Javad–Carlo Scientific ResearchOS

Humboldt Research Fellowship Project

Reproducibility and Perturbation Specificity of Genetic Regulatory Responses to DNA Damage in Human Immune Cells

Bridging primary blood experimental workflows and advanced statistical genetics: investigating genotype-by-perturbation regulatory effects in human CD8+ T cells vs. innate monocytes.

Applicant & Host

Dr. Javad Alizargar, MD, PhD

PD Dr. Carlo Maj (Marburg)

Live Operational Platform

Discovered

Screened

Included

Open Access

Evidence Recs

Research Gaps

Novelty Checks

Collab Actions

Scientific Quality Gates Audit (Section 17)

Every stage requires objective, verifiable supporting evidence before advancement.

Strict Governance

Loading quality gate audits...

Part 1: Immutable Scientific & Institutional Foundations

Confirmed Project Baseline & Institutional Roles

These parameters are confirmed and serve as the scientific anchor for all downstream development.

Institutional Roles & Core Objectives

Proposed Host: PD Dr. Carlo Maj

Head of Bioinformatics and Research Group Leader in Genetic Epidemiology, Center for Human Genetics, Philipps-University Marburg, Germany.

Applicant: Dr. Javad Alizargar, MD, PhD

Assistant Professor, National Taipei University of Nursing and Health Sciences, Taiwan. Clinical epidemiologist and medical researcher.

Pedagogical & Scientific Requirement:

The host has proposed beginning with available blood samples in Marburg so the applicant experiences the experimental workflow from the beginning, while retaining statistical genetics and response-eQTL mapping as the central scientific focus.

Confirmed Published Benchmarks

Seed Paper 1 • DDR exposure-eQTL

Bigge et al. (BMC Genomics 2024)

Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer. DOI: 10.1186/s12864-024-11068-6.

Direct precursor from Carlo Maj's research environment demonstrating feasibility of mapping genotoxic stress eQTLs.

Seed Paper 2 • Response-eQTL Benchmark

Fairfax et al. (Nature Communications 2014)

Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes. DOI: 10.1038/ncomms6236.

Gold standard for dynamic response-eQTL study designs in human blood-derived immune cells.

Federated Multi-API Literature Discovery

13 Structured Search Families (A–M) querying PubMed, Europe PMC, and OpenAlex in real-time.

Loading search families...

Reproducible Search Audit Log

Date (UTC)	Family	Database	Query Executed	Raw Results	New Papers
Loading search logs...

Curated Literature Library

FTS5 Full-Text Indexed • Deduplicated • Transparent Screening Status

BibTeX RIS CSV

Status	Title & Bibliographic Details	Journal / Year	Citations	Tags / Access	Actions
Loading publications...

Experimental Feasibility & Statistical Power Framework

Separating Confirmed Facts, Host Suggestions, Proposed Methods, and Unresolved Assumptions (Section 12).

Interaction eQTL (Genotype x Perturbation) Statistical Power Calculator

Simulates non-centrality parameters and statistical power for linear mixed-effects repeated measures models.

Number of Donors (N)

Minor Allele Frequency (MAF)

Interaction Effect Size (beta)

Ready to compute power model.

Marburg Laboratory Resource & Assumption Register

Parameter	Category	Status Classification	Description & Assumption	Carlo's Notes / Host Input
Loading feasibility register...

Encrypted API Vault & System Administration

AES-256-GCM Secure Credential Storage • Provider Health • Audit Trail • Zero Log Leakage

Scientific API Provider Registry

Provider	Category	Status	Active Key Preview	Update Credential
Loading providers...

Security & Audit Event Trail

Timestamp (UTC)	User Email	Action	IP Address	Details
Loading audit trail...

Reproducibility and Perturbation Specificity of Genetic Regulatory Responses to DNA Damage in Human Immune Cells

Scientific Quality Gates Audit (Section 17)

Confirmed Project Baseline & Institutional Roles

Institutional Roles & Core Objectives

Confirmed Published Benchmarks

Bigge et al. (BMC Genomics 2024)

Fairfax et al. (Nature Communications 2014)

Federated Multi-API Literature Discovery

Reproducible Search Audit Log

Curated Literature Library

Interactive Citation & Thematic Network

Structured Scientific Evidence Registry

Scientific Gap Identification Matrix

Adversarial Novelty Verification Engine

Run Targeted Adversarial Check

Experimental Feasibility & Statistical Power Framework

Interaction eQTL (Genotype x Perturbation) Statistical Power Calculator

Marburg Laboratory Resource & Assumption Register

Humboldt Fellowship Proposal Workspace

Summary of Changes & Revisions Log

Scientific Briefing for PD Dr. Carlo Maj

Grounded Multi-Model AI Research Assistant

Javad & Carlo Collaboration Workspace

Post Scientific Note or Decision

Encrypted API Vault & System Administration

Scientific API Provider Registry

Security & Audit Event Trail

Javad–Carlo ResearchOS

Reproducibility and Perturbation Specificity of Genetic Regulatory Responses to DNA Damage in Human Immune Cells

Scientific Quality Gates Audit (Section 17)

Confirmed Project Baseline & Institutional Roles

Institutional Roles & Core Objectives

Confirmed Published Benchmarks

Bigge et al. (BMC Genomics 2024)

Fairfax et al. (Nature Communications 2014)

Federated Multi-API Literature Discovery

Reproducible Search Audit Log

Curated Literature Library

Interactive Citation & Thematic Network

Structured Scientific Evidence Registry

Scientific Gap Identification Matrix

Adversarial Novelty Verification Engine

Run Targeted Adversarial Check

Experimental Feasibility & Statistical Power Framework

Interaction eQTL (Genotype x Perturbation) Statistical Power Calculator

Marburg Laboratory Resource & Assumption Register

Humboldt Fellowship Proposal Workspace

Summary of Changes & Revisions Log

Scientific Briefing for PD Dr. Carlo Maj

Grounded Multi-Model AI Research Assistant

Javad & Carlo Collaboration Workspace

Post Scientific Note or Decision

Encrypted API Vault & System Administration

Scientific API Provider Registry

Security & Audit Event Trail