Inferring active cis-regulatory modules to predict functional regulatory elements. Supplementary information on ChIP-GSM: ChIP-GSM User Manual and ChIP-GSM Package
Identifying differentially expressed isoforms using a novel joint model of RNA-seq data. Supplementary information on BayesIso: BayesIso User Manual and BayesIso Package
ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach. The ChIP_BIT2 package is available at http://sourceforge.net/projects/chipbitc/ [Click Here]
Inferring intracellular signaling modules by exploring pathway landscape. Supplementary information on IMPALA: IMPALA User Manual and IMPALA Package
IntAPT: Integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. The IntAPT package is available at https://github.com/henryxushi/IntAPT [Click Here]
CRNET: An efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data. Supplementary information on CRNET: CRNET User Manual (V2.2) and CRNET R Scripts (V2.2)
SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data. The SparseIso package is available at http://github.com/henryxushi/SparseIso Click Here
DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency. Supplementary information on DM-BLD: DM-BLD User Manual (V2.0) and DM-BLD Package (V2.0)
PSSV: A novel pattern-based probabilistic approach for somatic structural variation identification. Supplementary information on PSSV: PSSV User Manual (V2.1) and PSSV Package (V2.1)
ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles. Supplementary information on ChIP-BIT: ChIP-BIT Manual (V2.0), ChIP-BIT Package (V2.0), PBX1_chr1.bam, and Input_chr1.bam
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. The BMRF-Net package is available at http://sourceforge.net/projects/bmrfcjava/ Click Here
BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-seq data. Supplementary information on BADGE: BADGE Manual and BADGE Package
A bagging Markov random field (BMRF) approach for PPI subnetwork identification. Supplementary information on BMRF: BMRF Manual and BMRF Package
Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic. Supplementary information – a Gibbs sampler on outlier sum statistic (GibbsOS): GibbsOS Manual and GibbsOS Package (Version 3)
Multi-level Support Vector Regression (ml-SVR) Analysis to Identify Condition-Specific Regulatory Networks. Supplementary Information: free download ml-SVR software – ml-SVR Package
Motif-guided Sparse Decomposition (mSD) of Gene Expression Data for Regulatory Module Identification. Supplementary Information: free download mSD software – mSD Package
Coordinative Component Analysis (COCA). Supplementary Information on Coordinative Component Analysis (COCA): COCA Manual and COCA Package