Bioinformatics and Systems Medicine Laboratory

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We listed some previous and ongoing projects. Please contact us if you need more information or support.
  •    Important notice about our software maintenance.
    In these days, all our software has to perform data security scan due to the data policy of The University of Texas Systems. During this period, all software and databases are not available from outside users. We expect this process takes a few weeks, and we will work hard to make this available ASAP. Please come to visit our site soon. We will update on our web site after this process is complete. Thank you for your interest in our databases and tools, and your patience.
  • 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
  • VCUERGR An Ethanol Related Gene Resource database for VCU Alcohol Research Center sponsored by NIH/NIAAA grant P20-AA017828.
  • 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
  • InPrePPI A web-based application for the prediction of protein-protein interactions (PPIs) using one of the four genomic context based methods (Phylogenetic profile method, Gene cluster method, Gene fusion method, and Gene neighbor method) or an integration method (InPrePPI) based on these four methods.
  • SNPKS A statistical method to estimate the effective SNP size in vertebrate genomes.
  • 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" .
  • SNPMiner A SNP database and web interface with the functionalities including search, candidate SNP selections, and genetic analysis.
  • SNPNB A user-friendly application for analyzing the neighboring-nucleotide compositions and bias patterns of SNPs. It also evaluates statistically the effective size of SNPs which to represent the same patterns observed in a genome or on a chromosome. More functions will be added in the later versions.
  • SNPPEB (ongoing) A web based SNP information processing and primer design application. It will parse compressed XML file from NCBI website and display SNP info as required by lab molecular biologists. It will also design primers for selected SNPs and give user-friendly output. This application will automate related lab work and release biologists from some tedious manual work.
  • Warfarin PGx (under construction) A warfarin database and web interface with the functionalities including search patient information and prediction of initial warfarin dose amount.
 
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