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Core Team
Ben Collins 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 and innate immunity. 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 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 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 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.