Recent publications

Below some examples from recent publications. See ORCID for a full list. Full publication list is also available as bibtex Copies of most papers are available here, and we can share free copies upon request.

Computational and data science

Exit time as a measure of ecological resilience
Science 2021. (Free reprint)
Arani BMS, Carpenter S, Lahti L, van Nes E, Scheffer M.

Wrangling with Non-Standard Data
Proc. Digital Humanities in the Nordic Countries 2020.
Mäkelä E, Lagus K, Lahti L, Säily T, Tolonen M, Hämäläinen M, Kaislaniemi S, Nevalainen T.
Best long paper in DHN2020.

Three-species Lotka-Volterra model with respect to Caputo and Caputo-Fabrizio fractional operators
Symmetry 2021.
Khalighi M, Eftekhari L, Hosseinpour S, Lahti L.

Microbiome data science

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 JD, Long T, Salido R, Sanders K, Brennan C, Humphrey GC, Sanders JG, Jain M, Jousilahti P, Salomaa V, Knight R, Lahti L*, Niiranen T*.
Nature Communications 12:2671, May 2021.

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting
Liu Y, Meric G, Havulinna AS, Teo SM, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vazquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R, Inouye M.
Preprint at medRxiv: 2020.06.24.20138933

Links between gut microbiome composition and fatty liver disease in a large population sample
Ruuskanen MO, Åberg F, Männistö V, Havulinna AS, Méric G, Liu Y, Loomba R, Vázquez-Baeza Y, Tripathi A, Valsta LM, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti L, Niiranen TJ.
Gut Microbes 13(1):1-22, 2021.

Statistical and machine learning techniques in human microbiome studies: contemporary challenges and solutions
Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin GV, Adilovic M, Aydemir O, Bakir-Gungor B, Carrillo-de Santa Pau E, D'Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes MB, Marcos Zambrano LJ, Marques C, Mason M, May P, Pašić L, Pio G, Pongor S, Promponas VJ, Przymus P, Sáez-Rodríguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truică C-O, Vilne B, Vlachakis DP, Yılmaz E, Zeller G, Zomer A, Gómez-Cabrero D, Claesson M.
Frontiers in Microbiology 12:313, 2021.

Modeling spatial patterns in host-associated microbial communities
Ruuskanen M, Sommeria-Klein G, Havulinna A, Niiranen T, Lahti L.
Environmental Microbiology 23(5), 2021.

Computational humanities

Examining the Early Modern Canon: The English Short Title Catalogue and Large-Scale Patterns of Cultural Production
In: Baird I. (eds) Data Visualization in Enlightenment Literature and Culture. Palgrave Macmillan, Cham. pp. 63-119, 2021. Tolonen M, Hill MJ, Ijaz AZ, Vaara V, Lahti L.

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

Bibliographic Data Science and the History of the Book (c. 1500-1800)
Cataloging and classification quarterly, 2019. Lahti L, Marjanen J, Roivainen H, Tolonen M.

Open science

Alchemy & algorithms: perspectives on the philosophy and history of open science
RIO Journal 2017.
Lahti L, da Silva F, Laine MP, Lähteenoja V, Tolonen M.

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

Opening academic publishing: development and application of systematic evaluation criteria. Report on the openness of major scientific publishers
Finnish IT Center for Science (CSC) and Ministry of Education and Culture, Open Science and Research Initiative (ATT). 2018. Björk A, Paavolainen J-M, Ropponen T, Laakso M, Lahti L.

Opinion pieces (in Finnish)

Avoimuus voi vahvistaa päätöksenteon tieteellistä pohjaa
Invited opinion piece: University of Helsinki, ThinkOpen blog. August 2020.
Lahti L.

Aatehistoria ja digitaalisten aineistojen mahdollisuudet
Ennen & Nyt (Finland) 2015.
Tolonen M, Lahti L.

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