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

  • Bamnostic:
    A pure Python multi-version tolerant, runtime and OS-agnostic BAM file parser and random access tool. 
  • Broad-Enrich:
    test for enriched biological pathways, Gene Ontology terms, or other gene sets (Sartor)
  • Canny:
    assessing copy number variation genotypes (Mills)
  • 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)
  • Palmer
    Pre-mAsking Long reads for Mobile Element inseRtion
  • PePr:
    Peak Prioritization Pipeline, an analysis pipeline for ChIP-Seq experiments with biological replicates (Sartor)
  • RegulomeDB:
    a database that annotates SNPs (Boyle)
  • SAIGE:
    Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks [SAIGE-GENE] (Willer)
  • 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)
  • 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)
  • Crystal-C:
    A computational tool for refinement of open search results (Nesvizhskii)
  • DEMO:
    protein domain structure assembly (Zhang)
    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)
  • FragPipe:
    A complete proteomics pipeline with MSFragger search engine at heart
  • 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)
  • MAP-DIA:
    Model-based Analysis of Quantitative Proteomics from Data Independent Acquisition Mass Spectrometry (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)
  • MSFragger:
    Ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics (Nesvizhskii)
    protein threading program for identifying global structure template for target sequence (Zhang)
    construction of protein complexes (Nesvizhskii)
  • PD-Nodes
    The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes (Nesvizhskii)
  • Philosopher:
    A complete toolkit for shotgun proteomics data analysis (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)
  • SAINT:
    Significance Analysis of INTeractome (Nesvizhskii)
    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)
  • TMT-Integrator:
    A tool that integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis. (Nesvizhskii)
  • 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)