Speakers
Keynote speakers
Jan Hasenauer
Title of talk: Mechanistic modelling and machine learning: A love story
Abstract: In the realm of systems biology, the marriage between mechanistic modelling and machine learning has blossomed into a dynamic partnership, revolutionizing our understanding of complex biological systems. This presentation explores the intertwined relationship between mechanistic modelling and machine learning, highlighting their collaborative efforts in unraveling biological mysteries.
One of the key aspects of this love story is the utilization of machine learning methods for the optimization of mechanistic models. By harnessing the power of mini-batch optimisation, the training of comprehensive models for biological processes becomes feasible. Furthermore, the emergence of invertible neural networks has opened new avenues for Bayesian uncertainty analysis in systems biology. These innovative approaches enable researchers to unravel uncertainty in model predictions, providing deeper insights, e.g. into biological variability.
A second key aspect is the incorporation of biological priors in machine learning models and the formulation of hybrid models. This adds another layer of sophistication to this love story. By integrating prior knowledge derived from biological principles, machine learning algorithms can better adapt to the complexities and nuances of biological data, enhancing the predictive accuracy and interpretability of models.
Through a series of examples, this presentation will showcase the symbiotic relationship between mechanistic modelling and machine learning, demonstrating how their combined efforts are driving forward our understanding of complex biological systems and paving the way for future advancements in systems biology research.
Jan Hasenauer in short: Jan Hasenauer studied Technical Cybernetics at the University of Stuttgart, where he also obtained his doctoral degree in Engineering Sciences. He then worked at the Helmholtz Zentrum München and the Technical University of Munich as PostDoc and leader of a Young investigator group. Since 2017, he has been a Professor of Mathematics and Life Sciences at the University of Bonn, and since 2022, he has held one of the highly prestigious Schlegel professorships established within the framework of the Excellence Initiative. Jan Hasenauer received several awards, including the MTZ Award for Medical Systems Biology and is a member of the Excellence Clusters “Hausdorff Center for Mathematics” and “ImmunoSensation2” of the University of Bonn.
https://www.mathematics-and-life-sciences.uni-bonn.de/en/research/hasenauer-group
Belinda Nedjai
Title of talk: DNA methylation biomarkers for early detection, diagnosis, and prognosis of HPV-related cancer care
Abstract: Human Papilloma Virus (HPV ) infection has a critical role in common dermatologic and sexually transmitted diseases, as well as in some of the most frequent cancers worldwide. The HPV-associated disease burden is higher than that reported for any other infectious agent worldwide, with a larger burden observed in women than in men. The rapidly rising male share of the total burden underlines the prioritization of male HPV-related disease in prevention programmes, especially oropharyngeal and anal cancers. We have developed a triage classifier for the detection of HPV-related precancer lesions (anal, cervical, oropharyngeal), based on DNA methylation of HPV16, HPV18, HPV31 and HPV33 combined with the human gene EPB41L3. The classifier can predict the progression from normal to cervical cancer up to 5 years in advance. We also tested this classifier on two non-invasive cervical cancer specimens: a self-collected vaginal sample and urine. We demonstrated that S5 identify women who are CIN2+ using self-collected samples.
I will present here an overview of the performance of the DNA methylation classifier for the screening, diagnosis and as a test of cure for HPV-related cancers. These classifiers are useful in the context of Low resources and clinical setting or countries with no screening programmes in place.
Belinda Nedjai in short: Dr Belinda Nedjai is an Associate Professor in Cancer biomarker and Epigenetics and the Director of the Molecular Epidemiology Laboratory at Queen Mary University of London. She holds a PhD in genetics and functional genomics and has extensive experience in functional genomics, inflammation research, and biomarker discovery. Dr Nedjai has a background in both academia and industry, having spun out GeneU, a start-up focused on genetic research, where she spent 5 years as head of genetic research. Her current research focuses on developing DNA methylation biomarkers for the diagnosis and prognosis of cancers, including prostate, breast, colorectal and cervical cancer. Recent successes include improved methods to triage women infected by papillomavirus: Her group developed a classifier that combines DNA methylation of HPV and human genes, making it a strong contender for triaging women infected with carcinogenic HPV. They also created a 6-gene methylation classifier to improve the management of men diagnosed with prostate cancer who are on active surveillance.
https://www.qmul.ac.uk/wiph/people/profiles/nedjai-belinda.html
Andrew Daly
Title of talk: Bioprinting models of the human heart at CÚRAM, the Research Ireland Centre for Medical Devices
Abstract: Engineered biomaterials are enabling progress in numerous medical fields, ranging from medical device development to tissue engineering. This talk will provide an overview of CÚRAM, the Research Ireland Centre for Medical Devices at the University of Galway, and highlight its interdisciplinary approach to accelerating the translation of medical device research into impactful clinical solutions. I’ll then focus on my own research lab within CÚRAM, where we specialize in bioprinting models of the human heart. I’ll describe how incorporating principles of heart development into bioprinting strategies can enhance cell and tissue maturation, thereby enhancing physiological relevance for disease modelling, drug screening, and regenerative medicine applications.
