Rajendra Bahadur Shahi ShahiRB

Rajendra Bahadur Shahi

PhD · Senior Bioinformatics Scientist

RNA Therapeutics · Cancer Genomics · Personalised Medicine · Data Analysis · Machine Learning

`$ whoami`

researcher = {
    "name"        : "Rajendra Bahadur Shahi",
    "degree"      : "PhD · Medical Sciences (Cancer Genomics)",
    "institute"   : "Vrije Universiteit Brussel, Belgium",
    "current"     : "Scientist Bioinformatics · Etherna Immunotherapies",
    "expertise"   : [
        "End-to-end NGS pipeline development",
        "RNA design & mRNA therapeutics",
        "Cancer neoantigen prediction",
        "Germline / somatic variant analysis",
        "Machine learning · immunogenomics",
    ],
    "publications": 11,
    "fellowships" : ["EACR Travel Fellow", "MD Anderson Visiting Researcher"],
    "languages"   : ["English (Professional)", "Nepali (Native)", "Dutch (A1/A2)"],
}

Senior bioinformatics scientist with 15+ years of experience designing and deploying production-grade NGS pipelines across RNA therapeutics and oncogenomics. Currently leading computational efforts at Etherna Immunotherapies, supporting clinical-stage personalised cancer vaccine programmes. Author of 11 peer-reviewed publications in journals including BMC Cancer, International Journal of Cancer, and Oncogene. Internationally recognised with an EACR Travel Fellowship and a visiting research appointment at MD Anderson Cancer Center.

`$ cat skills.tsv`

🧬 Genomic Analysis

GATK · MuTect2 · VarScan · bcftools
VCFtools · STAR-Fusion · ANNOVAR · SnpEff
ClinVar · COSMIC · HGMD
NetMHC · NetMHCpan · pVACtools
cBioPortal · TCGA · ICGC

🔬 Transcriptomics & RNA

DESeq2 · edgeR · Kallisto · Salmon · Sleuth
ViennaRNA · RNAstructure · mfold
TargetScan · miRanda · miRBase · miRTarBase
GTEx · 1000 Genomes

🤖 Machine Learning

scikit-learn · TensorFlow · DeepChem · SHAP
PCA · t-SNE · Bayesian optimisation
ROC/AUC · Cross-validation
Logistic regression · Mixed models

🧪 Wet Lab (basic)

NGS library prep · DNA/RNA extraction
qPCR · RT-PCR · Western blot
ELISA · RIA · Cell culture · IF/IHC

⚙️ Programming & DevOps

Python (pandas · scikit-learn · Biopython)
R / Bioconductor · Bash · AWK · SQL · LaTeX
Git / GitHub · Snakemake · Docker
HPC: Slurm · PBS · Jupyter

📊 Visualisation & Reporting

Dash · Plotly · PowerBI
seaborn · matplotlib
IGV · UCSC Browser · Circos · PyMOL
Cytoscape

🗄️ Databases & Resources

ENSEMBL · NCBI · UniProt · GENCODE
dbSNP · dbNSFP · RefSeq
Reactome · KEGG · STRING · IEDB
BLAST · ExPASy · Clustal Omega

💬 Languages

English  ·  Professional
Nepali   ·  Native
Dutch    ·  A1/A2

`$ history | grep experience`

🔹 Scientist — Bioinformatics · Etherna Immunotherapies, Belgium · `2021 – Present`

Etherna Immunotherapies is a clinical-stage RNA therapeutics company developing personalised cancer vaccines.

Architected an end-to-end mRNA design and optimisation platform integrating UTR discovery, RNA secondary-structure prediction (ViennaRNA, RNAstructure), codon optimisation, and variant annotation — directly informing clinical-stage vaccine programmes
Developed an immunogenicity prediction pipeline combining neoantigen identification (pVACtools, NetMHCpan), HLA typing, and miRNA off-target analysis (TargetScan, miRanda), shortening candidate prioritisation cycles for internal R&D and external pharma partners
Deployed containerised (Docker) Snakemake workflows on HPC (Slurm), ensuring reproducibility and scalability across multi-cohort datasets
Delivered interactive reporting dashboards (Dash, Plotly, PowerBI) consolidating multi-omic outputs for scientific and clinical stakeholders

🔹 Scientific Collaborator · Lab. of Molecular & Cellular Therapy, VUB · `2019 – 2020`

Led development of a WES-based cancer neoantigen identification pipeline integrating variant calling, HLA typing, and epitope prediction for personalised tumour vaccine design
Co-authored peer-reviewed publications on neo-antigen mRNA vaccines (Vaccines 2020) and CRAF oncogene sensitivity to combined RAF/MEK inhibition (Oncogene 2019)

