Web Servers Packages
SeqATU: Predicting ATUs (alternative transcription units) of bacterial organisms. (2020)
LTMG: A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data. (2019)
DESSO: Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. (2019)
QUBIC2.0: A novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. (2019)
rSeqTU: A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units. (2019)
MetaQUBIC a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome. (2019)
EL-SMURF: An Ensemble Learning of SMOTE for Unbalancing samples and RF algorithm in PPI sites prediction. (2019)
GeneQC: A tool for gene expression level quality control. (2018)
SPP: A sigma-54 promoter predictor in prokaryotic genomes based on a machine learning method. (2018)
ViDGER: An R package for interpretation of differential gene expression results of RNA-seq data. (2018)
QUBIC-R package (2017)
GitHub Bioconductor Video Demonstration Publication
A phylogenetic model for understanding the effect of gene duplication on cancer progression. (2014)
Cancer-evolution: A phylogenetic model for understanding the effect of gene duplication on cancer progression. (2013)
supercoil: Bacterial chromosome folding structure under different conditions. (2013)
GitHub Google Code Publication
BoBro 2.0: An integrated toolkit for prediction and analysis of cis-regulatory motifs. (2011, 2013)
GitHub Publication(1.0) Publication(2.0)
GOST: An orthology mapping tool for prokaryotes. (2011)
GitHub Google Code Publication
QUBIC: A biclustering tool for microarray data. (2009)
UberOperon: Detecting uber-operons in prokaryotic genomes