Senior bioinformatics scientist with 15+ years designing and deploying production-grade NGS pipelines across RNA therapeutics and oncogenomics. Expert in end-to-end genomic analysis — from variant discovery and neoantigen prediction to mRNA design optimisation and transcriptomics. Author of 11 peer-reviewed publications in BMC Cancer, Int J Cancer and Oncogene. EACR Fellow · Visiting researcher, MD Anderson Cancer Center.

15+
Years
11
Publications
11
Awards
6
Presentations
LinkedIn Google Scholar GitHub ORCID
01

Featured Work

Clinical workflow Platform architecture

Personalized mRNA design platform

Unified UTR discovery, codon optimization, RNA secondary-structure scoring, and variant-aware annotation in one reproducible pipeline for candidate evaluation.

ViennaRNA RNAstructure Python Snakemake Docker
  • Turned fragmented design steps into versioned, auditable workflow stages.
  • Structured for cross-functional use across discovery, CMC, and partner-facing review.
Domain RNA therapeutics Outcome Reproducible design loop
Decision support Prioritization engine

Neoantigen prioritization workflow

Combined variant calling outputs, HLA typing, epitope ranking, and miRNA off-target filtering into a single analyst-friendly prioritization flow.

pVACtools NetMHCpan TargetScan Plotly Dash
  • Reduced manual handoffs by packaging ranking logic and report output together.
  • Presented results in formats that R&D teams and external collaborators could act on quickly.
Focus Cancer immunotherapy Output Partner-ready reports
Published impact Discovery pipeline

Cancer Genome Analysis

Built exome- and genome-scale interpretation workflows spanning germline and somatic variant calling, annotation, curation, and cohort- or family-level review across breast and lung cancer studies.

WES/WGS GATK bcftools R IGV
  • Supported both hereditary predisposition discovery and somatic cancer genome analysis, with outputs reflected in peer-reviewed breast and lung cancer publications.
  • Balanced research flexibility with rigor in interpretation, reproducibility, and publication-ready reporting.
Impact Translational genomics Proof Publication-backed outputs
02

Skills

Genomic
Analysis
GATKMuTect2VarScanbcftoolsVCFtoolsSTAR-FusionANNOVARSnpEffClinVarCOSMICHGMDNetMHCNetMHCpanpVACtoolscBioPortalTCGAICGC
Transcriptomics
& RNA
DESeq2edgeRKallistoSalmonSleuthViennaRNARNAstructuremfoldTargetScanmiRandaGTEx1000 GenomesmiRBasemiRTarBase
Machine
Learning
scikit-learnTensorFlowDeepChemSHAPPCAt-SNEBayesian optimisationROC / AUCCross-validationLogistic regressionMixed models
Programming
& DevOps
PythonR / BioconductorBashAWKSQLLaTeXGit / GitHubSnakemakeDockerSlurmPBSJupyter
Visualisation
& Reporting
DashPlotlyPowerBIseabornmatplotlibIGVUCSC BrowserCircosPyMOLCytoscape
Databases
& Resources
ENSEMBLNCBIUniProtGENCODEdbSNPdbNSFPReactomeKEGGSTRINGIEDBBLASTExPASyClustal Omega
Wet Lab
(basic)
NGS library prepDNA/RNA extractionqPCRRT-PCRWestern blotELISARIACell cultureIF/IHC
Languages
English — ProfessionalNepali — NativeDutch — A1/A2
Core tool
Proficient
03

Experience

2021
Present
Current
Scientist — Bioinformatics
Etherna Immunotherapies · Belgium
  • 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 personalised vaccine programmes.
  • Built an immunogenicity prediction pipeline combining neoantigen identification (pVACtools, NetMHCpan), HLA typing, and miRNA off-target analysis (TargetScan, miRanda), shortening candidate prioritisation cycles for internal and pharma partner teams.
  • 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 R&D stakeholders and external partners.
2019 – 2020
Scientific Collaborator
Lab. of Molecular & Cellular Therapy · Vrije Universiteit Brussel · Belgium
  • Led neoantigen identification pipeline development integrating WES 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 MEK inhibition (Oncogene 2019).
2012 – 2018
Scientific Researcher (PhD)
Lab. of Medical & Molecular Oncology · Vrije Universiteit Brussel · Belgium
  • Performed high-throughput WES/WGS analysis of hereditary breast cancer cohorts; identified RAD17 and novel predisposition gene candidates — published in BMC Cancer (2019, 2024) and Int J Cancer (2020).
  • Developed a generic PCR-based EGFR-TK mutation detection assay for NSCLC (Appl Immunohistochem Mol Morphol 2015).
  • Characterised germline/somatic mutation landscapes, CNV profiles, and mutational signatures across multiple tumour types.
  • EACR Travel Fellowship — visiting researcher at MD Anderson Cancer Center (2012–13). Received Prijs Kankeronderzoek (2016) and two OECI Awards.
2006 – 2009
Lecturer & Programme Coordinator
Tribhuvan University · St Xavier College · Lord Buddha Education Foundation · Nepal
  • Designed and taught courses in biotechnology, bioinformatics, and microbial genetics; led departmental strategy and curriculum development across three institutions.
2006
Research Trainee
Everest Biotech · Nepal
  • Antibody production workflow: goat immunisation, serum processing, and protein purification via affinity chromatography.
04

