Lab members

CBIO core

  • Laurent Gatto (ORCID: 0000-0002-1520-2268, Github: lgatto, fosstodon: @lgatto), head of the unit. He runs the CBIO group and teaches bioinformatics in the Facutly of Pharmacy and Biomedical Sciences (FASB).

  • Axelle Loriot (ORCID: 0000-0002-5288-8561, Github: aloriot) is a senior researcher at the de Duve Institute. Since 2001, she has been part of the epigenetics group led by Charles De Smet. She joined the CBIO group in 2018, focusing on transcriptomics and epigenetics. She developed algorithms to identify aberrant transcripts induced by DNA hypomethylation in tumor cells, and DNA hypermethylation events linked to overlapping expression. Axelle plays a major role in the bioinformatics core facility.

  • Philippe Hauchamps (Github: phauchamps) is, since September 2021, a PhD student working on flow cytometry data analyis. He joined the CBIO group in October 2019 as an intern and carried on with a Master’s project in computational proteomics, developing Bayesian models to analyse quantitative proteomics data. He has a Master degree in Computer Science Engineering and one in Biostatistics.

  • Julie Devis (Github: JulieDevis) did her master’s project in the CBIO lab and is now, since September 2022, a PhD student in biomedical sciences. She is working on deciphering complex mechanisms of epigenetic alterations in cancer genomes. She is pursuing her research in collaboration with Axelle Loriot and Prof. Charles De Smet from the epigenetics group.

  • Samuel Grégoire (Github: samgregoire) did his master’s project in the CBIO lab and is now, since September 2022, a PhD student in biomedical sciences. He is working on single-cell biology in AML, including single-cell proteomics, in collaboration with Didier Vertommen, who runs the institute’s mass spectrometry core facility.

  • Andrea Vicini (Github: andreavicini) joined the lab in October 2022 as a research assistant in bioinformatics. He focuses on integrative multi-omics approach to study infectious diseases as part of the large, inter-institute HYGIEIA project.

  • Enes Sefa Ayar (Github: EnesSefaAyar) joined the lab in November 2023 as a PhD student working on quantitative analysis of single-cell proteomics. He did a master’s in computational sciences and engineering at the Koç University. He is funded by a FNRS ‘Projet de Recherche’ (PDR) awarded to L. Gatto.

  • Jérôme Linden (GitHub: jerlinden) joined the lab in November 2023 as a Project Manager for e-OMIX, a CBIO-led project aiming at establishing a collaborative platform for the sharing and analyses of multiomics data. He has a PhD from ULiège and is funded by the European Regional Development Fund (ERDF) awarded to L. Gatto and S. Jodogne.

  • Loïc Guille (ORCID: 0000-0002-8387-1092, GitHub: loguille) joined the lab in May 2024 as a bioinformatician for e-OMIX a CBIO-led project. He has a master’s degree in bioinformatic from Lyon 1 university.

  • Riya Dogra (GitHub: rdogra8), is a PhD student at the de Duve Institute since June 2024, working on analysing PTMs using spatial and single cell proteomics approaches. She has a Master’s in Systems Biology and Bioinformatics from Panjab University, and worked in the Genomics Research lab at CSIR-CCMB.

  • Guillaume Deflandre (GitHub: guideflandre), did his Master’s thesis in the CBIO lab and is now pursuing a PhD in biomedical sciences at the de Duve institute since October 2024. His project is centered around the improvement of peptide identifications in single-cell proteomics. He has a Master’s degree in chemistry and bio-industries from the UCLouvain.

Undergraduates

  • Léopold Guyot (GitHub: leopoldguyot), is a final year Bioinformatics student at the “Université Libre de Bruxelles” (ULB). He is currently working on his Master’s thesis on single-cell proteomics in the CBIO lab under the supervision of Laurent Gatto and Matthieu Defrance.

CBIO lab photo

From left to right: Samuel, Riya, Enes, Andrea, Guillaume, Philippe, Axelle, Jérôme, Laurent, Loïc and Lieven (from the SMCS). Julie is missing. Picture taken at the de Duve Institute on 3 July 2024.

R for Mass Spectrometry core team

  • Sebastian Gibb, Department of Anesthesiology and Intensive Care, University Medicine Greifswald, Germany. Sebastian visited Laurent’s group in Cambridge 2014 and since then contributes to various projects, in particular MSnbase, Pbase and synapter.

  • Johannes Rainer, Center for Biomedicine, EURAC, Bolzano, Italy is a contributor to the MSnbase and Pbase packages.

Key collaborators

  • Manon Martin (ORCID: 0000-0003-4800-0942, Github: ManonMartin) is a research assistant in bioinformatics at the LIBST and ELI institues and the SMCS core facility on the Louvain-la-Neuve campus. She worked in the CBIO group from September 2020 to June 2022. She still collaborates with the lab as part of the bioinformatics core facility.

  • Lieven Clement, statOmics group, UGent, Belgium. We collaborate on statistical analyses of quantitative proteomics data, in particular the msqrob2 R/Bioconductor package.

