Matti Ruuskanen profile picture

Matti
Ruuskanen

University Lecturer, Department of Life Technologies
PhD, Docent
Microbiomes and health, microbiome data science

Contact

Links

ORCID

Areas of expertise

Microbiomes
bioinformatics
microbiology
data science

Biography

I received my MSc in Microbiology from University of Helsinki in 2014, where I studied e.g., the spread of antibiotic resistance genes during manure application. I completed my PhD research between 2015 and 2019 at University of Ottawa (Canada), where I investigated the sediment communities in Arctic lakes and how they respond to anthropogenic stresses. I started working at University of Turku in the groups of Teemu Niiranen as a postdoctoral researcher. Between 2021 and 2025 I continued my work in the group of Leo Lahti with postdoctoral funding from the Finnish Research Council and the Finnish Cultural Foundation. During my postdoc period I studied e.g., associations between incident and prevalent chronic diseases and human gut microbiomes in the FINRISK cohort. In 2023, I received the Title of Docent in Microbiology, from University of Helsinki.

Teaching

I have taught several laboratory and lecture courses as an assistant teacher at University of Helsinki and University of Ottawa (Canada) during my studies. Since 2019 I have been asked to give lectures on microbiome data science and related topics on courses at University of Helsinki, Karolinska Institutet (Sweden), Savitribai Phule Pune University (India), Universitas Gadjah Mada (Indonesia), University of Tirana (Albania). Additionally, I have organized and taught in several international workshops in Finland and in other European countries. At University of Turku, I was the main lecturer on the Machine Learning and Algorithmics course (TKO_3121) between 2021-2024.

I am currently teaching on Solu ja Biomolekyylit -teoria (BKEM5030), Elintarvikelainsäädäntö ja elintarvikevalvonta (ETEK0003), and Mikrobiologia (BKEM5013).

I have supervised 3 BSc theses, 3 MSc theses, and I am currently a co-supervisor for 2 PhD researchers.

I have a docent contract with University of Helsinki and I have completed the teacher's pedagogical studies (60 ECTS).

Publications

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Multi-omics time-series analysis in microbiome research: a systematic review (2025)

Briefings in Bioinformatics
Sherwani, Moiz Khan; Ruuskanen, Matti O.; Feldner-Busztin, Dylan; Nisantzis Firbas, Panos; Boza, Gergely; Móréh, Ágnes; Borman, Tuomas; Putu Erawijantari, Pande; Scheuring, István; Gopalakrishnan, Shyam; Lahti, Leo
(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä )

Integration of polygenic and gut metagenomic risk prediction for common diseases (2024)

Nature Aging
Liu Yang, Ritchie Scott C., Teo Shu Mei, Ruuskanen Matti O., Kambur Oleg, Zhu Qiyun, Sanders Jon, Vázquez-Baeza Yoshiki, Verspoor Karin, Jousilahti Pekka, Lahti Leo, Niiranen Teemu, Salomaa Veikko, Havulinna Aki S., Knight Rob, Méric Guillaume, Inouye Michael
(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä )

Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting (2022)

Cell Metabolism
Liu Yang, Méric Guillaume, Havulinna Aki S, Teo Shu Mei, Åberg Fredrik, Ruuskanen Matti, Sanders Jon, Zhu Qiyun, Tripathi Anupriya, Verspoor Karin, Cheng Susan, Jain Mohit, Jousilahti Pekka, Vázquez-Baeza Yoshiki, Loomba Rohit, Lahti Leo, Niiranen Teemu, Salomaa Veikko, Knight Rob, Inouye Michael
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))

Links between gut microbiome composition and fatty liver disease in a large population sample (2021)

Gut Microbes
Ruuskanen Matti O, Åberg Fredrik, Männistö Ville, Havulinna Aki S, Meric Guillaume, Liu Yang, Loomba Rohit, Vazquez-Baeza Yoshiki, Tripathi Anupriya, Valsta Liisa M, Inouye Michael, Jousilahti Pekka, Salomaa Veikko, Jain Mohit, Knight Rob, Lahti Leo, Niiranen Teemu J
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))
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