lahti.bib

@Article{Hekkala2026,
  title     = {Gut Microbiota-Derived Extracellular Vesicles in Patients With Obesity Undergoing Gastric Bypass Surgery},
  author    = {Hekkala, Jenni and Kaisanlahti, Anna and Tejesvi, Mysore V. and Turunen, Jenni and Virtanen, Nikke and Karikka, Sonja and Erawijantari, Pande Putu and Samoylenko, Anatoliy and Bart, Genevieve and Vainio, Seppo and Lahti, Leo and Hukkanen, Janne and Ruuska-Loewald, Terhi and Koivukangas, Vesa and Reunanen, Justus},
  year      = {2026},
  journal   = {Molecular Microbiology},
  doi       = {10.1111/mmi.70064},
  keywords  = {bioscience}
}

@Article{Kuukkanen2026,
  title     = {Application of mass spectrometry-based metabolomics and machine learning in the diagnostics of Lyme neuroborreliosis},
  author    = {Kuukkanen, Ilari and Muluh, Geraldson and Klisura, Đorđe and Kortela, Elisa and Pietikäinen, Annukka and Lahti, Leo and Hytönen, Jukka and Karonen, Maarit},
  year      = {2026},
  journal   = {{ACS Omega}},
  note      =  {In press.},
  keywords  = {bioscience}
}

@Article{pelto2026,
  title     = {A Bayesian approach to differential prevalence analysis with applications in microbiome studies},
  author    = {Juho Pelto and Kari Auranen and Janne V. Kujala and Leo Lahti},
  year      = {2026},
  journal   = {{arXiv}},
  pubstate  =	{preprint},
  doi       = {10.48550/arXiv.2602.05938},
  keywords  = {bioscience}
}

@Article{Han2026,
  title     = {Uncomplicated and complicated acute appendicitis induce different cytokine patterns},
  author    = {Han, Tatu and Borman, Tuomas and Vanhatalo, Sanja and Lahti, Leo and Löyttyniemi, Eliisa and Hurme, Saija and Munukka, Eveliina and Kallonen, Teemu and Hakanen, Antti and Hollmén, Maija and Salminen, Paulina},
  year      = {2026},
  month     = {02},
  journal   = {{APMIS}},
  volume    = {134},
  number    = {2},
  pages     = {e70168},
  doi       = {10.1111/apm.70168},
  keywords  = {bioscience}
}

@Article{Lahtinen2025,
  title     = {Robust Modelling of Ordinal Survey Data Using Probabilistic Programming},
  author    = {Aleksi Lahtinen and James Rhys Edwards and Marc Calmbach and Isabella Tautscher and Leo Lahti},
  year      = {2025},
  journal   = {Anthology of Computers and the Humanities},
  volume    = {3},
  pages     = {608--625},
  doi       = {10.63744/eCwMjQ976nWf},
  keywords  = {datascience}
}

@Article{Houttu2025b,
  author    = {Noora Houttu and Kati Mokkala and Himmi Lindgren and Mrunalini Lotankar and Chouaib Benchraka and Katariina Pärnänen and Lotta Saros and Ella Muhli and Tero Vahlberg and Leo Lahti and Kirsi Laitinen},
  title     = {The Relationship Between Gut Microbiota During Pregnancy and the Level of Postpartum Adiposity},
  journal   = {{MicrobiologyOpen}},
  year      = {2025},
  month     = {12},
  volume    = {14},
  number    = {6},
  pages     = {e70128},
  doi       = {10.1002/mbo3.70128},
  issn      = {2045-8827},
  keywords  = {bioscience}
}

@Article{Borman2025HR,
  author    = {Tuomas Borman and Artur Sannikov and Robert D. Finn  and Morten Tønsberg Limborg and Alexander B. Rogers and Varsha Kale and Kati Hanhineva and Leo Lahti},
  title     = {{HoloFoodR}: a statistical programming framework for holo-omics data integration workflows},
  journal   = {Bioinformatics},
  year      = {2025},
  month     = {11},
  volume    = {41},
  number    = {11},
  doi       = {10.1093/bioinformatics/btaf605},
  pages     = {btaf605},
  issn      = {1367-4811},
  keywords  = {bioscience}
}

@Article{Borman2025OMA,
  title   = {Orchestrating Microbiome Analysis with Bioconductor},
  author  = {Tuomas Borman and Giulio Benedetti and Geraldson Muluh and Aura Raulo and Benjamin Valderrama and Artur Sannikov and Stefanie Peschel and Yihan Liu and Rasmus Hindström and OMA OMA_consortium and Katariina Pärnänen and Christian L. Müller and Aki S. Havulinna and Sudarshan Shetty and Marcel Ramos and Domenick J. Braccia and Héctor Corrada Bravo and Felix M. Ernst and Levi Waldron and Thomaz F. S. Bastiaanssen and Himel Mallick and Leo Lahti},
  journal = {{bioRxiv}},
  pubstate =	 {preprint},
  year    = {2025},
  doi     = {10.1101/2025.10.29.685036},
  keywords  = {bioscience}
}

@Article{Manzoor2025,
  author    = {Muhammed Manzoor and Jukka Putaala and Svetislav Zaric and Jaakko Leskela and Anbo Dong and Eija Könönen and Leo Lahti and Susanna Paju and Pirkko Pussinen},
  title     = {Oral Microbial Determinants of Saliva and Serum Lipopolysaccharide Activity},
  journal   = {Journal of Dental Research},
  year      = {2025},
  month     = {10},
  volume    = {1},
  doi       = {10.1177/00220345251370995},
  issn      = {0022-0345},
  keywords  = {bioscience}
}

@Article{Sarkka2025,
  author    = {Mikko Särkkä and Sami Myöhänen and Kaloyan Marinov and Inka Saarinen and Leo Lahti and Vittorio Fortino and Jussi Paananen},
  title     =	{Comparison of missing data handling methods for variant pathogenicity predictors},
  journal   =	{{NAR} Genomics and Bioinformatics},
  year      = {2025},
  month     = {10},
  volume    = {7},
  number    = {4},
  pages     = {lqaf133},
  doi       = {10.1093/nargab/lqaf133},
  issn      = {2631-9268},
  keywords  = {bioscience}
}

@Article{Mostafa2025,
  author    = {Ali Mostafa and Akewak Jeba and Leo Lahti and Eleanor Coffey},
  title     =	{LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Analysis of Proteomics Data},
  journal   =	{Bioinformatics},
  year      = {2025},
  month     = {10},
  pages     = {btaf570},
  doi       = {10.1093/bioinformatics/btaf570},
  issn      = {1367-4811},
  keywords  = {bioscience}
}

@Article{Sherwani2025,
  author    = {Moiz Khan Sherwani and Matti O. Ruuskanen and Dylan Feldner-Busztin and Panos Nisantzis Firbas and Gergely Boza and Ágnes Móréh and Tuomas Borman and Pande Putu Erawijantari and István Scheuring and Shyam Gopalakrishnan and Leo Lahti},
  title     = {Multi-omics time-series analysis in microbiome research: a systematic review},
  journal   = {Briefings in Bioinformatics},
  year      = {2025},
  month     = {10},
  volume    = {26},
  number    = {5},
  pages     = {bbaf502},
  doi       = {10.1093/bib/bbaf502},
  keywords  = {bioscience}
}

@Article{Houttu2025,
  author    = {Veera Houttu and Dattatray Mongad and Noora Houttu and Lotta Saros and Chunpeng Zhang and Jenni Viitaharju and Tero Vahlberg and Leo Lahti and Kirsi Laitinen},
  title     = {The impact of maternal supplementation of fish oil and/or probiotics during pregnancy on the serum metabolomic profile from infancy to childhood: secondary analysis of a randomized placebo-controlled trial},
  journal   = {Current Developments in Nutrition},
  year      = {2025},
  month     = {10},
  volume    = {9},
  number    = {10},
  pages     = {107553},
  doi       = {10.1016/j.cdnut.2025.107553},
  issn      = {2475-2991},
  keywords  = {bioscience}
}

@Article{Aatsinki2025,
  author    = {Anna-Katariina Aatsinki and Santosh Lamichhane and Heidi Isokääntä and Partho Sen and Matilda Kråkström and Marina Amaral Alves and Anniina Keskitalo and Eveliina Munukka and Hasse Karlsson and Laura Perasto and Minna Lukkarinen and Matej Oresic and Henna-Maria Kailanto and Linnea Karlsson and Leo Lahti and Alex M. Dickens},
  title     = {Dynamics of Gut Metabolome and Microbiota Maturation during Early Life},
  journal   = {iScience},
  note      =  {In press.},
  year      = {2025},
  month     = {09},
  pages     = {113596},
  doi       = {10.1016/j.isci.2025.113596},
  issn      = {2589-0042},
  keywords  = {bioscience}
}

@Article{Seitz2025,
  author    = {Timo Seitz and Jenni Viitaharju and Chouaib Benchraka and Johannes Merilahti and Marko Kalliomäki and Lauri Polari and Diana Toivola and Leo Lahti and Otto Kauko and Kirsi Laitinen},
  title     = {Breast milk proteome: Changes in the different stages of lactation and impacts of gestational diabetes mellitus and body mass index},
  journal   = {Molecular Nutrition \& Food Research},
  year      = {2025},
  month     = {09},
  pages     = {e70225},
  doi       = {10.1002/mnfr.70225},
  issn      = {1613-4133},
  keywords  = {bioscience}
}

@Article{Hentila2025,
  author    = {Jaakko Hentilä and Jouni Tuisku and Ronja Ojala and Lihua Sun and Martin Lietzén and Heidi Virtanen and Riikka Lautamäki and Kalle Koskensalo and Lauri Nummenmaa and Eliisa Löyttyniemi and Semi Helin and Kirsi Pietiläinen and Jaakko Kaprio and Leo Lahti and Tarja Malm and Juha Rinne and Jarna Hannukainen},
  title     = {Obesity is associated with increased brain glucose uptake and activity but not neuroinflammation ({TSPO} availability) in monozygotic twin pairs discordant for {BMI} – exercise training reverses increased brain activity},
  journal   = {Diabetes, Obesity and Metabolism},
  year      = {2025},
  month     = {09},
  volume    = {27},
  number    = {12},
  pages     = {7097--7109},
  doi       = {10.1111/dom.70109},
  issn      = {1462-8902},
  keywords  = {bioscience}
}

@Article{Diab2025,
  author    = {Hassan Diab and Ville Langén and Li-Fang Yeo and Veikko Salomaa and Aki Havulinna and Leo Lahti and Katariina Pärnänen and Rob Knight and Sirpa Jalkanen and Marko Salmi and Teemu Niiranen and Joonatan Palmu},
  title     = {Associations between gut microbiome and circulating cytokines: a cross-sectional analysis in the FINRISK 2002 population cohort},
  journal   = {Gut Pathogens},
  year      = {2025},
  volume    = {17},
  number    = {1},
  pages     = {66},
  doi       = {10.1186/s13099-025-00742-z},
  issn      = {1757-4749},
  keywords  = {bioscience}

}

@Article{Myers2025,
  author  = {Tyler Myers and Se Jin Song, Yang Chen and Britta De Pessemier and Lora Khatib and Daniel McDonald and Shi Huang and Richard Gallo and Chris Callewaert and Aki S. Havulinna and Leo Lahti and Guus Roeselers and Manolo Laiola and Sudarshan A. Shetty and Scott T. Kelley and Rob Knight and Andrew Bartko},
  title   = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis},
  journal = {Communications Biology},
  year    = {2025},
  month   = {08},
  volume  = {8},
  number  = {1},
  pages   = {1159},
  doi     = {10.1038/s42003-025-08590-y},
  issn    = {2399-3642},
  keywords  = {bioscience}

}

@Article{Duhr2025,
  author    = {Hendrik Dühr and Katariina Pärnänen and Nina Kucháriková and Paulina Werner and Göran Pershagen and Leo Lahti and Harri Alenius and Anna Bergström and Matti O. Ruuskanen and Nanna Fyhrquist},
  title     = {Lifestyle associates with unique resistome and microbiome signatures in children},
  journal   = {{medRxiv}},
  pubstate =	 {In press.},
  year      = {2025},
  pages     = {2025.06.25.25330258},
  doi       = {10.1101/2025.06.25.25330258},
  keywords  = {bioscience}
}

@Article{Parnanen2025,
  author    = {Katariina Pärnänen and Matti O. Ruuskanen and Guilhem Sommeria-Klein and Ville Laitinen and Pyry Kantanen and Guillaume Méric and Camila Gazolla Volpiano and Michael Inouye and Rob Knight and Veikko Salomaa and Aki S. Havulinna and Teemu Niiranen and Leo Lahti},
  title     = {Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort},
  journal   = {Nature Communications},
  year      = {2025},
  month    = {07},
  volume    = {16},
  number    = {1},
  pages     = {5963},
  doi       = {10.1038/s41467-025-61137-x},
  keywords  = {bioscience}
}

@Article{Hieta2025,
  author    = {Janina Hieta and Chouaib Benchraka and Katariina Pärnänen and Noora Houttu and Kati Mokkala and Mrunalini Lotankar and Eeva-Leena Kataja and Leo Lahti and Kirsi Laitinen},
  title     = {Perinatal depressive and anxiety symptoms are associated with gut microbiota in pregnant women with overweight and obesity},
  journal   = {Brain, Behavior, \& Immunity - Health},
  volume    = {47},
  pages     = {101042},
  year      = {2025},
  month     =	 {06},
  doi       = {10.1016/j.bbih.2025.101042},
  issn      = {2666-3546},
  keywords  = {bioscience}
}

@Article{Escobarzepeda2025,
  author  = {Alejandra Escobar-Zepeda and Matti Olavi Ruuskanen and Martin Beracochea and Jennifer Lu and Dattatray Mongad and  Lorna Richardson and  Robert D. Finn and  Leo Lahti},
  title   = {Biome-specific genome catalogues reveal functional potential of shallow sequencing},
  journal =	 {{bioRXiv}},
  year    = {2025},
  month   =	 {06},
  doi     = {10.1101/2025.06.16.659887},
  keywords  = {bioscience}
}

@Article{kantanen2025,
  author  = {Pyry Kantanen and Erik Bülow and Aleksi Lahtinen and Måns Magnusson and Jussi Paananen and Leo Lahti},
  title   = {Validating and Extracting Information from National Identification Numbers in {R}: The Case of Finland and Sweden},
  journal = {The R Journal},
  year    = {2025},
  month     =	{05},
  volume  = {16},
  issue   = {3},
  pages   = {4--14},
  doi     = {10.32614/RJ-2024-023},
  issn    = {2073-4859},
  keywords  = {datascience}
}


@Article{Hellman2025,
  title     = {Gut Microbiome as a Risk Factor for Future CKD},
  author    = {Tapio Hellman and Li-Fang Yeo and Joonatan Palmu and Aki Havulinna and Pekka Jousilahti and Ville Laitinen and Katariina Pärnänen and Veikko Salomaa and Leo Lahti and Rob Knight and Teemu Niiranen},
  journal   = {Kidney International Reports},
  volume    = {10},
  number    = {6},
  pages     = {1673--1682},
  year      = {2025},
  month     =	{06},
  doi       = {10.1016/j.ekir.2025.04.007},
  issn      = {2468-0249},
  keywords  = {bioscience}
}

@Article{Boelius2025,
  author    = {Hanna-Mari Boelius and Anna-Katariina Aatsinki and Marja A. Heiskanen and Eero A. Haapala and Eveliina Munukka and Juha Mykkänen and Noora Kartiosuo and Leo Lahti and Anniina Keskitalo and Pentti Huovinen and Harri Niinikoski and Jorma Viikari and Tapani Rönnemaa and Hanna Lagström and Antti Jula and Suvi P. Rovio and Olli T. Raitakari and Katja Pahkala},
  title     = {Association of leisure time physical activity with gut microbiota composition in early adulthood},
  journal   = {Scientific Reports},
  year      = {2025},
  month     =	{06},
  volume    = {15},
  number    = {1},
  pages     = {19697},
  doi       = {10.1038/s41598-025-02287-2},
  issn      = {2045-2322},
  keywords  = {bioscience}
}

@Article{Metris2025,
  author    = {Aline Metris and Alan W. Walker and Alicia Showering and Andrea Doolan and Andrew J. McBain and Antonis Ampatzoglou and Barry Murphy and Catherine O'Neill and Colette Shortt and Elizabeth M. Darby and Gary Aldis and Greg G. Hillebrand and Helen L. Brown and Hilary P. Browne and Jay P. Tiesman and Joy Leng and Leo Lahti and Nicholas S. Jakubovics and Oliver Hasselwander and Robert D. Finn and Silvia Klamert and Tamas Korcsmaros and Lindsay J. Hall},
  title     = {Assessing the safety of microbiome perturbations},
  journal   = {Microbial Genomics},
  year      = {2025},
  month     =	{05},
  volume    = {11},
  number    = {5},
  publisher = {Microbiology Society},
  doi       = {10.1099/mgen.0.001405},
  issn      = {2057-5858},
  keywords  = {bioscience}
}

@Article{Salehi2025,
  author =	 {Mahkameh Salehi and Ville Laitinen and Shivang Bhanushali and Johan Bengtsson-Palme and Collignon P and John J Beggs and Katariina Pärnänen and Leo Lahti},
  title =	 {Gender differences in global antimicrobial resistance},
  journal =	 {npj Biofilms and Microbiomes},
  volume = {11},
  number = {1},
  pages = {79},
  issn = {2055-5008},
  year =	2025,
  month =	 05,
  doi = {10.1038/s41522-025-00715-9},
  keywords =  {bioscience}
}

