👨🔬 Welcome to My Academic Portfolio
Here, I showcase my lifelong journey in science 🔬, driven by curiosity, continuous learning, and a deep passion for data. I bring together a strong academic background 👨🔬 with hands-on expertise in both 🛠️ data engineering and analysis 📈 — a true data nerd 🤓 at my ❤️!
🔍 Want to see what I do daily?
To learn more about my current role as a Data Engineer at Solita, check out 👉🛠️ My Work Portfolio 👨🏻💻👈 or my resume 📑 (pdf).
Use the links below to jump to key sections!
I’d love to hear from you! Whether you have an exciting research idea where I could contribute—because science is fun!🤓—or just want to discuss my work, feel free to reach me out ✉︎.
For more insights into my research, you can also contact 👨🏻🏫 Professor Pasi Kallio from Tampere University, who leads Micro- and Nanosystems Research Group. More about their pretty cool research 🔬 can be found here.
🎓 Education
D. Sc. (Tech.), Tampere University of Technology, Sep 2018
- 📝 Doctoral dissertation ‘Modeling and Control of Microscale Cell Culture Environments’ available here
My Ph.D. work involved designing and implementing control systems, mathematical modeling and data handling using MATLAB and Simulink, FEM simulations with COMSOL, and laboratory work with microfluidics chips.
M. Sc. (Tech.), Tampere University of Technology, July 2010
- 📝 Thesis ‘Optically induced electric fields and their use in microfluidics and cell manipulation applications’ is available here and was presented in the 2nd European Conference on Microfluidics-Microfluidics 2010, Toulouse, December 8-10, 2010.
💼 My Research & Work Experience
Summarizing 15+ years in academia? Not the easiest task… but let’s try! 😆
- tl;dr: My 👨🔬 research focused on control engineering, microfluidics, mathematical modeling using both Simulink & MATLAB and FEM (COMSOL), and data analysis with MATLAB.
…without forgetting some hours of laboratory work! 😎👨🏻🔬🔬.
💡 Lifelong Researcher & Passionate Hobby Scientist (Jan 2025 – Present)
Currently, I focus on continuous learning and on my hobby projects, some of them listed below. But, please do not hesitate to contact me if you would have some research study in your mind. 👨🔬
NOTE: These are projects I’m actively working on—whether they’ll ever be truly finished is another story! 🤓 I also 📝 started blogging, and these will likely be my first topics. Stay tuned! ✍️
How to use GitHub Pages
- Sharing my tips & tricks how to set up GitHub Pages in my blog page. For example, how to make portfolio page, start blogging, or how to list your academic publications.
My Tips for Academy
- Sharing my tips & tricks for the academic career. For example, how to make “version control” clever in the case of you are not familiar with git etc. 👉 check more here
How to write scientific papers
- A follow-up to my Write LaTeX Documents using Word guide, this post explores how you can leverage VS Code, Markdown, Pandoc, LaTeX, and BibTeX to efficiently format and publish high-quality (scientific) papers, with the combination of Markdown and LaTeX ( link coming soon(ish))
- P.S. 🚀 Effortless writing not guaranteed—but at least the workflow is smooth(er)! 🤓
How to set up Python environments for data projects
- My proposal how to set up Python environment for (hobby) data projects by combining Miniconda, pip, VS Code,… 👉 more here
🤓 Visiting Scholar @Tampere University (Nov 2022 - Dec 2024)
Continued as a part-time researcher (approx. 10 hours/month) in Micro- and Nanosystems Research Group led by Professor Pasi Kallio.
- 🚀 Research areas: lab-on-a-chip, vascularization, data analysis, fuzzy control
- 🛠️ Main tools: MATLAB, Simulink, COMSOL (FEM)
During this period, we finished following three publications 📝
- 🧫 Vascularized Body-on-Chip development, doi: 10.1038/s41598-024-74493-3
- 🎚️ Fuzzy temperature control, doi: 10.1109/TASE.2023.3309668
- 📊 Understand field potential signals, doi: 10.5281/zenodo.10205591
👨🏼🎓 Postdoctoral Research Fellow @Tampere University (Sep 2018 - Nov 2022)
As a postdoc in Professor Pasi Kallio’s Micro- and Nanosystems Research Group, I developed data analysis methods for several challenging biosignals. Additionally, I worked as Professor Kallio’s Vice-PI in a multidisciplinary team combining cell biologists and engineers, and led a group of researchers developing a novel vascular-on-a-chip platform for 3D cell co-cultures. More info on CoEBoC-project section.
- 🚀 Research areas: lab-on-a-chip, data analysis, microfluidics, iPS-CM, fuzzy control
- 🛠️ Main tools: soft lithography (PDMS), MATLAB, Simulink, COMSOL (FEM)
👨🔬 Doctoral Researcher @Tampere University of Technology (Sep 2011 - Aug 2018)
My Ph.D. work in the multidisciplinary project involved implementing automation and control systems, designing microfluidics chips, developing mathematical models, and handling data analysis using MATLAB, Simulink, and COMSOL. More info about the project on Human Spare Parts section.
- 🚀 Research areas: microsystems, microfluidics, control engineering, heat control
- 🛠️ Main tools: soft lithography, MATLAB, Simulink, COMSOL (FEM)
- 📖 Thesis: Dissertation ‘Modeling and Control of Microscale Cell Culture Environments’ available here.
🧑🏼🔬 Project Researcher @Tampere University of Technology (Aug 2010 - Sep 2011)
My study was related to immunoassay in microchannels and how they could be used in patient diagnostics.
🧑🏼🔬 Thesis Worker and Research Assistant @Tampere University of Technology (June 2006 - Aug 2010)
I worked in OPTIMI (Optically actuated microfluidics) project funded by Academy of Finland and collaborated with researchers from Helsinki University of Technology. My task was to model and test optically induced electric fields and to study how they could be used in microfluidics applications.
- 📖 Master thesis (2010), titled ‘Optically induced electric fields and their use in microfluidics and cell manipulation applications’ is available here and was later presented 🗣 in the 2nd European Conference on Microfluidics-Microfluidics 2010, Toulouse, December 8-10, 2010
🗂️ Projects
🫀 CoEBoC (2018 - 2025)
CoEBoC, ‘Centre of Excellence in Body-on-Chip Research’, is Academy of Finland funded project for the years 2018-2025. The ultimate goal of CoEBoC is to revolutionize healthcare by developing and applying Body-on-Chip (BoC) technologies and enable more accurate and efficient drug testing, as well as by discovering new tools for diagnosing and treating diseases at the cellular level.
CoEBoC brought together six research groups from Tampere University: microsystems and microfluidics, biomaterials, adult stem cell research, cardiac and neural cell cultures, and computational biophysics and imaging. Below, I highlight some selected CoEBoC projects where I was involved.
- ⚡Own role: Postdoctoral Researcher, Vice Principal Investigator (Vice-PI), project lead in Vascularized Body-on-Chip development
- 🚀 Research areas: microfluidics, numerical simulations (FEM), data analysis, control engineering, cardiomyocyte culture, vascularization
Developing interconnected 3D microvascular networks
🚀 Bringing the future of tissue engineering one step closer! 🧫
I led a multidisciplinary research team that developed a groundbreaking “body-on-a-chip” platform for studying vascularized 3D cell co-cultures. Our team introduced an innovative open-top microfluidic chip that enables the cultivation of two distinct 3D cell cultures within a single device—without physical barriers. This breakthrough technology opens new possibilities for studying cell-cell interactions in a precisely controlled microenvironment and advancing drug testing applications. Read more:
When cardiomyocyte culture meets fuzzy controller
🎚️ Control the beating of cardiomyocyte cultures - by temperature! 🌡️
I developed fuzzy controllers and mathematical models to simulate and control temperature-dependency of beating human cardiomyocyte cultures. This research offers valuable guidance for scientists aiming to standardize experimental conditions and improve the reliability of cardiomyocyte cell cultures. Read more:
Study of field potential signals from cell cultures
📈 Truely understand the field potential signals 📊
I encapsulated my extensive experience in analyzing field potential (FP) signals derived from 2D human-induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) cultures.