Andrew Daly in short: Dr Andrew Daly is an Associate Professor in Biomedical Engineering at the University of Galway and a Principal Investigator at CÚRAM, the Research Ireland Centre for Medical Devices. He holds a BAI and PhD in Mechanical Engineering from Trinity College Dublin, Ireland. After a postdoctoral fellowship at the University of Pennsylvania, Dr. Daly returned to Ireland to establish his independent research group at the University of Galway. His highly-cited work has been published in leading journals such as Nature Communications, Nature Reviews Materials, Cell, and Biomaterials. He has secured over €2.4 million in research funding, including a prestigious European Research Council Starting Grant in 2022.
https://www.universityofgalway.ie/science-engineering/staff-profiles/andrewdaly/
https://www.biofabrication.ie/
MET Research Highlights speakers
Juulia Jylhävä
Title of talk: Decoding biological aging and frailty with AI and multiomics
Abstract: Biological age estimates how well our bodies are functioning compared to our chronological age. There are various ways to measure biological age at the cellular, organ, and system-wide levels, all of which offer insights into disease risk and mortality beyond chronological age. My group focuses on uncovering the drivers of biological aging using omics and causal inference approaches, and developing a system-wide biological aging measure for healthcare: the electronic frailty index.
Juulia Jylhävä in short: Juulia Jylhävä is a senior research fellow at the Institute for Advanced Study, Tampere, and a leader of the Systems Biology of Aging groups a Tampere University, Finland, and Karolinska Institutet, Stockholm, Sweden. She is passionate about unraveling the causes and consequences of biological aging, exploring its alignment with age-related diseases and discovering ways to promote healthier aging.
Soile Nymark
Title: Ionic activities in retinal pigment epithelium: From mechanisms to therapy development
Abstract: Visual perception depends on the integrative functions of retina and retinal pigment epithelium (RPE) in the eye. These functions are enabled and precisely regulated by complex ionic mechanisms and biochemical signaling. In RPE – being epithelial tissue – the ionic mechanisms have been severely overlooked in the past even though several retinal degenerative diseases are directly caused by mutations in the RPE ion channels. Our research group aims to unravel the concerted functioning of retina and RPE with focus on their ionic activities, and with an overarching goal to advance the development of new therapies. I will present our latest findings on the different ion channels and gap junctions of the RPE as well as their physiological relevance and disease associations.
Soile Nymark in short: Soile is an associate professor and Biophysics of the Eye research group leader in MET. She has a lifelong love for the amazing visual systems that there exist in the animal kingdom, and she strives to understand especially the electrical activities and biophysical phenomena that enable this fascinating sense.
Kaarlo Paakinaho
Title of talk: The Story of Biomendex
Abstract: Biomendex sprung out of the research done in Tampere University on Technology in a project aiming to develop new types of synthetic bone graft substitutes, to various clinical applications in the field ranging from orthopaedic to craniomaxillofacial surgery. Biomendex is now bringing a novel bone regeneration technology to the clinics and to the global markets. This new bone growth promoting composite material technology, Adaptos®, gives the surgeon the freedom to operate without material related restriction. Biomendex putting their full effort to to change the way bone voids are treated and enable better outcomes for surgical operations.
Kaarlo Paakinaho in short: Dr. Kaarlo Paakinaho is a founder of Biomendex, a company based in Tampere, Finland, that specializes in innovative tissue engineering technology. He earned his Doctor of Science (Technology) in the Tampere University of Technology. During his time at the University, Dr. Paakinaho focused on developing innovative materials for tissue engineering and regenerative medicine. His research has advanced the understanding and application of biodegradable polymers, particularly in creating scaffolds for tissue regeneration. Dr. Paakinaho is still doing research as a visiting researcher in Adult stem cell group (Prof Susanna Miettinen).
Research to Business (R2B) projects
Glue4Life
Glue4Life is a clinically compatible and biodegradable hydrogel which meets the needs of future biomedical applications. Regardless of the cell type you are working with, check out Glue4Life!
OrganAalytics
OrganAnalytics: Viability Analysis of Organ Transplants
Im.Engine
Im.Engine: Lensless, software-enabled, miniature microscope offering advanced live cell imaging solution that’s portable, cost-effective, and powered by AI. Transform the way you image and extract data from your samples with IMEN.
PaMo
PaMo is a novel wearable ward-wide patient monitoring system intended especially for early detection of respiratory depression in regular hospital wards.
L-Cell
L-Cell: Light-reconfigurable Substrates for Cell Cultures
VirNE
VirNE (Virtual Natural Environments) is a virtual reality relaxation application designed for pediatric use. It combines guided relaxation exercises with an immersive nature experience to offer a non-pharmacological method for reducing the stress of child patients.
MindFlow
Have you ever been in the zone? The MindFlow R2B project measures EEG signals through wearable devices, enabling real-time monitoring of your flow state in real-life situations