@Article{Benedetti2024,
  author =	 {Giulio Benedetti and Ely Seraidarian and Theotime Pralas and Akewak Jeba and Tuomas Borman and Leo Lahti},
  title =	 {{iSEEtree}: interactive explorer for hierarchical data},
  journal =	 {Bioinformatics Advances},
  year =	 2025,
  month =	 05,
  volume    = {5},
  number    = {1},
  pages = {vbaf107},
  issn  = {2635-0041},
  doi =   {10.1093/bioadv/vbaf107},
  keywords =    {datascience}
}

@Article{Drnevich2025,
  author =	 {Jenny Drnevich and Frederick J. Tan and Fabricio Almeida-Silva and
            Robert Castelo and Aedin C. Culhane and Sean Davis and Maria A. Doyle
            and Susan Holmes and Leo Lahti and Alexandru Mahmoud and Kozo Nishida
            and Marcel Ramos and Kevin Rue-Albrecht and David J.H. Shih and
            Laurent Gatto and Charlotte Soneson},
  title =	 {Learning and teaching biological data science in the Bioconductor community},
  journal =	 {{PLOS Computational Biology}},
  volume =   {21},
  number =   {4},
  year =	 2025,
  month =	 04,
  pages = {e1012925},
  doi =   {10.1371/journal.pcbi.1012925},
  keywords =    {bioscience}
}

@Article{Lotankar2025,
  author =	 {Mrunalini Lotankar and Noora Houttu and Chouaib Benchraka and Leo Lahti and Kirsi Laitinen},
  title =	 {Links between gut microbiota with specific serum metabolite groups in pregnant women with overweight or obesity},
  journal =	 {Nutrition, Metabolism and Cardiovascular Diseases},
  year =	 2025,
  month =	 04,
  pages = {104095},
  issn = {0939-4753},
  doi =  {10.1016/j.numecd.2025.104095},
  keywords =    {bioscience}
}

@Article{Kaisanlahti2025,
  author =	 {Anna Kaisanlahti and Jenni Turunen and Jenni Hekkala and Surbhi Mishra and Sonja Karikka and Sajeen Amatya and Niko Paalanne and Johanna Krüger and Anne Portaankorva and Jussi Koivunen and Arja Jukkola and Pia Vihinen and Päivi Auvinen and Sirpa Leppä and Peeter Karihtala and Vesa Koivukangas and Janne Hukkanen and Seppo Vainio and Anatoliy Samoylenko and Genevieve Bart and Leo Lahti and Justus Reunanen and Mysore Tejesvi and Terhi Ruuska-Loewald},
  title =	 {Gut microbiota-derived extracellular vesicles form a distinct entity from gut microbiota},
  journal =	 {mSystems},
  year =	 2025,
  month =	 04,
  volume    = {10},
  number    = {5},
  pages     = {e00311-25},
  doi       = {10.1128/msystems.00311-25},
  keywords =    {bioscience}
}

@Article{Koponen2025,
  author =	 {Kari Koponen and Daniel McDonald and Pekka Jousilahti and Guillaume Meric and Michael Inouye and Leo Lahti and Teemu Niiranen and Satu Männistö and Aki Havulinna and Rob Knight and Veikko Salomaa},
  title =	 {Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort},
  journal =	 {European Journal of Nutrition},
  volume =   {64},
  number  = {4},
  pages =   {153},
  issn = {1436-6215},
  year =	 2025,
  month =	 04,
  doi =   {10.1007/s00394-025-03668-z},
  keywords =    {bioscience}
}

@Article{Pelto2025,
  author =	 {Juho Pelto and Kari Auranen and Janne Kujala and Leo Lahti},
  title =	 {Elementary methods provide more replicable results in microbial differential abundance analysis},
  journal =	 {Briefings in Bioinformatics},
  volume =   {26},
  number = {2},
  pages = {bbaf130},
  issn = {1477-4054},
  year =	 2025,
  month =	 03,
  doi =   {10.1093/bib/bbaf130},
  keywords =    {bioscience}
}

@Article{Khalighi2025,
  author =	 {Moein Khalighi and Leo Lahti and Faïçal Ndaïrou and Peter Rashkov and Delfim F. M. Torres},
  title =	 {Fractional modelling of COVID-19 transmission incorporating asymptomatic and super-spreader individuals},
  journal =	 {Mathematical Biosciences},
  volume =   {380},
  pages = {109373},
  year =	 2025,
  issn = {0025-5564},
  month =	 01,
  doi =   {10.1016/j.mbs.2024.109373},
  keywords =    {datascience}
}

@Article{Jeyaram2025,
  author =	 {Kumaraswamy Jeyaram and Leo Lahti and Sebastian Tims and Hans Heilig and Antonie van Gelder and Willem M de Vos and Hauke Smidt and and Erwin Zoetendal},
  title =	 {Fermented foods affect the seasonal stability of gut bacteria in an {Indian} rural population},
  journal =	 {{Nature Communications}},
  volume =   {16},
  number = {1},
  pages =   {771},
  year =	 2025,
  month =	 01,
  issn = {2041-1723},
  doi =   {10.1038/s41467-025-56014-6},
  keywords =    {bioscience}
}

@Article{Potbhare2025,
  author =	 {Renuka Potbhare and Ameeta Ravikumar and Eveliina Munukka and Richa Ashma and Leo Lahti},
  title =	 {Skin microbiota variation in {Indian} families},
  journal =	 {PeerJ},
  volume =   {13},
  pages =   {e18881},
  year =	 2025,
  month =	 2,
  doi =   {10.7717/peerj.18881},
  keywords =    {bioscience}
}

@Article{Eckermann2025,
  author =	 {Henrik Eckermann and Hellen Lustermans and Katariina Parnanen and Leo Lahti and Carolina {de Weerth}},
  title =	 {Maternal Pre- and Postnatal Stress and Maternal and Infant Gut Microbiota Features.},
  journal =	 {Psychoneuroendocrinology},
  volume =   {172},
  pages = {107273},
  year =	 2025,
  issn = {0306-4530},
  doi = {10.1016/j.psyneuen.2024.107273},
  keywords =    {bioscience}
}

@Article{Joos2024,
  author =	 {Raphaela Joos and Katy Boucher and Aonghus Lavelle and
            Manimozhiyan Arumugam and Martin J. Blaser and Marcus J. Claesson and
            Gerard Clarke and Paul D. Cotter and Luisa De Sordi and Maria G. Dominguez-Bello and
            Bas E. Dutilh and Stanislav D. Ehrlich and Tarini Shankar Ghosh and Colin Hill and
            Christophe Junot and Leo Lahti and Trevor D. Lawley and Tine R. Licht and
            Emmanuelle Maguin and Thulani P. Makhalanyane and Julian R. Marchesi and
            Jelle Matthijnssens and Jeroen Raes and Jacques Ravel and Anne Salonen and
            Pauline D. Scanlan and Andrey Shkoporov and Catherine Stanton and Ines Thiele and
            Igor Tolstoy and Jens Walter and Bo Yang and Natalia Yutin and Alexandra Zhernakova and
            Hub Zwart and {Human Microbiome Action Consortium} and Joël Doré and R. Paul Ross},
  title =	 {Examining the healthy human microbiome concept},
  journal =	 {Nature Reviews Microbiology},
  year =	 2025,
  month =	 01,
  volume  = {23},
  number  = {3},
  pages   = {192--205},
  issn =    {1740-1534},
  doi         = {10.1038/s41579-024-01107-0},
  keywords =    {bioscience}
}

@Article{Khalighi2024acm,
  author =	 {Moein Khalighi and Giulio Benedetti and Leo Lahti},
  title =	 {Algorithm 1047: {FdeSolver}, a {Julia} Package for Solving Fractional Differential Equations},
  journal =	 {{ACM Transactions} on Mathematical Software},
  year =	 2024,
  month =	 10,
  volume =   {50},
  number =   {3},
  pages =    {22},
  issn =     {0098-3500},
  doi =      {10.1145/3680280},
  keywords =    {datascience}
}


@Article{Lietzén2024nut,
  author =	 {Martin S. Lietzén  and Maria Angela Guzzardi and Ronja Ojala and
            Jaakko Hentilä and Marja A. Heiskanen and Sanna M. Honkala and
            Riikka Lautamäki and Eliisa Löyttyniemi and Anna K. Kirjavainen and
            Johan Rajander and Tarja Malm and Leo Lahti and Juha O. Rinne and
            Kirsi H. Pietiläinen and Patricia Iozzo  and Jarna C. Hannukainen},
  title =	 {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}},
  journal =	 {Nutrients},
  year =	 2024,
  month =	 10,
  volume =   {16},
  issue  =   {10},
  pages =    {3554},
  doi         = {10.3390/nu16203554},
  keywords =    {bioscience}
}

@Article{Lietzén2024biom,
  author =	 {Martin S Lietzén and Andrea Mari and Ronja Ojala and Jaakko Hentilä
            and Kalle Koskensalo and Riikka Lautamäki and Eliisa Löyttyniemi and
            Riitta Parkkola and Virva Saunavaara and Anna K Kirjavainen and
            Johan Rajander and Tarja Malm and Leo Lahti and Juha O Rinne and
            Kirsi H Pietiläinen and Patricia Iozzo and Jarna C Hannukainen},
  title =	 {Effects of Obesity and Exercise on Hepatic and Pancreatic Lipid Content and Glucose Metabolism: {PET}-Studies in Twins Discordant for {BMI}},
  journal =	 {Biomolecules},
  volume =   {14},
  year =	 2024,
  number =   {9},
  month =	 08,
  issn =     {2218-273X},
  doi =      {10.3390/biom14091070},
  keywords =    {bioscience}
}

@Article{Jokela2024,
  author =	 {Roosa Jokela and Katariina MM Pärnänen and Alise J Ponsero and Leo Lahti and Kaija-Leena Kolho and Willem M de Vos and Anne Salonen},
  title =	 { 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},
  journal =	 {Gut Microbes},
  volume = {16},
  number = {1},
  pages = {2383746},
  issn = {1949-0976},
  year =	 2024,
  month = 	 08,
  doi = {10.1080/19490976.2024.2383746},
  keywords =    {bioscience}
}

@Article{Tiihonen2024,
  author =	 {Iiro Tiihonen and Leo Lahti and Mikko Tolonen},
  title =    {Print culture and economic constraints: A quantitative analysis of book prices in eighteenth-century Britain},
  journal =  {Explorations in Economic History},
  volume =   {94},
  pages =    {101614},
  month = 	 10,
  year =	 2024,
  issn =     {0014-4983},
  doi =      {10.1016/j.eeh.2024.101614},
  keywords =    {dh}
}

@Article{Grahnemo2024,
  author =	 {Louise Grahnemo and Oleg Kambur and Leo Lahti and Pekka Jousilahti
  and Teemu Niiranen and Rob Knight and Veikko Salomaa and Aki S. Havulinna and
  Claes Ohlsson },
  title =	 {Associations between gut microbiota and incident fractures in the FINRISK cohort},
  journal =	 {npj Biofilms and Microbiomes},
  volume = {10},
  number = {69},
  year =	 2024,
  volume  = {10},
  number = {1},
  pages = {69},
  issn  = {2055-5008},
  doi = {10.1038/s41522-024-00530-8},
  keywords =    {bioscience}
}

@Article{Khalighi2024,
  author    =	 {Moein Khalighi and Leo Lahti and Faïçal Ndaïrou},
  title     =	 {Epidemic Transmission Modeling with Fractional Derivatives and Environmental Pathogens},
  journal   =	 {International Journal of Biomathematics},
  year      =	 2024,
  pages     =  {2450085},
  doi       =  {10.1142/S1793524524500852},
  issn      =  {1793-5245},
  keywords  =  {datascience}
}

@Article{Manzoor2024,
  author =	 {Muhammed Manzoor and Jaakko Leskelä and Milla Pietiäinen and
  Nicolas Martinez-Majander and Pauli Ylikotila and Eija Könönen and
  Teemu Niiranen and Leo Lahti and Juha Sinisalo and Jukka Putaala and
  Pirkko J Pussinen and Susanna Paju},
  title =	 {Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke},
  journal =	 {ISME Communications},
  volume = {4},
  number = {1},
  pages = {ycae088},
  issn = {2730-6151},
  year =	 2024,
  month =	 06,
  doi =		 {10.1093/ismeco/ycae088},
  keywords =    {bioscience}
}

@Article{Kullberg2024,
  author =  {Robert F J Kullberg and Irina Wikki and Bastiaan W Haak and
  Anni Kauko and Henrike Galenkamp and Hessel Peters-Sengers and Joe M Butler and
  Aki S Havulinna and Joonatan Palmu and Daniel McDonald and Chouaib Benchraka and
  Mahmoud I Abdel-Aziz and Maria Prins and Anke H {Maitland van der Zee} and
  Bert-Jan {van den Born} and Pekka Jousilahti and Willem M {de Vos} and Veikko Salomaa and
  Rob Knight and Leo Lahti and Max Nieuwdorp and Teemu Niiranen and W Joost Wiersinga},
  title =   {Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies},
  journal = {{The Lancet Microbe}},
  year =    {2024},
  volume = {5},
  number = {9},
  pages = {100864},
  issn =    {2666-5247},
  doi =     {10.1016/S2666-5247(24)00079-X},
  keywords =	 {bioscience}
}

@Article{Bhanushali2024,
  author =	 {Shivang Bhanushali and Katariina Parnanen and Dattatray Mongad and Dhiraj Dhotre and Leo Lahti},
  title =	 {Biochemical analyses can complement sequencing-based ARG load monitoring: a case study in Indian hospital sewage networks},
  journal =	 {{medRxiv}},
  pubstate =	 {preprint},
  year =	 2024,
  month = 	 05,
  doi =		 {10.1101/2024.05.31.24308262},
  keywords =	 {bioscience}
}

@Article{Timmis2024,
  author =	 {Kenneth Timmis and John E. Hallsworth and Terry J. McGenity and
  Rachel Armstrong and María Francisca Colom and Zeynep Ceren Karahan and
  Max Chavarría and Patricia Bernal and Eric S. Boyd and Juan Luis Ramos and
  Martin Kaltenpoth and Carla Pruzzo and Gerard Clarke and
  Purificación López-Garcia and Michail M. Yakimov and Jessamyn Perlmutter and
  Chris Greening and Emiley Eloe-Fadrosh and Willy Verstraete and
  Olga C. Nunes and Oleg Kotsyurbenko and Pablo Iván Nikel and
  Paola Scavone and Max M. Häggblomand Rob Lavigne and Frédérique Le Roux and
  James K. Timmis and Victor Parro and Carmen Michán and José Luis García and
  Arturo Casadevall and Shelley M. Payne and Joachim Frey and Omry Koren and
  James I. Prosser and Leo Lahti and Rup Lal and Shailly Anand and
  Utkarsh Sood and Pierre Offre and Casey C. Bryce and Allen Y. Mswaka and
  Jörg Jores and Betül Kaçar and Lars Mathias Blank and Nicole Maaßen and
  Phillip B. Pope and Horia L. Banciu and Judith Armitage and Sang Yup Lee and
  Fengping Wang and Thulani P. Makhalanyane and Jack A. Gilbert and
  Thomas K. Wood and Branka Vasiljevic and Mario Soberón and Zulema Udaondo and
  Fernando Rojo and Jyoti Prakash Tamang and Tatiana Giraud and Jeanne Ropars and
  Thaddeus Ezeji and Volker Müller and Hirofume Danbara and Beate Averhoff and
  Angela Sessitsch and Laila Pamela Partida-Martínez and Wei Huang and Søren Molin and
  Pilar Junier and Ricardo Amils and Xiao-Lei Wu and Eliora Ron and Huseyin Erten and
  Elaine Cristina Pereira de Martinis and Alexander Rapoport and Maarja Öpik and
  W. Donald R. Pokatong and Courtney Stairs and Mohammad Ali Amoozegar and Jéssica Gil Serna},
  title =	 {A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society},
  journal =	 {Microbial Biotechnology},
  year =	 2024,
  month =	 05,
  volume = {17},
  number = {5},
  pages = {e14456},
  doi =		 {10.1111/1751-7915.14456},
  issn =     {1751-7915},
  keywords =    {bioscience}
}

@Article{Tito2024,
  author =	 {Raúl Y. Tito and Sara Verbandt and Marta Aguirre Vazquez and Leo Lahti and
                Chloe Verspecht and Verónica Lloréns-Rico and Sara Vieira-Silva and
                Janine Arts and Gwen Falony and Evelien Dekker and Joke Reumers and
                Sabine Tejpar and Jeroen Raes},
  title =	 {Microbiome confounders and quantitative profiling challenge predicted
                microbial targets in colorectal cancer development},
  journal =	 {Nature Medicine},
  year =	 2024,
  month =	 04,
  volume =   30,
  number = {5},
  pages =    {1339-1348},
  issn = {1546-170X},
  doi =		 {10.1038/s41591-024-02963-2},
  keywords =    {bioscience}
}

@Article{König2024,
  author =	 {Emilia König and Shea Beasley and Paulina Heponiemi and Sanni Kivinen and
                Jaakko Räkköläinen and Seppo Salminen and Maria Carmen Collado and
                Tuomas Borman and Leo Lahti and Virpi Piirainen and Anna Valros and
                Mari Heinonen},
  title =	 {Fecal microbiota profiles of growing pigs and their relation to
                growth performance},
  journal =	 {{PLoS One}},
  year =	 2024,
  month =	 05,
  volume =   19,
  number = {5},
  pages =    {1-20},
  doi =		 {10.1371/journal.pone.0302724},
  keywords =    {bioscience}
}

@Article{BarkerandNeil2024,
  author =	 {Michelle Barker and Neil Chue Hong},
  annotate = {Project leaders: Anna Mette Morthorst, Jean-Francois Nominé, Karsten Kryger Hansen,Laurents Sesink
              WG experts:  Birgit Schmidt, Birte Christensen-Dalsgaard, Daniel Roewenstrunk,Egon Heuson, Leo Lahti,
                            Loek Brinkman, Matt Jaquiery, Olivier Rouchon and Stefanie Mewes and Toumas Alatera},
  title =	 {Approaches to scaling up reproducibility in research organisations},
  journal =	 {Zenodo},
  year =	 2024,
  month =	 03,
  doi =		 {10.5281/zenodo.10663903},
  keywords =	 {{KE}}
}

@Article{Manzoora2024,
  author =	 {Muhammed Manzoora and Jaakko Leskelä and Milla Pietiäinen and
                Nicolas Martinez-Majander and Eija Könönen and Teemu Niiranen and
                Leo Lahti and Juha Sinisalo and Jukka Putaala and Pirkko J. Pussinen and
                Susanna Paju},
  title =	 {Shotgun metagenomic analysis of the oral microbiome in gingivitis: a nested case-control study},
  journal =	 {{Journal of Oral Microbiology (ZJOM)}},
  year =	 2024,
  volume =	 {16},
  number =	 1,
  month =	 03,
  doi =		 {10.1080/20002297.2024.2330867},
  keywords =	 {bioscience}
}

@Article{Liu2024,
  author =	 {Yang Liu and Scott C. Ritchie and Shu Mei Teo and Matti O. Ruuskanen and
                Oleg Kambur and Qiyun Zhu and Jon Sanders and Yoshiki Vázquez-Baeza and
                Karin Verspoor and Pekka Jousilahti and Leo Lahti and Teemu Niiranen and
                Veikko Salomaa and Aki S. Havulinna and Rob Knight and Guillaume Méric  and
                Michael Inouye},
  title =	 {Integration of polygenic and gut metagenomic risk prediction for common diseases},
  journal =	 {{Nature Aging}},
  year =	 2024,
  month =	 03,
  volume =   4,
  pages =    {584-594},
  doi =		 {10.1038/s43587-024-00590-7},
  issn =     {2662-8465},
  keywords =	 {bioscience}
}

@Article{Mishra2024,
  author =	 {Surbhi Mishra and Mysore Vishakantegowda Tejesvi and Jenni Hekkala and
                    Jenni Turunen and Niyati Kandikanti and Anna Kaisanlahti and
                    Marko Suokas and Sirpa Leppä and Pia Vihinen and Hanne Kuitunen and
                    Kaisa Sunela and Jussi Koivunen and Arja Jukkola and Ilja Kalashnikov and
                    Päivi Auvinen and Okko-Sakari Kääriäinen and T. Peñate Medina and
                    O. Peñate Medina and Juha Saarnio and Sanna Meriläinen and
                    Tero Rautio and Raila Aro and Reetta Häivälä and Juho Suojanen and
                    Mikael Laine and Pande Putu Erawijattari and Leo Lahti and
                    Peeter Karihtala and Terhi S. Ruuska and Justus Reunanen},
  title =	 {Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours},
  note =	 {Available online 7 March 2024},
  journal =	 {{Journal of Advanced Research}},
  year =	 2024,
  month =	 03,
  volume =   68,
  pages =    {375-386},
  issn = {2090-1232},
  doi =		 {10.1016/j.jare.2024.03.003},
  keywords =	 {bioscience}
}

@Article{Heiskanen2024,
  author =	 {Marja Heiskanen and Anna Aatsinki and Petra Hakonen and
                Noora Kartiosuo and Eveliina Munukka and Leo Lahti and
                Anniina Keskitalo and Pentti Huovinen and Harri Niinikoski and
                Jorma Viikari and Tapani Rönnemaa and Hanna Lagström and
                Antti Jula and Olli Raitakari and Suvi Rovio and Katja Pahkala},
  title =	 {Association of Long-Term Habitual Dietary Fiber Intake since Infancy with Gut Microbiota Composition in Young Adulthood},
  note =	 {Available online 12 January 2024},
  journal =	 {{The Journal of Nutrition}},
  year =	 2024,
  volume =	 {154},
  issue =	 2,
  pages =	 {744-754},
  month =	 01,
  doi =		 {10.1016/j.tjnut.2024.01.008},
  keywords =	 {bioscience}
}


@Article{Ojala2024,
  author =	 {Ronja Ojala and Jaakko Hentilä and Martin S. Lietzén and
                Milja Arponen and Marja A. Heiskanen and Sanna M. Honkala and
                Heidi Virtanen and Kalle Koskensalo and Riikka Lautamäki and
                Eliisa Löyttyniemi and Riitta Parkkola and Olli J. Heinonen and
                Tarja Malm and Leo Lahti and Juha Rinne and Olli Eskola and
                Johan Rajander and Kirsi H. Pietiläinen and Jaakko Kaprio and
                Kaisa K. Ivaska and Jarna C. Hannukainen},
  title =	 {Bone marrow metabolism is affected by body weight and response to exercise training varies according to anatomical location},
  note =	 {First published 11 October 2023},
  journal =	 {{Diabetes, Obesity and Metabolism}},
  year =	 2024,
  volume =	 {26},
  pages =	 {251-261},
  issue =	 1,
  month =	 01,
  doi =		 {10.1111/dom.15311},
  keywords =	 {bioscience}
}


@Article{Eckermann2024,
  author =	 {Henrik Andreas Eckermann and Jennifer Meijer and Kelly Cooijmans and
                Leo Lahti  and Carolina de Weerth},
  title =	 {Daily skin-to-skin contact alters microbiota development in
                healthy full-term infants},
  journal =	 {{Gut Microbes}},
  year =	 2024,
  volume = {16},
  number = {1},
  pages = {2295403},
  month =	 01,
  doi =		 {10.1080/19490976.2023.2295403},
  keywords =	 {bioscience}
}

@Article{König2024,
  author =	 {Emilia König and Paulina Heponiemi and Sanni Kivinen and
                Jaakko Räkköläinen and Shea Beasley and Tuomas Borman and
                Maria Carmen Collado and Vilja Hukkinen and Jouni Junnila and
                Leo Lahti and Marianna Norring and Virpi Piirainen and
                Seppo Salminen and Mari Heinonen and Anna Valros},
  title =	 {{Fewer culturable Lactobacillaceae species identified in faecal
                samples of pigs performing manipulative behaviour}},
  journal =	 {{Scientific Reports}},
  year =	 2024,
  volume =	 {14},
  number =	 {132},
  month =	 01,
  doi =		 {10.1038/s41598-023-50791-0},
  keywords =	 {bioscience}
}

@techreport{openedu2023,
  author       = {Open Science Coordination in Finland, Federation of Finnish Learned Societies},
  title        = {Open research data and methods. National policy and executive plan
                    by the higher education and research community for 2021–2025:
                    Policy component 1 (Open access to research data) and 2
                    (Open access to research methods and infrastructures)},
  publisher    = {The Committee for Public Information (TJNK) and Federation of Finnish Learned Societies (TSV)},
  volume       = 5,
  issn         = {2670-062X},
  isbn         = {978-952-5995-87-9},
  doi          = {10.23847/tsv.669},
  url          = {https://edition.fi/tsv/catalog/view/669/702/2461-1},
  keywords     = {openscience}
}

@Article{Huovinen2023,
  author =	 {Venla Huovinen and Anna-Katariina Aatsinki and Eeva-Leena Kataja
                and Eveliina Munukka and Anniina Keskitalo and Santosh Lamichhane and
                Peppi Raunioniemi and David J. Bridgett and Leo Lahti and
                Siobhain M. O’Mahony and Alex Dickens and Riikka Korja and
                Hasse Karlsson and Saara Nolvi and Linnea Karlsson},
  title =	 {Infant gut microbiota and negative and fear reactivity},
  journal =	 {Development and Psychopathology},
  year =	 2023,
  pages =	 {1-16},
  month =	 11,
  volume =	 36,
  number =	 4,
  pages =	 {2016-2031},
  doi =		 {10.1017/S0954579423001396},
  keywords =	 {bioscience}
}

@Article{MarcosZambrano2023,
  author =	 {Laura Judith Marcos-Zambrano and Víctor Manuel López-Molina and
                Burcu Bakir-Gungor and Marcus Frohme and Kanita Karaduzovic-Hadziabdic and
                Thomas Klammsteiner and Eliana Ibrahimi and Leo Lahti and Tatjana Loncar-Turukalo and
                Xhilda Dhamo and Andrea Simeon and Alina Nechyporenko and Gianvito Pio and
                Piotr Przymus and Alexia Sampri and Vladimir Trajkovik and Blanca Lacruz-Pleguezuelos and
                Oliver Aasmets and Ricardo Araujo and Ioannis Anagnostopoulos and Önder Aydemir and
                Magali Berland and M. Luz Calle and Michelangelo Ceci and Hatice Duman and
                Aycan Gündoğdu and Aki S. Havulinna and Kardokh Hama Najib Kaka Bra and
                Eglantina Kalluci and Sercan Karav and Daniel Lode and Marta B. Lopes and
                Patrick May and Bram Nap and Miroslava Nedyalkova and Inês Paciência and
                Lejla Pasic and Meritxell Pujolassos and Rajesh Shigdel and Antonio Susín and
                Ines Thiele and Ciprian-Octavian Truică and Paul Wilmes and Ercument Yilmaz and
                Malik Yousef and Marcus Joakim Claesson and Jaak Truu and Enrique Carrillo de Santa Pau},
  title =	 {A toolbox of machine learning software to support microbiome analysis},
  journal =	 {Frontiers in Microbiology},
  year =	 2023,
  month =	 11,
  volume =	 14,
  issn = {1664-302X},
  doi =		 {10.3389/fmicb.2023.1250806},
  keywords =	 {bioscience}
}

@Article{Koponen2023,
  author =	 {Kari Koponen and Oleg Kambur and Bijoy Joseph and Matti O. Ruuskanen and
                Pekka Jousilahti and Rodolfo Salido and Caitriona Brennan and
                Mohit Jain and Guillaume Meric and Michael Inouye and Leo Lahti and
                Teemu Niiranen and Aki S. Havulinna and Rob Knight and Veikko Salomaa},
  title =	 {{Role of Gut Microbiota in Statin-Associated New-Onset Diabetes—a Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort}},
  journal =	 {{Arteriosclerosis, Thrombosis, and Vascular Biology}},
  year =	 2023,
  month =	 11,
  volume =	 44,
  number =	 2,
  pages =	 {477-487},
  doi =		 {10.1161/ATVBAHA.123.319458},
  keywords =	 {bioscience}
}

@Article{Raulo2023,
  author =	 {Aura Raulo and Alexis Rojas and Björn Kröger and Antti Laaksonen and
                Carlos Lamuela Orta and Silva Nurmio and Mirva Peltoniemi and Leo Lahti
                    and Indrė Žliobaitė},
  title =	 {What are patterns of rise and decline?},
  journal =	 {{The Royal Society of Open Science}},
  year =	 2023,
  month =	 11,
  volume =	 10,
  issue =	 11,
  doi =		 {10.1098/rsos.230052},
  keywords =	 {bioscience}
}

@Article{Kaisanlahti2023,
  author =	 {Anna Kaisanlahti and Jenni Turunen and Nadiya Byts and Anatoliy Samoylenko and
  Genevieve Bart and Nikke Virtanen and Mysore V. Tejesvi and Artem Zhyvolozhnyi and
  Sonia Sarfraz and Sohvi Kumpula and Jenni Hekkala and Sonja Salmi and Olga Will and
  Johanna Korvala and Niko Paalanne and Pande Putu Erawijantari and Marko Suokas and
  Tuula Peñate Medina and Seppo Vainio and Oula Peñate Medina and Leo Lahti and
  Terhi Tapiainen and Justus Reunanen},
  title =	 {Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles},
  journal =	 {{BMC Microbiome}},
  url =		 {https://rdcu.be/dq2aL},
  year =	 2023,
  month =	 11,
  volume =	 11,
  number =	 249,
  doi =		 {10.1186/s40168-023-01694-9},
  keywords =	 {bioscience}
}

@Article{Erawijantari2023,
  author =	 {Pande Putu Erawijantari and Ece Kartal and José Liñares-Blanco and Teemu D. Laajala and
  Lily Elizabeth Feldman and The {FINRISK} Microbiome DREAM Challenge and {ML4Microbiome} Communities and
  Pedro Carmona-Saez and Rajesh Shigdel and Marcus and Joakim Claesson and Randi Jacobsen Bertelsen and
  David Gomez-Cabrero and Samuel Minot and Jacob Albrecht and Verena Chung and Michael Inouye and
  Pekka Jousilahti and Jobst-Hendrik Schultz and Hans-Christoph Friederich and Rob Knight and Veikko Salomaa and
  Teemu Niiranen and Aki S. Havulinna and Julio Saez-Rodriguez and Rebecca T. Levinson and Leo Lahti},
  title =	 {Microbiome-based risk prediction in incident heart failure: a community challenge},
  journal =	 {{medRxiv preprint}},
  year =	 2023,
  month =	 10,
  doi =		 {10.1101/2023.10.12.23296829},
  keywords =	 {bioscience}
}

@Article{Husso2023,
  author =	 {Aleksi Husso and Tiina Pessa-Morikawa and Ville Mikael and Olli Kärkkäinen and
                Hyuk Nam Kwon and Leo Lahti and Antti Iivanainen and Kati Hanhineva and Mikael Niku},
  title =	 {Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain, and placenta},
  journal =	 {BMC Biology},
  year =	 2023,
  month =	 10,
  volume =	 21,
  number =	 207,
  doi =		 {10.1186/s12915-023-01709-9},
  keywords =	 {bioscience}
}

@Article{DElia2023,
  author =	 {Domenica D’Elia and Jaak Truu and Leo Lahti and
            Magali Berland and Georgios Papoutsoglou and
            Michelangelo Ceci and Aldert Zomer and Marta B. Lopes and
            Eliana Ibrahimi and Aleksandra Gruca and Alina Nechyporenko and
            Marcus Frohme and Thomas Klammsteiner andEnrique Carrillo-de Santa Pau and
            Laura Judith Marcos-Zambrano and Karel Hron and Gianvito Pio and
            Andrea Simeon and Ramona Suharoschi and Isabel Moreno-Indias and
            Andriy Temko and Miroslava Nedyalkova and Elena-Simona Apostol and
            Ciprian-Octavian Truică and Rajesh Shigdel and Jasminka Hasić-Telalović and
            Erik Bongcam-Rudloff and Piotr Przymus and Naida Babić Jordamović and
            Laurent Falquet and Sonia Tarazona and Alexia Sampri and Gaetano Isola and
            David Pérez-Serrano and Vladimir Trajkovik and Lubos Klucar and
            Tatjana Loncar-Turukalo and Aki Havulinna and Christian Jansen and
            Randi Bertelsen andMarcus Claesson},
  title =	 {{Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action}},
  journal =	 {Frontiers in Microbiology},
  year =	 2023,
  month =	 09,
  volume =	 14,
  doi =		 {10.3389/fmicb.2023.1257002},
  keywords =	 {bioscience}
}

@Article{McDonald2023,
  author =	 {Daniel McDonald and Yueyu Jiang and Metin Balaban
                  and Kalen Cantrell and Qiyun Zhu and Antonio
                  Gonzalez and James Morton and Giorgia Nicolaou and
                  Donovan Parks and Søren Karst and Mads Albertsen and
                  Philip Hugenholtz and Todd DeSantis and Se-Jin Song
                  and Andrew Bartko and Aki Havulinna and Pekka
                  Jousilahti and Susan Cheng and Michael Inouye and
                  Teemu Niiranen and Mohit Jain and Veikko Salomaa and
                  Leo Lahti and Siavash Mirarab and Rob Knight},
  title =	 {Greengenes2 unifies microbial data in a single
                  reference tree},
  journal =	 {Nature Biotechnology},
  year =	 2023,
  month =	 07,
  volume =	 42,
  pages = {715-718},
  doi =		 {10.1038/s41587-023-01845-1},
  keywords =	 {bioscience}
}


@Article{Gao2023,
  author =	 {Yu Gao and Yağmur Şimşek and Emma Gheysen and Tuomas
                  Borman and Yi Li and Leo Lahti and Karoline Faust
                  and Daniel Garza},
  title =	 {{miaSim: an R/Bioconductor package to easily
                  simulate microbial community dynamics}},
  journal =	 {Methods in Ecology and Evolution},
  year =	 2023,
  month =	 05,
  volume =	 14,
  issue =	 8,
  pages =	 {1967-1980},
  doi =		 {10.1111/2041-210X.14129},
  keywords =	 {bioscience}
}


@Article{Aatsinki2023,
  author =	 {Anna-Katariina Aatsinki and Jetro Tuulari and Eveliina Munukka
                and Leo Lahti and Anniina Keskitalo and Henna-Maria Kailanto and
                  Saara Nolvi and Noora Scheinin and Jani Saunavaara and
                    Riitta Parkkola and John Lewis and Niloofar Hashempour and
                      Satu Shulist and Linnea Karlsson and Hasse Karlsson},
  title =	 {Infant Left Amygdala Volume Is Negatively Associated with Fecal Microbiota Diversity},
  journal =	 {bioRxiv preprint},
  year =	 2023,
  month = 	 04,
  doi =		 {10.1101/2023.04.23.537273},
  keywords =	 {bioscience}
}

