Using Graph-based Machine Learning Approach

scientific article published on 16 October 2024

lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine

scientific article published on 5 October 2015

m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome

scientific article published on 01 January 2022

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks

scientific article

List of works by Jia Meng

A nonparametric Bayesian approach for clustering bisulfate-based DNA methylation profiles.

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data

A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.

An Iterative Time Windowed Signature Algorithm for Time Dependent Transcription Module Discovery

Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks

Biclustering of time series microarray data.

Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics

Characterization and robust classification of EEG signal from image RSVP events with independent time-frequency features

Classification of imperfectly time-locked image RSVP events with EEG device

DRME: Count-based differential RNA methylation analysis at small sample size scenario

Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome

Direct and efficient cellular transformation of primary rat mesenchymal precursor cells by KSHV

Early remodeling of the neocortex upon episodic memory encoding.

Enhancing Epitranscriptome Module Detection from m6A-Seq Data Using Threshold-Based Measurement Weighting Strategy.

Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules

Epigenetic priming of memory updating during reconsolidation to attenuate remote fear memories.

Exome-based analysis for RNA epigenome sequencing data

Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation

Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods

Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features

HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome.

MeT-DB: a database of transcriptome methylation in mammalian cells

RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication

Robust inference of the context specific structure and temporal dynamics of gene regulatory network

Spatially Enhanced Differential RNA Methylation Analysis from Affinity-Based Sequencing Data with Hidden Markov Model

Tet1 is critical for neuronal activity-regulated gene expression and memory extinction

Topological Characterization of Human and Mouse m5C Epitranscriptome Revealed by Bisulfite Sequencing.

Viral and cellular N(6)-methyladenosine and N(6),2'-O-dimethyladenosine epitranscriptomes in the KSHV life cycle.

WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach

WITMSG: Large-scale Prediction of Human Intronic m6A RNA Methylation Sites from Sequence and Genomic Features

Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data

ac4CGE: Predicting N4-acetylcytidine (ac4C) RNA Modification Sites in Archaea Using Graph-based Machine Learning Approach

lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine

m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks