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 (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.

  • Theo Killian (Github: tfkillian) is a bioinformatician and research programmer at the de Duve Institute. Theo transitioned from biochemistry to bioinformatics and has developed computational protein design protocols at the KUL Biomolecular Modeling Lab.

  • 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 the FNRS fellowship.

  • Chong Tang (ORCID: 0000-0002-0482-8361 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 the a China Scholarship Council - FNRS scholarship.

  • Philippe Hauchamps (Github: phauchamps) is a Master student in Biostatistics. He joined the CBIO lab in October 2019 as an intern. He has a Master degree in Computer Science Engineering, has been previously working in the banking sector and is currently transitioning to Bioinformatics/Biostatistics.

Remote members

  • 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.

  • Oliver Crook is a Wellcome Trust PhD student at the University of Cambridge, jointly supervised with Paul Kirk from MRC Biostatistics Unit and Kathryn Lilley. Olly works on new Bayesian methods for spatial proteomics (Crook et al. 2018), formalising the theoretical foundations and implementing the algorithms that will be included in pRoloc.

MSnbase developers

  • 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

  • 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 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 is now a PhD student at Max Planck Institute of Molecular Plant Physiology.

  • Victoria Carr, Part III student in Systems Biology, applying graph-based methods to study protein sub-cellular localisation. Victoria is now pursuing a PhD at King’s College London.

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