@Article{Palmu2023,
  author =	 {Joonatan Palmu and Christin Börschel and Alfredo Ortega-Alonso
                and Markó Lajos and Michael Inouye and Pekka Jousilahti and
                  Rodolfo Salido and Karenina Sanders and Caitriona Brennan and
                    Gregory Humphrey and Jon Sanders and Friederike Gutmann and
                      Dominik Linz and Veikko Salomaa and Aki Havulinna and
                        Sofia Forslund and Rob Knight and Leo Lahti and
                          Teemu Niiranen and Renate Schnabel},
  title =	 {Gut microbiome and atrial fibrillation-results from a large population-based study},
  journal =	 {{eBioMedicine}},
  year =	 2023,
  month =   	 05,
  volume =	 91,
  pages = {104583},
  issn = {2352-3964},
  doi =		 {10.1016/j.ebiom.2023.104583},
  keywords =	 {bioscience}
}


@Article{Houttu2023,
  author =	 {Noora Houttu and Chouaib Benchraka and Mrunalini
                  Lotankar and Ella Muhli and Harri Niinikoski and Leo
                  Lahti and Kirsi Laitinen},
  title =	 {Gut microbiota composition and function in pregnancy
                  as determinants of prediabetes at two years’
                  postpartum},
  journal =	 {Acta Diabetologica},
  year =	 2023,
  month =	 04,
  volume =	 60,
  pages = {1045-1054},
  doi =		 {10.1007/s00592-023-02064-5},
  keywords =	 {bioscience}
}



@Article{Rahkola2023,
  author =	 {Ella-Noora Rahkola and Samuli Rautava and Henni
                  Hiltunen and Chandler Ross and Leo Lahti and Erika
                  Isolauri},
  title =	 {The preterm gut microbiota and administration routes
                  of different probiotics: a randomized controlled
                  trial},
  journal =	 {Pediatric research},
  year =	 2023,
  month =	 04,
  volume =	 94,
  pages = {1480–1487},
  doi =		 {10.1038/s41390-023-02560-y},
  keywords =	 {bioscience}
}

@Article{Liu2023,
  author =	 {Yang Liu and Shu Mei Teo and Guillaume Meric and
                  Howard HF Tang and Qiyun Zhu and Jon G Sanders and
                  Yoshiki Vazquez-Baeza and Karin Verspoor and Ville A
                  Vartiainen and Pekka Jousilahti and Leo Lahti and
                  Teemu Niiranen and Aki S Havulinna and Rob Knight
                  and Veikko Salomaa and Michael Inouye},
  title =	 {The gut microbiome is a significant risk factor for
                  future chronic lung disease},
  journal =	 {{Journal of Allergy and Clinical Immunology}},
  year =	 {2023},
  month =	 04,
  volume =	 151,
  issue =	 4,
  pages =	 943-952,
  doi =		 {10.1016/j.jaci.2022.12.810},
  keywords =	 {bioscience}
}

@Article{Muhli2023,
  author =	 {Ella Muhli and Chouaib Benchraka and Mrunalini
                  Lotankar and Noora Houttu and Harri Niinikoski and
                  Leo Lahti and Kirsi Laitinen},
  title =	 {Aberrations in the early pregnancy serum metabolic
                  profile in women with prediabetes at two years
                  postpartum},
  journal =	 {Metabolomics},
  year =	 2023,
  volume =	 19,
  number =	 29,
  doi =		 {10.1007/s11306-023-01994-z},
  keywords =	 {bioscience}
}


@Article{Ndairou2023,
  author =	 {Faïçal Ndaïrou and Moein Khalighi and Leo Lahti},
  title =	 {Ebola epidemic model with dynamic population and
                  memory},
  journal =	 {Chaos, Solitons and Fractals},
  year =	 2023,
  volume =	 170,
  pages = {113361},
  doi =		 {10.1016/j.chaos.2023.113361},
  keywords =	 {datascience}
}


@article{FeldnerBusztin2023,
  author =	 {Feldner-Busztin, Dylan and Firbas Nisantzis, Panos
                  and Edmunds, Shelley Jane and Boza, Gergely and
                  Racimo, Fernando and Gopalakrishnan, Shyam and
                  Limborg, Morten Tønsberg and Lahti, Leo and de
                  Polavieja, Gonzalo G},
  title =	 "{Dealing with dimensionality: the application of
                  machine learning to multi-omics data}",
  journal =	 {Bioinformatics},
  volume =	 39,
  number =	 2,
  year =	 2023,
  month =	 01,
  doi =		 {10.1093/bioinformatics/btad021},
  note =	 {btad021},
  keywords =	 {bioscience},
  eprint =  {https://academic.oup.com/bioinformatics/article-pdf/39/2/btad021/49124137/btad021.pdf}
}

@Article{Vaura2022,
  author =	 {Felix Vaura and Hyunkyung Kim and Miriam Udler and {FinnGen} and
                  Veikko Salomaa and Leo Lahti and Teemu Niiranen},
  title =	 {Multi-Trait Genetic Analysis Reveals Clinically Interpretable
                    Hypertension Subtypes},
  journal =	 {Circulation: Genomic and Precision Medicine},
  year =	 2022,
  volume =	 {15},
  number =	 {4},
  doi =		 {10.1161/CIRCGEN.121.003583},
  keywords =	 {bioscience}
}

@Article{Mikkonen2022,
  author =	 {Anna Mikkonen and Anne Kärki and Annina Lattu and Helena Puhakka-Tarvainen and
            Heli Lehtivuori and Inka Stormi and Leo Lahti and Maria Söderholm and
            Seliina Päällysaho, National Open Science & Research Coordination 2022},
  title =	 {Open science recommendation and checklist for research, {development and innovation activities in collaboration between research organisations and companies}},
  journal =	 {Vastuullisen tieteen julkaisusarja, Tieteellisten seurain valtuuskunta},
  year =	 {2022},
  month =	 {07},
  issn =     {2670-062X},
  doi =		 {10.23847/tsv.441},
  keywords =	 {openscience}
}

@Article{Palmu2022,
  author =	 {Joonatan Palmu and Emmi Tikkanen and Aki Havulinna and
                Erkki Vartiainen and Annamari Lundqvist and Matti Ruuskanen and
                Markus Perola and Mika Ala-Korpela and Pekka Jousilahti and
                Peter Würtz and Veikko Salomaa and Leo Lahti and Teemu Niiranen},
  title =	 {Comprehensive biomarker profiling of hypertension
              in 36 985 Finnish individuals},
  journal =	 {Journal of Hypertension},
  year =	 {2022},
  volume =	 {40},
  number =	 {3},
  pages =	 {579-587},
  doi =		 {10.1097/HJH.0000000000003051},
  keywords =	 {bioscience}
}

@Article{Khalighi2022,
  author =	 {Moein Khalighi and Guilhem Sommeria-Klein and Didier
                  Gonze and Karoline Faust and Leo Lahti},
  title =	 {Quantifying the impact of ecological memory on the
                  dynamics of interacting communities},
  journal =	 {{PLoS Computational Biology}},
  year =	 {2022},
  volume =	 {18},
  number =	 {6},
  pages =	 {e1009396},
  doi =		 {10.1371/journal.pcbi.1009396},
  keywords =	 {datascience}
}



@InProc{Laitinen2022,
  author =	 {Ville Laitinen and Leo Lahti},
  title =	 {Probabilistic multivariate early warning signals},
  book =	 {Proc. 20th International Conference on Computational
                  Methods in Systems Biology ({CMSB}). Lecture Notes
                  in Computer Science.},
  editor =	 {Ion Petre and Andrei Păun},
  year =	 {2022},
  pages =	 {259-274},
  month =	 {August},
  url =		 {https://arxiv.org/abs/2205.07576},
  doi =		 {10.1007/978-3-031-15034-0},
  pdf =
                  {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2022-Laitinen-CMSB.pdf},
  publisher =	 {Springer Cham.},
  keywords =	 {datascience},
  address =	 {Bucharest, Romania, September 14–16}
}

@Article{Keskitalo2022,
  author =	 {Anniina Keskitalo and Eveliina Munukka and Anna
                  Aatsinki and Wisam Saleem and Noora Kartiosuo and
                  Leo Lahti and Pentti Huovinen and Laura L. Elo and
                  Sami Pietilä and Suvi P. Rovio and Harri Niinikoski
                  and Jorma Viikari and Tapani Rönnemaa and Hanna
                  Lagström and Antti Jula and Olli Raitakari and Katja
                  Pahkala},
  title =	 {An Infancy-Onset 20-Year Dietary Counselling
                  Intervention and Gut Microbiota Composition in
                  Adulthood},
  journal =	 {Nutrients},
  year =	 2022,
  volume =	 14,
  number =	 13,
  pages =	 2667,
  keywords =	 {bioscience},
  doi =		 {10.3390/nu14132667}
}


@Article{Umerle2022,
  author =	 {Umerle, Tomasz and Colavizza, Giovanni and Herden,
                  Elżbieta and Jagersma, Rindert and Király, Péter and
                  Koper, Beata and Lahti, Leo and Lindemann, David and
                  Łubocki, Jakub Maciej and Malínek, Vojtěch and
                  Milanova, Alexandra and Péter, Róbert and
                  Rißler-Pipka, Nanette and Romanello, Matteo and
                  Roszkowski, Marcin and Siwecka, Dorota and Tolonen,
                  Mikko and Vimr, Ondřej},
  title =	 {An Analysis of the Current Bibliographical Data
                  Landscape in the Humanities. A Case for the Joint
                  Bibliodata Agendas of Public Stakeholders},
  journal =	 {Zenodo},
  year =	 2022,
  keywords =	 {dh},
  month =	 {May},
  doi =		 {10.5281/zenodo.6559857}
}


@Article{Ruuskanen2022emi,
  author =	 {Matti O. Ruuskanen and Deepti Vats and Renuka
                  Potbhare and Ameeta RaviKumar and Eveliina Munukka
                  and Richa Ashma and Leo Lahti},
  title =	 {Towards standardized and reproducible research in
                  skin microbiomes},
  journal =	 {Environmental Microbiology},
  year =	 2022,
  volume =	 24,
  number =	 9,
  pages =	 {3840--3860},
  month =	 {March},
  keywords =	 {bioscience},
  doi =		 {10.1111/1462-2920.15945}
}


@Article{Lahti2022,
  author =	 {Leo Lahti},
  title =	 {Enhancing biomarkers with co-abundance},
  journal =	 {Nature Computational Science},
  year =	 2022,
  month =	 {May},
  keywords =	 {review},
  doi =		 {10.1038/s43588-022-00254-9},
  note =	 {Invited News & Views.}
}




@article{Houttu2022,
  title =	 {Potential pathobionts in vaginal microbiota are
                  affected by fish oil and/or probiotics intervention
                  in overweight and obese pregnant women},
  journal =	 {Biomedicine & Pharmacotherapy},
  volume =	 149,
  pages =	 112841,
  year =	 2022,
  doi =		 {10.1016/j.biopha.2022.112841},
  url =
                  {https://www.sciencedirect.com/science/article/pii/S0753332222002293},
  author =	 {Noora Houttu and Kati Mokkala and Wisam Tariq Saleem
                  and Seppo Virtanen and Juuso Juhila and Ella
                  Koivuniemi and Outi Pellonperä and Kristiina Tertti
                  and Paula Luokola and Timo Sorsa and Anne Salonen
                  and Leo Lahti and Kirsi Laitinen},
  keywords =	 {bioscience}
}

@Article{Potbhare2022,
  author =	 {Renuka Potbhare and Ameeta RaviKumar and Eveliina Munukka and
                  Leo Lahti and Richa Ashma},
  title =	 {Skin microbiota diversity among genetically
                  unrelated individuals of Indian origin},
  journal =	 {PeerJ},
  year =	 2022,
  volume =	 10,
  pages =	 {e13075},
  doi =		 {10.7717/peerj.13075},
  keywords =	 {bioscience}
}


@Article{Eckermann2022,
  author =	 {Henrik Andreas Eckermann and Yangwenshan Ou and Leo
                  Lahti and Carolina de Weerth},
  title =	 {Can gut microbiota throughout the first 10 years of
                  life predict executive functioning in childhood?},
  journal =	 {Developmental Psychobiology},
  year =	 2022,
  volume =	 64,
  number =	 3,
  pages =	 {e22226},
  month =	 {March},
  doi =		 {10.1002/dev.22226},
  keywords =	 {bioscience}
}


@article{Zhu2022,
  title =	 {Phylogeny-aware analysis of metagenome community
                  ecology based on matched reference genomes while
                  bypassing taxonomy},
  author =	 {Zhu, Qiyun and Huang, Shi and Gonzalez, Antonio and
                  McGrath, Imran and McDonald, Daniel and Haiminen,
                  Niina and Armstrong, George and V{\'a}zquez-Baeza,
                  Yoshiki and Yu, Julian and Kuczynski, Justin and
                  Sepich-Poore, Gregory D and Swafford, Austin D and
                  Das, Promi and Shaffer, Justin P and Lejzerowicz,
                  Franck and Belda-Ferre, Pedro and Havulinna, Aki S
                  and M{\'e}ric, Guillaume and Niiranen, Teemu and
                  Lahti, Leo and Salomaa, Veikko and Kim, Ho-Cheol and
                  Jain, Mohit and Inouye, Michael and Gilbert, Jack
                  and Knight, Rob},
  year =	 2022,
  journal =	 {mSystems},
  volume =	 7,
  issue =	 22,
  pages =	 {e0016722},
  keywords =	 {bioscience},
  doi =		 {10.1128/msystems.00167-22}
}

@Article{Lotankar2022,
  author =	 {Mrunalini Lotankar and Kati Mokkala and Noora Houttu
                  and Ella Koivuniemi and Nikolaj Sørensen and Henrik
                  Nielsen and Eveliina Munukka and Leo Lahti and Kirsi
                  Laitinen},
  title =	 {Distinct diet-microbiota-metabolism interactions in
                  overweight and obese pregnant women: a metagenomics
                  approach},
  journal =	 {Microbiology Spectrum},
  volume =	 10,
  issue =	 2,
  year =	 2022,
  pages =	 {e00893-21},
  doi =		 {10.1128/spectrum.00893-21},
  URL =
                  {https://journals.asm.org/doi/abs/10.1128/spectrum.00893-21},
  eprint =
                  {https://journals.asm.org/doi/pdf/10.1128/spectrum.00893-21},
  keywords =	 {bioscience}
}


@Article{Qin2022,
  author =	 {Youwen Qin and Aki S. Havulinna and Yang Liu and
                  Pekka Jousilahti and Scott C. Ritchie and Alex
                  Tokolyi and Jon G. Sanders and Liisa Valsta and
                  Marta Brożyńska and Qiyun Zhu and Anupriya Tripathi
                  and Yoshiki Vázquez-Baeza and Rohit Loomba and Susan
                  Cheng and Mohit Jain and Teemu Niiranen and Leo
                  Lahti and Rob Knight and Veikko Salomaa and Michael
                  Inouye and Guillaume Méric},
  title =	 {Combined effects of host genetics and diet on human
                  gut microbiota and incident disease in a single
                  population cohort},
  journal =	 {Nature Genetics},
  year =	 2022,
  volume =	 54,
  number =	 2,
  pages =	 {134--142},
  month =	 {Feb},
  doi =		 {10.1038/s41588-021-00991-z},
  keywords =	 {bioscience}
}

@Article{Ruuskanen2022dc,
  author =	 {Matti O. Ruuskanen and Pande P. Erawijantari and Aki
                  S. Havulinna and Yang Liu and Guillaume Méric and
                  Jaakko Tuomilehto and Michael Inouye and Pekka
                  Jousilahti and Veikko Salomaa and Mohit Jain and Rob
                  Knight and Leo Lahti* and Teemu J. Niiranen*},
  title =	 {Gut microbiome composition is predictive of incident
                  type 2 diabetes in a population cohort of 5 572
                  Finnish adults},
  journal =	 {Diabetes Care},
  year =	 2022,
  volume =	 45,
  number =	 4,
  pages =	 {811--818},
  doi =		 {10.2337/dc21-2358},
  keywords =	 {bioscience}
}


@Article{Armstrong2021,
  author =	 {George W Armstrong and Kalen Cantrell and Shi Huang
                  and Daniel McDonald and Niina Haiminen and Anna
                  Paola Carrieri and Qiyun Zhu and Antonio Gonzalez
                  and Imran McGrath and Kristen Beck and Daniel Hakim
                  and Aki S Havulinna and Guillaume Méric and Teemu
                  Niiranen and Leo Lahti and Veikko Salomaa and Mohit
                  Jain and Michael Inouye and Austin D Swafford and
                  Ho-Cheol Kim and Laxmi Parida and Yoshiki
                  Vázquez-Baeza and and Rob Knight},
  title =	 {Efficient computation of {Faith's} phylogenetic
                  diversity with applications in characterizing
                  microbiomes},
  journal =	 {Genome Research},
  year =	 2021,
  keywords =	 {bioscience},
  volume =	 31,
  pages =	 {2131--2137},
  doi =		 {10.1101/gr.275777.121}
}


@article{Mokkala2021,
	title        = {Impact of combined consumption of fish oil and probiotics on the serum metabolome in pregnant women with overweight or obesity},
	author       = {Kati Mokkala and Tero Vahlberg and Noora Houttu and Ella Koivuniemi and Leo Lahti and Kirsi Laitinen},
	year         = 2021,
	month        = 11,
	journal      = {EbioMedicine},
	volume       = 73,
	pages        = 103655,
	doi          = {10.1016/j.ebiom.2021.103655},
	keywords     = {bioscience}
}




@article{Laitinen2021ews,
	title        = {Probabilistic early warning signals},
	author       = {Ville Laitinen and Vasilis Dakos and Leo Lahti},
	year         = 2021,
	month        = 9,
	journal      = {Ecology & Evolution},
	volume       = 11,
	number       = 20,
	pages        = {14101--14114},
	doi          = {10.1002/ece3.8123},
	keywords     = {datascience}
}

