Computational Biology Services

Quantitative Science,
Powered by Data

QSP modeling, PK/PD analysis, and custom Shiny app development — bridging translational biology with computational rigor.

GitHub
15+ yrs
Translational neuroscience: spinal cord injury, stroke, Parkinson's, glaucoma, glioblastoma
What We Do
Computational Services

From interactive bioinformatics tools to full quantitative systems pharmacology pipelines.

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Shiny App Development
Custom interactive R Shiny applications to streamline bioinformatics analysis and visualization pipelines for internal teams and external stakeholders.
scRNA-seqMulti-omicsBiomarker viz NCA / popPKSpatial transcriptomics
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QSP Modeling
Mechanistic systems pharmacology models built on literature synthesis and experimental data — including sensitivity, identifiability analysis, and Bayesian calibration.
Literature synthesisODE systemsSensitivity analysis IdentifiabilityABC-SMC BayesianExperiment design
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PK/PD Analysis
Non-compartmental analysis, population PK, TMDD, and model-informed drug development — with interactive Shiny apps for dose optimization and therapeutic drug monitoring.
NCAPopulation PKTMDD MIDDSAEM / FOCEiVPCBayesian TDM
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CDISC Data Programming
End-to-end SDTM → ADaM → TLG pipelines built to CDISC standards with the pharmaverse — including custom domain design, controlled terminology, and independent validation for regulatory-ready datasets.
SDTMADaMTLG sdtm.oakadmiralxportrValidation
Work
Portfolio Highlights

Open-source models, pipelines, and Shiny apps available on GitHub and shinyapps.io.

QSP Model
Glaucoma Complement-Microglia QSP
14-state ODE system with ABC-SMC Bayesian calibration for complement pathway in glaucoma.
↗ github.com/tjmb03/ODEs-QSP
QSP Model
GBM Tumor-Immune QSP
13-state model for glioblastoma tumor-immune dynamics with rAAV-shRNA gene therapy arm.
↗ github.com/tjmb03/ODEs-QSP
QSP Model
CAR-T BCMA QSP Model
Quantitative systems pharmacology model for CAR-T cell therapy targeting BCMA in multiple myeloma.
↗ github.com/tjmb03/CAR-T-BCMA-QSP
Shiny App Suite
PK/PD Interactive Apps
NCA, population PK (SAEM/FOCEi/VPC), Bayesian TDM, and 2D dose optimization — all interactive.
↗ github.com/tjmb03/PK-PD-model
PK/PD Model
AAV Intrathecal DMPK Model
DMPK and biodistribution modeling for intrathecally administered AAV gene therapy.
↗ github.com/tjmb03/AAV-IT-DMPK
MIDD
Model-Informed Molecule Selection
Mechanistic first-in-human dosability screen for tumor-targeted bispecific antibodies — go/no-go and dosability-margin ranking computed from binding parameters, before any dose exists.
↗ github.com/tjmb03/bispecific-fih-dosability
CDISC Pipeline
OPT Trial — CDISC Pipeline
SDTM → ADaM → TLG pipeline built on a real published NEJM trial (823 subjects) from non-CDISC source data, with 38 validation checks recomputed from raw.
↗ github.com/tjmb03/opt-cdisc-pipeline
Pipeline
Spatial Transcriptomics Pipeline
Nextflow DSL2 pipeline: STARsolo → Seurat v5 → scVI → CellRank 2 → Moran's I → GSEApy.
↗ Spatial-transcriptomic
Shiny App
Multi-Omics Shiny App
MOFA+, scVI, CellRank, Random Forest — interactive multi-omics analysis and visualization.
↗ Live demo
YouTube
QSPplus Explainer Channel
Publish animated videos on QSP, PK/PD, spatial transcriptomics, CellRank, BANKSY, and multi-omics.
↗ YouTube @QSPplus
Background
About QSPplus

Built on deep translational biology with intensive quantitative modeling — bridging bench and algorithm.

QSPplus is a computational biology consultancy built on 15+ years of translational neuroscience and intensive quantitative modeling — spanning QSP, PK/PD analysis, Shiny app development, and CDISC data programming — bridging biological insight with rigorous quantitative methods to accelerate drug development.

Ready to collaborate?

Reach out to discuss your computational biology project — modeling, analysis, or app development.

✉ qspplus@gmail.com ◆ github.com/tjmb03 ▶ QSPplus on YouTube