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.

All publications

Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain and placenta
Husso A, Pessa-Morikawa T, Koistinen V, Karkkainen O, Lahti L, Iivanainen A, Hanhineva K & Niku M.
bioRxiv Cold Spring Harbor Laboratory, 2022
10.1101/2022.07.01.498433 | URL

Probabilistic multivariate early warning signals
Laitinen V & Lahti L.
2022 Preprint

The gut microbiome is a significant risk factor for future chronic lung disease
Liu Y, Teo S, Meric G, Tang H, Zhu Q, Sanders J, Vazquez-Baeza Y, Verspoor K, Vartiainen V, Jousilahti P, Lahti L, Niiranen T, Havulinna A, Knight R, Salomaa V & Inouye M.
2022 Preprint

An infancy-onset 20-year dietary counselling intervention and gut microbiota composition in adulthood
Keskitalo A, Munukka E, Aatsinki A, Saleem W, Kartiosuo N, Lahti L, Huovinen P, Elo L, Pietilä S, Rovio S, Niinikoski H, Viikari J, Rönnemaa T, Lagström H, Jula A, Raitakari O & Pahkala K.
Nutrients 14(13), 2022

An analysis of the current bibliographical data landscape in the humanities. A case for the joint bibliodata agendas of public stakeholders
Umerle T, Colavizza G, Herden E, Jagersma R, Király P, Koper B, Lahti L, Lindemann D, Łubocki J, Malínek V, Milanova A, Péter R, Rißler-Pipka N, Romanello M, Roszkowski M, Siwecka D, Tolonen M & Vimr O.
Zenodo 2022

Towards standardized and reproducible research in skin microbiomes
Ruuskanen M, Vats D, Potbhare R, RaviKumar A, Munukka E, Ashma R & Lahti L.
Environmental Microbiology 2022

Enhancing biomarkers with co-abundance
Lahti L
Nature Computational Science 2022
Invited News & Views.

Potential pathobionts in vaginal microbiota are affected by fish oil and/or probiotics intervention in overweight and obese pregnant women
Houttu N, Mokkala K, Saleem W, Virtanen S, Juhila J, Koivuniemi E, Pellonperä O, Tertti K, Luokola P, Sorsa T, Salonen A, Lahti L & Laitinen K.
Biomedicine & Pharmacotherapy 149, 2022
10.1016/j.biopha.2022.112841 | URL

Skin microbiota diversity among genetically unrelated individuals of indian origin
Potbhare R, RaviKumar A, Munukka E, Lahti L & Ashma R.
PeerJ 10, 2022

Can gut microbiota throughout the first 10 years of life predict executive functioning in childhood?
Eckermann H, Ou Y, Lahti L & Weerth C.
Developmental Psychobiology 64(3), 2022

Phylogeny-aware analysis of metagenome community ecology based on matched reference genomes while bypassing taxonomy
Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore G, Swafford A, Das P, Shaffer J, Lejzerowicz F, Belda-Ferre P, Havulinna A, Méric G, Niiranen T, Lahti L, Salomaa V, Kim H, Jain M, Inouye M, Gilbert J & Knight R.
mSystems 2022

Distinct diet-microbiota-metabolism interactions in overweight and obese pregnant women: A metagenomics approach
Lotankar M, Mokkala K, Houttu N, Koivuniemi E, Sørensen N, Nielsen H, Munukka E, Lahti L & Laitinen K.
Microbiology Spectrum 2022
10.1128/spectrum.00893-21 | URL

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 2022

Gut microbiome composition is predictive of incident type 2 diabetes in a population cohort of 5 572 finnish adults
Ruuskanen M, Erawijantari P, Havulinna A, Liu Y, Méric G, Tuomilehto J, Inouye M, Jousilahti P, Salomaa V, Jain M, Knight R, Lahti* L & Niiranen* T.
Diabetes Care 2022