  • Thomas Burger, BIG-BGE (Université Grenoble Alpes, CNRS, CEA, INSERM), France. We collaborate with Thomas and his group on various proteomics data analysis (for example missing data in Lazar et al 2016) and software (see Wieczorek et al. 2016). Thomas contributed the perTurbo algorithms to pRoloc.

  • Christophe Vanderaa, statOmics group, UGent, Belgium. We pursue our collaboration on the development of computational solutions for the analysis of single-cell proteomics data.

Alumni

  • Christophe Vanderaa (ORCID: 0000-0001-7443-5427, Github: cvanderaa) is a former PhD student working on single-cell assay bioinformatics. He did a masters in biomedical sciences at the UCLouvain and followed up with a masters in bioinformatics at the KULeuven before conducting his PhD training in the lab funded by an FNRS fellowship. Chris then enrolled as a postdoc at the UGent in the statOmics group (headed by Lieven Clement) to develop statistical frameworks for the analysis of single-cell proteomics data.

  • Badr-Ali Mouaden finished his engineering degree in 2023 and did his master’s project under the co-supervision of Laurent Gatto, Philippe Hauchamps and Prof Michel Versleysen from the Louvain Engineering School (EPL). He worked on the development and application of deep convolution neural network on flow cytometry data.

  • Kristína Gömöryová (Github:KristinaGomoryova) joined the lab in September 2022 as an OpenMS intern. She is doing her PhD in Animal Physiology and Immunology in the lab of prof. Bryja at Masaryk University. In CBIO lab she focuses on the analysis of DIA proteomics data within the HYGIEIA project.

  • Charlotte Léonard (Github: chachaleo) did her Master’s project in applied mathematics, working on single-cell multi-modal data integration. She is co-supervised by Michel Verleysen from the Machine Learning Group at UCLouvain.

  • Manojkumar Selvaraju (ORCID: 0000-0001-6439-5652, Github: manogenome) worked from September 2020 to May 2022 on software infrastructure for the integration of genomics, transcriptomics and proteomics data.

  • Chong Tang (ORCID: 0000-0002-0482-8361, Github: plantton) was part of the CBIO lab from the very beginning in 2019 to 2021. He worked on mass spectrometry-based proteomics software development with a special focus on using databases to store and retrieve massive MS datasets.

  • Aayush Grover (ORCID: 0000-0002-3716-2850, Github: AayushGrover) is a PhD student at the Institute for Machine Learning of ETH Zurich where he is working on computational epigenetics of cancer. He was a master thesis student at the CBIO lab after completing his summer internship (2020) at the CBIO lab. He worked on predicting protein subcellular location using deep learning techniques during his internship and focused on the task of survival prediction in cancer using multi-omics integration and few-shot learning.

  • Kilian Maes (Github: KilianMaes) did his Master’s project in software engineering in the lab working on the clustering of mass spectrometry data. He was co-supervised by Prof Pierre Dupont from the Machine Learning Group. He now works part-time as a software engineer and continues his medical degree at the UCLouvain.

  • Oliver Crook, was a Wellcome Trust PhD student at the University of Cambridge, jointly supervised with Paul Kirk from MRC Biostatistics Unit and Kathryn Lilley. Olly worked on new Bayesian methods for spatial proteomics (see for example Crook et al. 2018), formalising the theoretical foundations and implementing the algorithms in the pRoloc package. He is now pursuing post-doctoral research at the Protein Informatics Group in the Department of Statistics at the University of Oxford.

  • Lisa Breckels, Post-Doctoral Research Associa in the Cambridge Centre for Proteomics, at the University of Cambridge (UK). Her work focuses on the application and development of machine learning and pattern recognition methods to enable robust analysis of high-throughput quantitative proteomics data. All her methods and algorithms form part of the pRoloc framework for protein localisation prediction.

  • Theo Killian was a bioinformatician and research programmer in the CBIO group at the de Duve Institute. Theo developes and maintains the depmap package. He now works as a Bioinformatics scientist at the Laboratory of Translational Genetics at the KULeuven.

  • Robin Kohze comes from the Radboud University Nijmegen and visits the group in the frame of his master’s internship. He developed a new infrastructure to facilitate the dissemination of spatial proteomics data. He currently pursues a PhD in the Department of Genetics at the University of Cambridge, UK.

  • Thomas Naake, visited the group in Cambridge in Spring 2014 as an ERASMUS student affiliated to the University of Freiburg. He developed the first version of pRolocGUI, an interactive visualisation tools for organelle proteomics data. Thomas has since earner a PhD from the Max Planck Institute of Molecular Plant Physiology.

  • Victoria Carr, was a Part III student in Systems Biology at the University of Cambridge, applying graph-based methods to study protein sub-cellular localisation. Vicky went on doing a PhD at King’s College London and is now working as a Scientific Programmer in the Pathogen Informatics Unit at the Wellcome Sanger Institute.