Bioinformatics and Systems Medicine Laboratory

We listed some previous and ongoing projects. Please contact us if you need more information or support.
  • DrVAEN: Drug response prediction through deep Variational Autoencoder model followed by Elastic Net.
  • CSEA-DB: Cell-type-Specific Enrichment Analysis DataBase.
  • INSCT: Integrating millions of single cells using batch-aware triplet neural networks.
  • Deep4mC: A deep learning method for systematic assessment and computational prediction of DNA N4-methylcytosine sites.
  • DeepFun: A tissue and cell type specific deep learning sequence-based model to decipher noncoding variant effects.
  • DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data.
  • 6mA-Finder: Computational prediction of 6mA sites in the DNA sequences
  • TSEA-DB: A trait-tissue association map for human complex traits and diseases.
  • VISDB: A knowledgebase containing the most comprehensive DNA virus integration sites and also the integration sites for several typical RNA retrovirus.
  • CleftGeneDB: The cleft gene annotation database aiming to provide a resource or reference for the midfacial development and the related disease studies for mouse and human.
  • MotifPredictor: With miRNA-TF, miRNA-gene, TF-miRNA, and TF-gene interactions as input, this C package can identify specific motifs (miRNA-TF-gene feed-forward and feedback loops) from networks.
  • ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence
  • deTS: An R package to identify the most relevant tissues for candidate genes or for gene expression profiles.
  • CNet: A JAVA package that detects groups of genomic signatures that are associated with clinical and phenotypical outcomes.
  • TissGDB: Tissue-specific Gene annotation DataBase in cancer for better understanding tissue-specificity and identifying targetable alterations of tissue-specific genes.
  • scRNASeqDB: A database for gene expression profiling in human single cell by RNA-seq.
  • SZGR: Schizophrenia Gene Resource provides a comprehensive online resource for schizophrenia genetics studies.>
  • ccmGDB: Cancer Cell Metabolism Gene Database. A comprehensive database for cataloging cancer cell metabolism genes for better understanding of mutational landscapes of all metabolism genes and identifying potential druggable cancer cell metabolism targets in cancerous cells.
  • TSGene 2.0: Tumor Suppressor Gene Database version 2.0 A comprehensive database for tumor suppressor genes in multiple model organisms and their related biological information (tumor types, gene expression, mutations, pathways, protein-protein interactions, and non-coding genes, etc). Major updates include: added and curated hundreads more TSGenes (1022 coding and 192 non-coding genes now), added pan-cancer gene expression, somatic mutation, miRNA data, added many pre-computed results (e.g. differential expression, mutation hotspots, networks, loss of function), data visulization, among others.
  • EW_dmGWAS Edge-weighted dense module search for genome-wide association studies and gene expression profiles. This is an upgraded algorithm of our previous dmGWAS to boost GWAS signals in a node- and edge-weighted protein-protein interaction network. In EW_dmGWAS, we utilize condition-specific gene expression profiles for edge weights. Tool is available by clicking here.
  • CCG: The Catalogue of Cancer Genes database is an integrated Interactome of Cancer Genes.
  • DESnowball: method to identify downstream target genes that are affected by a recurrent driver mutation.
  • PAHKB: Pulmonary Arterial Hypertension KnowledgeBase.
  • VirusFinder: software to detect viruses and their integration sites in host genomes through next generation sequencing data.
  • CNVannotator: A comprehensive annotation server for copy number variation (CNV) in humans.
  • TSGene: Tumor Suppressor Gene Database: A comprehensive database for tumor suppressor genes in multiple model organisms and their related biological information (tumor types, gene expression, mutations, pathways, protein-protein interactions, and non-coding genes, etc).
  • NGS Catalog: A Database of Next Generation Sequencing Studies in Humans
  • DTome: a web-based tool for drug-target interactome construction
  • GenRev a Python package for subnetwork extraction
  • glad (gene length bias detection in GWAS datasets): source code to detect gene length bias as in Jia et al.
  • dmGWAS an R package for genome-wide association studies (GWAS) analysis
  • SZGR Schizophrenia Gene Resource
  • ERGR Ethanol Related Gene Resource
  • Suppl. for Genomics (2004) 84:785-795 " The influence of neighboring nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs" .
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