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

Impact of combined consumption of fish oil and probiotics on the serum metabolome in pregnant women with overweight or obesity
Mokkala K, Vahlberg T, Houttu N, Koivuniemi E, Lahti L & Laitinen K.
EbioMedicine 73, 2021

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

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

Xylo-oligosaccharides in prevention of hepatic steatosis and adipose tissue inflammation: Associating taxonomic and metabolomic patterns in fecal microbiomes with biclustering
Hintikka J, Lensu S, Mäkinen E, Karvinen S, Honkanen M, Linden J, Garrels T, Pekkala S & Lahti L.
International Journal of Environmental Research and Public Health 18(8), 2021

Gut microbiota diversity but not composition is related to saliva cortisol stress response at the age of 2.5 months
Keskitalo A, Aatsinki A, Kortesluoma S, Pelto J, Korhonen L, Lahti L, Lukkarinen M, Munukka E, Karlsson H & Karlsson L.
Stress 24(5), 2021
In press.

Microbiome data science in the SummarizedExperiment universe
Lahti L, Ernst F, Shetty S & others.
F1000Research 10(748), 2021
(slides); version 1; not peer reviewed

Laki estää tehokkaiden tutkimusmenetelmien käytön
Mäkelä E, Lahti L, Lilja J & Heikkinen P.
HS Mielipide, 2021

Applications of machine learning in human microbiome studies: A review on feature selection, biomarker identification, disease prediction and treatment
Marcos-Zambrano L, Karaduzovic-Hadziabdic K, Loncar Turukalo T, Przymus P, Trajkovik V, Aasmets O, Berland M, Gruca A, Hasic J, Hron K, Klammsteiner T, Kolev M, Lahti L, Lopes M, Moreno V, Naskinova I, Org E, Paciência I, Papoutsoglou G, Shigdel R, Stres B, Vilne B, Yousef M, Zdravevski E, Tsamarindos I, Santa Pau E, Claesson M, Moreno-Indias I & Truu J.
Frontiers in Microbiology 12, 2021
10.3389/fmicb.2021.634511 | URL

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

Targeting gut microbiota to treat hypertension: A systematic review
Palmu J, Lahti L & Niiranen T.
International Journal of Environmental Research and Public Health 18(3), 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

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

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

Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors
Sarhadi V, Mathew B, A A, Karla T, Tikkanen M, Rautelin H, Lahti L, Puolakkainen P & Knuutila S.
Gut Pathogens 13, 2021

Examining the early modern canon: The english short title catalogue and large-scale patterns of cultural production.
Tolonen M, Hill M, Ijaz A, Vaara V & Lahti L.
Data visualization in enlightenment literature and culture Palgrave Macmillan, Cham., 2021
Book chapter in: Data Visualization in Enlightenment Literature and Culture

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).

Corpus linguistics and eighteenth century collections online (ECCO)
Tolonen M, Mäkelä E, Ijaz A & Lahti L.
Research in Corpus Linguistics 9(1), 2021

Systemic cross-talk between brain, gut, and peripheral tissues in glucose homeostasis: Effects of exercise training (CROSSYS): Exercise training intervention in monozygotic twins discordant for body weight
Heiskanen M, Honkala S, Ojala R, Lautamäki R, Koskensalo K, Lietzén M, Hentilä J, Saunavaara V, Saunavaara J, Helmiö M, Löyttyniemi E, Nummenmaa L, Collado M, Malm T, Lahti L, Pietiläinen K, Kaprio J, Rinne J & Hannukainen J.
BMC Sports Science, Medicine and Rehabilitation 13, 2021

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting
Liu Y, Méric G, Havulinna A, Teo S, Åberg F, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vázquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R & Inouye M.
Cell Metabolism 2022

Maternal prenatal psychological distress and hair cortisol levels associate with infant fecal microbiota composition at 2.5 months of age
Aatsinki A, Keskitalo A, Laitinen V, Munukka E, Uusitupa H, Lahti L, Kortesluoma S, Mustonen P, Rodrigues A, Coimbra B, Huovinen P, Karlsson H & Karlsson L.
Psychoneuroendocrinology 119, 2020

Three-species lotka-volterra model with respect to caputo and caputo-fabrizio fractional operators
Khalighi M, Eftekhari L, Hosseinpour S & Lahti L.
Symmetry 13, 2020

Partial restoration of normal intestinal microbiota in morbidly obese women six months after bariatric surgery
Koffert J, Lahti L, Nylund L, Salminen S, Hannukainen J, Salminen P, Vos W & Nuutila P.
PeerJ – Life & Environment 8, 2020
Shared first authorship.

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

Laskentamallit eivät lähtökohtaisesti ole salassa pidettävää tietoa
Lahti L, Wallgren T & Kulmala M.
HS Mielipide 2020

Lähdekoodin sisältämien yksityiskohtien avoimuus on keskeistä päätöksenteon läpinäkyvyydelle.
Lahti L
HS Mielipide 2020

Tietopyyntö epidemialaskelmien lähdekoodeista
Lahti L & Toikkanen T.
Open Knowledge Finland Blog 2020

Päätös epidemialaskelmien salaamisesta vastoin valtioneuvoston avoimuuslinjausta
Lahti L
Open Knowledge Finland Blog 2020

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

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

Diet, perceived intestinal well-being, fecal microbiota and short chain fatty acids in oat-using subjects with celiac disease or gluten sensitivity.
Nylund L, Hakkola S, Lahti L, Salminen S, Kalliomäki M, Yang B & Linderborg K.
Nutrients 12, 2020
Special issue.

Association between the gut microbiota and blood pressure in a population cohort of 6953 individuals
Palmu J, Salosensaari A, Havulinna A, Cheng S, Inouye M, Jain M, Salido R, Sanders K, Brennan C, Humphrey G, Sanders J, Vartiainen E, Laatikainen T, Jousilahti P, Salomaa V, Knight R, Lahti L & Niiranen T.
Journal of the American Heart Association 2020

Eicosanoid inflammatory mediators are robustly associated with blood pressure in the general population
Palmu J & others.
Journal of American Heart Association 9, 2020

Prebiotic xylo-oligosaccharides targeting faecalibacterium prausnitzii prevent high fat diet-induced hepatic steatosis in rats
Lensu S, Pariyani R, Mäkinen E, Yang B, Saleem W, Munukka E, Lehti M, Yang B, Linden J, Tiirola M, Lahti L & Pekkala S.
Nutrients 12(11), 2020

Gut microbiota and host gene mutations in colorectal cancer patients and controls of iranian and finnish origin
Sarhadi V, Lahti L, Saberi F, Youssef O, Kokkola A, Karla T, Tikkanen M, Rautelin H, Puolakkainen P, Salehi R & Knuutila S.
Anticancer Research 40(3), 2020
10.21873/anticanres.14074 | PDF

Unsupervised hierarchical clustering identifies a metabolically challenged subgroup of hypertensive individuals
Vaura F, Salomaa V, Kantola I, Kaaja R, Lahti L & Niiranen T.
Journal of Clinical Hypertension 22(9), 2020

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

Gut microbiota composition is associated with temperament traits in infants
Aatsinki A, Lahti L, Uusitupa H, Munukka E, Anniina Keskitalo S, O’Mahony S, Pietilä S, Elo L, Eerola E, Karlsson H & Karlsson L.
Brain Behavior and Immunity 80, 2019
10.1016/j.bbi.2019.05.035 | PDF

Reconstructing intellectual networks: From the ESTC’s bibliographic metadata to historical material
Hill M, Vaara V, Säily T, Lahti L & Tolonen M.
Proc. Digital humanities in the nordic countries 2364, 2019
Best paper award.

Analytical edition detection in bibliographic metadata
Ijaz A, Roivainen H & Lahti L.
Proceedings of the digital humanities (DH2019) 2019
In press.