While developing the DatAnalyzer software, explained here, I observed a wide array of methodologies used for FP signal analysis across various studies. Driven by realization of this inconsistency, I dedicated significant effort to produce an academically rigorous report that—despite not undergoing formal peer-review process—offers valuable insights and guidance for researchers analyzing FP signals. More information on DatAnalyzer repo and in the following article:
List of Selected CoEBoC Articles
Show Selected Articles
Mäki, Antti-Juhana and Koivumäki, Jussi and Hyttinen, Jari and Kallio, Pasi . "Simulation-Based Study of Control Strategies for Beating of Human Cardiomyocyte Cultures" IEEE Transactions on Automation Science and Engineering, 2024. doi: 10.1109/TASE.2023.3309668
Häkli, Martta and Kreutzer, Joose and Mäki, Antti-Juhana and Välimäki, Hannu and Cherian, Reeja Maria and Kallio, Pasi and Aalto-Setälä, Katriina and Pekkanen-Mattila, Mari . "Electrophysiological Changes of Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes during Acute Hypoxia and Reoxygenation" Stem cells international, 2022. doi: 10.1155/2022/9438281
Skogberg, Anne and Siljander, Sanna and Mäki, Antti-Juhana and Honkanen, Mari and Efimov, Alexander and Hannula, Markus and Lahtinen, Panu and Tuukkanen, Sampo and Björkqvist, Tomas and Kallio, Pasi . "Self-assembled cellulose nanofiber–carbon nanotube nanocomposite films with anisotropic conductivity" Nanoscale, 2022. doi: 10.1039/d1nr06937c
🦾 Human Spare Parts (2011 - 2019)
In this Business Finland (former TEKES) Human Spare Parts - project (2011-2019), the goal was to develop stem cell-based advanced in vitro models and solutions for cardiac, neural, bone, and adipose diseases and traumas. It combined tens of experts from different research fields, such as microsystems, stem cells, biomaterials, and biomedical engineering, and produced several leading edge in vitro models and solutions.
- ⚡Own role: Doctoral Researcher
- 🚀 Research areas: microsystems, numerical simulations (FEM), control engineering
👨💻 Own projects
Here, I list some of my research projects I have created during my academic career.
🚀 DatAnalyzer: The correct way to analyze FP signals 📊
- ⚡ Role: Creator
- ✅ Key Contributions: Developed tools to load, analyze, and visualize data, especially electrical biosignals
- 🛠️ Tech Stack: MATLAB
- 🏷️ Key Words: data analysis, MEA, field potential, hiPS-CM
- 🔗 References: DatAnalyzer home page and publication Opinion: The correct way to analyze FP signals in Zenodo
I developed DatAnalyzer software to analyze field potential (FP) signals from human induced pluripotent stem cells derived cardiomyocyte (hiPSC-CM) cultures. Furthermore, I summarized how FP signals have been analyzed various, sometimes even contradictory, ways in the literature, and proposed new methdod for the proper analysis.
List of Publications using DatAnalyzer
Gaballah, Mahmoud and Penttinen, Kirsi and Kreutzer, Joose and Mäki, Antti-Juhana and Kallio, Pasi and Aalto-Setälä, Katriina . "Cardiac Ischemia On-a-Chip: Antiarrhythmic Effect of Levosimendan on Ischemic Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes" Cells, 2022. doi: 10.3390/cells11061045
Häkli, Martta and Kreutzer, Joose and Mäki, Antti-Juhana and Välimäki, Hannu and Lappi, Henna and Huhtala, Heini and Kallio, Pasi and Aalto-Setälä, Katriina and Pekkanen-Mattila, Mari . "Human induced pluripotent stem cell-based platform for modeling cardiac ischemia" Scientific reports, 2021. doi: 10.1038/s41598-021-83740-w
🚀 Write LaTeX documents together with co-authors that use MS Word ✍️
- ⚡ Role: Creator
- ✅ Key Contributions: Developed conversion tool to work with MS Word using Pandoc & Markdowns & LaTeX
- 🛠️ Tech Stack: Powershell, Pandoc, LaTeX, Markdown
- 🏷️ Key Words: automation, publish
- 🔗 References: Project repo
Do you want to use LaTeX for your (scientific) paper, but struggling when co-authors, such as you supervisor, do not use it, thus Word is preferred? This is tool for you! Minimize hassle of exporting files in different formats and copy-paste text from one format to another, while still be able to write LaTeX-documents. And you are ready to publish high-quality papers like the following that was written using this tool! 😎
Method used in the following publication:
🚀 Plot Fluke Ti400 thermal images 🌡️
- ⚡ Role: Creator, co-author
- ✅ Key Contributions: Plot thermal images for the analysis
- 🛠️ Tech Stack: MATLAB, PowerShell, thermal images
- 🏷️ Key Words: automation, publish
- 🔗 References: Project repo
In the following publication, thermal images from Fluke Ti400 device were plotted using this tool.
Languages and merits
Language
- Finnish: Mother tongue
- English: C2 (full professional working proficiency)
- Swedish: A2
- German: A1
- Mandarin: A1
Academic Merits
- Invention disclosures
- TKS0222022 Kudosteknologisen lihaskimpun kehikko (”Frame of an engineered skeletal muscle bundle”), granted 08/2022 (second author)
- TKS0222021 MEA-signaalin analyysityökalu (”MEA analysis tool”), granted 05/2021
- TKS0612020 Pilarivapaa 3D monisolukasvatuschippi (”Barrier-free 3D co-culture chip”), granted 06/2020
- Member of the Organizing Committee, Nordic Organ on a Chip Symposium 2019, 08/2019
- Member of Future Finders network, Tampere University 2019-2022
- Doctoral Programme of the President of the Tampere University of Technology, 09/2021 – 08/2015; personal salary
📚 Publications
In this section, I list my journal articles. For more, including my conference papers, check out the links below:
Next, I’ve selected a few key articles 📝 to showcase my 🎓 academic journey.
