Microbial Functional Genomics
and Systems Biology
Bacterial functional genomics
The functional determinants in the organization of bacterial genomes
DOOR: a prokaryotic operon database for genome analyses and functional inference
Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum
A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli
A novel computational framework for genome-scale alternative transcription units prediction
Integrated and systematic views of regulatory DNA motif identification and analyses
A web server for identification of bacterial transcription units
Presenting operons and their functions through dynamic and integrated views
Microbial systems biology
Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions
Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes
GAAP: genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes
Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis
Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses
Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency
Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective
Physical properties of DNA may direct the binding of nucleoid-associated proteins along the E. coli genome
Metagenomics & metatranscriptomics
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes
Network analyses in microbiome based on high-throughput multi-omics data
A computational pipeline for gene-level functional profiling of metagenome and metatranscriptome
Linking Microbiota Functions with Medicine Therapeutics