Analytical determination of editions from bibliographic metadata
Ijaz A, Tolonen M & Lahti L.
Proceedings of the research data in the humanities conference 2019

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

Best practices in bibliographic data science
Lahti L, Vaara V, Marjanen J & Tolonen M.
Proceedings of the research data in the humanities conference 2019

Interdisciplinary collaboration in studying newspaper materiality
Mäkelä E, Tolonen M, Marjanen J, Kanner A, Vaara V & Lahti L.
Proc. Twin talks workshop. Digital humanities in the nordic countries 2365, 2019

A national public sphere? Analyzing the language, location, and form of newspapers in finland, 1771–1917
Marjanen J, Vaara V, Kanner A, Roivainen H, Mäkelä E, Lahti L & Tolonen M.
Journal of European Periodical Studies 4(1), 2019
Special issue: Digital Approaches Towards Serial Publications
10.21825/jeps.v4i1.10483 | PDF

Microbiome data science
Shetty S & Lahti L.
Journal of Biosciences 44, 2019
10.1007/s12038-019-9930-2 | PDF

Microbiome yarns: The global phenotype-genotype survey. Episode III: Importance of microbiota diversification for microbiome function and biome health
Timmis K, Jebok F, Rohde M, Lahti L & Molinari G.
Microbial Biotechnology 2019

Scaling up bibliographic data science
Tolonen M, Marjanen J, Roivainen H & Lahti L.
Proceedings of the digital humanities in the nordics (DHN2019) 2019

The emerging paradigm of bibliographic data science
Vaara V, Ijaz A, Tiihonen I, Hengchen S, Kanner A, Säily T & Lahti L.
Proceedings of the digital humanities (DH2019) 2019
In press.

Microbial communities in a dynamic it in vitro model for the human ileum resemble the human ileal microbiota
Stolaki M, Minekus M, Venema K, Lahti L, Smid E, Kleerebezem M & Zoetendal E.
FEMS Microbiology Ecology(8), 2019
10.1093/femsec/fiz096 | PDF

A quantitative approach to book-printing in sweden and finland, 1640–1828
Tolonen M, Lahti L, Roivainen H & Marjanen J.
Historical Methods: A Journal of Quantitative and Interdisciplinary History 52 Routledge, 2019
10.1080/01615440.2018.1526657 | PDF

Gut microbiota composition in mid-pregnancy is associated with gestational weight gain but not prepregnancy body mass index
Aatsinki A, Uusitupa H, Munukka E, Pesonen H, Rintala A, Pietilä S, Lahti L, Eerola E, Karlsson L & Karlsson H.
Journal of Womens Health 2018
Epub ahead of print.
10.1089/jwh.2017.6488 | PDF

Stability estimation of autoregulated genes under michaelis-menten type kinetics
Arani B, Mahmoudi M, Lahti L, González J & Wit E.
Physical Review E 97(6) American Physical Society, 2018
10.1103/PhysRevE.97.062407 | PDF

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

Signatures of ecological processes in microbial community time series
Faust K, Bauchinger F, Laroche B, Buyl S, Lahti L, Washburne A, Gonze D & Widder S.
Microbiome 6(120), 2018
10.1186/s40168-018-0496-2 | PDF

Microbial communities as dynamical systems
Gonze D, Coyte K, Lahti L & Faust K.
Current Opinion in Microbiology 44, 2018
10.1016/j.mib.2018.07.004 | PDF

Spheres of “public” in eighteenth-century britain
Hill M, Kanner A, Marjanen J, Vaara V, Mäkelä E, Lahti L & Tolonen M.
Proceedings of the digital humanities in the nordics conference 2018

Open data science
Lahti L
Advances in intelligent data analysis XVII. Lecture notes in computer science 11191. 11191 Springer Nature, 2018
Conference proceedings.

A hierarchical ornstein-uhlenbeck model for stochastic time series analysis
Laitinen V & Lahti L.
Advances in intelligent data analysis XVII. Lecture notes in computer science 11191. Springer, 2018
Conference proceedings.

