Dual-caller strategy
GATK and DeepVariant calls are merged with Spark/Glow, reaching 0.99 F1/recall on GIAB benchmarks.
Bioinformatician · Medical Geneticist
Fardad DanaeeFard
I build production-grade genomics pipelines that turn raw sequencing reads into ▍
- 0
- F1 / recall on GIAB truth sets
- <0h
- to process each exome
- 0
- peer-reviewed publications
- 0st
- of 65,333 in the national M.Sc. exam
01
From the hematology bench to the command line.
I started out in a hematology lab, running blood tests for patients with leukemia. Today I write the software that reads their genomes.
I trained in Medical Laboratory Sciences and Human Genetics, and my work now sits where clinical genetics meets software engineering. I design scalable Nextflow pipelines, benchmark variant callers against GIAB truth sets, and write clinical reports that help families get a diagnosis.
My research covers hereditary spastic paraplegia, rare neurological disorders, cancer transcriptomics, and endogenous retroviruses in Parkinson’s disease at single-cell resolution.
- Based inIstanbul, Türkiye
- DegreeM.Sc. Human Genetics
- EnglishIELTS 8 · TOEFL 110
- HonorMSCA DISCOVER PhD Scholarship
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##INFO=<ID=ROLE,Description="Current calling">
#CHROM POS ID REF ALT
chrIR 2015 fardad MedLab Bioinformatics
QUAL FILTER
99 PASS
INFO
ROLE=Bioinformatician,Medical_Geneticist;
FOCUS=Rare_Disease,Cancer_Genomics,scRNA;
STACK=Nextflow,GATK,DeepVariant,Spark;
LANG=Python,Rust,R,Bash,Groovy;
ACMG=Pathogenic # for bad pipelines
02
PAPCO: FASTQ to clinic in under an hour.
The Nextflow (DSL2) suite I designed and built at Genomist Ltd. It is containerized, versioned and benchmarked, and it runs in clinical production.
FASTQraw reads · QC
DRAGMAPalt-masked ref
Scattercontig-aware · gender-aware
GATKHaplotypeCaller
DeepVariantCNN caller
Spark · Glowcallset merge
ReportACMG · HPO
Scatter / gather at scale
Parallel processing brings each exome under one hour, fast enough for high-throughput cohorts.
Phenotype-aware CNV
HPO-integrated CNV calling plus cancer biomarker modules for TMB, MSI, ROH and LOH.
Reproducible by design
Every module is pinned with Docker and DSL2 versioning. DRAGMAP replaces BWA to resolve complex regions better.
03
Experience, mapped like a chromosome.
q36.1 · 2025–2026
Bioinformatician & Medical Geneticist
Genomist Ltd. · Tehran
- Designed and built PAPCO, a production Nextflow DSL2 suite using DRAGMAP and an alt-masked reference.
- Built the GATK + DeepVariant dual-caller workflow with Spark/Glow merging. It scores 0.99 F1 on GIAB.
- Developed the HPO-aware CNV module and the TMB / MSI / ROH / LOH biomarker modules.
- Wrote clinical reports for Mendelian disorders, recurrent pregnancy loss, ACMG secondary findings and carrier status.
q32.2 · 2025
Research Consultant
BOKU University, Vienna · Remote
- Built a PacBio long-read pipeline that detects SNVs, indels, STRs and CNVs in grapevine.
- Designed the case-control statistics for identifying disease variants, and advised on PhD pipeline methods.
p21.3 · 2024–2025
Research Assistant
Shahid Sadoughi University of Medical Sciences · Remote
- Led pipeline development to map the transcriptional landscape of colorectal cancer from NCBI-GEO data.
