Lab members

CBIO core

  • Laurent Gatto (ORCID: 0000-0002-1520-2268, Github: lgatto, Twitter @lgatt0), 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.

  • Manon Martin (ORCID: 0000-0003-4800-0942, Github: ManonMartin) is a research assistant in bioinformatics with a focus on transcriptomics and other omics data analysis. She joined the CBIO group in September 2020 and holds a PhD is biostatistics. During her thesis, she worked on several aspects of NMR metabolomics data treatment, mostly based on multivariate data analysis.

  • Christophe Vanderaa (ORCID: 0000-0001-7443-5427, Github: cvanderaa) is a 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. He is funded by a FNRS fellowship.

  • Chong Tang (ORCID: 0000-0002-0482-8361, Github: plantton) is a PhD student working on mass spectrometry-based proteomics software development. He has a bachelor degree in biotechnology from the Central South University of Forestry and Technology in China and a masters in bioinformatics from KULeuven. He is funded by a China Scholarship Council - FNRS scholarship.

  • Manojkumar Selvaraju (ORCID: 0000-0001-6439-5652, Github: manogenome, Twitter: manogenome) is a PhD student working on the Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data. He joined the CBIO group in September 2020 and holds an Engineering degree in Industrial Biotechnology from A.C.Tech, Anna University, Chennai. Previously, he worked as a Bioinformatician for several years at the academia-industry interface. He is funded by the de Duve Institute’s doctoral scholarship.

  • 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) is a master 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 the epigenetics group and is co-supervised by Axelle.

  • Samuel Grégoire is a master student in biomedical sciences who is benchmarking single cell mass spectrometry-based proteomics analysis pipelines. He is co-supervised by Sébastien Pyr dit Ruys from the proteomics group.

CBIO lab photo

From left to right: Chong, Philippe, Christophe, Manoj, Laurent, Julie, Samuel, Manon and Axelle. Picture taken at the de Duve Institute on 08 September 2021.

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

  • Paul Kirk, MRC Biostatistics Unit, University of Cambridge, UK. Paul is part of the team developing principled Bayesian model for spatial proteomics, such as the T-Augmented Gaussian Mixture (TAGM) model (Crook et al. 2018).
  • 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.

  • Lieven Clement, statOmics group, UGent, Belgium. We collaborate on statistical analyses of quantitative proteomics data.

Alumni

  • 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 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.

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