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Recent publications

Recent publications below. See ORCID for a full list. Full publication list is also available as bibtex. Copies of most papers are available here, and we share free copies upon request (contact the first/corresponding author).

Computational and data science

What are patterns of rise and decline?
Raulo A, Rojas A, Kröger B, Laaksonen A, Orta C, Nurmio S, Peltoniemi M, Lahti L & Žliobaitė I.
The Royal Society of Open Science 10, 2023

Quantifying the impact of ecological memory on the dynamics of interacting communities
Khalighi M, Sommeria-Klein G, Gonze D, Faust K & Lahti L.
PLoS Computational Biology 18(6), 2022

Exit time as a measure of ecological resilience
Arani B, Nes E, Lahti L, Carpenter S & Scheffer M.
Science 372(6547), 2021

Probabilistic early warning signals
Laitinen V, Dakos V & Lahti L.
Ecology & Evolution 11(20), 2021

Efficient computation of Faith’s phylogenetic diversity with applications in characterizing microbiomes
Armstrong G, Cantrell K, Huang S, McDonald D, Haiminen N, Carrieri A, Zhu Q, Gonzalez A, McGrath I, Beck K, Hakim D, Havulinna A, Méric G, Niiranen T, Lahti L, Salomaa V, Jain M, Inouye M, Swafford A, Kim H, Parida L, Vázquez-Baeza Y & Rob Knight .
Genome Research 31, 2021

Wrangling with non-standard data
Mäkelä E, Lagus K, Lahti L, Säily T, Tolonen M, Hämäläinen M, Kaislaniemi S & Nevalainen T.
Proc. Digital humanities in the nordic countries 2612, 2020

Microbiome data science

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort
Qin Y, Havulinna A, Liu Y, Jousilahti P, Ritchie S, Tokolyi A, Sanders J, Valsta L, Brożyńska M, Zhu Q, Tripathi A, Vázquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M & Méric G.
Nature Genetics 54(2), 2022

Taxonomic signatures of cause-specific mortality risk in human gut microbiome
Salosensaari* A, Laitinen* V, Havulinna A, Meric G, Cheng S, Perola M, Valsta L, Alfthan G, Inouye M, Watrous J, Long T, Salido R, Sanders K, Brennan C, Humphrey G, Sanders J, Jain M, Jousilahti P, Salomaa V, Knight R, Lahti* L & Niiranen* T.
Nature Communications 12, 2021

Statistical and machine learning techniques in human microbiome studies: Contemporary challenges and solutions
Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, Bakir-Gungor B, Pau E, D’Elia D, Desai M, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes M, Zambrano L, Marques C, Mason M, May P, Pašić L, Pio G, Pongor S, Promponas V, Przymus P, Sáez-Rodríguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truică C, Vilne B, Vlachakis D, Yılmaz E, Zeller G, Zomer A, Gómez-Cabrero D & Claesson M.
Frontiers in Microbiology 12, 2021

Computational humanities

Probabilistic analysis of early modern british book prices
Tiihonen I, Tolonen M & Lahti L.
Proc. CEUR Workshop Proceedings on Computational Humanities Research 2989, 2021
In M Ehrmann, F Karsdorp et al. (eds).

Quantifying bias and uncertainty in historical data collections with probabilistic programming
Lahti L, Mäkelä E & Tolonen M.
Proc. CEUR Workshop Proceedings on Computational Humanities Research 2020

Bibliographic data science and the history of the book (c. 1500–1800)
Lahti L, Marjanen J, Roivainen H & Tolonen M.
Cataloging & Classification Quarterly 57(1) Routledge, 2019
Special issue.
10.1080/01639374.2018.1543747 | PDF

Open science

Alchemy & algorithms: Perspectives on the philosophy and history of open science
Lahti L, Silva F, Laine M, Lähteenoja V & Tolonen M.
RIO Journal 3, 2017
Review of the international conference, including electronic material (video interviews, lectures and podcasts.
10.3897/rio.3.e13593 | PDF

National policy and executive plan by the higher education and research community for 2021-2025 - policy component 1: Open access to educational resources.
Finland) E
Responsible Research Series 16 Committee for Public Information (TJNK) and Federation of Finnish Learned Societies (TSV)., 2020

Opening academic publishing: Development and application of systematic evaluation criteria
Björk A, Paavolainen J, Ropponen T, Laakso M & Lahti L.
unknown; Open Science and Research Initiative (ATT), 2018
Report on the openness of major scientific publishers commissioned by Finnish Ministry of Education and Culture

Opinion pieces (in Finnish)

Avoimuus voi vahvistaa päätöksenteon tieteellistä pohjaa
Lahti L
University of Helsinki, ThinkOpen blog 2020

Aatehistoria ja digitaalisten aineistojen mahdollisuudet
Tolonen M & Lahti L.
Ennen & Nyt 2 2, 2015