- Found new pathways through functional annotation and enrichment analysis, supervised by Prof. Mahta Mazaheri.
p16.1 · 2023
NGS Data Analyst
MOM Fertility Clinic · Remote
- Identified variants in Mendelian disease, cancer and familial infertility, and wrote clinical reports for genetic counseling.
p13 · 2021
Course Instructor
Salvia Medical Sciences · CytoCity · Royan Institute
- Taught NGS and WES analysis, from FASTQ to clinical insight, to 30+ students online during COVID-19.
p11.2 · 2016–2019
Medical Laboratory Technician, Hematology
Zagross Medical Laboratory · Kermanshah
- Ran hematology tests for patients with ALL, AML and CLL, and managed the department's daily QC.
M.Sc. Human Genetics
University of Social Welfare and Rehabilitation Sciences, Tehran
Thesis: whole-exome sequencing in five Iranian families with hereditary spastic paraplegia to find disease-causing variants. Supervised by Dr. Afagh Alavi and Prof. Hossein Najmabadi.
B.Sc. Medical Laboratory Sciences
Kermanshah University of Medical Sciences
Full scholarship recipient.
04
Research & publications.
Rare neurological disease genetics, cancer genomics and single-cell sequencing.
Apr 2025
Expanding the phenotypic spectrum of RNASEH2B mutations: a new case of pure hereditary spastic paraplegia and a systematic review
Current Journal of Neurology
↗ Aug 2021Anticipation can be more common in hereditary spastic paraplegia with SPAST mutations than it appears
Canadian Journal of Neurological Sciences
↗ Jun 2021Neurodegeneration with brain iron accumulation and a brief report of the disease in Iran
Canadian Journal of Neurological Sciences
↗ Feb 2021Clinical spectrum in multiple families with primary COQ10 deficiency
American Journal of Medical Genetics Part A
↗Projects & presentations
ClinLR: clinical long-read genomic analysis
I built a PacBio HiFi pipeline for small and structural variants, tandem repeat expansions, long-range phasing and native DNA methylation analysis.
Explore ClinLR documentation ↗HERV footprints in Parkinson’s disease at single-cell scale
I built a custom composite reference of the human genome plus known HERVs to detect endogenous retroviruses in single-cell data from several Parkinson’s cohorts. This is a collaboration with Dr. Michael Lappe at BRIC, University of Copenhagen.
New molecular & cellular pathways of IDH1 mutation in glioblastoma
Seurat-based scRNA-seq analysis of GSE103224 showing adipocyte accumulation and weakened immune responses in IDH1 R132H tumors.
AD-HSP, SPAST variations & evidence for anticipation
Presented at the 4th International and 16th Iranian Genetics Congress.
Genetic heterogeneity & novel genes in Iranian HSP patients
European Human Genetics Conference 2022.
RNASEH2B-related disorders: a network for differential diagnosis
A systematic review using network analysis of clinical findings. Presented with a companion talk on HSP heterogeneity.
05
Toolkit, expressed.
Shown as an expression heatmap. Brighter cells mean deeper experience.
Genomics
Germline & somatic variant calling · CNV · STR · PacBio long-read · WES · scRNA-seq · bulk RNA-seq · ChIP-seq · GIAB validation
Pipelines
Nextflow DSL2 · Docker / Singularity · scatter/gather · Spark / Glow · SLURM & HPC
Clinical
ACMG classification · HPO integration · TMB / MSI / ROH / LOH · clinical reporting
AI engineering
Model development & deployment · RAG · LLM fine-tuning · agentic AI · MLOps
GATKDeepVariantMutect2NeuSomaticDRAGMAPBWASAMtoolsBCFtoolsVEPANNOVARExomiserSeuratScanpy
DESeq2edgeRlimmaGSEAGSVAEnsemblClinVardbSNPHPOGEOSRAdbGaPGIABGit
MSCA
DISCOVER PhD Scholarship, H2020 Marie Skłodowska-Curie (2022)
★
Best Poster Award, Iranian Genetics Congress (2020)
#21
Out of 65,333 applicants, M.Sc. entrance exam (2019)
KAUST
Fundamental Skills in Bioinformatics, plus courses from Google, Imperial, Fred Hutch and IBM