Research

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.

Microbiome data science: selected examples

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
10.1038/s41467-021-22962-y

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
10.3389/fmicb.2021.635781

Microbiome data science in the SummarizedExperiment universe
Lahti L, Ernst F, Shetty S & others.
F1000Research 10(748), 2021
(slides); version 1; not peer reviewed
10.7490/f1000research.1118712.1

Modeling spatial patterns in host-associated microbial communities
Ruuskanen M, Sommeria-Klein G, Havulinna A, Niiranen T & Lahti L.
Environmental Microbiology 23(5), 2021
10.1111/1462-2920.15462

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

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

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

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

More microbiome data science and life science applications

Examining the healthy human microbiome concept
Joos R, Boucher K, Lavelle A, Arumugam M, Blaser M, Claesson M, Clarke G, Cotter P, Sordi L, Dominguez-Bello M, Dutilh B, Ehrlich S, Ghosh T, Hill C, Junot C, Lahti L, Lawley T, Licht T, Maguin E, Makhalanyane T, Marchesi J, Matthijnssens J, Raes J, Ravel J, Salonen A, Scanlan P, Shkoporov A, Stanton C, Thiele I, Tolstoy I, Walter J, Yang B, Yutin N, Zhernakova A, Zwart H, , Doré J & Ross R.
Nature Reviews Microbiology 2024
10.1038/s41579-024-01107-0

Regular exercise training induces more changes on intestinal glucose uptake from blood and microbiota composition in leaner compared to heavier individuals in monozygotic twins discordant for BMI
Lietzén M, Guzzardi M, Ojala R, Hentilä J, Heiskanen M, Honkala S, Lautamäki R, Löyttyniemi E, Kirjavainen A, Rajander J, Malm T, Lahti L, Rinne J, Pietiläinen K, Iozzo P & Hannukainen J.
Nutrients 16, 2024
10.3390/nu16203554

Learning and teaching biological data science in the bioconductor community
Drnevich J, Tan F, Almeida-Silva F, Castelo R, Culhane A, Davis S, Doyle M, Holmes S, Lahti L, Mahmoud A, Nishida K, Ramos M, Rue-Albrecht K, Shih D, Gatto L & Soneson C.
arXiv 2024
10.48550/arXiv.2410.01351

Effects of obesity and exercise on hepatic and pancreatic lipid content and glucose metabolism: PET-studies in twins discordant for BMI
Lietzén M, Mari A, Ojala R, Hentilä J, Koskensalo K, Lautamäki R, Löyttyniemi E, Parkkola R, Saunavaara V, Kirjavainen A, Rajander J, Malm T, Lahti L, Rinne J, Pietiläinen K, Iozzo P & Hannukainen J.
Biomolecules 14(9), 2024
10.3390/biom14091070

A cohort study in family triads: Impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life
Jokela R, Pärnänen K, Ponsero A, Lahti L, Kolho K, Vos W & Salonen A.
Gut Microbes 16(1), 2024
10.1080/19490976.2024.2383746

Associations between gut microbiota and incident fractures in the FINRISK cohort
Grahnemo L, Kambur O, Lahti L, Jousilahti P, Niiranen T, Knight R, Salomaa V, Havulinna A & Ohlsson C.
npj Biofilms and Microbiomes 10(69), 2024
10.1038/s41522-024-00530-8

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke
Manzoor M, Leskelä J, Pietiäinen M, Martinez-Majander N, Ylikotila P, Könönen E, Niiranen T, Lahti L, Sinisalo J, Putaala J, Pussinen P & Paju S.
ISME Communications 4(1), 2024
10.1093/ismeco/ycae088

Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: Results from two observational, population-based microbiome studies
Kullberg R, Wikki I, Haak B, Kauko A, Galenkamp H, Peters-Sengers H, Butler J, Havulinna A, Palmu J, McDonald D, Benchraka C, Abdel-Aziz M, Prins M, Maitland van der Zee A, Born B, Jousilahti P, Vos W, Salomaa V, Knight R, Lahti L, Nieuwdorp M, Niiranen T & Wiersinga W.
The Lancet Microbe 2024
https://doi.org/10.1016/S2666-5247(24)00079-X

Biochemical analyses can complement sequencing-based ARG load monitoring: A case study in indian hospital sewage networks
Bhanushali S, Parnanen K, Mongad D, Dhotre D & Lahti L.
medRxiv 2024
10.1101/2024.05.31.24308262