Digitaaliset ihmistieteet ja historiantutkimus
Tolonen M & Lahti L.
Menneisyyden rakentajat Gaudeamus, 2018
(in Finnish). In: Hannikainen, MO and Danielsbacka, M and Tepora, T (eds.). Menneisyyden rakentajat. Gaudeamus, Helsinki, 2018.

Stool microbiota composition differs in patients with stomach, colon, and rectal neoplasms
Youssef O, Lahti L, Kokkola A, Karla T, Tikkanen M, Ehsan H, Carpelan‑Holmström M, Koskensalo S, Böhling T, Rautelin H, Puolakkainen P, Knuutila S & Sarhadi V.
Digestive Diseases and Sciences 63(11), 2018
10.1007/s10620-018-5190-5 | PDF

Turun yliopiston avoimen tutkimuksen politiikka / open research policy

unknown University of Turku; Report, 2018
(in Finnish)

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
Buelow E, González T, Fuentes S, Steenhuijsen Piters W, Lahti L, Bayjanov J, Majoor E, Braat J, Mourik M, Oostdijk E, Willems R, Bonten M, Passel M, Smidt H & Schaik W.
Microbiome 5(1), 2017
10.1186/s40168-017-0309-z | PDF

Multi-stability and the origin of microbial community types
Gonze D, Lahti L, Raes J & Faust K.
ISME Journal 11, 2017
10.1038/ismej.2017.60 | PDF

Linking statistical and ecological theory: Hubbell’s unified neutral theory of biodiversity as a hierarchical dirichlet process
Harris K, Parsons T, Ijaz U, Lahti L, Holmes I & Quince C.
Proceedings of the IEEE 105(3), 2017
10.1109/JPROC.2015.2428213 | PDF

Retrieval and analysis of eurostat open data with the eurostat package
Lahti L, Huovari J, Kainu M & Biecek P.
The R Journal 9(1), 2017

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

Intestinal microbiome landscaping: Insight in community assemblage and implications for microbial modulation strategies
Shetty S, Hugenholtz F, Lahti L, Smidt H, Vos W & Danchin A.
FEMS Microbiology Reviews 41, 2017
10.1093/femsre/fuw045 | PDF

Printing in a periphery: A quantitative study of finnish knowledge production, 1640-1828
Tolonen M, Ilomäki N, Roivainen H & Lahti L.
Digital humanities 2016: Conference abstracts Jagiellonian University & Pedagogical University, Kraków, 2016

The open science peer review oath
Aleksic J, Alexa A, Attwood T, Hong N, Dahlö M, Davey R, Dinkel H, Förstner K, Grigorov I, Hériché J, Lahti L, MacLean D, Markie M, Molloy J, Schneider M, Scott C, Smith-Unna R & Vieira B.
F1000Research 3, 2015
AllBio: Open Science & Reproducibility Best Practice Workshop
10.12688/f1000research.5686.2 | PDF

Metagenomics meets time series analysis: Unraveling microbial community dynamics
Faust K, Lahti L, Gonze D, Vos W & Raes J.
Current Opinion in Microbiology 25, 2015
10.1016/j.mib.2015.04.004 | PDF

A quantitative study of history in the english short-title catalogue (ESTC) 1470-1800
Lahti L, Ilomäki N & Tolonen M.
LIBER Quarterly 25(2), 2015
10.18352/lq.10112 | PDF

Beyond open access - the changing culture of producing and disseminating scientific knowledge
Laine H, Lahti L, Lehto A, Ollila S & Miettinen M.
Proceedings of the 19th international academic mindtrek conference in tampere, finland, september 22-24 AcademicMindTrek’15: Proceedings of the 19th International Academic Mindtrek Conference; ACM, 2015

Fat, fiber and cancer risk in african, americans and rural africans
O’Keefe S, Li J, Lahti L, Ou J, Carbonero F, Mohammed K, Posma J, Kinross J, Wahl E, Ruder E, Vipperla K, Naidoo V, Mtshali L, Tims S, PGB Puylaert J, Krasinskas A, Benefiel A, Kaseb H, Newton K, Nicholson J, Vos W, Gaskins H & Zoetendal E.
Nature Communications 6, 2015
Top science article in Guardian on the release day.
10.1038/ncomms7342 | PDF

