IRIBHM computational biology groups

Hello, I am Diego ! I started my PhD journey in September 2023. I achieved a master in Biomedical Sciences at the University of Mons in the Neurosciences and Physiology labs where I investigated the effects of different training conditions on neurogenesis and their relatioship with a myokine called the irisin.

Meanwhile, I contributed to the modeling of an in vitro hypothalamus at the Karolinska Institutet, working under the guidance of Professor Ceccatelli.

Next, I pursued a master in bioinformatics at the Université Libre de Bruxelles under the supervision of Pr. Detours, where I layed the groundwork to histological quantitative trait loci (histoQTL).

Currently, I am dedicated to my master thesis project related to the the histological quantitative trait loci. I am exploring the genomic relationships with histology, employing an in-lab developped AI pipeline.

My upcoming PhD project, titled "Single-cell Resolution 3D Molecular Histology of Papillary Thyroid Cancer and Adjacent Healthy Tissues," aims to construct a 3D model of papillary thyroid cancer (PTC) and healthy thyroid tissues. The project bridges the gap between 3D histology and molecular biology techniques, incorporating spatial transcriptomics, snRNA-seq, and spatially resolved genomics.

If you want to know more about my research, do not hesitate to come and talk to me !

Hi, I am Maxime. I'm a PhD student in IRIBHM computational biology lab. I have a background in biomedical sciences and bioinformatics.

I achieved a master in Biomedical Sciences at the University of Mons (UMONS) during which I contributed to two research projects. For my master's thesis, in the Laboratory of Metabolic and Molecular Biochemistry of UMONS, I studied of C1qBP functions in healthy and FSHD skeletal muscle cells with a specific focus on autophagy. During my Erasmus internship, in the Department of Paediatrics at Oxford University, I worked on the development of new delivery methods for microdystrophin gene therapy.

Then, I achieved a second master in Bioinformatics and Modelling at ULB. During this master I performed a company internship at GSK in the Research and Development department in order to characterize protein’s antigenic surface attribute. Finally, I performed my master's thesis under the supervision of Maxime T. in the computational biology lab of IRIBHM where I studied the genome-wide differences in mutability between parental sets of chromosomes.

I started my PhD 1st October 2023 under the supervision of Maxime T. I'm currently working on two projects:

1. My master's thesis project: Genome-wide differences in mutability between parental sets of chromosomes. Basically, my goal is to find a new methodology to phase the whole genome of cancer patients in order to quantify somatic mutation and structural variants in each copy of the genome.
2. My PhD project: Characterization of genetic variations in repeated regions of the genome with short-read sequencing. Basically, my goal is to develop a suite of bioinformatics tools to call somatic and de-novo indels and substitutions from short read sequencing data including the non-unique genome (not well characterized), validate the tools apply it to a set of normal and cancer datasets. The final goal is to publish the tool as open source software for the general scientific community and will also make all the calls available for others to be able to mine the retrieved calls.

Hello world!

I am Dalil, a PhD student and member of the Computational Biology lab at the IRIBHM.

I completed my master’s in biomedical sciences at the Free University of Brussels. Despite being in a bioinformatic lab, my background primarily lies in the wetlab world. During my master's, I undertook several internships. Firstly, at the ULB Center for Diabetes Research, a laboratory of experimental medicine where I participated in investigating the non-canonical pathway of Nf-KB, specifically focusing on the role of the NIK protein in that pathway. Additionally, I interned at the Jules Bordet Institute, where I worked on deciphering the role of myeloid cells during human cancer development, with a significant emphasis on breast cancer.

In my current project, my main focus lies on genomic events occurring during human development. Through a robust collaboration with the Jules Bordet Institute, our current screening involves various aggressive human cancer biopsies. Our aim is to study the occurrence of copy-number events, particularly focusing on whole-genome doubling events.

Hello! My name is Oier and I am doing my PhD since October 2022. After studying the Bsc of Biochemistry, I decided to start coding by studying the Msc in Computational Methods in Bioinformatics, both in the University of Navarra of Pamplona, Spain.

My Msc project was based on the transcriptomic characterization of different cholangiocarcinoma mouse models and the analysis of different state of the art drug-target interaction methods based on graph methodology.

Actually, in my PhD project I am trying to decipher the intratumoral heterogeneity in resected PDAC. For that, I am trying to confirm that ] can co-exist in the same patient’s tumour and could impact therapeutic purpose. To finish, I al studying also the pathogenic mechanisms involved in the treatment resistance.

If you want to know more about my project, contact me whenever you want!

Hello, I am Ruben, a PhD student working in the computational lab of Vincent Detours. I completed a bachelor’s degree in Biomedical Sciences at the University of Mons and a master in Bioinformatics at the University of Bruxelles where I worked during my internship and my master thesis in Vincent Detours ‘lab.

I’m working on an RNA-editing enzyme, ADAR, converting adenosine to inosine in double stranded RNA substrates. While ADAR nucleoplasm and cytoplasmic functions are well-studied, little is known about its nucleolar enrichment. My goal is to understand the potential role of ADAR nucleolar location and reciprocally, the potential nucleolar role on ADAR functions.

I’m mainly specialized in the processing and analyzes of RNA-sequencing data. During my thesis, we worked in collaboration with the laboratory of Denis Lafontaine, which gave me the opportunity to conduct wet lab experiments and acquire new knowledge.