🔹 Scientific Researcher · Lab. of Medical & Molecular Oncology, VUB · `2012 – 2018`

Performed high-throughput WES/WGS analysis of hereditary breast cancer cohorts; identified RAD17 and additional novel predisposition gene candidates — results published in BMC Cancer (2019, 2024) and Int J Cancer (2020)
Developed a generic PCR-based EGFR-TK mutation detection assay for NSCLC, improving clinical diagnostic workflow sensitivity (Appl Immunohistochem Mol Morphol 2015)
Characterised germline/somatic mutation landscapes, CNV profiles, and mutational signatures across multiple tumour types
Awarded EACR Travel Fellowship for a visiting research stay at MD Anderson Cancer Center (2012–13); received Prijs Kankeronderzoek (2016) and two OECI Awards (2012, 2015)

🔹 Lecturer & Programme Coordinator · Multiple Institutions, Nepal · `2006 – 2009`

Designed and taught courses in biotechnology, bioinformatics, and microbial genetics across Tribhuvan University, St Xavier College, and Lord Buddha Education Foundation
Directed departmental strategy and curriculum development; supervised laboratory practicals

🔹 Research Trainee · Everest Biotech, Nepal · `2006`

Antibody production workflow including goat immunisation, serum processing, and protein purification via affinity chromatography

`$ cat education.tsv`

Degree	Institution	Result
PhD · Medical Sciences (Cancer Genomics)	Faculty of Medicine & Pharmacy, Vrije Universiteit Brussel	—
M.Sc. Biomedical Sciences (Cell & Gene Therapy)	Faculty of Medicine & Pharmacy, Vrije Universiteit Brussel	Great Distinction
M.Sc. Biotechnology	T. Hans Roever College, Bharathidasan University, India	Distinction
PG Diploma · Bioinformatics	T. Hans Roever College, Bharathidasan University, India	Distinction

`$ bibtex --list publications.bib`

11 peer-reviewed publications · View full list on Google Scholar →

#	Authors	Title	Journal	Year
1	Joris S, Giron P, …, Shahi RB, …, Hes FJ	Identification of RAD17 as a candidate cancer predisposition gene…	BMC Cancer	2024
2	Massart A, Danger R, …, Shahi RB, …, Brouard S	An exome-wide study of renal operational tolerance	Front Med	2022
3	Boeckx B ``, Shahi RB* `*`, …, De Greve J	The genomic landscape of NSCLC in never smokers	Int J Cancer	2020
4	Esprit A, de Mey W, Shahi RB, …, Breckpot K	Neo-Antigen mRNA Vaccines	Vaccines	2020
5	Noeparast A, …, Shahi RB, …, Teugels E	CRAF mutations in lung cancer predict sensitivity to RAF/MEK inhibition	Oncogene	2019
6	Joris S, Shahi RB, De Brakeleer S, …, De Grève J	Clinical characteristics of breast cancers with familial risk and no BRCA1/2 mutations	J Mol Genet Med	2019
7	Shahi RB, De Brakeleer S, …, De Grève J	Candidate cancer predisposing variants by WES in BRCA1/2-negative families	BMC Cancer	2019
8	De Grève J, Decoster L, Shahi RB, …, Teugels E	PARP inhibitors	Belg J Med Oncol	2016
9	Shahi RB, De Brakeleer S, …, Teugels E	EGFR-TK domain-activating mutations in NSCLC via generic PCR methods	Appl Immunohistochem Mol Morphol	2015
10	Pokharel K, …, Shahi RB, …, Poudel BH	Antibacterial activities of medicinal plants of Nepal	J Inst Med	2009
11	Shahi RB	Exome-wide identification of rare variants in BRCA1/2-negative breast cancer families	In preparation	—

* Equal contribution

`$ ls awards/`

2016  🏆  Prijs Kankeronderzoek (Cancer Research Prize)
          ORC–VUB, Oncology Research Center, Vrije Universiteit Brussel

2015  🎖️  OECI Award – 4th Joint Training Course
          Organisation of European Cancer Institutes, Belgium

2015  ✈️  Travel Grant – SABCS Symposium, San Antonio, TX
          Doctoral School of Life Sciences & Medicine, VUB

2012  ✈️  EACR Travel Fellowship – MD Anderson Cancer Center, Houston
2013      European Association for Cancer Research, UK

2012  ✈️  Travel Grant – Visiting Research
2013      Doctoral School of Life Sciences & Medicine, VUB

2012  🎖️  OECI Award – 2nd Joint Training Course
          Organisation of European Cancer Institutes, Belgium