@article{Arani2021,
	title        = {Exit Time as a Measure of Ecological Resilience},
	author       = {Babak M.S. Arani and Egbert van Nes and Leo Lahti and Stephen R. Carpenter and Marten Scheffer},
	year         = 2021,
	month        = 6,
	journal      = {Science},
	volume       = 372,
	number       = 6547,
	pages        = {eaay4895},
	doi          = {10.1126/science.aay4895},
	keywords     = {datascience}
}
@article{Hintikka2021,
	title        = {Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering},
	author       = {Hintikka, J and Lensu, S and Mäkinen, E and Karvinen, S and Honkanen, M and Linden, J and Garrels, T and Pekkala, S and Lahti, L},
	year         = 2021,
	month        = 4,
	journal      = {International Journal of Environmental Research and Public Health},
	volume       = 18,
	number       = 8,
	pages        = 4049,
	doi          = {10.3390/ijerph18084049},
	keywords     = {bioscience}
}
@article{Keskitalo2021,
	title        = {Gut microbiota diversity but not composition is related to saliva cortisol stress response at the age of 2.5 months},
	author       = {Keskitalo, A and Aatsinki, A-K and Kortesluoma, S and Pelto, J and Korhonen, L and Lahti, L and Lukkarinen, M and Munukka, E and Karlsson, H and Karlsson, L},
	year         = 2021,
	month        = 3,
	journal      = {Stress},
	volume       = 24,
	number       = 5,
	pages        = {551--560},
	doi          = {10.1080/10253890.2021.1895110},
	keywords     = {bioscience}
}
@article{Lahti2021bioc,
	title        = {Microbiome data science in the {\it SummarizedExperiment} universe},
	author       = {Leo Lahti and Felix G.M. Ernst and Sudarshan A. Shetty and others},
	year         = 2021,
	journal      = {F1000Research},
	volume       = 10,
	number       = 748,
	doi          = {10.7490/f1000research.1118712.1},
	note         = {(slides); version 1; not peer reviewed},
	keywords     = {bioscience}
}
@misc{Makela2021hs,
	title        = {Laki estää tehokkaiden tutkimusmenetelmien käytön},
	author       = {Eetu Mäkelä and Leo Lahti and Johanna Lilja and Pekka Heikkinen},
	year         = 2021,
	month        = 10,
	url          = {https://www.hs.fi/mielipide/art-2000008325656.html?share=6421b425ce95dfc19d87511d90f6d3c4},
	howpublished = {HS Mielipide},
	keywords     = {opinion}
}
@article{MarcosZambrano2021,
	title        = {Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment},
	author       = {Marcos-Zambrano, Laura Judith and Karaduzovic-Hadziabdic, Kanita and Loncar Turukalo, Tatjana and Przymus, Piotr and Trajkovik, Vladimir and Aasmets, Oliver and Berland, Magali and Gruca, Aleksandra and Hasic, Jasminka and Hron, Karel and Klammsteiner, Thomas and Kolev, Mikhail and Lahti, Leo and Lopes, Marta B and Moreno, Victor and Naskinova, Irina and Org, Elin and Paciência, Inês and Papoutsoglou, Georgios and Shigdel, Rajesh and Stres, Blaz and Vilne, Baiba and Yousef, Malik and Zdravevski, Eftim and Tsamarindos, Ioannis and Carrillo de Santa Pau, Enrique and Claesson, Marcus J. and Moreno-Indias, Isabel and Truu, Jaak},
	year         = 2021,
	journal      = {Frontiers in Microbiology},
	volume       = 12,
	pages        = 313,
	doi          = {10.3389/fmicb.2021.634511},
	issn         = {1664-302X},
	url          = {https://www.frontiersin.org/article/10.3389/fmicb.2021.634511},
	keywords     = {bioscience}
}
@article{MorenoIndias2021,
	title        = {Statistical and machine learning techniques in human microbiome studies: contemporary challenges and solutions},
	author       = {Isabel Moreno-Indias and Leo Lahti and Miroslava Nedyalkova and Ilze Elbere and Gennady V. Roshchupkin and Muhamed Adilovic and Onder Aydemir and Burcu Bakir-Gungor and Enrique Carrillo-de Santa Pau and Domenica D'Elia and Magesh S. Desai and Laurent Falquet and Aycan Gundogdu and Karel Hron and Thomas Klammsteiner and Marta B. Lopes and Laura J. Marcos Zambrano and Cláudia Marques and Michael Mason and Patrick May and Lejla Pašić and Gianvito Pio and Sándor Pongor and Vasilis J. Promponas and Piotr Przymus and Julio Sáez-Rodríguez and Alexia Sampri and Rajesh Shigdel and Blaz Stres and Ramona Suharoschi and Jaak Truu and Ciprian-Octavian Truică and Baiba Vilne and Dimitrios P. Vlachakis and Ercüment Yılmaz and Georg Zeller and Aldert Zomer and David Gómez-Cabrero and Marcus Claesson},
	year         = 2021,
	month        = 2,
	journal      = {Frontiers in Microbiology},
	volume       = 12,
	pages        = 277,
	doi          = {10.3389/fmicb.2021.635781},
	keywords     = {bioscience}
}
@article{Palmu2021ijerph,
	title        = {Targeting gut microbiota to treat hypertension: a systematic review},
	author       = {Joonatan Palmu and Leo Lahti and Teemu Niiranen},
	year         = 2021,
	month        = 1,
	journal      = {International Journal of Environmental Research and Public Health},
	volume       = 18,
	number       = 3,
	pages        = 1248,
	doi          = {10.3390/ijerph18031248},
	keywords     = {bioscience},
	tag          = {review}
}
@article{Ruuskanen2021,
	title        = {Modeling spatial patterns in host-associated microbial communities},
	author       = {Matti Ruuskanen and Guilhem Sommeria-Klein and Aki Havulinna and Teemu Niiranen and Leo Lahti},
	year         = 2021,
	month        = 5,
	journal      = {Environmental Microbiology},
	volume       = 23,
	number       = 5,
	pages        = {2374--2388},
	doi          = {10.1111/1462-2920.15462},
	keywords     = {bioscience}
}
@article{Ruuskanen2021gutmicrobes,
	title        = {Links between gut microbiome composition and fatty liver disease in a large population sample},
	author       = {Matti O. Ruuskanen and Fredrik Åberg and Ville Männistö and Aki S. Havulinna and Guillaume Méric and Yang Liu and Rohit Loomba and Yoshiki Vázquez-Baeza and Anupriya Tripathi and Liisa M. Valsta and Michael Inouye and Pekka Jousilahti and Veikko Salomaa and Mohit Jain and Rob Knight and Leo Lahti and Teemu J. Niiranen},
	year         = 2021,
	month        = 3,
	journal      = {Gut Microbes},
	volume       = 13,
	doi          = {10.1080/19490976.2021.1888673},
	issue        = 1,
	keywords     = {bioscience}
}

@article{Salosensaari2021,
	title        = {Taxonomic signatures of cause-specific mortality risk in human gut microbiome},
	author       = {Aaro Salosensaari* and Ville Laitinen* and Aki S Havulinna and Guillaume Meric and Susan Cheng and Markus Perola and Liisa Valsta and Georg Alfthan and Michael Inouye and Jeramie D Watrous and Tao Long and Rodolfo Salido and Karenina Sanders and Caitriona Brennan and Gregory C Humphrey and Jon G Sanders and Mohit Jain and Pekka Jousilahti and Veikko Salomaa and Rob Knight and Leo Lahti* and Teemu Niiranen*},
	year         = 2021,
	journal      = {Nature Communications},
	volume       = 12,
	pages        = 2671,
	doi          = {10.1038/s41467-021-22962-y},
	keywords     = {bioscience},
	annote       = {Preprint featured in HS Tiede Jan 30, 2020. Featured in Science Magazine Jan 22, 2020 https://www.sciencemag.org/news/2020/01/microbes-your-gut-could-predict-whether-you-re-likely-die-next-15-years}
}

@article{Sarhadi2021,
	title        = {Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors},
	author       = {Virinder Sarhadi and Binu Mathew and Arto Kokkola A and Tiina Karla and Milja Tikkanen and Hilpi Rautelin and Leo Lahti and Pauli Puolakkainen and Sakari Knuutila},
	year         = 2021,
	journal      = {Gut Pathogens},
	volume       = 13,
	pages        = {1--9},
	doi          = {10.1186/s13099-021-00403-x},
	keywords     = {bioscience},
	issue        = 11
}


@incollection{Tolonen2021canon,
	title        = {Examining the Early Modern Canon: The English Short Title Catalogue and Large-Scale Patterns of Cultural Production.},
	author       = {Mikko Tolonen and Mark J. Hill and Ali Zeeshan Ijaz and Ville Vaara and Leo Lahti},
	year         = 2021,
	month        = 3,
	booktitle    = {Data Visualization in Enlightenment Literature and Culture},
	publisher    = {Palgrave Macmillan, Cham.},
	doi          = {10.1007/978-3-030-54913-8_3},
	note         = {Book chapter in: Data Visualization in Enlightenment Literature and Culture},
	editor       = {Baird, I.},
	chapter      = 3,
	keywords     = {dh}
}

@inproceedings{Tiihonen2021chr,
  title =	 {Probabilistic Analysis of Early Modern British Book
                  Prices},
  author =	 {Iiro Tiihonen and Mikko Tolonen and Leo Lahti},
  year =	 2021,
  booktitle =	 {{Proc. CEUR Workshop Proceedings on Computational
                  Humanities Research}},
  pages =	 {39--48},
  pdf =
                  {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2021-Tiihonen-CHR.pdf},
  note =	 {In M Ehrmann, F Karsdorp et al. (eds).},
  month =	 {Nov},
  address =	 {Aachen},
  volume =	 2989,
  url =		 {http://ceur-ws.org/Vol-2989/short_paper9.pdf},
  keywords =	 {dh}
}

@article{Tolonen2021rcl,
  title =	 {Corpus Linguistics and Eighteenth Century
                  Collections Online (ECCO)},
  author =	 {Tolonen, M and M{\"a}kel{\"a}, E and Ijaz, A and
                  Lahti, L},
  year =	 2021,
  journal =	 {Research in Corpus Linguistics},
  volume =	 9,
  number =	 1,
  pages =	 {19--34},
  doi =		 {10.32714/ricl.09.01.03},
  keywords =	 {dh}
}

@article{crossys2021,
	title        = {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},
	author       = {Marja A. Heiskanen and Sanna M. Honkala and Ronja A. Ojala and Riikka Lautamäki and Kalle Koskensalo and Martin Lietzén and Jaakko Hentilä and Virva Saunavaara and Jani Saunavaara and Mika Helmiö and Eliisa Löyttyniemi and Lauri Nummenmaa and Maria C. Collado and Tarja Malm and Leo Lahti and Kirsi H. Pietiläinen and Jaakko Kaprio and Juha O. Rinne and Jarna C. Hannukainen},
	year         = 2021,
	journal      = {BMC Sports Science, Medicine and Rehabilitation},
	volume       = 13,
	pages        = 16,
	doi          = {10.1186/s13102-021-00241-z},
	keywords     = {bioscience}
}



@article{Liu2022liver,
  title =	 {Early prediction of liver disease using conventional
                  risk factors and gut microbiome-augmented gradient
                  boosting},
  author =	 {Yang Liu and Guillaume Méric and Aki S. Havulinna
                  and Shu Mei Teo and Fredrik Åberg and Matti
                  Ruuskanen and Jon Sanders and Qiyun Zhu and Anupriya
                  Tripathi and Karin Verspoor and Susan Cheng and
                  Mohit Jain and Pekka Jousilahti and Yoshiki
                  Vázquez-Baeza and Rohit Loomba and Leo Lahti and
                  Teemu Niiranen and Veikko Salomaa and Rob Knight and
                  Michael Inouye},
  journal =	 {Cell Metabolism},
  volume =	 34,
  issue =	 5,
  pages =	 {719-730.e4},
  year =	 2022,
  doi =		 {10.1016/j.cmet.2022.03.002},
  keywords =	 {bioscience}
}

@article{Aatsinki2020,
	title        = {Maternal prenatal psychological distress and hair cortisol levels associate with infant fecal microbiota composition at 2.5 months of age},
	author       = {Anna-Katariina Aatsinki and Anniina Keskitalo and Ville Laitinen and Eveliina Munukka and Henna-Maria Uusitupa and Leo Lahti and Susanna Kortesluoma and Paula Mustonen and Ana João Rodrigues and Bárbara Coimbra and Pentti Huovinen and Hasse Karlsson and Linnea Karlsson},
	year         = 2020,
	journal      = {Psychoneuroendocrinology},
	volume       = 119,
	pages        = 104754,
	doi          = {10.1016/j.psyneuen.2020.104754},
	keywords     = {bioscience}
}