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database
Ritari J, Salojärvi J, Lahti L & Vos W.
BMC Genomics 16, 2015
10.1186/s12864-015-2265-y | PDF

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river
Atashgahi S, Aydin R, Dimitrov M, Sipkema D, Hamonts K, Lahti L, Maphosa F, Kruse T, Saccenti E, Dirk Springael W & Smidt H.
Scientific Reports 5(17284), 2015
10.1038/srep17284 | PDF

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging
Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J & Ola Hansson .
Skeletal Muscle 5(35), 2015
10.1186/s13395-015-0059-1 | PDF

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

Binning metagenomic contigs by coverage and composition
Alneberg J, Bjarnason B, Bruijn I, Schirmer M, Quick J, Ijaz U, Lahti L, Loman N, Andersson A & Quince C.
Nature Methods 11(1144–1146), 2014
CONCOCT algorithm
10.1038/nmeth.3103 | PDF

Systematic use of computational methods allows stratifying treatment responders in glioblastoma multiforme
Louhimo R, Aittomäki V, Faisal A, Laakso M, Chen P, Ovaska K, Valo E, Lahti L, Rogojin V, Kaski S & Hautaniemi. S.
Systems Biomedicine (special issue) 1, 2014
Critical Assessment of Massive Data Analysis (CAMDA) workshop
10.4161/sysb.28904 | PDF

Tipping elements in the human intestinal ecosystem
Lahti L, Salojärvi J, Salonen A, Scheffer M & Vos W.
Nature Communications 5, 2014
10.1038/ncomms5344 | PDF

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men
Salonen A, Lahti L, Salojärvi J, Holtrop G, Korpela K, Duncan S, Date P, Johnstone A, Lobley G, Louis P, Flint H & Vos W.
ISME Journal 8, 2014
10.1038/ismej.2014.63 | PDF

Copy number alterations and neoplasia specific mutations in MELK, PDCD1LG2, TLN1, and PAX5 at 9p in different neoplasias
Sarhadi V, Lahti L, Scheinin I, Ellonen P, Kettunen E, Serra M, Scotlandi K, Picci P & Knuutila S.
Genes, Chromosomes and Cancer 53(7), 2014

rOpenGov: Open source ecosystem for computational social sciences and digital humanities
Leo Lahti J & Kainu M.
software, 2013
ICML/MLOSS workshop (Int’l Conf. on Machine Learning - Open Source Software workshop).

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases
Lahti L, Torrente A, Elo L, Brazma A & Rung J.
Nucleic Acids Research 41(10), 2013
Implementation available through Bioconductor RPA package.
10.1093/nar/gkt229 | PDF

Associations between the human intestinal microbiota, lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data
Lahti L, Salonen A, Kekkonen R, Salojärvi J, Jalanka-Tuovinen J, Palva A, Orešič M & Vos W.
PeerJ 1, 2013
Highly accessed, featured in PeerJ journal blog and Top-10 Microbiology collection.
10.7717/peerj.32 | PDF

Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: A comparative review
Lahti L, Schäfer M, Klein H, Bicciato S & Dugas M.
Briefings in Bioinformatics 14(1), 2013
10.1093/bib/bbs005 | PDF

Targeted resequencing of 9p in acute lymphoblastic leukemia yields concordant results with array CGH and reveals novel genomic alterations
Sarhadi V, Lahti L, Scheinin I, Tyybäkinoja A, Savola S, Usvasalo A, Räty R, Elonen E, Ellonen P, Saarinen-Pihkala U & Knuutila S.
Genomics 102(3), 2013
10.1016/j.ygeno.2013.01.001 | PDF

