Members

About me

Jaruri Hyttinen is full professor and head of BioMediTech unit at the Faculty of Medicine

and Health Technology, Tampere University. His research group Computational

Biophysics and Imaging Group https://research/tuni.fi/cbig develops novel computer simulations (in-silico)

on cellular biophysics and in-vitro based electrophysiology and 3D imaging methods

for future personalized medicine and tissue engineering. Previously he has been a

visiting researcher at University of Pennsylvania, University of Tasmania, Duke

University and as visiting professor at University of Wollongong 2017 and ETH

Zurich 2018.   

Responsibilities

Profesessor of Biomedical Eningeering, Head of Biomeditech unit, Head of Computational Biophysics and Imaging group CBIG https://research.tuni.fi/cbig  

Field of expertise

Biomedical Engineering, bioelectronics, bioelectric phenomena and signals, biophysics, computational modelling and biological/physiological system analysis, bio- and medical imaging, 

Research fields

Biomedical Engineering, bioimaging, computational biophysics, Body on Chip Technologies

About me

Postdoctoral research fellow working on non-invasive and label-free methods for analysis and quantification of cell culture structure and function. My special focus is on cardiac myocytes and their biomechanics. I have supervised different research projects and B.Sc/M.Sc. theses on these topics. Feel free to contact me about collaborations!  

Technical coordinator of the EU-funded SMASH-HCM project.

Subsitute project manager of the Business Finland funded L-Cell project.

Research topics

• Quantification of cardiomyocyte contractility using video methods
• Brightfield microscopy -based methods for structural and functional assessments using deep learning methods
• Light-activated cell culture surface topographies

Research unit

Computational Biophysics and Imaging Group

Research fields

• Signal processing
• Image processing
• In vitro electrical stimulation
• Machine learning

Responsibilities

I'm the responsible teacher in the following courses:

BBT.022​ Essentials of Anatomy and Physiology

BBT.029​ Biomedical Engineering Principles

BBT.OPN.011 Kandidaatintyö ja seminaari, biolääketieteen tekniikka​

BBT.HTI.506​ Measurements of Physiological Systems​

BBT.HTI.507​ Modelling of Physiological Systems​

Research topics

• Atrial fibrillation (AFib): cellular mechanisms causing and maintaining arrhythmias and contractile dysfunction
• The gender gap in heart disease: sex-dependent differences in cardiac disorders
• Electromechanical alterations in hypertrophic cardiomyopathy (HCM)
• Translation of hiPSC-based findings to human context.

Research unit

Computational Biophysics and Imaging Group

Research fields

• computational cardiology
• mathematical modelling
• systemsphysiology
• excitation-contraction coupling
• arrhythmias
• intracellular Ca2+ dynamics

Research career

• University Lecturer; Tampere University, FI; current position
• Visiting Researcher; IEPT, UKE, DE; 04-05/2018
• Postdoctoral Researcher; Tampere University, FI; --> 12/2020
• Postdoctoral Researcher; University of Eastern Finland, FI; --> 02/2018
• Visiting Researcher; UC Davis, USA; 10-11/2016
• Researcher Scientist (part-time); Fibrux Ltd (startup company), FI; 03-06/2015
• Researcher Scientist (full-time consulting); Stanford School of Medicine, USA; 01-03/2015
• Postdoctoral Fellow; Simula Research Laboratory, NO; --> 12/2014
• Visiting Researcher; KIT, Karlsruhe, DE; 01-02/2012
• Postdoctoral Researcher; University of Eastern Finland, FI; --> 07/2011
• Graduate Student; University of Oulu, FI; --> 12/2009

Responsibilities

OrganAnalytics — Viability Analysis of Organ Transplants R2B Project Team Leader

Research unit

Computational Biophysics and Imaging Group

About me

I am a biophysicist with background in signal processing and telecommunications. I completed my doctoral study in Tampere University of Technology in January 2016 with prof. Andre Ribeiro. Later, I worked as a postdoc with prof. Aleksandra Walczak (École Normale Supérieure) and prof. Nathalie Dostatni (Institut Curie) in Paris, France. In 2021, I returned to Finland to work in MET faculty as a postdoc researcher and from 2023 as the Research Council of Finland’s Research fellow.

I have always been fascinated by living organisms as dynamic systems, in which individual cells’ nonlinear convoluting behaviors are hidden in the population and steady-state statistics. Many behaviors, tailored over billions of years of evolution to ensure the organisms’ survival, operate either in equilibrium with their environments or at the physical limit. My research goal is to uncover these design principles in different organisms and cell types through the use of modeling and quantitative in vitro experiments. These principles can help redefine what “healthy” should be rather than metric means.