If you’re curious, you can also check out my all journal articles listed at the end.
🧫 A Special One!
This must-have first article is extra special—it’s the first (and maybe last!) time I’m listed as the last author! This study even made it to Finnish news! More about it here.
🎚️ Fuzzy Logic Meets Beating Heart Cells
One of my deepest dives into control systems happened when I combined fuzzy controllers with cardiomyocyte cell cultures in a simulation environment I built from scratch. Check this part to find out more.
🫀 Biosignals, Ischemia & Data Science
This study uncovered key biological insights—like how hiPSC-CMs, despite their immature phenotype, can be used to model ischemia–reperfusion injury. On a personal level, it was also a milestone for me:
✅ I built DatAnalyzer, software designed for this research.
✅ It marked my first experience analyzing complex cardiomyocyte biosignals.
✅ This journey eventually led me to explore 📈 field potential signals from cell cultures, opening up a whole new world of bioelectric data analysis. 📊
✅ It pushed me further into data-driven science—the foundation of what I do today! 🤓
Truely understand the field potential signals 📊
🌱 My Most Cited Paper!
Had to include this one—it’s my most cited article! 😎 Beyond citations, it stands out because we successfully oriented cells using aligned cationic cellulose nanofiber (c-CNF) surfaces, a method that has potential in guiding cellular growth. Personally, I had a blast analyzing the data for this project.
🎓 Wrapping Up My Doctoral Work
These two papers sum up my PhD research quite well:
🎛️ The first one brings together control engineering, indirect measurement methods, mathematical modeling, electronics, and data analysis—all powered by MATLAB & Simulink. Pretty cool, if you ask me. 😎
✍🏻 The second one is a deep dive into computational modeling, mathematics, chemistry, and microfluidics 🧮🧪💧, primarily using COMSOL. During my PhD defense, this work received great feedback from my opponents. 🏆🤓
Mäki, Antti-Juhana and Peltokangas, Mikko and Kreutzer, Joose and Auvinen, Sanna and Kallio, Pasi . "Modeling carbon dioxide transport in PDMS-based microfluidic cell culture devices" Chemical Engineering Science, 2015. doi: 10.1016/j.ces.2015.06.065
📚 All Journal Articles
Click below to see list of all journal articles I am involved in.
📚 Show All Journal Articles
Mäki, Antti-Juhana and Koivumäki, Jussi and Hyttinen, Jari and Kallio, Pasi . "Simulation-Based Study of Control Strategies for Beating of Human Cardiomyocyte Cultures" IEEE Transactions on Automation Science and Engineering, 2024. doi: 10.1109/TASE.2023.3309668
Mäki, Antti-Juhana . "Opinion: The correct way to analyze FP signals" Zenodo, 2023. doi: 10.5281/zenodo.10205591
Häkli, Martta and Kreutzer, Joose and Mäki, Antti-Juhana and Välimäki, Hannu and Cherian, Reeja Maria and Kallio, Pasi and Aalto-Setälä, Katriina and Pekkanen-Mattila, Mari . "Electrophysiological Changes of Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes during Acute Hypoxia and Reoxygenation" Stem cells international, 2022. doi: 10.1155/2022/9438281
Peussa, Heidi and Kreutzer, Joose and Mäntylä, Elina and Mäki, Antti-Juhana and Nymark, Soile and Kallio, Pasi and Ihalainen, Teemu . "Pneumatic equiaxial compression device for mechanical manipulation of epithelial cell packing and physiology" PloS one, 2022. doi: 10.1371/journal.pone.0268570
Tornberg, Kaisa and Välimäki, Hannu and Valaskivi, Silmu and Mäki, Antti-Juhana and Jokinen, Matias and Kreutzer, Joose and Kallio, Pasi . "Compartmentalized organ-on-a-chip structure for spatiotemporal control of oxygen microenvironments." Biomedical Microdevices, 2022. doi: 10.1007/s10544-022-00634-y