@article{Khalighi2021,
	title        = {Three-species Lotka-Volterra model with respect to Caputo and Caputo-Fabrizio fractional operators},
	author       = {Moein Khalighi and Leila Eftekhari and Soleiman Hosseinpour and Leo Lahti},
	year         = 2020,
	month        = {January},
	journal      = {Symmetry},
	volume       = 13,
	pages        = 368,
	doi          = {10.3390/sym13030368},
	issue        = 3,
	keywords     = {datascience}
}
@article{Koffert2020,
	title        = {Partial restoration of normal intestinal microbiota in morbidly obese women six months after bariatric surgery},
	author       = {Jukka Koffert and Leo Lahti and Lotta Nylund and Seppo Salminen and Jarna C Hannukainen and Paulina Salminen and Willem de Vos and Pirjo Nuutila},
	year         = 2020,
	journal      = {PeerJ – Life & Environment},
	volume       = 8,
	pages        = {e10442},
	doi          = {10.7717/peerj.10442},
	note         = {Shared first authorship.},
	keywords     = {bioscience}
}
@inproceedings{Lahti2020chr,
	title        = {Quantifying bias and uncertainty in historical data collections with probabilistic programming},
	author       = {Leo Lahti and Eetu Mäkelä and Mikko Tolonen},
	editor       = {Karsdorp, Folgert and McGillivray, Barbara and Nerghes, Adina and Wevers, Melvin},
	year         = 2020,
	month        = {Nov},
	booktitle    = {{CHR2020: Proc. CEUR Workshop Proceedings on Computational Humanities Research}},
	address      = {Amsterdam, The Netherlands},
  publisher    = {CEUR-WS.org},
  series       = {CEUR Workshop Proceedings},
  volume       = {2723},
	pages        = {80--89},
	url          = {http://ceur-ws.org/Vol-2723/short46.pdf},
	keywords     = {dh}
}
@article{Lahti2020hs1,
	title        = {Laskentamallit eivät lähtökohtaisesti ole salassa pidettävää tietoa},
	author       = {Leo Lahti and Thomas Wallgren and Markku Kulmala},
	year         = 2020,
	month        = {May},
	journal      = {HS Mielipide},
	url          = {https://www.hs.fi/mielipide/art-2000006494641.html},
	keywords     = {opinion}
}
@article{Lahti2020hs2,
	title        = {Lähdekoodin sisältämien yksityiskohtien avoimuus on keskeistä päätöksenteon läpinäkyvyydelle.},
	author       = {Leo Lahti},
	year         = 2020,
	month        = {June},
	journal      = {HS Mielipide},
	url          = {https://www.hs.fi/mielipide/art-2000006545770.html},
	keywords     = {opinion}
}
@article{Lahti2020okf1,
	title        = {Tietopyyntö epidemialaskelmien lähdekoodeista},
	author       = {Leo Lahti and Tarmo Toikkanen},
	year         = 2020,
	month        = {May},
	journal      = {Open Knowledge Finland Blog},
	url          = {https://www.okf.fi/fi/2020/05/13/tietopyynto-thln-epidemialaskelmien-lahdekoodeista},
	keywords     = {opinion}
}
@article{Lahti2020okf2,
	title        = {Päätös epidemialaskelmien salaamisesta vastoin valtioneuvoston avoimuuslinjausta},
	author       = {Leo Lahti},
	year         = 2020,
	month        = {June},
	journal      = {Open Knowledge Finland Blog},
	url          = {https://www.okf.fi/fi/2020/06/15/thln-paatos-epidemialaskelmien-salaamisesta-vastoin-valtioneuvoston-avoimuuslinjausta/},
	keywords     = {opinion}
}
@article{Lahti2020thinkopen,
	title        = {Avoimuus voi vahvistaa päätöksenteon tieteellistä pohjaa},
	author       = {Leo Lahti},
	year         = 2020,
	month        = {August},
	journal      = {University of Helsinki, ThinkOpen blog},
	url          = {https://blogs.helsinki.fi/thinkopen/lahdekoodin-avoimuus-paatoksenteossa/},
	keywords     = {opinion}
}
@inproceedings{Makela2020,
	title        = {Wrangling with Non-Standard Data},
	author       = {Mäkelä, E and Lagus, K and Lahti, L and Säily, T and Tolonen, M and Hämäläinen, M and Kaislaniemi, S and Nevalainen, T},
	year         = 2020,
	month        = {March},
	booktitle    = {Proc. Digital Humanities in the Nordic Countries},
	series       = {CEUR Workshop Proceedings},
	volume       = 2612,
	pages        = {81--96},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2020-Makela-DHN.pdf},
	editor       = {Sanita Reinsone and Inguna Skadiņa and Anda Baklāne and Jānis Daugavietis},
	keywords     = {dh}
}
@article{Nylund2020,
	title        = {Diet, perceived intestinal well-being, fecal microbiota and short chain fatty acids in oat-using subjects with celiac disease or gluten sensitivity.},
	author       = {Lotta Nylund and Salla Hakkola and Leo Lahti and Seppo Salminen and Marko Kalliomäki and Baoru Yang and Kaisa M. Linderborg},
	year         = 2020,
	month        = {August},
	journal      = {Nutrients},
	volume       = 12,
	pages        = 2570,
	doi          = {10.3390/nu12092570},
	note         = {Special issue.},
	issue        = 9,
	keywords     = {bioscience}
}
@article{Palmu2020,
	title        = {Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals},
	author       = {Joonatan Palmu and Aaro Salosensaari and Aki S. Havulinna and Susan Cheng and Michael Inouye and Mohit Jain and Rodolfo A. Salido and Karenina Sanders and Caitriona Brennan and Gregory C. Humphrey and Jon G. Sanders and Erkki Vartiainen and Tiina Laatikainen and Pekka Jousilahti and Veikko Salomaa and Rob Knight and Leo Lahti and Teemu J. Niiranen},
	year         = 2020,
	month        = {July},
	journal      = {Journal of the American Heart Association},
	doi          = {10.1161/JAHA.120.016641},
	keywords     = {bioscience}
}
@article{Palmu2020JAHA,
	title        = {Eicosanoid Inflammatory Mediators Are Robustly Associated with Blood Pressure in the General Population},
	author       = {Joonatan Palmu and others},
	year         = 2020,
	journal      = {Journal of American Heart Association},
	volume       = 9,
	pages        = {e016641},
	doi          = {10.1161/JAHA.120.017598},
	issue        = 15,
	keywords     = {bioscience}
}
@article{Pekkala2020,
	title        = {Prebiotic Xylo-oligosaccharides Targeting Faecalibacterium prausnitzii Prevent High Fat Diet-induced Hepatic Steatosis in Rats},
	author       = {Sanna Lensu and Raghunath Pariyani and Elina Mäkinen and Baoru Yang and Wisam Saleem and Eveliina Munukka and Maarit Lehti and Baoru Yang and Jere Linden and Marja Tiirola and Leo Lahti and Satu Pekkala},
	year         = 2020,
	month        = 10,
	journal      = {Nutrients},
	volume       = 12,
	number       = 11,
	pages        = 3225,
	doi          = {10.3390/nu12113225},
	keywords     = {bioscience}
}
@article{Sarhadi2020,
	title        = {Gut Microbiota and Host Gene Mutations in Colorectal Cancer Patients and Controls of Iranian and Finnish Origin},
	author       = {Sarhadi, V and Lahti, L and Saberi, F and Youssef, O and Kokkola, A and Karla, T and Tikkanen, M and Rautelin, H and Puolakkainen, P and Salehi, R and Knuutila, S},
	year         = 2020,
	month        = 3,
	journal      = {Anticancer Research},
	volume       = 40,
	number       = 3,
	pages        = {1325--1334},
	doi          = {10.21873/anticanres.14074},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2020-Sarhadi-Anticanc.pdf},
	keywords     = {bioscience}
}
@article{Vaura2020jch,
	title        = {Unsupervised hierarchical clustering identifies a metabolically challenged subgroup of hypertensive individuals},
	author       = {Felix C. Vaura and Veikko V. Salomaa and Ilkka M. Kantola and Risto Kaaja and Leo Lahti and Teemu J. Niiranen},
	year         = 2020,
	month        = 8,
	journal      = {Journal of Clinical Hypertension},
	volume       = 22,
	number       = 9,
	pages        = {1546--1553},
	doi          = {10.1111/jch.13984},
	keywords     = {bioscience}
}
@techreport{openedu2020,
	title        = {National policy and executive plan by the higher education and research community for 2021-2025 - Policy component 1: Open access to educational resources.},
	author       = {Expert Panel in Open Education (Open Science Coordination in Finland)},
	year         = 2020,
	journal      = {Responsible Research Series},
	publisher    = {Committee for Public Information (TJNK) and Federation of Finnish Learned Societies (TSV).},
	address      = {Helsinki, Finland},
	volume       = 16,
	keywords     = {openscience}
}
@article{Aatsinki2019,
	title        = {Gut microbiota composition is associated with temperament traits in infants},
	author       = {Anna Aatsinki and Leo Lahti and Henna Uusitupa and Eveliina Munukka and Anniina Keskitalo, Saara Nolvi and Siobhain O'Mahony and Sami Pietilä and Laura Elo and Erkki Eerola and Hasse Karlsson and Linnea Karlsson},
	year         = 2019,
	month        = {May},
	journal      = {Brain Behavior and Immunity},
	volume       = 80,
	pages        = {849--858},
	doi          = {10.1016/j.bbi.2019.05.035},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Aatsinki.pdf},
	keywords     = {bioscience}
}
@inproceedings{Hill2019dhn,
	title        = {Reconstructing intellectual networks: from the {ESTC}'s bibliographic metadata to historical material},
	author       = {Mark J Hill and Ville Vaara and Tanja S{\"a}ily and Leo Lahti and Mikko Tolonen},
	year         = 2019,
	month        = {March},
	booktitle    = {Proc. Digital Humanities in the Nordic Countries},
	address      = {Copenhagen},
	series       = {CEUR Workshop Proceedings},
	volume       = 2364,
	pages        = {201--219},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Hill-DHN.pdf},
	note         = {Best paper award.},
	editor       = {Costanza Navarretta and Manex Agirrezabal and Bente Maegaard},
	keywords     = {dh}
}
@inproceedings{Ijaz2019dh,
	title        = {Analytical Edition Detection In Bibliographic Metadata},
	author       = {Ali Ijaz and Hege Roivainen and Leo Lahti},
	year         = 2019,
	month        = {July},
	booktitle    = {Proceedings of the Digital Humanities (DH2019)},
	doi          = {10.34894/IWQ5BO},
	keywords     = {dh}
}
@inproceedings{Ijaz2019rdhum,
	title        = {Analytical determination of editions from bibliographic metadata},
	author       = {Ali Ijaz and Mikko Tolonen and Leo Lahti},
	year         = 2019,
	month        = {August},
	booktitle    = {Proceedings of the Research Data in the Humanities Conference},
	address      = {Oulu},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Ijaz-RDHum.pdf},
	keywords     = {dh}
}
@article{Lahti2019bds,
	title        = {Bibliographic Data Science and the History of the Book (c. 1500–1800)},
	author       = {Leo Lahti and Jani Marjanen and Hege Roivainen and Mikko Tolonen},
	year         = 2019,
	month        = {January},
	journal      = {Cataloging \& Classification Quarterly},
	publisher    = {Routledge},
	volume       = 57,
	number       = 1,
	pages        = {5--23},
	doi          = {10.1080/01639374.2018.1543747},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Lahti-CCQ.pdf},
	note         = {Special issue.},
	keywords     = {dh}
}
@inproceedings{Lahti2019rdhum,
	title        = {Best practices in bibliographic data science},
	author       = {Leo Lahti and Ville Vaara and Jani Marjanen and Mikko Tolonen},
	year         = 2019,
	month        = {August},
	booktitle    = {Proceedings of the Research Data in the Humanities Conference},
	address      = {Oulu},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Lahti-RDHUM.pdf},
	keywords     = {dh}
}
@inproceedings{Makela2019dhn,
	title        = {Interdisciplinary collaboration in studying newspaper materiality},
	author       = {Eetu M{\"a}kel{\"a} and Mikko Tolonen and Jani Marjanen and Antti Kanner and Ville Vaara and Leo Lahti},
	year         = 2019,
	month        = {March},
	booktitle    = {Proc. Twin Talks workshop. Digital Humanities in the Nordic Countries},
	address      = {Copenhagen},
	series       = {CEUR Workshop Proceedings},
	volume       = 2365,
	pages        = {55--66},
	url          = {http://ceur-ws.org/Vol-2365/07-TwinTalks-DHN2019_paper_7.pdf},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Makela-DHN.pdf},
	editor       = {Steven Krauwer and Darja Fišer},
	pubstate     = {dh},
	keywords     = {dh}
}
@article{Marjanen2019,
	title        = {A National Public Sphere? Analyzing the Language, Location, and Form of Newspapers in Finland, 1771–1917},
	author       = {Jani Marjanen and Ville Vaara and Antti Kanner and Hege Roivainen and Eetu Mäkelä and Leo Lahti and Mikko Tolonen},
	year         = 2019,
	month        = {June},
	journal      = {Journal of European Periodical Studies},
	volume       = 4,
	number       = 1,
	doi          = {10.21825/jeps.v4i1.10483},
	url          = {https://ojs.ugent.be/jeps/article/view/10483},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Marjanen-JEPS.pdf},
	note         = {Special issue: Digital Approaches Towards Serial Publications},
	pubstate     = {dh},
	keywords     = {dh}
}
@article{Shetty2019,
	title        = {Microbiome data science},
	author       = {Sudarshan Shetty and Leo Lahti},
	year         = 2019,
	month        = {October},
	journal      = {Journal of Biosciences},
	volume       = 44,
	pages        = 115,
	doi          = {10.1007/s12038-019-9930-2},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Shetty-MDS.pdf},
	category     = {review},
	keywords     = {bioscience}
}
@article{Timmis2019,
	title        = {Microbiome yarns: The Global Phenotype-Genotype Survey. Episode III: importance of microbiota diversification for microbiome function and biome health},
	author       = {Timmis, K and Jebok, F and Rohde, M and Lahti, L and Molinari, G},
	year         = 2019,
	month        = {April},
	journal      = {Microbial Biotechnology},
	doi          = {10.1111/1751-7915.13406},
	keywords     = {misc},
	annote       = {Comics piece for the popularization of microbiome research.}
}
@inproceedings{Tolonen2019dhn,
	title        = {Scaling up bibliographic data science},
	author       = {Mikko Tolonen and Jani Marjanen and Hege Roivainen and Leo Lahti},
	year         = 2019,
	month        = {March},
	booktitle    = {Proceedings of the Digital Humanities in the Nordics (DHN2019)},
	address      = {Copenhagen},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Tolonen-DHN.pdf},
	editor       = {Costanza Navarretta and Manex Agirrezabal and Bente Maegaard},
	pubstate     = {dh},
	keywords     = {dh}
}
@inproceedings{Vaara2019dh,
	title        = {The Emerging Paradigm of Bibliographic Data Science},
	author       = {Ville Vaara and Ali Ijaz and Iiro Tiihonen and Simon Hengchen and Antti Kanner and Tanja S{\"a}ily and Leo Lahti},
	year         = 2019,
	month        = {July},
	booktitle    = {Proceedings of the Digital Humanities (DH2019)},
	keywords     = {dh}
}
@article{stolaki2019,
	title        = {Microbial communities in a dynamic {it in vitro} model for the human ileum resemble the human ileal microbiota},
	author       = {Stolaki, Maria and Minekus, Mans and Venema, Koen and Lahti, Leo and Smid, Eddy J. and Kleerebezem, Michiel and Zoetendal, Erwin G},
	year         = 2019,
	month        = {August},
	journal      = {FEMS Microbiology Ecology},
	number       = 8,
	pages        = {fiz096},
	doi          = {10.1093/femsec/fiz096},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Stolaki-FEMS.pdf},
	keywords     = {bioscience},
	vol          = 95
}
@article{tolonen2019,
	title        = {A Quantitative Approach to Book-Printing in Sweden and Finland, 1640–1828},
	author       = {Mikko Tolonen and Leo Lahti and Hege Roivainen and Jani Marjanen},
	year         = 2019,
	journal      = {Historical Methods: A Journal of Quantitative and Interdisciplinary History},
	publisher    = {Routledge},
	volume       = 52,
	pages        = {57--78},
	doi          = {10.1080/01615440.2018.1526657},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2019-Tolonen.pdf},
	issue        = 1,
	keywords     = {dh}
}
@article{Aatsinki2018,
	title        = {Gut Microbiota Composition in Mid-Pregnancy Is Associated with Gestational Weight Gain but Not Prepregnancy Body Mass Index},
	author       = {Anna-Katariina Aatsinki and Henna-Maria Uusitupa and Eveliina Munukka and Henri Pesonen and Anniina Rintala and Sami Pietilä and Leo Lahti and Erkki Eerola and Linnea Karlsson and Hasse Karlsson},
	year         = 2018,
	month        = {May},
	journal      = {Journal of Womens Health},
	doi          = {10.1089/jwh.2017.6488},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2018-Aatsinki.pdf},
	note         = {Epub ahead of print.},
	keywords     = {bioscience}
}
@article{Arani2018,
	title        = {Stability estimation of autoregulated genes under {Michaelis-Menten} type kinetics},
	author       = {Arani, Babak M. S. and Mahmoudi, Mahdi and Lahti, Leo and Gonz\'alez, Javier and Wit, Ernst C.},
	year         = 2018,
	month        = {Jun},
	journal      = {Physical Review E},
	publisher    = {American Physical Society},
	volume       = 97,
	number       = 6,
	pages        = 062407,
	doi          = {10.1103/PhysRevE.97.062407},
	issn         = {2470-0045},
	url          = {https://link.aps.org/doi/10.1103/PhysRevE.97.062407},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2018-Arani-PhysRevE.pdf},
	numpages     = 10,
	keywords     = {datascience}
}
@techreport{Bjork2018,
	title        = {Opening academic publishing: development and application of systematic evaluation criteria},
	author       = {Anna Björk and Juho-Matti Paavolainen and Teemu Ropponen and Mikael Laakso and Leo Lahti},
	year         = 2018,
	month        = {January},
	publisher    = {Open Science and Research Initiative (ATT)},
	url          = {http://urn.fi/URN:NBN:fi-fe201802123334},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2018-Bjork-ATT.pdf},
	category     = {report},
	note         = {Report on the openness of major scientific publishers commissioned by Finnish Ministry of Education and Culture},
	institution  = {unknown},
	authorship   = {corresponding},
	pubstate     = {openscience},
	keywords     = {openscience}
}
@article{Faust2018,
	title        = {Signatures of ecological processes in microbial community time series},
	author       = {Karoline Faust and Franziska Bauchinger and Beatrice Laroche and Sophie de Buyl and Leo Lahti and Alex D Washburne and Didier Gonze and Stefanie Widder},
	year         = 2018,
	month        = {June},
	journal      = {Microbiome},
	volume       = 6,
	number       = 120,
	doi          = {10.1186/s40168-018-0496-2},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2018-Faust-Microbiome.pdf},
	keywords     = {bioscience}
}
@article{Gonze2018,
	title        = {Microbial communities as dynamical systems},
	author       = {Didier Gonze and Katharine Z Coyte and Leo Lahti and Karoline Faust},
	year         = 2018,
	month        = {July},
	journal      = {Current Opinion in Microbiology},
	volume       = 44,
	pages        = {41--49},
	doi          = {10.1016/j.mib.2018.07.004},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2018-Gonze.pdf},
	keywords     = {bioscience}
}
@inproceedings{Hill2018,
	title        = {Spheres of “public” in eighteenth-century Britain},
	author       = {Mark J Hill and Antti Kanner and Jani Marjanen and Ville Vaara and Eetu Mäkelä and Leo Lahti and Mikko Tolonen},
	year         = 2018,
	month        = 3,
	booktitle    = {Proceedings of the Digital Humanities in the Nordics Conference},