2011  🎓  Ph.D. Research Scholarship
2016      LMMO, Vrije Universiteit Brussel

2009  🎓  Master's Fellowship in Biomedicine
2011      Vrije Universiteit Brussel

2004  🎓  Undergraduate Scholarship in Microbiology
2006      Tri-Chandra College, Tribhuvan University, Nepal

2000  🎓  M.Sc. Scholarship in Biotechnology
2003      T. Hans Roever College, Bharathidasan University, India

1997  🎓  Pre-University Scholarship in Biology
1999      Tri-Chandra College, Tribhuvan University, Nepal

`$ grep -r "presentations" ./`

Year	Conference	Type
2017	19th Annual BSMO Meeting — Belgian Society of Medical Oncology	`Oral`
2016	Centrum Medische Genetica, UZ Brussel: Beyond BRCA & NGS	`Seminar`
2015	SABCS — San Antonio Breast Cancer Symposium	`Oral + Poster`
2014	Dept. of Hematology, UZ Brussel: NGS in Clinical Molecular Oncology	`Seminar`
2013	WIN Symposium — Worldwide Innovative Networking in Personalised Cancer Medicine, Paris	`Poster`
2012	BRIGHTcore, UZ Brussel–VUB: NGS Technologies	`Seminar`

`$ git log --stats`

Primary languages & tools used across research pipelines

`$ curl -s contact.json`


💼 LinkedIn	linkedin.com/in/rajendra-bahadur-shahi-a820a6112
📚 Google Scholar	scholar.google.com/citations?user=ziLEJd8AAAAJ
🔬 ORCID	orcid.org/0000-0002-7751-6852
🌐 Profile website	shahirb.github.io

─── A ── T ── C ── G ── A ── T ── C ── G ── A ── T ── C ── G ───
   PhD · Medical Sciences · Vrije Universiteit Brussel
   Scientist Bioinformatics · Etherna Immunotherapies
─── G ── C ── T ── A ── G ── C ── T ── A ── G ── C ── T ── A ───

Selected skills and experiences are presented · * Equal contribution

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Rajendra Bahadur Shahi ShahiRB

Highlights

Block or report ShahiRB

Rajendra Bahadur Shahi

`$ whoami`

`$ cat skills.tsv`

`$ history | grep experience`

🔹 Scientist — Bioinformatics · Etherna Immunotherapies, Belgium · `2021 – Present`

🔹 Scientific Collaborator · Lab. of Molecular & Cellular Therapy, VUB · `2019 – 2020`

🔹 Scientific Researcher · Lab. of Medical & Molecular Oncology, VUB · `2012 – 2018`

🔹 Lecturer & Programme Coordinator · Multiple Institutions, Nepal · `2006 – 2009`

🔹 Research Trainee · Everest Biotech, Nepal · `2006`

`$ cat education.tsv`

`$ bibtex --list publications.bib`

`$ ls awards/`

`$ grep -r "presentations" ./`

`$ git log --stats`

`$ curl -s contact.json`

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Rajendra Bahadur Shahi ShahiRB

Highlights

Rajendra Bahadur Shahi

$ whoami

$ cat skills.tsv

$ history | grep experience

🔹 Scientist — Bioinformatics · Etherna Immunotherapies, Belgium · 2021 – Present

🔹 Scientific Collaborator · Lab. of Molecular & Cellular Therapy, VUB · 2019 – 2020

🔹 Scientific Researcher · Lab. of Medical & Molecular Oncology, VUB · 2012 – 2018

🔹 Lecturer & Programme Coordinator · Multiple Institutions, Nepal · 2006 – 2009

🔹 Research Trainee · Everest Biotech, Nepal · 2006

$ cat education.tsv

$ bibtex --list publications.bib

$ ls awards/

$ grep -r "presentations" ./

$ git log --stats

$ curl -s contact.json

Pinned Loading

Uh oh!

`$ whoami`

`$ cat skills.tsv`

`$ history | grep experience`

🔹 Scientist — Bioinformatics · Etherna Immunotherapies, Belgium · `2021 – Present`

🔹 Scientific Collaborator · Lab. of Molecular & Cellular Therapy, VUB · `2019 – 2020`

🔹 Scientific Researcher · Lab. of Medical & Molecular Oncology, VUB · `2012 – 2018`

🔹 Lecturer & Programme Coordinator · Multiple Institutions, Nepal · `2006 – 2009`

🔹 Research Trainee · Everest Biotech, Nepal · `2006`

`$ cat education.tsv`

`$ bibtex --list publications.bib`

`$ ls awards/`

`$ grep -r "presentations" ./`

`$ git log --stats`

`$ curl -s contact.json`