Our research focuses on computational analysis of
complex natural and social systems. There is a great demand for
targeted computational techniques to extract information and insights
from rich data collections based on clever combinations of human and
machine intelligence. We blend elements from fields such as machine
learning/AI, probabilistic programming, statistical ecology, and data
science, and drive open developer communities that help to translate
latest theoretical advances into accessible methods to inform
modeling, experimentation, and decision-making. For a full list of publications check this page.
Preprints
A Bayesian approach to differential prevalence analysis with applications in microbiome studies
Pelto, J., Auranen, K., Kujala, J.V. & Lahti, L.
arXiv
2026
10.48550/arXiv.2602.05938
Orchestrating microbiome analysis with Bioconductor
Borman, T., Benedetti, G., Muluh, G., Raulo, A., Valderrama, B., Sannikov, A., Peschel, S., Liu, Y., Hindström, R., OMA consortium, Pärnänen, K., Müller, C.L., Havulinna, A.S., Shetty, S.A., Ramos, M., Braccia, D.J., Corrada Bravo, H., Ernst, F.G.M., Waldron, L., Bastiaanssen, T.F.S., Mallick, H. & Lahti, L.
bioRxiv
2025
10.1101/2025.10.29.685036
Biochemical analyses can complement sequencing-based ARG load monitoring: A case study in indian hospital sewage networks
Bhanushali, S., Pärnänen, K., Mongad, D., Dhotre, D. & Lahti, L.
medRxiv
2024
10.1101/2024.05.31.24308262
Microbiome-based risk prediction in incident heart failure: A community challenge
Erawijantari, P.P., Kartal, E., Liñares-Blanco, J., Laajala, T.D., Feldman, L.E., Challenge, T.F.M.D., Communities, M., Carmona-Saez, P., Shigdel, R., Claesson, M.J., Bertelsen, R.J., Gómez-Cabrero, D., Minot, S., Albrecht, J., Chung, V., Inouye, M., Jousilahti, P., Schultz, J.H., Friederich, H.C., Knight, R., Salomaa, V., Niiranen, T., Havulinna, A.S., Saez-Rodriguez, J., Levinson, R.T. & Lahti, L.
medRxiv
2023
10.1101/2023.10.12.23296829
Infant left amygdala volume is negatively associated with fecal microbiota diversity
Aatsinki, A.K., Tuulari, J.J., Munukka, E., Lahti, L., Keskitalo, A., Kailanto, H.M., Nolvi, S., Scheinin, N.M., Saunavaara, J., Parkkola, R., Lewis, J.D., Hashempour, N., Shulist, S.J., Karlsson, L. & Karlsson, H.
bioRxiv
2023
10.1101/2023.04.23.537273
A brief overview on the BioPAX and SBML standards
Lahti, L.
arXiv,
2007
Overview of machine-readable representations of biological processes (in Finnish).
10.48550/arXiv.1109.4919
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URL
A unified framework for batch correction and missing data handling in large-scale and single-cell mass spectrometry proteomics
Anwar, A.M., Bayoumi, S., Lahti, L. & Coffey, E.
bioRxiv
2026
10.64898/2026.05.19.726178
Gut microbiome signatures associated with self-reported allergic symptoms among Finnish adults
Lindgren, H., Vartiainen, V.A., Muluh, G., Bayal, N., Pärnänen, K., Méric, G., Jousilahti, P., Ruuskanen, M.O., Knight, R., Niiranen, T., Havulinna, A.S., Salomaa, V., Erawijantari, P.P. & Lahti, L.
medRxiv
2026
10.64898/2026.07.03.26357002