Ming Chen

mirCCC: Repression-aware graph learning for miRNA-mediated cell-cell communication inference

mirCCC infers microRNA-mediated cell-cell communication from single-cell RNA sequencing by detecting coordinated gene expression changes and models miRNA activity and transfer capacity.

AWmeta empowers adaptively-weighted transcriptomic meta-analysis

AWmeta improves transcriptomic meta-analysis by adaptively weighting studies, yielding more accurate differentially expressed genes with fewer samples and reduced false positives.

Cross-Species Prediction of Histone Modifications in Plants via Deep Learning

This study uses deep learning to predict histone modifications across plant species, showing improved cross-species performance with family-level models.

Mapping the comorbid landscape of Parkinson's disease and Crohn's disease along the gut-blood-brain axis

This study maps the comorbid landscape of Parkinson's disease and Crohn's disease through a multi-omics approach, revealing shared genetic and transcriptional mechanisms along the gut-blood-brain axis.

GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells

GraphVelo extends RNA velocity inference to multimodal data by using graph-based machine learning to preserve vector information across different data representations.

SoyOD: An Integrated Soybean Multi-omics Database for Mining Genes and Biological Research

SoyOD integrates soybean multi-omics data and provides tools for gene mining and analysis, with a focus on agronomic traits like plant height.

iSeq: An integrated tool to fetch public sequencing data

iSeq is a tool for retrieving public sequencing data from multiple databases, supporting various accession formats and enabling parallel downloads and metadata retrieval.

Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition

This study systematically analyzes single-cell data to show how transposable elements dynamically regulate the endothelial-to-hematopoietic transition through epigenetic changes and inflammatory signaling.

A Statistical Framework to Identify Cell Types Whose Genetically Regulated Proportions are Associated with Complex Diseases

This paper introduces a statistical framework, cWAS, to identify cell types with genetically regulated proportions associated with complex diseases using integrated genetic and transcriptomics data.

T4SEpp: a pipeline integrated with protein language models effectively predicting bacterial type IV secreted effectors

T4SEpp predicts bacterial type IV secreted effectors using protein language models and integrates multiple modules, achieving high sensitivity and specificity.

Integrated aqueous humor ceRNA and miRNA-TF-mRNA network analysis reveals potential molecular mechanisms governing primary open-angle glaucoma pathogenesis

The paper identifies key genes and regulatory networks in aqueous humor of POAG patients using bioinformatics analysis of gene expression data.

A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys

This study creates a single-cell regulomic and transcriptomic map of cynomolgus monkeys, revealing cell-type similarities to humans over mice.

Genome-wide discovery of hidden genes mediating known drug-disease association using KDDANet

KDDANet identifies hidden genes mediating known drug-disease associations by analyzing genome-wide functional gene interaction networks, revealing both known and novel candidates in diseases like Alzheimer's and obesity.

Genomic selection to optimize doubled haploid-based hybrid breeding in maize

The paper applies genomic selection to optimize doubled haploid breeding in maize by improving prediction accuracy for DH production and agronomic traits.

A Novel Riboswitch Classification based on Imbalanced Sequences achieved by Machine Learning

The paper addresses riboswitch classification challenges using machine learning on imbalanced datasets, showing improved performance with balanced data and identifying biologically relevant k-mers.

ChIP-Hub: an Integrative Platform for Exploring Plant Regulome

ChIP-Hub provides a web-based platform integrating and visualizing reanalyzed ChIP-seq data from over 40 plant species to explore plant regulomes.

FPD: A comprehensive phosphorylation database in fungi

The paper introduces FPD, a database of phosphorylation sites in fungi, containing 62,272 non-redundant sites across eight species.