Research topics

My research has always been at the interface between theoreticians (myself included) and experimentalists, where we combine state-of-the-art tools of genetics, imaging, machine learning and computational modeling to achieve mechanistic understandings of biological phenomena. The central theme of my study is the balance between speed, accuracy and energy consumption in biological phenomena and how different cell types navigate within this balance to perform their respective functions.

Cell-to-cell communication via Calcium signaling cascades.

with Teemu Ihalainen, Soile Nymark, Arri Priimägi and Jari Hyttinen

Tightly connected epithelial tissues achieve complex behaviors largely by coordinating electrophysiological activities across individual cells through ion channels. These electrophysiological activities, with the most well-known being calcium signaling, determine cells’ immediate response to external stimuli by triggering transduction signaling pathways. Electrophysiological signals, despite the short time scale (from milliseconds to tens of minutes), are rarely static. Transduction signaling molecules such as calcium can also introduce latent but much longer-term changes in cells by affecting the Gene Regulatory Network (GRN), which operates at a much slower time scale (in hours or days). This can alter drastically, sometimes irreversibly, subsequent cellular behaviors by modulating protein subunits involved in the electrophysiological responses.

In this multidisciplinary spearhead, we aim to study the linkage between these two very different yet intertwining components and their roles in tissue behaviors. We will employ state-of-the-art measurement techniques, particularly in live imaging, to simultaneously apply stimulations to the tissues and capture the triggered calcium dynamics. The captured calcium responses to stimuli of different scales are then combined by integrating the principles of statistical biophysics and machine learning to characterize the trajectory of tissue behaviors over time. We first focus on epithelial cells, in particular Madin-Darby Canine Kidney and Retina Pigment Epithelium, as model tissues.

Gene expression in development

Postdoc project, with Aleksandra Walczak and Nathalie Dostatni

During my post-doctoral training, I studied the formation of gap genes’ expression patterns and its robustness in Drosophila melanogaster earlier embryogenesis. This concerns how cell identity, usually determined by the expression of specific genes, is established at the correct time and correct location in space to ensure the reproducibility of developmental patterns and the emergence of properly proportioned individuals despite their varying size and growth rate. The work is at the very interface between biology and physics, with the aim to explain quantitatively the mechanisms responsible for the pattern formation via means of modelling and explore/validate them via MS2-MCP RNA-tagging approach for live monitoring of transcription.

Dynamics of genetic circuits

Doctoral thesis with Andre Ribeiro

In genetic circuits, the constituent genes do not interact only between themselves but also with regulatory molecules of the host cells that support the circuits’ operation and by the environmental conditions. These factors, along with the intrinsic noise in gene expression, govern the functioning of the circuits. As such, to understand the structure of natural circuits and to engineer functional synthetic circuits, one needs to characterize thoroughly how external factors and perturbations from the environment may affect their behavior. In my doctoral studies, I focused on two major topics: (1) the dynamics of genetic circuits in specific contextual settings and (2) regulatory mechanisms of transcription in bacterium Escherichia coli.

Research unit

Computational Biopyshics and Imaging Group

Research fields

Biomedical Engineering

3D histopathology

Cancer 

About me

I am an engineer, I try to solve problems. Tools used tell what things I work with . If I solve problems using code I do it in c/c++, python, haskell, MATLAB, javascript, bash, lua. Sometimes I put things parellel with omp, cuda, openGL or slurm. Text I edit with neovim. For documents I use LaTex, sometimes with overleaf. To figure out how heart works, I write ODE's, with Matlab, easyML (openCARP), or CellML. To document my work, and for version control, I use git. Currently, I am trying to understand Hypertrophic cardiomyopathy with mathematical models.

About me

Doctoral researcher in Computational Biophysics and Imaging Group, with research focus in cardiac muscle (cardiomyocyte) computational modelling and simulation using MATLAB programming language. 

Research topics

Computational modelling of cardiomyocytes (heart muscle cells)

Research unit

Computational Biophysics and Imaging Group

Research fields

• Computational biology
  • Modelling and simulation of cell electrophysiology
• Tissue engineering & biomaterials
• Regulation & commercialisation of medical devices

Research career

• Doctoral researcher, simulation and modelling of cardiac muscle cell electrophysiology; Computational Biophysics and Imaging Group, Tampere University, 01/2025 →
• Master of Science (Tech.), Tissue Engineering and biomaterials (Computational biology & Regulation and commercialisation of medical devices); Tampere University, 05/2024
  • Exchange studies: Mahidol University International College, Thailand, Nakhon Pathom, Functional Histology and General Microbiology; Autumn 2022
• Bachelor of Science (Tech.), Biomedical Engineering (Biotechnology); Tampere University, 03/2020