Advisory & Scientific Consulting

Computational Biology Leadership for Research Labs

Turn complex single-cell, spatial, and multi-omics data into reproducible findings and a clear next experimental step. Transparent milestones, publication-grade deliverables, and fixed-scope pricing.

Built for Research LabsAcademic PIs, medical institutes & biotech R&D
Scientist-to-Scientist SupportBiological questions before method lists · 15+ yrs experience
Fixed-Scope DeliverablesClear milestones, explicit boundaries & zero hidden fees
The Project Icebreaker Protocol

Have a Public Cohort or Sequencing Plan? Start With a 1-Page Feasibility Audit.

Before committing to a multi-week contract, test my scientific judgment. Provide a GEO accession, SRA ID, or planned sample design matrix, and schedule a confidential 30-minute scoping discussion.

01
Share Your Accession or Plan

Enter your GEO/SRA ID or sample allocation schema when booking your scoping call.

02
30-Minute Scoping Discussion

I evaluate your biological hypothesis, study design constraints, and technical failure modes with you.

03
Receive Your 1-Page Audit Memo

Within 48 hours, you receive an expert memorandum evaluating power, batch confounding, and next steps.

Scientific Boundary: This is a rigorous diagnostic audit to establish whether your hypothesis is computationally defensible. I diagnose feasibility and statistical validity upfront to protect your grant budget from unviable pipelines.
Book Scoping Call & Claim Free Audit ↗
Transparent Pricing Framework

Structured Engagement Models

No vague hourly billing or runaway retainers. Every project operates on defined milestones, explicit deliverables, and publication-grade standards.

The IcebreakerTier 01

Pilot Feasibility & Risk Audit

Complimentary*

*With a 30-min scoping call for qualified academic labs & biotech teams

48 Hours – 3 Business Days

Test data viability, statistical power, and batch risks before spending grant budget.

Best For

PIs formulating grants, labs considering a GEO/SRA re-analysis, and teams designing new sequencing runs.

Key Deliverables
  • 1-Page Data Feasibility & Confounding Risk Memorandum
  • Experimental design matrix & sample size power verification
  • Identification of hidden batch effects and platform-specific artifacts
  • Fixed-scope technical execution roadmap with upfront pricing
Book Scoping Call & Request Audit ↗
Recommended
Most PopularTier 02

Fixed-Scope Analysis Sprint

$3,500 – $7,500

Per defined deliverable · Zero scope drift

2 – 4 Weeks

Turn raw or uncurated omics datasets into publication-grade, decision-ready findings.

Best For

Translational labs, target discovery groups, and research consortia needing definitive multi-omics results.

Key Deliverables
  • Publication-ready, vector-quality figure panels & statistical tables
  • Annotated, fully documented AnnData / Seurat / Bioconductor objects
  • Reproducible analysis package (version-locked Nextflow / Snakemake)
  • Formal Methods & Materials manuscript text with full provenance
Inquire About a Sprint ↗
Long-Term AdvisoryTier 03

Translational Milestone Partnership

From $8,000

Phased milestone payments tied to validated biological milestones

1 – 3 Months

End-to-end computational leadership for major grants, trial cohorts, and reviewer rebuttals.

Best For

Biotech R&D leads, clinical trial investigators, and PIs navigating high-stakes manuscript revisions.

Key Deliverables
  • Longitudinal cohort integration across single-cell, spatial, and multiome assays
  • Custom predictive machine learning classifiers with rigorous cross-validation
  • Comprehensive response-to-reviewers computational re-analysis memos
  • Bi-weekly scientific strategy meetings and direct PI-to-PI communication
Schedule Partnership Discussion ↗
Pillar Expertise

Four Core Consulting Domains

From grant-stage cohort discovery to sub-micron spatial multi-omics and advanced institutional workshops.

01Grant Planning · For PIs

Grant-Ready Preliminary Evidence

Use public data to test hypotheses and build credible preliminary evidence before sequencing

Identify suitable public cohorts and datasets (GEO, SRA, UK Biobank, TCGA, HCA) to test the biological signal behind your grant question and generate proposal-ready figures.

Who This Is For

Principal Investigators, laboratory heads, and grant applicants planning NIH/CIHR proposals.

Typical Engagements

  • Public cohort discovery, harmonization, and statistical power check
  • Preliminary evidence figure generation adhering to grant review standards
  • Biological hypothesis validation in clinical or knockout datasets
  • Definition of next experimental milestones and analysis boundaries

Key Deliverables

  • Proposal-ready high-resolution figure panels and statistical summaries
  • Methods text, cohort accession documentation, and citations
  • Explicit statement of statistical power, sample sizes, and study limitations
  • Reproducible Nextflow/Snakemake analysis code package
Verified Case EvidenceCase: Interactive Decision Audit for RNA-seq Reports →
02Primary Advisory · 2-3 Wks

Single-Cell & Spatial Omics

Resolve cell states, tissue microenvironments, and treatment responses across platforms

Turn complex single-cell and spatial runs (10x Chromium, Visium HD, Xenium, MERFISH, GeoMx) into interpretable cellular neighborhoods, receptor-ligand communication networks, and disease states.

Who This Is For

Translational medicine teams, disease consortia, and biotech target discovery leads.