Hello, I am Aida, a PhD student student since April 2023. I did my bachelor in Biology in the University of Extremadura in Spain. In the final year of my bachelor, I developed an interest in bioinformatics, which led me to pursue a Master’s degree in Bioinformatics at KU Leuven in Belgium. My favorite area of study was the analysis of sequencing data, particularly within the field of cancer research. To further specialize in this area, I began my PhD at the Laboratory of Histology at Université Libre de Bruxelles (ULB) in Belgium.

My PhD project is centered on understanding the malignant progression of squamous cell carcinoma (SCC), the second most common type of skin cancer. Through sequencing of normal skin, actinic keratosis (premalignant lesion) and SCC, our goal is to understand the initiation and progression of malignancy leading to SCC, while defining the different cell-types and cell-states present on each stage of the progression.

This would bring new insights, not only to get an effective treatment for SCC but also for the prevention and early diagnosis.

Hi, I'm Antonia and I started my PhD in October 2023, under the supervision of Dr. Maxime Tarabichi. I have a background in computer science and a master’s in bioinformatics and modeling at ULB. During my master thesis I worked on developing a database of copy number profiles, inferred from raw microarray data of thousands of tumor samples.

My PhD thesis mainly consists of developing and improving an in-house copy number calling R package called ASCAT.sc. This aims to allow the retrieval of copy number profiles of tumors from a wide array of raw data types, such as methylation arrays, single cell ATAC sequencing and Tapestri sequencing.

I’m also collaborating with PhD student Maxime Lefèbvre on a project aiming to uncover genomic variation in the non-unique regions of the genome using short read sequencing.

Hello, my name is Valeriia, and I am a postdoc at the Computational Biology Lab in IRIBHM. I am originated from Kazakhstan (Karaganda), but all my high education I obtained in Russia starting from Medical Biochemistry in Siberian State Medical University (Tomsk) and finalizing with PhD degree in biology at Far Eastern Federal University (Vladivostok). In between I also received master’s degree in biomedical sciences at the University of Maastricht (Netherlands), where I was testing the efficacy of a bispecific antibody in inducing immune response against breast cancer.

My PhD project was investigating the broad molecular effect of the two single nucleotide mutations in brain tumours (gliomas). During my PhD I had opportunities to go abroad to learn very interesting methods as single nucleus transcriptomics in the University of Copenhagen (Denmark) and CRISPR/Cas9-editing by deamination with base-editors in the Dresden University of Technology (Germany)

Currently, I am working with Vincent Detours and Maxime Tarabichi on performing spatial transcriptomics on Illumina flow cells with tissue fixed in PaxGene. This project is challenging as it demands specific knowledge that I never had before, such as how to engrave or cut the glass, 3D-printing of tools for pipetting, choosing polymeric material sustaining high temperature and still having good thermal transduction, and so on. I have started my position in the February 2023 and now, one year later, I have learned exorbitant number of things which are very far from molecular biology (including a little bit of bioinformatics and a tiny bit of French language), and this is something that makes me feel good about my work.

If you want to know more about spatial transcriptomics with a new non-commercial approach, please connect me!

I am Mathieu! I am a member of the Computational Biology lab at IRIBHM. I hold a Master's degree in Bioengineering in Chemistry and Bioindustries from the University of Louvain-la-Neuve. My master’s thesis focused on creating fusion protein nets designed to polymerize around pathogenic bacteria, under the supervision of Patrice Soumillion.

In addition, I participated in the International Genetically Engineered Machine (iGEM) competition in 2018 with UCLouvain. Our project, BactWars: A New Hope for Antimicrobial Resistance and Global Epidemics, involved designing and engineering a conjugative plasmid equipped with a CRISPR-Cas9 system and one or more guide RNAs. This plasmid would propagate within bacteria and neutralize specific genes to either re-sensitize or kill the bacteria. Afterward, I completed a second Master's degree in Bioinformatics at ULB.

My current project continues the work of my previous thesis and aims to study the spatio-temporal evolution and (epi)genomics of anaplastic thyroid cancer, under the supervision of Maxime Tarabichi.

Hi, I am Zhao, I started my PhD in October 2021. My initial academic background was biopharmaceutical engineering, with master thesis acomplished at GSK (Title : High throughput screening of protein formulation stability: Oxidation by metals and light. The goal of the study was to develop a high throughput screening protocol allowing testing protein stability in these oxidative conditions and finding the most suitable Then I've worked 5 and half years as associate manager consultant at GSK (Wavre), successively held 3 different positions: Global Validation Coordinator, Project Coordinator, Technical Regulatory Expert. formulation to stabilize proteins from a large library of different antioxidants formulations).

After that, I returned to China for a PhD training in stem cell biology (Project title: Expansion of cardiovascular progenitors derived from human pluripotent stem cells. The aim of the project was to find the appropriate in vitro culture condition allowing human cardiovascular progenitor cells expansion and differentiation, without genetic manipulation; and once this step achieved, their molecular identity could be further analyzed) In 2019 I returned back in Belgium and did master in bioinformatics and modelling (Master thesis title: Computational study of shift work schedules. A non-negligible percentage of population is involved in shift work and could suffer from a chronic jet lag. Based on existing 16-variables molecular model, an organism-level variable core body temperature is added, enabling simulation of shift work conditions varying on shift light intensity, magnitude, direction and rotation speed.) During this master training, I did an intership under the supervision of Pr. Detours, and worked on a prototype of my PhD project.

My current PhD project consists in an unbiased quantitative artificial intelligence (AI)-based survey of histological variation in human asymptomatic thyroids, with AI enabling the quantitative analysis of expressed histological morphologies, we can compute associated transcriptional and genetic variations and reveals morphological changes related to risk-associated loci.