A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society
Timmis K, Hallsworth J, McGenity T, Armstrong R, Colom M, Karahan Z, Chavarría M, Bernal P, Boyd E, Ramos J, Kaltenpoth M, Pruzzo C, Clarke G, López-Garcia P, Yakimov M, Perlmutter J, Greening C, Eloe-Fadrosh E, Verstraete W, Nunes O, Kotsyurbenko O, Nikel P, Scavone P, Lavigne M, Roux F, Timmis J, Parro V, Michán C, García J, Casadevall A, Payne S, Frey J, Koren O, Prosser J, Lahti L, Lal R, Anand S, Sood U, Offre P, Bryce C, Mswaka A, Jores J, Kaçar B, Blank L, Maaßen N, Pope P, Banciu H, Armitage J, Lee S, Wang F, Makhalanyane T, Gilbert J, Wood T, Vasiljevic B, Soberón M, Udaondo Z, Rojo F, Tamang J, Giraud T, Ropars J, Ezeji T, Müller V, Danbara H, Averhoff B, Sessitsch A, Partida-Martínez L, Huang W, Molin S, Junier P, Amils R, Wu X, Ron E, Erten H, Martinis E, Rapoport A, Öpik M, Pokatong W, Stairs C, Amoozegar M & Serna J.
Microbial Biotechnology 17(5), 2024
10.1111/1751-7915.14456

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development
Tito R, Verbandt S, Vazquez M, Lahti L, Verspecht C, Lloréns-Rico V, Vieira-Silva S, Arts J, Falony G, Dekker E, Reumers J, Tejpar S & Raes J.
Nature Medicine 2024
10.1038/s41591-024-02963-2

Fecal microbiota profiles of growing pigs and their relation to growth performance
König E, Beasley S, Heponiemi P, Kivinen S, Räkköläinen J, Salminen S, Collado M, Borman T, Lahti L, Piirainen V, Valros A & Heinonen M.
PLoS One 19, 2024
10.1371/journal.pone.0302724

Elementary methods provide more replicable results in microbial differential abundance analysis
Pelto J, Auranen K, Kujala J & Lahti L.
arXiv 2024
10.48550/arXiv.2404.02691 | URL

Shotgun metagenomic analysis of the oral microbiome in gingivitis: A nested case-control study
Manzoora M, Leskelä J, Pietiäinen M, Martinez-Majander N, Könönen E, Niiranen T, Lahti L, Sinisalo J, Putaala J, Pussinen P & Paju S.
Journal of Oral Microbiology (ZJOM) 16, 2024
10.1080/20002297.2024.2330867

Integration of polygenic and gut metagenomic risk prediction for common diseases
Liu Y, Ritchie S, Teo S, Ruuskanen M, Kambur O, Zhu Q, Sanders J, Vázquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna A, Knight R, Méric G & Inouye M.
Nature Aging 2024
10.1038/s43587-024-00590-7

Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours
Mishra S, Tejesvi M, Hekkala J, Turunen J, Kandikanti N, Kaisanlahti A, Suokas M, Leppä S, Vihinen P, Kuitunen H, Sunela K, Koivunen J, Jukkola A, Kalashnikov I, Auvinen P, Kääriäinen O, Medina T, Medina O, Saarnio J, Meriläinen S, Rautio T, Aro R, Häivälä R, Suojanen J, Laine M, Erawijattari P, Lahti L, Karihtala P, Ruuska T & Reunanen J.
Journal of Advanced Research 2024
Available online 7 March 2024
10.1016/j.jare.2024.03.003

Association of long-term habitual dietary fiber intake since infancy with gut microbiota composition in young adulthood
Heiskanen M, Aatsinki A, Hakonen P, Kartiosuo N, Munukka E, Lahti L, Keskitalo A, Huovinen P, Niinikoski H, Viikari J, Rönnemaa T, Lagström H, Jula A, Raitakari O, Rovio S & Pahkala K.
The Journal of Nutrition 154, 2024
Available online 12 January 2024
10.1016/j.tjnut.2024.01.008

Bone marrow metabolism is affected by body weight and response to exercise training varies according to anatomical location
Ojala R, Hentilä J, Lietzén M, Arponen M, Heiskanen M, Honkala S, Virtanen H, Koskensalo K, Lautamäki R, Löyttyniemi E, Parkkola R, Heinonen O, Malm T, Lahti L, Rinne J, Eskola O, Rajander J, Pietiläinen K, Kaprio J, Ivaska K & Hannukainen J.
Diabetes, Obesity and Metabolism 16, 2024
First published 11 October 2023
10.1111/dom.15311

Daily skin-to-skin contact alters microbiota development in healthy full-term infants
Eckermann H, Meijer J, Cooijmans K, Lahti L & Weerth C.
Gut Microbes 16(2295403, 1), 2024
10.1080/19490976.2023.2295403