Typical Engagements

  • Atlas-scale multi-sample batch correction (Harmony, scVI, BBKNN)
  • Spatial neighborhood and cellular niche mapping (Squidpy, cell2location)
  • TCR/BCR clonotype expansion paired with single-cell phenotypes
  • Ligand-receptor cell crosstalk and microenvironmental barrier analysis

Key Deliverables

  • Integrated AnnData / Seurat objects with full provenance tracking
  • Interactive spatial and single-cell visualization dashboards
  • Cell-state frequency shifts and differential abundance statistics
  • Decision memo evaluating biological plausibility and follow-up validation
Verified Case EvidenceCase: 128-Sample Kidney Spatial Transcriptomics (5 Platforms) →
03Advanced Analysis · High Impact

Biomarker Validation & Multimodal Mechanism

Test signature transferability and connect multi-omics layers to clinical outcomes

Test whether a molecular signature remains robust and predictive across external cohorts, different sequencing platforms, and longitudinal time points. Connect RNA, ATAC, and proteomics layers.

Who This Is For

Clinical trial investigators, biotech teams, and core facility computational groups.

Typical Engagements

  • Independent-cohort cross-platform validation and signature transferability
  • Joint chromatin accessibility (scATAC) and transcriptomic enhancer linkage
  • Longitudinal treatment-response and drug-resistance trajectory tracking
  • Confounder, batch, and sensitivity checks before clinical advancement

Key Deliverables

  • Comprehensive Validation Report with clear go / refine / stop criteria
  • Machine learning classifier scripts and cross-validated AUROC/AUPRC scores
  • Prioritized regulatory targets, candidate enhancers, and mechanism ranking
  • Response-to-reviewers computational re-analysis and audit trails
Verified Case EvidenceCase: GCAR1 CAR-T Trial Visium HD & TCR Repertoire Re-Analysis →
04Institutional Training · Bespoke

Advanced Training & Private Workshops

Private workshops, institutional training, and advanced bioinformatics programs

Intensive, bespoke computational biology training engineered for wet-lab biologists transitioning to dry-lab, core facility bioinformaticians, and dry-lab scientists advancing to predictive modeling.

Who This Is For

Academic departments, biotech R&D organizations, graduate programs, and research institutes.

Typical Engagements

  • Multi-day hands-on intensive workshops in single-cell & spatial transcriptomics
  • Nextflow DSL2 and reproducible pipeline engineering for research teams
  • Statistical reasoning and experimental design for translational scientists
  • Custom training cohorts focused on specific disease areas or platforms

Key Deliverables

  • Interactive code notebooks and guided laboratory exercises
  • Containerized workshop computing environments ready for AWS / SLURM
  • Recorded lecture archives and comprehensive reference handbooks
  • Post-workshop office hours and implementation code reviews
Verified Case EvidenceCase: Clinical Trial Expression Benchmark & Audit Memo →
Proven Technical Breadth

Delivered Project Modalities

Standardized workflows, reproducible pipelines, and figure-ready deliverables across spatial, single-cell, and multi-omics architectures.

Spatial Transcriptomics

Visium HD, Xenium & GeoMx Microenvironments

Multi-platform spatial deconvolution, Squidpy neighborhood graphs, ligand-receptor interaction modeling, and perivascular barrier mapping in complex tissues.

View Multi-Platform Spatial Case →
Single-Cell & V(D)J

CAR-T Dynamics & Exhaustion Trajectories

Spatiotemporal cellular kinetics, TCR clonotype expansion tracking, multi-checkpoint exhaustion characterization, and immunotherapy resistance mechanisms.

View CAR-T Clinical Trial Case →
scMultiome & Epigenomics

TF Regulatory Networks & Enhancer Linkage

Joint chromatin accessibility (scATAC) and RNA embedding, transcription factor motif enrichment, peak-to-gene cis-linkage, and prioritized enhancer targets.

View Atherosclerosis Single-Cell Case →
Deep Generative AI

scVI Unified Atlas Integration

HPC-scale data harmonization, batch-corrected deep latent space integration across disease states, rare subpopulation classification, and deployable prediction scripts.

View Organ Atlas scVI Integration Case →
Initiate Contact

How a Project Starts

Scoping Call & 1-Page Audit → Data Feasibility Review → Fixed-Scope Proposal → Reproducible Deliverables.

1
30-Minute Scoping Call & Icebreaker Audit

Book a direct 30-minute scoping call. Provide your GEO ID, SRA accession, or sample plan to receive a complimentary 1-Page Feasibility Memo.

2
Data & Feasibility Review

I review technical viability, statistical power, confounder risks, and metadata completeness without charging an upfront retainer.

3
Fixed-Scope Proposal

You receive a formal memorandum with defined deliverables, milestone timeline, computational specifications, and fixed milestone pricing.

Direct Booking & Inquiry

Schedule a confidential 30-minute discussion directly on Dr. Zhang's calendar:

Book a 30-Minute Scoping Call ↗
Audit Protocol Note

Include your target GEO / SRA accession or sequencing outline in the Calendly booking notes so I can inspect the metadata prior to the call.

Direct EmailContact by email ↗
Colleague Referral
LinkedInDr. Qingzhou Zhang ↗
GitHubgithub.com/zqzneptune ↗

Helpful context for scoping:

  • Biological system and key hypotheses
  • Assay types (e.g. 10x Chromium 3' scRNA, Visium HD, bulk RNA-seq)
  • Sample sizes, batch structure, and current stage (pre-sequencing vs. existing FASTQs)
  • Desired timeline and primary objective (grant, manuscript, discovery, decision)