Team
If you are interested in discussing potential projects please Contact Us
Core Team | |
Ben Collins Group Leader |
Since 2019 Ben is a Reader (equiv. Assoc. Prof.) in the the School of Biological Sciences, Queen’s University of Belfast, UK. His research focuses on broadly on 3 topics: (i) method development and applications in data independent acquisition mass spectrometry; (ii) method development and applications in the analysis of protein interaction networks and protein complexes; and (iii) applications of these strategies in host-pathogen biology, innate immunity, cancer biology, and drug discovery. Ben’s PhD was completed at University College Dublin in 2009 where he remained for 1 year as the Agilent Technologies Newman Fellow (postdoctoral) in Quantitative Proteomics. Ben moved to the Institute of Molecular Systems Biology at ETH Zurich in Autumn 2010 as postdoctoral researcher under the supervision of Prof. Ruedi Aebersold, where his research focused on the application of quantitative interaction proteomics in signaling and the development of DIA/SWATH mass spectrometry. Following this Ben was a Group Leader and SNF Ambizione Fellow at IMSB, ETH Zurich with a focus on applying methods developed as a postdoc to relevant problems in host-pathogen biology. |
Mohammad Arefian Postdoctoral Research Associate |
I obtained my Ph.D. from Ferdowsi University of Mashhad, Iran in 2018; wherein I evaluated the effect of salinity stress on plants at physiological, gene expression, and proteome levels. I continued my research as a Postdoctoral Fellow at Yenepoya research center in India, where my research mostly focused on kinase-mediated signaling pathways (de)activated in rice and Arabidopsis upon stress and during flowering. Besides post-translational modifications, my researches were also involved proteomic, proteogenomic, and metabolomic approaches to investigate cancers and infectious diseases in human, as well as stress-responsive mechanisms in model plants. |
Jack Penny PhD Student |
Project: A map of host cell rewiring by pathogens. Jack is a second year PhD student investigating host cell rewiring by pathogens with a particular interest in the ubiquitin system. Jack completed his undergraduate degree in Biochemistry and Master of Research at Aberystwyth University in 2018. His previous projects involved metabolomics and natural product drug discovery with an interest in antimicrobials and overcoming resistance mechanisms. Co-supervisors Gunnar Schroeder and José Bengoechea |
Emma Mckay PhD Student |
Project: Protein complex dynamics in innate immunity. Emma is a PhD student investigating the dynamics of protein interactions and post translational modifications in the NLRP3 inflammasome system, a central signalling hub of the innate immune system. Emma completed her undergraduate degree in Biological Sciences at Queens University Belfast, graduating in 2021. Co-supervisor Rebecca Coll |
Co-Supervision |
Simran Cheema PhD Student |
Project: Maximizing the clinical impact of Human Milk on Prevention of Necrotizing Enterocolitis. Co-supervised with Simon Cameron and Natalie Shenkar |
Ruan O’Tiarnaigh PhD Student |
Project: A machine learning approach to a combinatorics solution for complex Protein Protein Interaction (PPI) problems specifically in the Proteome-Dense Lipoproteins (PDL) space. Co-supervised with Gary Hardiman and Brian Green |
Daniel Lockwood PhD Student |
Subversion of innate immune defences by intracellular bacterial pathogens. Co-supervised with Gunnar Schroeder and Miguel Valvano |
Alumni | |
Charlotte Nicod PhD graduated 2020 (ETH Zurich) |
Unraveling host-pathogen interactions upon Mycobacterium tuberculosis infections using quantitative mass spectrometry. Now Associate at Flagship Pioneering. |
Amir Banaei-Esfahani PhD graduated 2019 (ETH Zurich) |
Deconvolution of Biochemical Pathways in Genetically Diverse Mycobacterium tuberculosis. Now Senior Bioinformatics Scientist at Universitätsspital Zürich. |
Shruti Jha Research Assistent 2017-2019 (ETH Zurich) |
Host-pathogen interactions upon Mycobacterium tuberculosis infections. Now Research Associate at DewPoint Therapeutics. |
Project students | |
Meaghan King MSc Student 2022 |
Assembly of a Mycobacterium tuberculosis host-pathogen protein-protein interaction network. |
Olivia Mulderrig BSc Student 2022 |
Novel post translational modifications in cardiomyopathy. |
Daniel Cosby BSc Student 2022 |
Novel post translational modifications in the VCP/p97 signalling system. |
Katie Marshall BSc Student 2022 |
Epitope mapping of cell surface proteins of Mycobacterium tuberculosis complex organisms. |
Cansu Uygun MSc Student 2021 |
Mass spectrometry based proteomics – longitudinal evaluation and quality control of analytical methods. |
Noemi Casaferniza Ochoa MSc Student 2021 |
Novel post translational modifications in the interactome of 14-3-3β. |
Clare-Ann Nelson BSc Student 2021 |
Novel Post Translational Modifications in the Macrophage Proteins Targeted by Mycobacterium tuberculosis. |
Emily Lecky BSc Student 2021 |
Quantitative Aspects of Ion Mobility – Mass Spectrometry in Proteomics. |
Megan Taylor BSc Student 2021 |
Proteome analysis of macrophages infected with Mycobacterium tuberculosis RD1 mutant. |
Caolán Doran MSc Student 2020 |
Assembly of a p97 cofactor protein-protein interaction network. |
Jun Cai MSc 2018 (ETH Zurich) |
Elucidating Host-Pathogen Protein-Protein Interactions in the Context of Mycobacterium Tuberculosis Infections. |