Fewer culturable Lactobacillaceae species identified in faecal samples of pigs performing manipulative behaviour
König E, Heponiemi P, Kivinen S, Räkköläinen J, Beasley S, Borman T, Collado M, Hukkinen V, Junnila J, Lahti L, Norring M, Piirainen V, Salminen S, Heinonen M & Valros A.
Scientific Reports 14(132), 2024
10.1038/s41598-023-50791-0

Infant gut microbiota and negative and fear reactivity
Huovinen V, Aatsinki A, Kataja E, Munukka E, Keskitalo A, Lamichhane S, Raunioniemi P, Bridgett D, Lahti L, O’Mahony S, Dickens A, Korja R, Karlsson H, Nolvi S & Karlsson L.
Development and Psychopathology 2023
10.1017/S0954579423001396

A toolbox of machine learning software to support microbiome analysis
Marcos-Zambrano L, López-Molina V, Bakir-Gungor B, Frohme M, Karaduzovic-Hadziabdic K, Klammsteiner T, Ibrahimi E, Lahti L, Loncar-Turukalo T, Dhamo X, Simeon A, Nechyporenko A, Pio G, Przymus P, Sampri A, Trajkovik V, Lacruz-Pleguezuelos B, Aasmets O, Araujo R, Anagnostopoulos I, Aydemir Ö, Berland M, Calle M, Ceci M, Duman H, Gündoğdu A, Havulinna A, Bra K, Kalluci E, Karav S, Lode D, Lopes M, May P, Nap B, Nedyalkova M, Paciência I, Pasic L, Pujolassos M, Shigdel R, Susín A, Thiele I, Truică C, Wilmes P, Yilmaz E, Yousef M, Claesson M, Truu J & Santa Pau E.
Frontiers in Microbiology 14, 2023
10.3389/fmicb.2023.1250806 | URL

Role of Gut Microbiota in Statin-Associated New-Onset Diabetes—a Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort
Koponen K, Kambur O, Joseph B, Ruuskanen M, Jousilahti P, Salido R, Brennan C, Jain M, Meric G, Inouye M, Lahti L, Niiranen T, Havulinna A, Knight R & Salomaa V.
Arteriosclerosis, Thrombosis, and Vascular Biology 2023
10.1161/ATVBAHA.123.319458

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
10.1098/rsos.230052

Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles
Kaisanlahti A, Turunen J, Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi M, Zhyvolozhnyi A, Sarfraz S, Kumpula S, Hekkala J, Salmi S, Will O, Korvala J, Paalanne N, Erawijantari P, Suokas M, Medina T, Vainio S, Medina O, Lahti L, Tapiainen T & Reunanen J.
BMC Microbiome 249, 2023
10.1186/s40168-023-01694-9 | URL

Microbiome-based risk prediction in incident heart failure: A community challenge
Erawijantari P, Kartal E, Liñares-Blanco J, Laajala T, Feldman L, Challenge T, Communities M, Carmona-Saez P, Shigdel R, Marcus , Claesson J, Bertelsen R, Gomez-Cabrero D, Minot S, Albrecht J, Chung V, Inouye M, Jousilahti P, Schultz J, Friederich H, Knight R, Salomaa V, Niiranen T, Havulinna A, Saez-Rodriguez J, Levinson R & Lahti L.
medRxiv preprint 2023
10.1101/2023.10.12.23296829 | URL

Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain, and placenta
Husso A, Pessa-Morikawa T, Mikael V, Kärkkäinen O, Kwon H, Lahti L, Iivanainen A, Hanhineva K & Niku M.
BMC Biology(207), 2023
10.1186/s12915-023-01709-9

Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action
D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes M, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Carrillo-de Santa Pau T, Marcos-Zambrano L, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol E, Truică C, Shigdel R, Hasić-Telalović J, Bongcam-Rudloff E, Przymus P, Jordamović N, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna A, Jansen C & Claesson R.
Frontiers in Microbiology 14, 2023
10.3389/fmicb.2023.1257002

Greengenes2 unifies microbial data in a single reference tree
McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton J, Nicolaou G, Parks D, Karst S, Albertsen M, Hugenholtz P, DeSantis T, Song S, Bartko A, Havulinna A, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S & Knight R.
Nature Biotechnology 2023
10.1038/s41587-023-01845-1

miaSim: an R/Bioconductor package to easily simulate microbial community dynamics
Gao Y, Şimşek Y, Gheysen E, Borman T, Li Y, Lahti L, Faust K & Garza D.
Methods in Ecology and Evolution 14, 2023
10.1111/2041-210X.14129

Infant left amygdala volume is negatively associated with fecal microbiota diversity
Aatsinki A, Tuulari J, Munukka E, Lahti L, Keskitalo A, Kailanto H, Nolvi S, Scheinin N, Saunavaara J, Parkkola R, Lewis J, Hashempour N, Shulist S, Karlsson L & Karlsson H.
bioRxiv preprint 2023
10.1101/2023.04.23.537273

