Avatar

Pieter Moris

Postdoctoral Researcher Bioinformatics

Institute of Tropical Medicine Antwerp


I’m a biologist at heart with a passion for machine learning, statistics and scientific reproducibility.

After an education in both biology and statistical bioinformatics, I embarked upon my journey as a PhD student in the field of bioinformatics at the Adrem Data Lab of the University of Antwerp and the Biomina Research Network , where I leveraged machine learning and data mining methods to study molecular host-pathogen interactions and the immune system. My next role was that of Data Scientist in the Bioinformatics Unit at Galapagos , with a focus on improving scientific reproducibility and throughput via pipelines and containerization on cloud infrastructure, as well as assisting in drug target discovery projects by analysing transcriptomics experiments. Currently, I am a Postdoctoral Researcher Bioinformatics in the Unit of Malariology at the Institute of Tropical Medicine , where I am working on the molecular surveillance of malaria in travelers using whole-genome sequencing and machine learning approaches.

Interests

  • Bioinformatics ∪ computational biology
  • Machine learning & artificial intelligence
  • Data pipelines & scientific reproducibility
  • Genomics
  • Statistics
  • Systems biology
  • Immunoinformatics
  • Infectious diseases and parasitology

Education

  • PhD in Bioinformatics, 2021

    UAntwerpen

  • MSc Statistics - Bioinformatics, 2016

    UHasselt

  • MSc in Biology, 2014

    KU Leuven

  • BSc in Biology, 2012

    KU Leuven

Skills

Machine learning and deep learning

Bioinformatics / computational biology

Statistics

Python

R

Unix

Git version control

(Nextflow) Pipelines

Containerization

Server administration

High performance computing (VSC)

Cloud computing

LaTeX / Quarto / Knitr / Jupyter

Science communication

Education

Projects

Some things I’ve worked on

*
All Educational Bioinformatics Machine learning Computational Git

SUMMIT

A GeoSentinel-ITM project for surveilling the genomic epidemiology of malaria in travelers.
PDF

Introduction to unix and sequencing pipelines

Course notes offering an introduction to (l)unix and the bioinformatics analysis of sequencing assays for malaria molecular …
Link to course notes

Nf-core institutional config for CalcUA VSC

A config profile for using nf-core pipelines on the CalcUA HPC.
Link to config on nf-core

Workshop on collaborating in git

A workshop to introduce git to researchers with a focus on collaboration.
Link to workshop

ImRex - CNN

Convolutional neural network for TCR-epitope recognition prediction using a combined sequence input represention.
Link to code repository

MILES Subgraph Miner

A Java tool for mining subgraphs that are associated with a specific set of nodes in a network.
Link to code repository

Docker primer

A hands-on introductory tutorial to Docker.
Link to primer

Computational skills primer

An overview of computational skills and tools required for suriving a PhD in bioinformatics.
Link to slides

Biomolecular id remapper

A Python script for remapping biomolecular identifiers via the UniProt API.
Link to code repository

Tutorial on git internals

A light-hearted presentation on the inner workings of the git version control system
Link to slides

TCRex (server back end)

A web tool for the prediction of TCR–epitope recognition.
TCRex website

Gene Ontology scripts

A Python package and script for handling Gene Ontology data and performing enrichment tests.
Link to code repository

Publications

Journal Current Challenges for Unseen-Epitope TCR Interaction Prediction and a New Perspective Derived from Image Classification.
Pieter Moris, Joey De Pauw, Anna Postovskaya, Sofie Gielis, Nicolas De Neuter, Wout Bittremieux, Benson Ogunjimi, Kris Laukens, Pieter Meysman. Briefings in Bioinformatics, 2020.

Code DOI

Journal Detection of enriched T cell epitope specificity in full T cell receptor sequence repertoires.
Sofie Gielis, Pieter Moris, Wout Bittremieux, Nicolas De Neuter, Benson Ogunjimi, Kris Laukens, Pieter Meysman. Frontiers in Immunology, 2019.

Project DOI

Journal MILES: a Java tool to extract node-specific enriched subgraphs in biomolecular networks.
Pieter Moris, Danh Bui-Thi, Kris Laukens, Pieter Meysman. Bioinformatics, 2019.

Code Project DOI

Journal No barrier breakdown between human and cattle schistosome species in the Senegal River Basin in the face of hybridisation.
Nele Boon, Moustapha Mbow, Linda Paredis, Pieter Moris, Ibrahima Sy, Tim Maes, Bonnie L. Webster, Moussa Sacko, Filip A.M. Volckaert, Katja Polman, Tine Huyse. International Journal for Parasitology, 2019.

DOI

Journal Grasping frequent subgraph mining for bioinformatics applications.
Aida Mrzic, Pieter Meysman, Wout Bittremieux, Pieter Moris, Boris Cule, Bart Goethals, Kris Laukens. BioData Mining, 2018.

DOI

Journal The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology.
Conor J. Meehan, Pieter Moris, Thomas A. Kohl, Jūlija Pečerska, Suriya Akter, Matthias Merker, Christian Utpatel, Patrick Beckert, Florian Gehre, Pauline Lempens, Tanja Stadler, Michel K. Kaswa, Denise Kühnert, Stefan Niemann, Bouke C. de Jong. EBioMedicine, 2018.

DOI

Journal On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition.
Nicolas De Neuter, Wout Bittremieux, Charlie Beirnaert, Bart Cuypers, Aida Mrzic, Pieter Moris, Arvid Suls, Viggo Van Tendeloo, Benson Ogunjimi, Kris Laukens, Pieter Meysman. Immunogenetics, 2018.

DOI

Contact

  • Message me on Linkedin
  • My GitHub
  • ORCID
  • Google Scholar
  • PGP fingerprint: 3DA4 8C04 4736 4796 0490 D6D5 BD3B 7810 4AE1 D801 ()