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ZYNEX BIOComputing Biology
Computational Offerings

Our Expertise & Services

Computational approaches designed for modern biological research, structure-based drug discovery, and systems-level omics analysis.

Service 1Transcriptomics

RNA-seq & Transcriptomics

End-to-end transcriptomic analysis workflows including quality control, preprocessing, alignment or quantification, differential expression analysis, functional enrichment, pathway analysis, and publication-ready visualization.

Key Deliverables & Analysis Steps:

Quality control & raw read trimming
Genome alignment & transcriptome quantification
Differential gene expression (DGE) statistical modeling
Gene Ontology (GO) & KEGG pathway enrichment
Publication-ready heatmaps, volcano plots, and PCA visualizations
Software & Tools Pipeline
FastQCMultiQCFastpTrimmomaticSTARHISAT2featureCountsDESeq2RPython
Standard Output Artifacts
Statistical data tables, publication-ready vector figures (SVG/PDF), method logs, and technical reports.
Service 2Genomics & Sequencing

NGS & Bioinformatics

Computational analysis of high-throughput sequencing data using reproducible workflows and established bioinformatics tools.

Key Deliverables & Analysis Steps:

Quality control & read preprocessing
High-performance sequence alignment & mapping
Gene and transcript quantification
Variant-oriented workflows & genomic annotations
Biological data interpretation & reporting
Software & Tools Pipeline
BWASAMtoolsBEDtoolsGATKSnakemakeNextflowPythonBash
Standard Output Artifacts
Statistical data tables, publication-ready vector figures (SVG/PDF), method logs, and technical reports.
Service 3Systems Pharmacology

Network Pharmacology

Systems-level analysis integrating compounds, therapeutic targets, protein–protein interactions, biological pathways, and functional enrichment to investigate complex disease mechanisms.

Key Deliverables & Analysis Steps:

Target prediction for natural phytocompounds & synthetic small molecules
Disease target identification & intersection analysis
Protein-Protein Interaction (PPI) network construction
Hub gene identification & topological centrality analysis
GO enrichment & KEGG pathway mapping
Network visualization & modular analysis
Software & Tools Pipeline
CytoscapeSTRING DBSwissTargetPredictionDisGeNETOMIMClusterProfilerR
Standard Output Artifacts
Statistical data tables, publication-ready vector figures (SVG/PDF), method logs, and technical reports.
Service 4Structural Bioinformatics

Molecular Docking

Structure-based computational analysis of protein–ligand interactions to investigate potential binding modes and molecular interactions.

Key Deliverables & Analysis Steps:

Target protein structure preparation & protonation
3D ligand conformer generation & energy minimization
Grid box definition & binding pocket characterization
Molecular docking simulation & binding energy calculations
Interaction analysis (H-bonds, hydrophobic, electrostatic)
Structural visualization & 3D figure generation
Software & Tools Pipeline
AutoDockAutoDock VinaMGLToolsPyMOLDiscovery StudioOpen Babel
Standard Output Artifacts
Statistical data tables, publication-ready vector figures (SVG/PDF), method logs, and technical reports.
Service 5Structure Analysis

Structural Bioinformatics

Computational investigation of protein structures, sequence–structure relationships, binding pockets, molecular interactions, and structural features relevant to biological research.

Key Deliverables & Analysis Steps:

PDB structure retrieval & validation analysis
Protein structure cleaning & missing loop refinement
Active site & binding pocket prediction
Homology modeling & comparative structural analysis
Non-covalent interaction profiling
Software & Tools Pipeline
PyMOLPDBChimeraXProSAPROCHECKMODELLERFoldseek
Standard Output Artifacts
Statistical data tables, publication-ready vector figures (SVG/PDF), method logs, and technical reports.
Service 6Visual Analytics

Scientific Data Analysis

Publication-oriented biological data visualization designed to communicate complex computational results clearly and effectively.

Key Deliverables & Analysis Steps:

High-resolution heatmaps & hierarchical clustering
Volcano plots & MA plots for differential expression
Principal Component Analysis (PCA) & UMAP projection
Gene Ontology & KEGG pathway enrichment plots
Protein interaction network visualizations
Sankey & chord diagrams for multi-variable interactions
Custom scientific vector figures for manuscript submission
Software & Tools Pipeline
ggplot2ComplexHeatmapSeuratMatplotlibSeabornPlotlyGraphviz
Standard Output Artifacts
Statistical data tables, publication-ready vector figures (SVG/PDF), method logs, and technical reports.
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