Lab members

CPU core

  • Laurent Gatto, head of the unit. He moved to Cambridge in January 2010 to work in the Cambridge Centre for Proteomics on various aspects of quantitative and spatial proteomics, developing methodological advances and implementing computational tools with a strong emphasis on rigorous and reproducible data analysis. He is also a visiting scientist in the PRIDE team at the European Bioinformatics Institute, affiliate teaching staff at the Cambridge Computational Biology Institute, a Software Sustainability Institute fellow and a Software and Data Carpentry instructor.

  • Lisa Breckels, Post-Doctoral Research Associate. Lisa joined the Cambridge Centre for Proteomics in November 2010 and CPU in August 2013. 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.

Remote members

  • Sebastian Gibb, Department of Anesthesiology and Intensive Care, University Medicine Greifswald, Germany. Sebastian visited the group 2014 and since then contributes to various projects, in particular MSnbase, Pbase and synapter, which he is currently leading the development of.

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

Key collaborators

  • Kathyn S. Lilley, Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UL. Kathryn’s lab developed the state-of-the art LOPIT (Dunkley et al. 2006) and hyperLOPIT (Christoforou et al. 2016) technologies. Her lab is at the origin of some of the very best spatial proteomics datasets in the world, which we help to analyse and interpret by applying our dedicated software (see for example Breckels et al. 2016 in F1000Research).

  • Sean Holden, Computer Laboratory. We collaborate with Sean on the development and application of machine learning algorithms to solve problems in spatial proteomics. A recent example is transfer learning (Breckels et al. 2016).

  • Thomas Burger, BIG-BGE (Université Grenoble Alpes, CNRS, CEA, INSERM), 38000 Grenoble, 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.

Alumni

  • 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.

  • Vicky Butt, Part III student in Systems Biology, applying graph-based methods to study protein sub-cellular localisation. Vicky is now pursuing a PhD at UCL.

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