	address      = {Helsinki, Finland},
	category     = {abstract},
	keywords     = {dh}
}
@inproceedings{Lahti2018IDA,
	title        = {Open Data Science},
	author       = {Lahti, Leo},
	year         = 2018,
	month        = {October},
	booktitle    = {Advances in Intelligent Data Analysis XVII. Lecture Notes in Computer Science 11191.},
	publisher    = {Springer},
	publisher    = {Springer Nature},
	address      = {India},
	volume       = 11191,
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2018-Lahti-IDA.pdf},
	category     = {perspective},
	note         = {Conference proceedings.},
	keywords     = {openscience},
	authorship   = {first}
}
@inproceedings{Laitinen2018IDA,
	title        = {A hierarchical Ornstein-Uhlenbeck model for stochastic time series analysis},
	author       = {Laitinen, Ville and Lahti, Leo},
	year         = 2018,
	month        = {October},
	booktitle    = {Advances in Intelligent Data Analysis XVII. Lecture Notes in Computer Science 11191.},
	publisher    = {Springer},
	address      = {India},
	url          = {https://github.com/velait/OUP},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2018-Laitinen-IDA.pdf},
	note         = {Conference proceedings.},
	keywords     = {datascience},
	authorship   = {pi}
}
@article{Tolonen2018gaudeamus,
	title        = {Digitaaliset ihmistieteet ja historiantutkimus},
	author       = {Mikko Tolonen and Leo Lahti},
	year         = 2018,
	journal      = {Menneisyyden rakentajat},
	booktitle    = {Menneisyyden rakentajat},
	publisher    = {Gaudeamus},
	url          = {https://www.gaudeamus.fi/menneisyyden-rakentajat/},
	note         = {(in Finnish). In: Hannikainen, MO and Danielsbacka, M and Tepora, T (eds.). Menneisyyden rakentajat. Gaudeamus, Helsinki, 2018.},
	authorship   = {second},
	language     = {Finnish},
	editor       = {Hannikainen, MO and Danielsbacka, M and Tepora, T},
	journaltitle = {Menneisyyden rakentajat},
	keywords     = {dh},
	annote       = {This is a book chapter but classified as article as could not find a way to include this to CSL automatically generated bibliography yet.}
}
@article{Youssef2018,
	title        = {Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms},
	author       = {Omar Youssef and Leo Lahti and Arto Kokkola and Tiina Karla and Milja Tikkanen and Homa Ehsan and Monika Carpelan‑Holmström and Selja Koskensalo and Tom Böhling and Hilpi Rautelin and Pauli Puolakkainen and Sakari Knuutila and Virinder Sarhadi},
	year         = 2018,
	month        = {July},
	journal      = {Digestive Diseases and Sciences},
	volume       = 63,
	number       = 11,
	pages        = {2950--2958},
	doi          = {10.1007/s10620-018-5190-5},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2018-Youssef.pdf},
	authorship   = {shared first},
	keywords     = {bioscience}
}
@techreport{openutu2018,
	title        = {Turun yliopiston avoimen tutkimuksen politiikka / Open Research Policy},
	author       = {{OpenUTU work group}},
	year         = 2018,
	month        = {May},
	journal      = {unknwown},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2018-avoimen-tutkimuksen-politiikka-fi.pdf},
	category     = {report},
	note         = {(in Finnish)},
	key          = {report},
	institution  = {University of Turku},
	howpublished = {Report},
	journaltitle = {unknown},
	keywords     = {openscience},
	annote       = {Member in the work group that developed the report.}
}
@article{Buelow2017,
	title        = {Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects},
	author       = {Elena Buelow and Teresita {d.J.} Bello González and Susana Fuentes and Wouter A.A. {de Steenhuijsen Piters} and Leo Lahti and Jumamurat R. Bayjanov and Eline A.M. Majoor and Johanna C. Braat and Maaike S. van Mourik and Evelien A.N. Oostdijk and Rob J.L. Willems and Marc J.M. Bonten and Mark W.J. van Passel and Hauke Smidt and Willem van Schaik},
	year         = 2017,
	month        = {Aug},
	journal      = {Microbiome},
	volume       = 5,
	number       = 1,
	pages        = 88,
	doi          = {10.1186/s40168-017-0309-z},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2017-Buelow-Microbiome.pdf},
	keywords     = {bioscience}
}
@article{Faust2017,
	title        = {Multi-stability and the origin of microbial community types},
	author       = {Didier Gonze and Leo Lahti and Jeroen Raes and Karoline Faust},
	year         = 2017,
	month        = {may},
	journal      = {ISME Journal},
	volume       = 11,
	pages        = {2159--2166},
	doi          = {10.1038/ismej.2017.60},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2017-Faust-ISME.pdf},
	keywords     = {bioscience}
}
@article{Harris17,
	title        = {Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process},
	author       = {Keith Harris and Todd L Parsons and Umer Z Ijaz and Leo Lahti and Ian Holmes and Christopher Quince},
	year         = 2017,
	month        = {March},
	journal      = {Proceedings of the IEEE},
	volume       = 105,
	number       = 3,
	pages        = {516--529},
	doi          = {10.1109/JPROC.2015.2428213},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2017-Harris-IEEE.pdf},
	keywords     = {bioscience}
}
@article{Lahti17eurostat,
	title        = {Retrieval and Analysis of Eurostat Open Data with the eurostat Package},
	author       = {Leo Lahti and Janne Huovari and Markus Kainu and Przemysław Biecek},
	year         = 2017,
	journal      = {The R Journal},
	volume       = 9,
	number       = 1,
	pages        = {385--392},
	url          = {https://journal.r-project.org/archive/2017/RJ-2017-019/index.html},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2017-Lahti-RJournal.pdf},
	keywords     = {dh},
	software     = {yes},
	authorship   = {first, corresponding},
	annote       = {R package homepage URL: http://ropengov.github.io/eurostat/}
}
@article{Lahti17phos,
	title        = {Alchemy & algorithms: perspectives on the philosophy and history of open science},
	author       = {Leo Lahti and Filipe da Silva and Markus Petteri Laine and Viivi Lähteenoja and Mikko Tolonen},
	year         = 2017,
	month        = {May},
	journal      = {RIO Journal},
	volume       = 3,
	pages        = {e13593},
	doi          = {10.3897/rio.3.e13593},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2017-Lahti-PHOS.pdf},
	category     = {perspective},
	note         = {Review of the international conference, including electronic material (video interviews, lectures and podcasts.},
	authorship   = {first, corresponding},
	keywords     = {openscience},
	pubstate     = {openscience},
	keywords     = {dh}
}
@article{Shetty2017,
	title        = {Intestinal microbiome landscaping: Insight in community assemblage and implications for microbial modulation strategies},
	author       = {Shetty, SA and Hugenholtz, F and Lahti, L and Smidt, H and de Vos, WM and Danchin, A},
	year         = 2017,
	month        = {March},
	journal      = {FEMS Microbiology Reviews},
	volume       = 41,
	pages        = {182--199},
	doi          = {10.1093/femsre/fuw045},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2017-Shetty-FEMS.pdf},
	note         = {fuw045},
	note         = {review},
	issue        = 2,
	keywords     = {bioscience}
}
@inproceedings{Tolonen16dh,
	title        = {Printing in a Periphery: a Quantitative Study of Finnish Knowledge Production, 1640-1828},
	author       = {Mikko Tolonen and Niko Ilom{\"a}ki and Hege Roivainen and Leo Lahti},
	year         = 2016,
	month        = 7,
	booktitle    = {Digital Humanities 2016: Conference Abstracts},
	publisher    = {Jagiellonian University & Pedagogical University, Kraków},
	address      = {Krakow, Poland},
	pages        = {383--385},
	url          = {http://dh2016.adho.org/abstracts/9},
	category     = {abstract},
	keywords     = {dh}
}
@article{Aleksic14,
	title        = {The Open Science Peer Review Oath},
	author       = {Jelena Aleksic and Adrian Alexa and Teresa K Attwood and Neil Chue Hong and Martin Dahl{\"o} and Robert Davey and Holger Dinkel and Konrad U F{\"o}rstner and Ivo Grigorov and Jean-Karim Hériché and Leo Lahti and Dan MacLean and Michael L Markie and Jenny Molloy and Maria Victoria Schneider and Camille Scott and Richard Smith-Unna and Bruno Miguel Vieira},
	year         = 2015,
	month        = 1,
	journal      = {F1000Research},
	volume       = 3,
	pages        = 271,
	doi          = {10.12688/f1000research.5686.2},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2014-Aleksic.pdf},
	category     = {perspective},
	note         = {AllBio: Open Science & Reproducibility Best Practice Workshop},
	keywords     = {openscience}
}
@article{Faust15,
	title        = {Metagenomics meets time series analysis: unraveling microbial community dynamics},
	author       = {Karoline Faust and Leo Lahti and Didier Gonze and Willem M de Vos and Jeroen Raes},
	year         = 2015,
	month        = 6,
	journal      = {Current Opinion in Microbiology},
	volume       = 25,
	pages        = {56--66},
	doi          = {10.1016/j.mib.2015.04.004},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2015-Faust-CurrOpMicrob.pdf},
	category     = {review},
	keywords     = {bioscience},
	authorship   = {shared first}
}
@article{Lahti15LIBER,
	title        = {A quantitative study of history in the English short-title catalogue (ESTC) 1470-1800},
	author       = {Leo Lahti and Niko Ilom{\"a}ki and Mikko Tolonen},
	year         = 2015,
	month        = 12,
	journal      = {LIBER Quarterly},
	volume       = 25,
	number       = 2,
	pages        = {87--116},
	doi          = {10.18352/lq.10112},
	issn         = {2213-056X},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2015-Lahti-LIBERQuarterly.pdf},
	pubstate     = {dh},
	authorship   = {first},
	keywords     = {dh}
}
@inproceedings{Laine15,
	title        = {Beyond Open Access - The Changing Culture of Producing and Disseminating Scientific Knowledge},
	author       = {Heidi Laine and Leo Lahti and Anne Lehto and Samuli Ollila and Markus Miettinen},
	year         = 2015,
	booktitle    = {Proceedings of the 19th International Academic Mindtrek Conference in Tampere, Finland, September 22-24},
	location     = {Tampere, Finland},
	publisher    = {ACM},
	address      = {ACM New York, NY, USA},
	address      = {New York, NY, USA},
	isbn         = {978-1-4503-3948-3},
	url          = {http://dl.acm.org/citation.cfm?id=2818187},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2015-Laine-Mindtrek.pdf},
	organization = {AcademicMindTrek'15: Proceedings of the 19th International Academic Mindtrek Conference},
	authorship   = {second},
	keywords     = {openscience}
}
@article{OKeefe15,
	title        = {Fat, Fiber and Cancer Risk in African, Americans and Rural Africans},
	author       = {SJD O'Keefe and JV Li and L Lahti and J Ou and F Carbonero and K Mohammed and JM Posma and J Kinross and E Wahl and E Ruder and K Vipperla and V Naidoo and L Mtshali and S Tims and PGB Puylaert, J DeLany and A Krasinskas and AC Benefiel and HO Kaseb and K Newton and JK Nicholson and WM de Vos and HR Gaskins and EG Zoetendal},
	year         = 2015,
	month        = {Apr},
	journal      = {Nature Communications},
	volume       = 6,
	pages        = 6342,
	doi          = {10.1038/ncomms7342},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2015-OKeefe-NComms.pdf},
	note         = {Top science article in Guardian on the release day.},
	keywords     = {gut},
	keywords     = {bioscience},
	annote       = {Guardian: http://www.theguardian.com/science/2015/apr/28/bowel-cancer-risk-may-be-reduced-by-rural-african-diet-study-finds}
}
@article{Ritari15,
	title        = {Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database},
	author       = {Jarmo Ritari and Jarkko Salojärvi and Leo Lahti and Willem M. de Vos},
	year         = 2015,
	month        = 12,
	journal      = {BMC Genomics},
	volume       = 16,
	pages        = 1056,
	doi          = {10.1186/s12864-015-2265-y},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2015-Ritari-BMCGenomics.pdf},
	keywords     = {bioscience}
}
@article{Siavash15,
	title        = {Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river},
	author       = {Siavash Atashgahi and Rozelin Aydin and Mauricio R. Dimitrov and Detmer Sipkema and Kelly Hamonts and Leo Lahti and Farai Maphosa and Thomas Kruse and Edoardo Saccenti and Dirk Springael, Winnie Dejonghe and Hauke Smidt},
	year         = 2015,
	month        = 11,
	journal      = {Scientific Reports},
	volume       = 5,
	number       = 17284,
	doi          = {10.1038/srep17284},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2015-Atagashi.pdf},
	keywords     = {bioscience}
}
@article{Su2015,
	title        = {A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging},
	author       = {Jing Su and Carl Ekman and Nikolay Oskolkov and Leo Lahti and Kristoffer Ström and Alvis Brazma and Leif Groop and Johan Rung and and Ola Hansson},
	year         = 2015,
	month        = 10,
	journal      = {Skeletal Muscle},
	volume       = 5,
	number       = 35,
	doi          = {10.1186/s13395-015-0059-1},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2015-Su-SkeletalMuscle.pdf},
	keywords     = {bioscience}
}
@article{Tolonen15EnnenNyt,
	title        = {Aatehistoria ja digitaalisten aineistojen mahdollisuudet},
	author       = {Mikko Tolonen and Leo Lahti},
	year         = 2015,
	month        = 8,
	journal      = {Ennen \& Nyt 2},
	volume       = 2,
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2015-EnnenNyt-Tolonen.pdf},
	authorship   = {shared first},
	language     = {Finnish},
	keywords     = {dh}
}
@article{Alneberg14,
	title        = {Binning metagenomic contigs by coverage and composition},
	author       = {Johannes Alneberg and Brynjar Smári Bjarnason and Ino de Bruijn and Melanie Schirmer and Joshua Quick and Umer Z Ijaz and Leo Lahti and Nicholas J Loman and Anders F Andersson and Christopher Quince},
	year         = 2014,
	journal      = {Nature Methods},
	volume       = 11,
	number       = {1144--1146},
	doi          = {10.1038/nmeth.3103},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2014-Alneberg-NatMeth.pdf},
	note         = {CONCOCT algorithm},
	keywords     = {bioscience}
}
@article{Louhimo14,
	title        = {Systematic Use of Computational Methods Allows Stratifying Treatment Responders in Glioblastoma Multiforme},
	author       = {Riku Louhimo and Viljami Aittom{\"a}ki and Ali Faisal and Marko Laakso and Ping Chen and Kristian Ovaska and Erkka Valo and Leo Lahti and Vladimir Rogojin and Samuel Kaski and Sampsa Hautaniemi.},
	year         = 2014,
	month        = 4,
	journal      = {Systems Biomedicine (special issue)},
	volume       = 1,
	pages        = {130--136},
	doi          = {10.4161/sysb.28904},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2014-Louhimo.pdf},
	note         = {Critical Assessment of Massive Data Analysis (CAMDA) workshop},
	issue        = 2,
	keywords     = {bioscience}
}
@article{lahti14natcomm,
	title        = {Tipping elements in the human intestinal ecosystem},
	author       = {Leo Lahti and Jarkko Saloj{\"a}rvi and Anne Salonen and Marten Scheffer and Willem M. de Vos},
	year         = 2014,
	month        = 7,
	journal      = {Nature Communications},
	volume       = 5,
	pages        = 4344,
	doi          = {10.1038/ncomms5344},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2014-Lahti-NatComm.pdf},
	authorship   = {first},
	keywords     = {bioscience}
}
@article{salonen14,
	title        = {Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men},
	author       = {Anne Salonen and Leo Lahti and Jarkko Saloj{\"a}rvi and Grietje Holtrop and Katri Korpela and Sylvia Duncan and Priya Date and Alexandra Johnstone and Gerald Lobley and Petra Louis and Harry Flint and Willem M. de Vos},
	year         = 2014,
	journal      = {ISME Journal},
	volume       = 8,
	pages        = {2218--2230},
	doi          = {10.1038/ismej.2014.63},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2014-Salonen-ISME.pdf},
	keywords     = {bioscience},
	authorship   = {second}
}
@article{sarhadi14,
	title        = {Copy Number Alterations and Neoplasia Specific Mutations in MELK, PDCD1LG2, TLN1, and PAX5 at 9p in Different Neoplasias},
	author       = {Virinder Sarhadi and Leo Lahti and Ilari Scheinin and Pekka Ellonen and Eeva Kettunen and Massimo Serra and Katia Scotlandi and Pierro Picci and Sakari Knuutila},
	year         = 2014,
	month        = 7,
	journal      = {Genes, Chromosomes and Cancer},
	volume       = 53,
	number       = 7,
	pages        = {579--588},
	doi          = {10.1002/gcc.22168},
	keywords     = {bioscience},
	authorship   = {second}
}
@misc{Lahti13icml,
	title        = {rOpenGov: open source ecosystem for computational social sciences and digital humanities},
	author       = {Leo Lahti, Juuso Parkkinen, Joona Lehtomäki and Markus Kainu},
	year         = 2013,
	month        = 12,
	url          = {http://ropengov.github.io},
	category     = {abstract},
	note         = {ICML/MLOSS workshop (Int'l Conf. on Machine Learning - Open Source Software workshop).},
	keywords     = {dh},
	howpublished = {software},
	keywords     = {datascience}
}
@article{Lahti13nar,
	title        = {A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases},
	author       = {Leo Lahti and Aurora Torrente and Laura L Elo and Alvis Brazma and Johan Rung},
	year         = 2013,
	journal      = {Nucleic Acids Research},
	volume       = 41,
	number       = 10,
	pages        = {e110},
	doi          = {10.1093/nar/gkt229},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2013-Lahti-NAR.pdf},
	note         = {Implementation available through Bioconductor RPA package.},
	authorship   = {first, corresponding},
	keywords     = {bioscience}
}
@article{Lahti13provasI,
	title        = {Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data},
	author       = {Leo Lahti and Anne Salonen and Riina A. Kekkonen and Jarkko Salojärvi and Jonna Jalanka-Tuovinen and Airi Palva and Matej Orešič and Willem M. de Vos},
	year         = 2013,
	journal      = {PeerJ},
	volume       = 1,
	pages        = {e32},
	doi          = {10.7717/peerj.32},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2013-Lahti-PeerJ.pdf},
	note         = {Highly accessed, featured in PeerJ journal blog and Top-10 Microbiology collection.},
	keywords     = {bioscience},
	authorship   = {corresponding, shared first},
	pmid         = 23638368
}
@article{Lahti2012intcomp,
	title        = {Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review},
	author       = {Leo Lahti and Martin Sch{\"a}fer and Hans-Ulrich Klein and Silvio Bicciato and Martin Dugas},
	year         = 2013,
	month        = 6,
	journal      = {Briefings in Bioinformatics},
	volume       = 14,
	number       = 1,
	pages        = {27--35},
	doi          = {10.1093/bib/bbs005},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2013-Lahti-BriefBioinf.pdf},
	category     = {review},
	keywords     = {bioscience},
	authorship   = {first, corresponding}
}
@article{Sarhadi13,
