DCMB Software and Bioinformatics Tools

 Below is a listing of software and bioinformatics tools developed by DCMB faculty and researchers.

Genomics, regulatory genomics and epigenomics

  • Broad-Enrich:
    test for enriched biological pathways, Gene Ontology terms, or other gene sets (Sartor)
  • Canny:
    assessing copy number variation genotypes (Mills)
  • ConceptGen:
    gene set enrichment testing and concept mapping tool (Sartor)
  • Dinumt:
    identification and genotyping of nuclear insertions of mitochondrial origin (Mills)
  • F-seq:
    individual sequence data summarization and display (Boyle)
  • Gene2MeSH:
    gene annotation with the concepts defined in MeSH (Athey)
    evaluation of global enrichment of trait-associated variants (Willer)
  • Islet eQTL variants:
    exploration of variants in islet expression quantitative trait loci (Parker)
  • LocusZoom:
    plotting regional association results (Willer)
  • LRpath:
    gene set enrichment testing using logistic regression (Sartor)
  • MethylSig:
    analyzing bisulfite sequencing data (Sartor)
  • Nephroseq:
    analysis of publicly available renal gene expression data (Kretzler)
  • PePr:
    Peak Prioritization Pipeline, an analysis pipeline for ChIP-Seq experiments with biological replicates (Sartor)
  • RegulomeDB:
    a database that annotates SNPs (Boyle)
  • Self Organizing Maps:
    exploration of the combinatorial space of transcription factor binding (Boyle)
  • Svelter:
    identification of rearrangements from paired-end sequencing data (Mills)

Protein structure, proteomics, and alternative splicing

  • 3DRobot:
    protein decoy structure generator (Zhang)
    extraction of label-free quantitative information from MS/MS data sets (Nesvizhskii)
  • AggMod:
    an online model repository of mathematical models of protein aggregation (Schnell) 
    protein backbone torsion angle prediction (Zhang)
  • BatMass:
    mass spectrometry data visualization (Nesvizhskii)
  • Bio3D:
    open-source R package for structural bioinformatics and molecular biophysics (Grant)
  • Bio3D-nma:
    online tool for normal mode analysis of protein structures (Grant)
  • Bio3D-web:
    online interactive server for comparative protein structural analysis (Grant)
  • BSpred:
    sequence-base protein-protein binding site prediction (Zhang)
  • COACH:
    protein ligand binding site prediction (Zhang)
    structure based protein function prediction (Zhang)
  • CRAPome:
    Contaminant Repository for Affinity Purification (Nesvizhskii)
    analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data (Nesvizhskii)
  • Disorder Atlas:
    interpretation of intrinsic disorder predictions using proteome-based descriptive statistics (Schnell)
  • EDTsurf:
    construction of macromolecular surface (Zhang)
  • HAAD:
    hydrogen atom addition for protein structures (Zhang)
    protein structure prediction and structure-base function annotation (Zhang)
    determining phase of X-ray crystallography using structure prediction (Zhang)
  • IonCom:
    Protein Ion ligand binding site prediction (Zhang)
    meta-server for protein threading and fold-recognition (Zhang)
  • Luciphor:
    localization of post-translational modifications on peptide sequences (Nesvizhskii)
  • Luciphor2:
    an expansion of Luciphor in JAVA (Nesvizhskii)
    Multiple Alignment of Protein Structures and Consensus Identification (Ye)
    Method for Inferring Kinetics and Network Architecture of biochemical reactions (Schnell)
  • MM-align:
    protein-protein complex structural alignment (Zhang)
  • ModRefiner:
    high resolution protein structure refinement program (Zhang)
    protein threading program for identifying global structure template for target sequence (Zhang)
    construction of protein complexes (Nesvizhskii)
    a Laboratory Management System (LIMS) for interaction proteomics (Nesvizhskii)
  • PSSpred:
    protein secondary structure prediction (Zhang)
  • QPROT:
    analysis of differential protein expression (Nesvizhskii)
  • QSPEC:
    analysis of differential protein expression with label-free spectral count data (Nesvizhskii)
  • QUARK:
    ab initio protein structure prediction (Zhang)
  • REMO:
    reconstructing full-atom protein structure model from C-alpha trace (Zhang)
  • ResQ:
    estimating B-factor and residue-level quality of protein structure (Zhang)
  • RW and RWplus:
    atomic-level potential for protein structure recognition (Zhang)
    protein threading program for identifying local conserved structure motifs (Zhang)
  • Spectre:
    identification of regions of active translation from ribosome profiling sequence data (Mills)
    protein decoy selection through structure clustering (Zhang)
  • STRUM:
    prediction of protein stability change upon single point mutation (Zhang)
    protein residue-residue contact prediction by Support Vector Machine (Zhang)
  • ThreaDom:
    threading-based protein domain boundary prediction (Zhang)
  • TM-align:
    protein structural alignment (Zhang)
  • TM-score:
    quantitative assessment of protein structure similarity (Zhang)
  • Trans-Proteomic Pipeline:
    primary processing of mass spectrometry-based proteomic data (Nesvizhskii)

Systems biology and networks analysis

  • MetDisease Plugin for Cytoscape:
    annotation of a metabolic network with MeSH disease terms (Karnovsky)
  • MetScape3:
    the visualization and interpretation of metabolomic and expression profiling data (Karnovsky)
  • Network WorkBench:
    a large-scale network analysis, modeling and visualization toolkit (Schnell)

Biomedical data science, translational bioinformatics, and pharmacogenomics

  • ConceptMetab:  
    mapping and exploring the relationships among metabolite sets (Sartor)
  • Metab2Mesh:
    compound annotation with the concepts defined in MeSH (Athey, Karnovsky, Sartor)
  • MetDisease Plugin for Cytoscape:
    annotation of a metabolic network with MeSH disease terms (Karnovsky)
  • MetScape3:
    the visualization and interpretation of metabolomic and expression profiling data (Karnovsky)

Methodological development in computational biology

  • Discriminant Multiple Kernel Learning:
  • DPC:
    Dual Projection onto Convex Sets for screening (Ye)
  • LONI Pipeline:
    graphical Workflow Environment for Imaging, Informatics and Genomics Computing (Dinov)
  • LSCCA:
    Least Squares Canonical Correlation Analysis package (Ye)
    Multi-tAsk Learning via StructurAl Regularization (Ye)
  • MLDR:
    Multi-Label Dimensionality Reduction (Ye)