Education

PhD
Ph.D. in Medical Sciences (Cancer Genomics)
Faculty of Medicine & Pharmacy · Vrije Universiteit Brussel · Brussels, Belgium
Great Distinction
M.Sc. Biomedical Sciences (Cell and Gene Therapy)
Faculty of Medicine & Pharmacy · Vrije Universiteit Brussel · Brussels, Belgium
Distinction
M.Sc. Biotechnology
T. Hans Roever College · Bharathidasan University · Tamil Nadu, India
Distinction
Postgraduate Diploma in Bioinformatics
T. Hans Roever College · Bharathidasan University · Tamil Nadu, India
05

Publications

01
Joris S, Giron P, Olsen C, Seneca S, Gheldof A, Staessens S, Shahi RB, De Brakeleer S, … De Grève J, Hes FJ.
Identification of RAD17 as a candidate cancer predisposition gene in families with histories of pancreatic and breast cancers.
BMC Cancer2024; 24(1):723↗ Open
02
Massart A, Danger R, Olsen C, …, Shahi RB, …, Pirson I, Brouard S.
An exome-wide study of renal operational tolerance.
Frontiers in Medicine2022; 9:976248↗ Open
03
Boeckx Bequal, Shahi RBequal, Smeets D, …, Lambrechts D, De Greve J.
The genomic landscape of non-small cell lung carcinoma in never smokers.
International Journal of Cancer2020; 146(11):3207–3218↗ Open
04
Esprit A, de Mey W, Shahi RB, Thielemans K, …, Franceschini L, Breckpot K.
Neo-Antigen mRNA Vaccines.
Vaccines2020; 8(4):776↗ Open
05
Noeparast A, Giron P, Noor A, Shahi RB, De Brakeleer S, …, De Grève J, Teugels E.
CRAF mutations in lung cancer can be oncogenic and predict sensitivity to combined type II RAF and MEK inhibition.
Oncogene2019; 38(31):5933–5941↗ Open
06
Joris S, Shahi RB, De Brakeleer S, …, Teugels E, De Grève J.
Clinical characteristics of breast cancers with familial risk in which no BRCA1/2 mutations were found are sometimes suggestive for a genetic etiology.
Journal of Molecular and Genetic Medicine2019; 13(2):423↗ Open
07
Shahi RB, De Brakeleer S, Caljon B, …, Teugels E, De Grève J.
Identification of candidate cancer predisposing variants by performing whole-exome sequencing on index patients from BRCA1 and BRCA2-negative breast cancer families.
BMC Cancer2019; 19(1):313↗ Open
08
De Grève J, Decoster L, Shahi RB, Fontaine C, …, De Brakeleer S, Teugels E.
PARP inhibitors.
Belgian Journal of Medical Oncology2016; 10(7):263–275↗ Open
09
Shahi RB, De Brakeleer S, …, In't Veld P, Teugels E.
Detection of EGFR-TK domain-activating mutations in NSCLC with generic PCR-based methods.
Applied Immunohistochemistry & Molecular Morphology2015; 23(3):163–171↗ Open
10
Pokharel K, Dhungana BR, Tiwari KB, Shahi RB, Yadav BK, …, Shrestha D, Poudel BH.
Antibacterial activities of medicinal plants of Nepal.
Journal of the Institute of Medicine2009; 30(2):28–32↗ Open
11
Shahi RB.
Exome-wide identification of rare variants in BRCA1/2-negative breast cancer families.
Manuscript in preparation

* Equal contribution

06

Awards & Honours

2016
Prijs Kankeronderzoek (Cancer Research Prize)
ORC–VUB (Oncology Research Center – Vrije Universiteit Brussel), Belgium
2015
OECI Award – 4th Joint Training Course
Organisation of European Cancer Institutes, Belgium
2015
Travel Grant – SABCS Symposium, San Antonio
Doctoral School of Life Sciences & Medicine – VUB, Belgium
2012–13
EACR Travel Fellowship – MD Anderson Cancer Center
European Association for Cancer Research, UK
2012–13
Travel Grant – Visiting Research
Doctoral School of Life Sciences & Medicine – VUB, Belgium
2012
OECI Award – 2nd Joint Training Course
Organisation of European Cancer Institutes, Belgium
2011–16
Ph.D. Research Scholarship
LMMO–VUB, Belgium
2009–11
Master's Fellowship in Biomedicine
Vrije Universiteit Brussel, Belgium
2004–06
Undergraduate Scholarship in Microbiology
Tri-Chandra College – Tribhuvan University, Nepal
2000–03
M.Sc. Scholarship in Biotechnology
T. Hans Roever College – Bharathidasan University, India
1997–99
Pre-University Scholarship in Biology
Tri-Chandra College – Tribhuvan University, Nepal
07

Presentations

2017
19th Annual BSMO Meeting (Belgian Society of Medical Oncology)
Brussels, Belgium
Oral
2016
Centrum Medische Genetica, UZ Brussel: Beyond BRCA & NGS
Brussels, Belgium
Seminar
2015
SABCS — San Antonio Breast Cancer Symposium
San Antonio, TX, USA
Oral + Poster
2014
Department of Hematology, UZ Brussel: NGS in Clinical Molecular Oncology
Brussels, Belgium
Seminar
2013
WIN Symposium — Worldwide Innovative Networking in Personalized Cancer Medicine
Paris, France
Poster
2012
BRIGHTcore, UZ Brussel–VUB: NGS Technologies
Brussels, Belgium
Seminar