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The Team

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Prof. Ines Thiele

Principal Investigator

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Dr. Ines Thiele is a Personal Professor at the National University of Ireland, Galway. Her research interests include the diet-gut-brain-axis in neurodegenerative diseases.

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Dr. Cyrille Thinnes

Engagement Manager and Research Fellow

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Dr. Cyrille Thinnes cultivates the Virtual Metabolic Human business case, integrating the technology, stakeholder, and organisational capabilities for enhancing user experience.

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Dr. Mohammad Faiz Khan

Postdoctoral fellow

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Dr Mohammad Faiz possesses expertise in integrating two significant modelling paradigms: COBRA and PBPK. He focuses on developing a comprehensive whole-body metabolic modelling framework for assessing drug effectiveness and toxicity, while also predicting optimal dosages for systems biomedicine application.

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Dr. Wiley Barton

Postdoctoral fellow

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Dr. Wiley Barton earned his PhD in Computational Biology from University College Cork. His focus is on building a pipeline for constructing a microbial model for the cow microbiome.

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Joe Desbonnet

Computer scientist

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Joe Desbonnet is responsible for maintaining the computational infrastructure of the research group.

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Flippo Martinelli

PhD Student

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Filippo obtained his Master's degree in pharmaceutical chemistry with a thesis focused on doping analysis. His research interests include the application of constraint-based models to investigate diet-drugs-microbiota-host interactions.

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Timothy O. Hulshof

PhD student

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Timothy obtained his Master's degree in bioinformatics from the University College Cork, Ireland. His work includes enabling the large-scale integration of metagenomic data with microbiome-level metabolic models. 

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Tim Hensen

PhD student

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Tim is a PhD student with a background in systems biology. His research focuses on applying the constrained-based modelling framework to investigate the role of the gut-brain axis in neurodegenerative diseases. 

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Bram Nap

PhD student

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Bram obtained his Master's degree in biotechnology at Wageningen University. His research area is in the role of gut microbes in the context of cognitive health and is part of the ITN SmartAge project.

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Anna Sheehy

PhD student

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Anna obtained her BSc in biomedical science at the University of Galway. She is interested in using COBRA modelling to advance our understanding of host-microbe co-metabolism along the gut-brain axis.

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Jadzia Murphy

PhD student

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Jadzia graduated with a BSc in microbiology from University of Galway. She is working on the modelling inherited metabolic diseases.

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Mohammad Reza Moghimi

PhD student

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Reza holds a master's degree in Chemical Engineering from Shiraz University and possesses expertise in Cancer Systems Biology, Bioinformatics, In-silico and Computational Modelling, as well as Metabolic Engineering.

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Research Assistant

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Catherine obtained her Master’s degree in Integrated System Biology from the University of Luxembourg. Her interests lie in the cross between the application of whole-body computational models of metabolism for in-silico trials and drug-discovery.

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Joanne Cooney

Research Assistant

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​Joanne obtained her Bachelor’s degree in Science, specializing in microbiology from the University of Galway. Her interests lie in the in microbial and human metabolism, and microbiome studies. Her focus in the research group is to curate drug metabolism pathways, for the integration into the Whole-body Metabolic reconstruction.

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Natalia Makosa

Research Assistant

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Natalia obtained her Bachelor's in Science from the University of Galway, majoring in microbiology. Her keen interest lie in drug-host-microbiome interactions. She is working to curate drug metabolism pathways, for the integration into the whole-body metabolic reconstruction.

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Tushar Purushothaman Namboodiri

Research Assistant

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Tushar is a Master student at the University of Galway, pursuing MSc in Artificial Intelligence. He focuses on using large language models (LLMs) for early diagnosis of inherited metabolic diseases and exploring AI to uncover species relationships through metabolic data.

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Umera Wajeed Pasha

Research Assistant

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Umera Pasha work to explores techniques to scrape, separate, and embed patient data into a comprehensive database, enhancing its performance and embedding sources along with citations. Focusing on inherited metabolic diseases, she combines clinical presentations with research papers to improve data management accuracy.

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Naveen James

Research Assistant

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Naveen James works with ChatIMD, exploring various techniques to enhance its performance and discovering methods to embed sources and citations into the respective answers.

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Hemanth Harikrishnan

Research Assistant

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Hemanth Harikrishnan, a Research Assistant, aims to utilize inherited metabolic disease information to aid in early-stage diagnosis using LLMs. His work also involves exploring AI to uncover intrinsic relationships among species using their metabolic data. 

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Anusha Shivamadhu

Research Assistant

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Anusha Shivamadhu, in her role as a Research Assistant, is tasked with enhancing the VMH's clinical interface and capabilities. Her responsibilities encompass developing APIs and exploring AI techniques to enhance the performance of ChatIMD.

Previous Team Members

PhD students:

Dr. Almut Heinken - Research fellow, now Associate Professor, Nantes University, France.

Dr. Johannes Hertel - Research fellow, now Junior Professor, University of Greifswald, Germany

Dr. Bronson Weston - Research fellow

Dr. Dmitry A. Ravcheev - Research fellow

Visiting PhD students:

Arianna Basile - Post-doctoral fellow at Cambridge University.

Gwendolyn Gusak

Elaine Zaunseder

Visiting master students:

Thibault Vangeneugden

Research Assistants:

Subashini Kennedy

David Sharkey 

Marcus Hogan 

Renee Waschkowitz 

Summer students:

Liveta, Natalia, Roisin, Adam, Joanne Cooney, Joanne Malone

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© 2024 by Ines Thiele. 

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