Gaballah, Mahmoud and Penttinen, Kirsi and Kreutzer, Joose and Mäki, Antti-Juhana and Kallio, Pasi and Aalto-Setälä, Katriina . "Cardiac Ischemia On-a-Chip: Antiarrhythmic Effect of Levosimendan on Ischemic Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes" Cells, 2022. doi: 10.3390/cells11061045
Mykuliak, Anastasiia and Yrjänäinen, Alma and Mäki, Antti-Juhana and Gebraad, Arjen and Lampela, Ella and Kääriäinen, Minna and Pakarinen, Toni-Karri and Kallio, Pasi and Miettinen, Susanna and Vuorenpää, Hanna . "Vasculogenic potency of bone marrow-and adipose tissue-derived mesenchymal stem/stromal cells results in differing vascular network phenotypes in a microfluidic chip" Frontiers in Bioengineering and Biotechnology, 2022. doi: 10.3389/fbioe.2022.764237
Skogberg, Anne and Siljander, Sanna and Mäki, Antti-Juhana and Honkanen, Mari and Efimov, Alexander and Hannula, Markus and Lahtinen, Panu and Tuukkanen, Sampo and Björkqvist, Tomas and Kallio, Pasi . "Self-assembled cellulose nanofiber–carbon nanotube nanocomposite films with anisotropic conductivity" Nanoscale, 2022. doi: 10.1039/d1nr06937c
Häkli, Martta and Kreutzer, Joose and Mäki, Antti-Juhana and Välimäki, Hannu and Lappi, Henna and Huhtala, Heini and Kallio, Pasi and Aalto-Setälä, Katriina and Pekkanen-Mattila, Mari . "Human induced pluripotent stem cell-based platform for modeling cardiac ischemia" Scientific reports, 2021. doi: 10.1038/s41598-021-83740-w
Rajan, Dhanesh Kattipparambil and Mäki, Antti-Juhana and Pekkanen-Mattila, Mari and Kreutzer, Joose and Ryynänen, Tomi and Välimäki, Hannu and Verho, Jarmo and Koivumäki, Jussi T and Ihalainen, Heimo and Aalto-Setälä, Katriina and Kallio, Pasi and Lekkala, Jukka . "Cardiomyocytes: Analysis of Temperature Response and Signal Propagation Between Dissociated Clusters Using Novel Video-Based Movement Analysis Software" IEEE Access, 2020. doi: 10.1109/ACCESS.2020.3001191
Mäki, Antti-Juhana and Verho, Jarmo and Kreutzer, Joose and Ryynänen, Tomi and Rajan, Dhanesh and Pekkanen-Mattila, Mari and Ahola, Antti and Hyttinen, Jari and Aalto-Setälä, Katriina and Lekkala, Jukka and Kallio, Pasi . "A Portable Microscale Cell Culture System with Indirect Temperature Control" SLAS Technology, 2018. doi: 10.1177/2472630318768710
Skogberg, Anne and Mäki, Antti-Juhana and Mettänen, Marja and Lahtinen, Panu and Kallio, Pasi . "Cellulose Nanofiber Alignment Using Evaporation-Induced Droplet-Casting, and Cell Alignment on Aligned Nanocellulose Surfaces" Biomacromolecules, 2017. doi: 10.1021/acs.biomac.7b00963
Kreutzer, Joose and Ylä-Outinen, Laura and Mäki, Antti-Juhana and Ristola, Mervi and Narkilahti, Susanna and Kallio, Pasi . "Cell culture chamber with gas supply for prolonged recording of human neuronal cells on microelectrode array" Journal of Neuroscience Methods, 2017. doi: 10.1016/j.jneumeth.2017.01.019
Mäki, Antti-Juhana and Ryynänen, Tomi and Verho, Jarmo and Kreutzer, Joose and Lekkala, Jukka and Kallio, Pasi J . "Indirect temperature measurement and control method for cell culture devices" IEEE Transactions on Automation Science and Engineering, 2016. doi: 10.1109/TASE.2016.2613912
Mäki, Antti-Juhana and Hemmilä, Samu and Hirvonen, Juha and Girish, Nathaniel Narra and Kreutzer, Joose and Hyttinen, Jari and Kallio, Pasi . "Modeling and Experimental Characterization of Pressure Drop in Gravity-Driven Microfluidic Systems" Journal of Fluids Engineering, 2015. doi: 10.1115/1.4028501
Mäki, Antti-Juhana and Peltokangas, Mikko and Kreutzer, Joose and Auvinen, Sanna and Kallio, Pasi . "Modeling carbon dioxide transport in PDMS-based microfluidic cell culture devices" Chemical Engineering Science, 2015. doi: 10.1016/j.ces.2015.06.065