Intestinal microbiota, individuality and health. In: Computational methods aiding early-stage drug design (dagstuhl seminar 13212)
Lahti L
Dagstuhl Reports 3(5) Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, 2013
10.4230/DagRep.3.5.78 | URL

The adult intestinal core microbiota is determined by analysis depth and health status
Salonen A, Salojärvi J, Lahti L & Vos .
Clinical Microbiology and Infection 18(Suppl. 4), 2012
10.1111/j.1469-0691.2012.03855.x | PDF

MicroRNA profiling predicts survival in anti-EGFR treated chemorefractory metastatic colorectal cancer patients with wild-type KRAS and BRAF
Mosakhani N, Lahti L, Borze I, Karjalainen-Lindsberg M, Sundstrom J, Ristamaki R, Osterlund P, Knuutila S & Virinder Kaur Sarhadi .
Cancer Genetics 205(11), 2012
10.1016/j.cancergen.2012.08.003 | PDF

MicroRNA profiling in pediatric acute lymphoblastic leukemia: Novel prognostic tools
Mosakhani N, Sarhadi V, Usvasalo A, Karjalainen-Lindsberg M, Lahti L, Tuononen K, Saarinen-Pihkala U & Knuutila S.
Leukemia & Lymphoma 53(12), 2012
10.3109/10428194.2012.685731 | PDF

Homozygous deletions of cadherin genes in chondrosarcoma – an array CGH study
Niini T, Scheinin I, Lahti L, Savola S, Mertens F, Hollmén J, Böhling T, Kivioja A, Nord K & Knuutila S.
Cancer Genetics 205(11), 2012

MicroRNA microarrays on archive bone marrow core biopsies of leukemias - method validation
Borze I, Guled M, Musse S, Raunio A, Elonen E, Saarinen-Pihkala U, Karjalainen-Lindsberg M, Lahti L & Knuutila. S.
Leukemia Research 35, 2011

Biomarker discovery via dependency analysis of multi-view functional genomics data
Faisal A, Louhimo R, Lahti L, Hautaniemi S & Kaski S.
NIPS 2011 workshop from statistical genetics to predictive models in personalized medicine 2011

Intestinal microbiota in healthy adults: Temporal analysis reveals individual and common core and relation to intestinal symptoms
Jalanka-Tuovinen J, Salonen A, Nikkilä J, Immonen O, Kekkonen R, Lahti L, Palva A & Vos W.
PLoS One 6(7), 2011

Intcomp: A benchmarking pipeline for integrative cancer gene detection algorithms
Lahti L, Schäfer M, Klein H, Bicciato S & Dugas M.
software, 2011

Probabilistic dependency models for data integration in functional genomics
Lahti L & Kaski S.
2011 Machine Learning for Systems Biology workshop, ISMB, Vienna, Austria

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays
Lahti L, Elo L, Aittokallio T & Kaski S.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(1) IEEE Computer Society, 2011
10.1109/TCBB.2009.38 | PDF

Array comparative genomic hybridization reveals frequent alterations of G1/s checkpoint genes in undifferentiated pleomorphic sarcoma of bone
Niini T, Lahti L, Michelacci F, Ninomiya S, Hattinger C, Guled M, Böhling T, Picci P, Serra M & Knuutila S.
Genes, Chromosomes and Cancer 50(5), 2011
10.1002/gcc.20851 | PDF

Integrative analysis of microRNA, mRNA and aCGH data reveals asbestos- and histology-related changes in lung cancer
Nymark P, Guled M, Borze I, Faisal A, Lahti L, Salmenkivi K, Kettunen E, Anttila S & Knuutila S.
Genes, Chromosomes and Cancer 50(8), 2011
10.1002/gcc.20880 | PDF

Global modeling of transcriptional responses in interaction networks
Lahti L, Knuuttila J & Kaski S.
Bioinformatics 26, 2010
R/Matlab implementations available at
10.1093/bioinformatics/btq500 | PDF

Dependency modeling toolkit
Lahti L, Tripathi A & Huovilainen O.
software; ICML workshop, 2010
CRAN: dmt

