About Experience Publications Posters Presentations Software Articles Awards
Ruben Van Paemel

Ruben Van Paemel

MD · PhD

Pediatrician with experience in pediatric oncology, hematology, precision medicine, with a PhD in cancer genomics, biomarkers, big data analysis and artificial intelligence.

View Publications Get in Touch

About

I'm a pediatrician with additional expertise in pediatric hematology and oncology, currently working as a Fellow at Ghent University Hospital.

My PhD (Research Foundation – Flanders, 2017–2021) focused on expanding the diagnostic toolbox in paediatric oncology through exploration of the cell-free DNA methylome. This work combined wet-lab techniques (plasma preparation, RRBS library prep, qPCR quantification) with large-scale bioinformatics pipelines built in Bash, R, Python and Snakemake on HPC infrastructure.

I am passionate about bridging bench-side research and bedside clinical care, and about building open, reproducible data-analysis tools for the scientific community.

Contact & Links

Email
Ghent University Hospital, Belgium
—
Citations
—
h-index
—
i10-index

Source: OpenAlex

Experience & Education

▶
Oct 2024 – Present
Fellow in Pediatric Hematology & Oncology
Ghent University Hospital, Ghent, Belgium
  • Diagnosis and treatment of patients on the hematology, oncology and stem cell transplantation ward
  • Communicating diagnosis, treatment and prognosis to patients and caregivers
  • Management of complications of chemotherapy, CAR-T therapy, bone marrow transplantation, cancer and surgery in a multidisciplinary team
  • Leading the medical and paramedical team during on-call weeks
  • Enrolment of patients in phase I/II clinical trials (ICF forms, safety monitoring, adverse event reporting)
  • GCP ICH E6(R3) certified
●
June 2017 – 2024
Residency & Master in Specialist Medicine – Pediatrics
Ghent University & AZ Sint-Lucas, Ghent, Belgium
7-year specialist training programme covering general pediatrics, neonatology (NICU), pediatric intensive care (PICU), and pediatric hematology & oncology (in- and outpatient). Gained proficiency in general pediatrics, neonatal resuscitation, critical care management, coordination of oncology follow-up.
  • Developed and deployed two clinical decision-support apps in the UZ Gent NICU: bilicurve (bilirubin nomogram) and Fenton growth curves (premature infant growth monitoring)
●
2020 – 2021
Student Supervision
Ghent University
  • "Computational deconvolution of the methylation signal of heterogeneous mixtures: A benchmarking study" — Master of Bioinformatics, 2021
  • "Deconvolution of Cell-free DNA methylation in Pediatric Cancer" — Master of Bioinformatics, 2021
  • "Methylation Calling and Tumor Classification from cfDNA of Pediatric and Adult Cancer types" — Design Project Bioinformatics, 2020
  • Jury member: "Liquid biopsy analysis in neuroblastoma patients" — Master of Biomedical Sciences, 2020
●
2017 – 2020
PhD Courses & Training
Various institutions
  • Statistical Rethinking: A Bayesian Course with Examples in R and Stan — Richard McElreath, 2020
  • Computational Systems Biology in Cancer — Institut Curie, France, 2018
  • Advanced Academic English Writing Course — Doctoral Schools, Ghent University, 2018
  • Introduction to Deep Learning and Machine Learning — Ghent University & Jülich Supercomputing Center, 2017
  • Digital Droplet PCR Course — Doctoral Schools, Ghent University, 2017
●
Sept 2017 – 2021
PhD Fellowship
Research Foundation – Flanders (FWO)
Thesis: "Expanding The Diagnostic Toolbox in Pediatric Oncology: Exploration of the Value of the Cell-Free DNA Methylome."
Promotor: Prof. dr. B. De Wilde · Co-promotor: Prof. dr. K. De Preter
  • Patient recruitment, IRB approval, sample processing (plasma prep, DNA isolation, SOP development)
  • Sequencing library preparation: WGS, WES, bulk RNA-seq; qPCR quantification; capillary electrophoresis QC
  • Large-scale bioinformatics pipelines (Snakemake / HPC); data analysis in Bash, R, R-Shiny, Python; variant calling and copy number variant (CNV) analysis
  • Hands-on linear regression modelling with frequentist and Bayesian statistics
  • Version control with git; development of open-source tools
●
June 2013 – 2017
Master in Medicine — Summa cum laude
Ghent University
Thesis: "Identification of genetic aberrations predisposing to familial Burkitt lymphoma using whole genome sequencing." Promotor: Prof. Dr. G. Laureys
●
June 2010 – 2013
Bachelor in Medicine — Magna cum laude
Ghent University

Publications

Co-authored peer-reviewed articles.

No publications match your search.