Gut microbiome and atrial fibrillation-results from a large population-based study
Palmu J, Börschel C, Ortega-Alonso A, Lajos M, Inouye M, Jousilahti P, Salido R, Sanders K, Brennan C, Humphrey G, Sanders J, Gutmann F, Linz D, Salomaa V, Havulinna A, Forslund S, Knight R, Lahti L, Niiranen T & Schnabel R.
eBioMedicine 2023
10.1016/j.ebiom.2023.104583

Gut microbiota composition and function in pregnancy as determinants of prediabetes at two years’ postpartum
Houttu N, Benchraka C, Lotankar M, Muhli E, Niinikoski H, Lahti L & Laitinen K.
Acta Diabetologica 2023
10.1007/s00592-023-02064-5

The preterm gut microbiota and administration routes of different probiotics: A randomized controlled trial
Rahkola E, Rautava S, Hiltunen H, Ross C, Lahti L & Isolauri E.
Pediatric research 2023
10.1038/s41390-023-02560-y

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.
Journal of Allergy and Clinical Immunology 151, 2023
10.1016/j.jaci.2022.12.810

Aberrations in the early pregnancy serum metabolic profile in women with prediabetes at two years postpartum
Muhli E, Benchraka C, Lotankar M, Houttu N, Niinikoski H, Lahti L & Laitinen K.
Metabolomics 19(29), 2023
10.1007/s11306-023-01994-z

Dealing with dimensionality: the application of machine learning to multi-omics data
Feldner-Busztin D, Firbas Nisantzis P, Edmunds S, Boza G, Racimo F, Gopalakrishnan S, Limborg M, Lahti L & Polavieja G.
Bioinformatics 39(2), 2023
btad021
10.1093/bioinformatics/btad021 | URL

Multi-trait genetic analysis reveals clinically interpretable hypertension subtypes
Vaura F, Kim H, Udler M, , Salomaa V, Lahti L & Niiranen T.
Circulation: Genomic and Precision Medicine 15(4), 2022
10.1161/CIRCGEN.121.003583

Comprehensive biomarker profiling of hypertension in 36 985 finnish individuals
Palmu J, Tikkanen E, Havulinna A, Vartiainen E, Lundqvist A, Ruuskanen M, Perola M, Ala-Korpela M, Jousilahti P, Würtz P, Salomaa V, Lahti L & Niiranen T.
Journal of Hypertension 40(3), 2022
10.1097/HJH.0000000000003051

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

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
10.3390/nu14132667

Towards standardized and reproducible research in skin microbiomes
Ruuskanen M, Vats D, Potbhare R, RaviKumar A, Munukka E, Ashma R & Lahti L.
Environmental Microbiology 24(9), 2022
10.1111/1462-2920.15945

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
10.7717/peerj.13075

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
10.1002/dev.22226

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 7, 2022
10.1128/msystems.00167-22

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 10, 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 54(2), 2022
10.1038/s41588-021-00991-z

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 45(4), 2022
10.2337/dc21-2358

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
10.1101/gr.275777.121

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
10.1016/j.ebiom.2021.103655

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
10.3390/ijerph18084049

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.
10.1080/10253890.2021.1895110

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

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
10.3390/ijerph18031248

Modeling spatial patterns in host-associated microbial communities
Ruuskanen M, Sommeria-Klein G, Havulinna A, Niiranen T & Lahti L.
Environmental Microbiology 23(5), 2021
10.1111/1462-2920.15462

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
10.1080/19490976.2021.1888673

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
10.1186/s13099-021-00403-x

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
10.1186/s13102-021-00241-z

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 34, 2022
10.1016/j.cmet.2022.03.002

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
10.1016/j.psyneuen.2020.104754

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.
10.7717/peerj.10442

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.
10.3390/nu12092570

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
10.1161/JAHA.120.016641

Eicosanoid inflammatory mediators are robustly associated with blood pressure in the general population
Palmu J & others.
Journal of American Heart Association 9, 2020
10.1161/JAHA.120.017598

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
10.3390/nu12113225

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
10.1111/jch.13984

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

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

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

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

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

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

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

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
review
10.1093/femsre/fuw045 | 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

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

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
10.1002/gcc.22168

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
10.1016/j.cancergen.2012.09.007

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
10.1016/j.leukres.2010.08.005

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
PDF

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
PDF

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

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

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 http://netpro.r-forge.r-project.org/
10.1093/bioinformatics/btq500 | PDF

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

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)
URL

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
10.1186/1471-2164-8-62

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 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
PDF