NetResponse (functional network analysis)
Lahti L, Gusmao A & Huovilainen O.
software, 2010
R/Bioconductor: netresponse

Pairwise integration of functional genomics data
Huovilainen O & Lahti L.
software, 2010
R/BioConductor: pint

Probabilistic analysis of the human transcriptome with side information
Lahti L
Aalto University School of Science and Technology, Faculty of Information and Natural Sciences, Department of Information and Computer Science, 2010
LaTeX sources and the pdf version are openly available:; Press release:

Unique microRNA profile in dupuytren’s contracture supports deregulation of beta-catenin pathway
Mosakhani N, Guled M, Lahti L, Borze I, Forsman M, Ryhänen J & Knuutila S.
Modern Pathology 23, 2010
International Dupuytren Award for best research paper in 2011
10.1038/modpathol.2010.146 | PDF

CDKN2A, NF2 and JUN are dysregulated among other genes by miRNAs in malignant mesothelioma - a miRNA microarray analysis
Guled M, Lahti L, Lindholm P, Salmenkivi K, Bagwan I, Nicholson A & Knuutila S.
Genes, Chromosomes and Cancer 48(7), 2009
10.1002/gcc.20669 | PDF

Concerning blackburn’s quasi-realism in securing moral discussion
Lahti L
B.Sc. thesis. University of Helsinki, Faculty of Political Sciences, 2009
(In Finnish)

Dependency detection with similarity constraints
Lahti L, Myllykangas S, Knuutila S & Kaski S.
Proc. MLSP’09 IEEE international workshop on machine learning for signal processing XIX software, 2009
R/Bioconductor: pint

RPA: Probe reliability and differential gene expression analysis
Lahti L
software, 2009
R/Bioconductor: RPA
10.18129/B9.BIOC.RPA | URL

A brief overview on the BioPAX and SBML standards
Lahti L
arXiv, 2007
(in Finnish)

Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines
Nymark P, Lindholm P, Korpela M, Lahti L, Ruosaari S, Kaski S, Hollmen J, Anttila S, Kinnula V & Knuutila S.
BMC Genomics 8(62), 2007

Integrating probe-level expression changes across generations of affymetrix arrays
Elo L, Lahti L, Skottman H, Kyläniemi M, Lahesmaa R & Aittokallio T.
Nucleic Acids Research 33(22), 2005
10.1093/nar/gni193 | PDF

Associative clustering for exploring dependencies between functional genomics data sets
Kaski S, Nikkilä J, Sinkkonen J, Lahti L, Knuuttila J & Roos C.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2(3), 2005
Special Issue on Machine Learning for Bioinformatics – Part 2
10.1109/TCBB.2005.32 | PDF

Associative clustering (AC): Technical details
Sinkkonen J, Kaski S, Nikkilä J & Lahti L.
Helsinki University of Technology, 2005
Publications in Computer and Information Science

Associative clustering
Sinkkonen J, Nikkilä J, Lahti L & Kaski S.
Proceedings of the ECML’04, 15th european conference on machine learning Springer, 2004

Comparative functional genome analysis using associative clustering
Lahti L
Helsinki University of Technology, 2003
(in Finnish)

Associative clustering by maximizing a Bayes factor
Sinkkonen J, Nikkilä J, Lahti L & Kaski S.
Helsinki University of Technology and Laboratory of Computer and Information Science, 2003

Itsesimilaaristen joukkojen hausdorffin dimension määrittäminen
Lahti L
2002 Special assignment in Mathematics (in Finnish)

Julian joukko iteraatioden valuma-altaan reunana
Lahti L
2001 Special assignment in Mathematics (in Finnish)

Opencomp blog
Lahti L

Louhos blog
Lahti L, Lehtomäki J, Parkkinen J & others.
Open government data analytics blog (in Finnish)

rOpenGov blog
Lahti L, Lehtomäki J, Kainu M, Parkkinen J & others.
Open government data analytics blog