Academic Posters

Ten years of CAR-T cell therapy: real-world experience from the Belgian cohort
INSPIRED 2025 · Chicago, USA
Ten Years of CAR-T Cell Therapy: Real-world Experience from the Belgian Cohort
Retrospective analysis of all paediatric BCP-ALL patients treated with CAR-T cell therapy in Belgium between 2015 and 2025
Download PDF ↓
Fatal HLH in a 5 year old girl as a complication of secondary histiocytic sarcoma treated with trametinib and chemotherapy
CCLS 2025 · Budapest, Hungary
Fatal HLH as a Complication of Secondary Histiocytic Sarcoma Treated with Trametinib and Chemotherapy
Case report: 5-year-old girl with T-ALL developing necrotising pleuropneumonia and HLH secondary to histiocytic sarcoma sharing the same TCR rearrangement
Download PDF ↓
Mycobacterium abscessus as a complication of immunosuppression after allogeneic stem cell transplantation for congenital neutropenia
eBMT 2026 · Madrid, Spain
Mycobacterium abscessus as a Complication of Immunosuppression after Allogeneic Stem Cell Transplantation for Congenital Neutropenia
Case report: 3-year-old boy with CSF3R mutation, post-alloSCT disseminated M. abscessus infection with pulmonary GvHD
Download PDF ↓
Minimally-Invasive Classification of Pediatric Solid Tumors Using Reduced Representation Bisulfite Sequencing of Cell-free DNA
SIOP 2019 · Lyon, France
Minimally-Invasive Classification of Pediatric Solid Tumors Using Reduced Representation Bisulfite Sequencing of Cell-free DNA: A Proof-of-Principle Study
Download PDF ↓

Presentations

2026

Lymphadenopathy work-up

Master of Specialist Medicine – Pediatrics

2025

Unmasking Familial Hemophagocytic Lymphohistiocytosis type 3: Chronic Disseminated Rubella Infection Following MMR Vaccination Travel grant

eBMT Inborn Error Working Party

2025

Acute management of sickle cell anemia

National Meeting - Pediatrics

2020

Liquid Biopsies: ready for prospective evaluation

SIOPEN Meeting · September 2020

2019

Non-invasive classification of pediatric tumor types using reduced representation bisulfite sequencing of cell-free DNA: a proof-of-principle study

EACR-ESMO Joint Conference on Liquid Biopsies · Bergamo, Italy

2019

Precision Oncology Masterclass

Master of Biomedical Sciences · Ghent University · November 2019

Software & Tools

Open-source projects available on GitHub

clinAnnotR R

Harmonise treatment and lab values of multiple cases on one figure

GitHub → Live app →

EU Pediatric Trial Monitor R

Interactive EU clinical trial dashboard

GitHub → Live app →

fenton-shiny R

Fenton growth curve visualiser with GET support — deployed at UZ Gent NICU

GitHub → Live app →

bilicurve-shiny R

Bilirubin nomogram app for neonatal jaundice — deployed at UZ Gent NICU

Live app →

Stolling HTML

Interactive overview of the clotting cascade

Live app →

More projects on GitHub

Articles & Blog Posts

Published on Medium / Towards Data Science

2021

My Workflow for Open and Reproducible Science as an Academic Researcher in Biomedicine

Version control, reproducible pipelines and open-science tools for biomedical researchers.

2020

Scanning and Converting Old Black-and-White Film Negatives to Color Using DeepAI

Applying AI colorisation to analogue film photography.

2020

Kaplan Madness: Dichotomising Continuous Variables

The statistical pitfalls of binarising continuous predictors in survival analysis.

2019

Kaplan-Meier Curves: An Introduction

Primer on survival functions and their interpretation in clinical research.

2018

My Journey Into Programming and Bioinformatics: Part 3

Advanced bioinformatics workflows and HPC pipelines.

2018

My Journey Into Programming and Bioinformatics: Part 2 — Sequencing Crash Course

DNA/RNA sequencing technologies explained for the coding clinician.

2018

My Journey Into Data Science and Bioinformatics

From clinician to coder — first steps into programming and genomics.

Awards & Certificates

Awards

  • Award for Oral Presentation — Oncopoint, 2019
  • Award for Flash Presentation — Institut Curie, Paris, 2018
  • Best Poster Presentation by Young Investigator — BeSHG, 2018
  • Award for Storm Session Presentation — Oncopoint, 2018

Certificates

  • Electrocardiography
  • Newborn Life Support (NLS) Provider
  • European Pediatric Advanced Life Support (EPALS) Provider
  • European Board of Paediatricians (EPB)-Certified
  • GCP ICH E6(R3) Certified
CV (full) CV (lite)