	title        = {Targeted Resequencing of 9p in Acute Lymphoblastic Leukemia Yields Concordant Results with Array CGH and Reveals Novel Genomic Alterations},
	author       = {Virinder Kaur Sarhadi and Leo Lahti and Ilari Scheinin and Anne Tyyb{\"a}kinoja and Suvi Savola and Anu Usvasalo and Riikka R{\"a}ty and Erkki Elonen and Pekka Ellonen and Ulla M Saarinen-Pihkala and Sakari Knuutila},
	year         = 2013,
	month        = 9,
	journal      = {Genomics},
	volume       = 102,
	number       = 3,
	pages        = {182--188},
	doi          = {10.1016/j.ygeno.2013.01.001},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2013-Sarhadi-Genomics.pdf},
	keywords     = {bioscience},
	authorship   = {shared first}
}
@article{bender13,
	title        = {Intestinal microbiota, individuality and health. In: Computational Methods Aiding Early-Stage Drug Design (Dagstuhl Seminar 13212)},
	author       = {Leo Lahti},
	year         = 2013,
	journal      = {Dagstuhl Reports},
	publisher    = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
	address      = {Dagstuhl, Germany},
	volume       = 3,
	number       = 5,
	pages        = {78--94},
	doi          = {10.4230/DagRep.3.5.78},
	issn         = {2192-5283},
	url          = {http://drops.dagstuhl.de/opus/volltexte/2013/4179},
	category     = {abstract},
	keywords     = {bioscience},
	editor       = {Andreas Bender and Hinrich G{\"o}hlmann and Sepp Hochreiter and Ziv Shkedy},
	urn          = {urn:nbn:de:0030-drops-41791},
	annote       = {Keywords: Bioinformatics, Chemoinformatics, Machine learning, Statistics, Interdisciplinary applications. Short abstract for the Dagstuhl seminar.}
}
@article{Lahti12cmi,
	title        = {The adult intestinal core microbiota is determined by analysis depth and health status},
	author       = {Anne Salonen and Jarkko Saloj{\"a}rvi and Leo Lahti and and Willem M. de Vos},
	year         = 2012,
	journal      = {Clinical Microbiology and Infection},
	volume       = 18,
	number       = {Suppl. 4},
	pages        = {16–20},
	doi          = {10.1111/j.1469-0691.2012.03855.x},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2012-Salonen-CMI.pdf},
	keywords     = {bioscience}
}
@article{Mosakhani12,
	title        = {MicroRNA profiling predicts survival in anti-EGFR treated chemorefractory metastatic colorectal cancer patients with wild-type KRAS and BRAF},
	author       = {Neda Mosakhani and Leo Lahti and Ioana Borze and Marja-Liisa Karjalainen-Lindsberg and Jari Sundstrom and Raija Ristamaki and Pia Osterlund and Sakari Knuutila and and Virinder Kaur Sarhadi},
	year         = 2012,
	month        = 11,
	journal      = {Cancer Genetics},
	volume       = 205,
	number       = 11,
	pages        = {545--51},
	doi          = {10.1016/j.cancergen.2012.08.003},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2012-Mosakhani-CG.pdf},
	keywords     = {bioscience},
	authorship   = {second}
}
@article{Mosakhani12LL,
	title        = {MicroRNA profiling in pediatric acute lymphoblastic leukemia: novel prognostic tools},
	author       = {N Mosakhani and VK Sarhadi and A Usvasalo and ML Karjalainen-Lindsberg and L Lahti and K Tuononen and UM Saarinen-Pihkala and S Knuutila},
	year         = 2012,
	month        = {Dec},
	journal      = {Leukemia \& Lymphoma},
	volume       = 53,
	number       = 12,
	pages        = {2517--2520},
	doi          = {10.3109/10428194.2012.685731},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2012-Mosakhani-LL.pdf},
	keywords     = {bioscience}
}
@article{Niini12,
	title        = {Homozygous Deletions of Cadherin Genes in Chondrosarcoma – an Array CGH Study},
	author       = {Tarja Niini and Ilari Scheinin and Leo Lahti and Suvi Savola and Fredrik Mertens and Jaakko Hollmén and Tom Böhling and Aarne Kivioja and Karolin H Nord and Sakari Knuutila},
	year         = 2012,
	month        = 11,
	journal      = {Cancer Genetics},
	volume       = 205,
	number       = 11,
	pages        = {588--93},
	doi          = {10.1016/j.cancergen.2012.09.007},
	keywords     = {bioscience},
	pmid         = 23146407
}
@article{Borze11,
	title        = {MicroRNA microarrays on archive bone marrow core biopsies of leukemias - method validation},
	author       = {Ioana Borze and Mohamed Guled and Suad Musse and Anna Raunio and Erkki Elonen and Ulla Saarinen-Pihkala and Marja-Liisa Karjalainen-Lindsberg and Leo Lahti and Sakari Knuutila.},
	year         = 2011,
	month        = 2,
	journal      = {Leukemia Research},
	volume       = 35,
	pages        = {188--195},
	doi          = {10.1016/j.leukres.2010.08.005},
	issue        = 2,
	keywords     = {bioscience}
}
@inproceedings{Faisal2011,
	title        = {Biomarker discovery via dependency analysis of multi-view functional genomics data},
	author       = {Ali Faisal and Riku Louhimo and Leo Lahti and Sampsa Hautaniemi and Samuel Kaski},
	year         = 2011,
	booktitle    = {NIPS 2011 workshop From Statistical Genetics to Predictive Models in Personalized Medicine},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2011-Faisal-NIPS.pdf},
	category     = {abstract},
	keywords     = {bioscience}
}
@article{Jalanka-Tuovinen11,
	title        = {Intestinal microbiota in healthy adults: Temporal analysis reveals individual and common core and relation to intestinal symptoms},
	author       = {Jonna Jalanka-Tuovinen and Anne Salonen and Janne Nikkil{\"a} and Outi Immonen and Riina Kekkonen and Leo Lahti and Airi Palva and Willem M. de Vos},
	year         = 2011,
	month        = 7,
	journal      = {PLoS One},
	volume       = 6,
	number       = 7,
	pages        = {e23035},
	url          = {10.1371/journal.pone.0023035},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2011-JalankaTuovinen-PLoS.pdf},
	keywords     = {bioscience}
}
@misc{Lahti11intcomp,
	title        = {intcomp: a benchmarking pipeline for integrative cancer gene detection algorithms},
	author       = {Leo Lahti and Martin Schäfer and Hans-Ulrich Klein and Silvio Bicciato and Martin Dugas},
	year         = 2011,
	month        = 2,
	url          = {http://intcomp.r-forge.r-project.org/},
	note         = {R-forge},
	howpublished = {software},
	keywords     = {bioscience}
}
@misc{Lahti11ismb,
	title        = {Probabilistic dependency models for data integration in functional genomics},
	author       = {Leo Lahti and Samuel Kaski},
	year         = 2011,
	month        = {July},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2011-MLSB-Lahti.pdf},
	category     = {abstract},
	note         = {Machine Learning for Systems Biology workshop, ISMB, Vienna, Austria},
	authorship   = {first, corresponding},
	keywords     = {bioscience}
}
@article{Lahti11rpa,
	title        = {Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays},
	author       = {Leo Lahti and Laura L. Elo and Tero Aittokallio and Samuel Kaski},
	year         = 2011,
	month        = {Jan.-Mar.},
	journal      = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
	publisher    = {IEEE Computer Society},
	address      = {Los Alamitos, CA, USA},
	volume       = 8,
	number       = 1,
	pages        = {217--225},
	doi          = {10.1109/TCBB.2009.38},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2011-Lahti-TCBB.pdf},
	keywords     = {bioscience},
	authorship   = {first, corresponding},
	annote       = {R/Bioconductor: RPA}
}
@article{Niini11mfh,
	title        = {Array Comparative Genomic Hybridization Reveals Frequent Alterations of G1/S Checkpoint Genes in Undifferentiated Pleomorphic Sarcoma of Bone},
	author       = {Tarja Niini and Leo Lahti and Francesca Michelacci and Shinsuke Ninomiya and Claudia Maria Hattinger and Mohamed Guled and Tom B{\"o}hling and Piero Picci and Massimo Serra and Sakari Knuutila},
	year         = 2011,
	month        = 5,
	journal      = {Genes, Chromosomes and Cancer},
	volume       = 50,
	number       = 5,
	pages        = {291--306},
	doi          = {10.1002/gcc.20851},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2011-Niini-GCC.pdf},
	authorship   = {second},
	keywords     = {bioscience}
}
@article{Nymark11,
	title        = {Integrative Analysis of microRNA, mRNA and aCGH Data Reveals Asbestos- and Histology-Related Changes in Lung Cancer},
	author       = {Penny Nymark and Mohamed Guled and Ioana Borze and Ali Faisal and Leo Lahti and Kaisa Salmenkivi and Eeva Kettunen and Sisko Anttila and Sakari Knuutila},
	year         = 2011,
	month        = 8,
	journal      = {Genes, Chromosomes and Cancer},
	volume       = 50,
	number       = 8,
	pages        = {585--597},
	doi          = {10.1002/gcc.20880},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2011-Nymark-GCC.pdf},
	keywords     = {bioscience}
}
@article{Lahti10bioinf,
	title        = {Global modeling of transcriptional responses in interaction networks},
	author       = {Leo Lahti and Juha E.A. Knuuttila and Samuel Kaski},
	year         = 2010,
	month        = 11,
	journal      = {Bioinformatics},
	volume       = 26,
	pages        = {2713--2720},
	doi          = {10.1093/bioinformatics/btq500},
	url          = {http://bioinformatics.oxfordjournals.org/content/early/2010/09/02/bioinformatics.btq500.abstract.html?ijkey=N1zzjtUBRng3wCM&keytype=ref},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2010-Bioinformatics-Lahti-NetResponse.pdf},
	note         = {R/Matlab implementations available at http://netpro.r-forge.r-project.org/},
	issue        = 21,
	keywords     = {bioscience},
	authorship   = {first},
	annote       = {ArXiv: http://arxiv.org/abs/1202.0501; R/Matlab source code http://netpro.r-forge.r-project.org}
}
@misc{Lahti10dmt,
	title        = {Dependency modeling toolkit},
	author       = {Leo Lahti and Abhishek Tripathi and Olli-Pekka Huovilainen},
	year         = 2010,
	month        = 6,
	publisher    = {ICML workshop},
	url          = {http://dmt.r-forge.r-project.org/},
	note         = {CRAN: dmt},
	howpublished = {software},
	keywords     = {datascience}
}
@misc{Lahti10netresponse,
	title        = {NetResponse (functional network analysis)},
	author       = {Leo Lahti and Antonio Gusmao and Olli-Pekka Huovilainen},
	year         = 2010,
	month        = {October},
	doi          = {10.18129/B9.BIOC.NETRESPONSE},
	url          = {http://www.bioconductor.org/help/bioc-views/devel/bioc/html/netresponse.html},
	note         = {R/Bioconductor: netresponse},
	keywords     = {datascience},
	howpublished = {software}
}
@misc{Lahti10pint,
	title        = {Pairwise integration of functional genomics data},
	author       = {Olli-Pekka Huovilainen and Leo Lahti},
	year         = 2010,
	month        = {April},
	url          = {http://bioconductor.org/packages/devel/bioc/html/pint.html},
	note         = {R/BioConductor: pint},
	keywords     = {datascience},
	howpublished = {software}
}
@phdthesis{Lahti10thesis,
	title        = {Probabilistic analysis of the human transcriptome with side information},
	author       = {Leo Lahti},
	year         = 2010,
	month        = 12,
	address      = {Espoo},
	series       = {TKK Dissertations in Information and Computer Science},
	number       = {TKK-ICS-D19},
	issn         = {1797-5069},
	url          = {http://lib.tkk.fi/Diss/2010/isbn9789526033686/},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2010-Lahti-thesis.pdf},
	category     = {thesis},
	note         = {LaTeX sources and the pdf version are openly available: https://github.com/antagomir/thesis/tree/master/phd10; Press release: https://github.com/antagomir/thesis/blob/master/phd10/Vaitostiedote-LeoLahti-20101207.pdf},
	school       = {Aalto University School of Science and Technology, Faculty of Information and Natural Sciences, Department of Information and Computer Science},
	language     = {Finnish},
	keywords     = {thesis, probabilistic models, Bayesian analysis, data integration, gene expression, microarrays, computational science, data analysis, machine learning, computational biology, open source, open access, creative commons},
	abstract     = {Recent advances in high-throughput measurement technologies and efficient sharing of biomedical data through community databases have made it possible to investigate the complete collection of genetic material, the genome, which encodes the heritable genetic program of an organism. This has opened up new views to the study of living organisms with a profound impact on biological research. Functional genomics is a subdiscipline of molecular biology that investigates the functional organization of genetic information.  This thesis develops computational strategies to investigate a key functional layer of the genome, the transcriptome. The time- and context-specific transcriptional activity of the genes regulates the function of living cells through protein synthesis. Efficient computational techniques are needed in order to extract useful information from high-dimensional genomic observations that are associated with high levels of complex variation. Statistical learning and probabilistic models provide the theoretical framework for combining statistical evidence across multiple observations and the wealth of background information in genomic data repositories.  This thesis addresses three key challenges in transcriptome analysis. First, new preprocessing techniques that utilize side information in genomic sequence databases and microarray collections are developed to improve the accuracy of high-throughput microarray measurements.  Second, a novel exploratory approach is proposed in order to construct a global view of cell-biological network activation patterns and functional relatedness between tissues across normal human body. Information in genomic interaction databases is used to derive constraints that help to focus the modeling in those parts of the data that are supported by known or potential interactions between the genes, and to scale up the analysis. The third contribution is to develop novel approaches to model dependency between co-occurring measurement sources. The methods are used to study cancer mechanisms and transcriptome evolution; integrative analysis of the human transcriptome and other layers of genomic information allows the identification of functional mechanisms and interactions that could not be detected based on the individual measurement sources. Open source implementations of the key methodological contributions have been released to facilitat e their further adoption by the research community.}
}
@article{Mosakhani10,
	title        = {Unique microRNA profile in Dupuytren's contracture supports deregulation of beta-catenin pathway},
	author       = {Neda Mosakhani and Mohamed Guled and Leo Lahti and Ioana Borze and Minna Forsman and Jorma Ryh{\"a}nen and Sakari Knuutila},
	year         = 2010,
	month        = 11,
	journal      = {Modern Pathology},
	volume       = 23,
	pages        = {1544--1522},
	doi          = {10.1038/modpathol.2010.146},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2010-ModernPathology-Mosakhani-Dupuytre.pdf},
	note         = {International Dupuytren Award for best research paper in 2011},
	keywords     = {bioscience}
}
@article{Guled09,
	title        = {CDKN2A, NF2 and JUN Are Dysregulated Among Other Genes by miRNAs in Malignant Mesothelioma - a miRNA Microarray Analysis},
	author       = {Mohamed Guled and Leo Lahti and Pamela M. Lindholm and Kaisa Salmenkivi and Izhar Bagwan and Andrew G. Nicholson and Sakari Knuutila},
	year         = 2009,
	month        = 7,
	journal      = {Genes, Chromosomes and Cancer},
	volume       = 48,
	number       = 7,
	pages        = {615--623},
	doi          = {10.1002/gcc.20669},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2009-GCC-Guled-miRNA.pdf},
	keywords     = {bioscience}
}
@misc{Lahti09bsc,
	title        = {Concerning Blackburn's quasi-realism in securing moral discussion},
	author       = {Leo Lahti},
	year         = 2009,
	month        = 7,
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/theses/LeoLahti-BSc-2008.pdf},
	category     = {thesis},
	note         = {(In Finnish)},
	keywords     = {thesis},
	howpublished = {B.Sc. thesis. University of Helsinki, Faculty of Political Sciences},
	language     = {Finnish}
}
@inproceedings{Lahti09mlsp,
	title        = {Dependency detection with similarity constraints},
	author       = {Leo Lahti and Samuel Myllykangas and Sakari Knuutila and Samuel Kaski},
	year         = 2009,
	booktitle    = {Proc. MLSP'09 IEEE International Workshop on Machine Learning for Signal Processing XIX},
	address      = {Piscataway, NJ},
	pages        = {198--203},
	url          = {http://arxiv.org/abs/1101.5919},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2009-MLSP-Lahti-SimCCA.pdf},
	note         = {R/Bioconductor: pint},
	editor       = {Adali T, Chanussot J, Jutten C, and Larsen J},
	howpublished = {software},
	authorship   = {first, corresponding},
	arxiv        = {1101.5919},
	keywords     = {datascience}
}
@misc{Lahti09rpa,
	title        = {RPA: probe reliability and differential gene expression analysis},
	author       = {Leo Lahti},
	year         = 2009,
	month        = {October},
	doi          = {10.18129/B9.BIOC.RPA},
	url          = {http://bioconductor.org/packages/release/bioc/html/RPA.html},
	note         = {R/Bioconductor: RPA},
	howpublished = {software},
	keywords     = {bioscience}
}
@misc{Lahti2006biopax,
	title        = {A brief overview on the BioPAX and SBML standards},
	author       = {Leo Lahti},
	year         = 2007,
	url          = {https://arxiv.org/abs/1109.4919},
	category     = {thesis},
	note         = {Overview of machine-readable representations of biological processes.},
	note         = {(in Finnish)},
	howpublished = {arXiv},
	authorship   = {first},
	keywords     = {bioscience},
	arxiv        = {arXiv:1109.4919 [cs.DS]},
	language     = {Finnish}
}
@article{Nymark07,
	title        = {Gene Expression Profiles in Asbestos-exposed Epithelial and Mesothelial Lung Cell Lines},
	author       = {Penny Nymark and Pamela M. Lindholm and Mikko V. Korpela and Leo Lahti and Salla Ruosaari and Samuel Kaski and Jaakko Hollmen and Sisko Anttila and Vuokko L. Kinnula and Sakari Knuutila},
	year         = 2007,
	month        = 3,
	journal      = {BMC Genomics},
	volume       = 8,
	number       = 62,
	doi          = {10.1186/1471-2164-8-62},
	keywords     = {bioscience},
	annote       = {CCA on two asbestos-exposed cell lines.}
}
@article{Elo05,
	title        = {Integrating probe-level expression changes across generations of Affymetrix arrays},
	author       = {Elo, Laura L. and Lahti, Leo and Skottman, Heli and Kyl{\"a}niemi, Minna and Lahesmaa, Riitta and Aittokallio, Tero},
	year         = 2005,
	month        = 12,
	journal      = {Nucleic Acids Research},
	volume       = 33,
	number       = 22,
	pages        = {e193},
	doi          = {10.1093/nar/gni193},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2005-Elo-NAR.pdf},
	authorship   = {second},
	keywords     = {bioscience}
}
@article{Kaski05,
	title        = {Associative clustering for exploring dependencies between functional genomics data sets},
	author       = {Samuel Kaski and Janne Nikkil{\"a} and Janne Sinkkonen and Leo Lahti and Juha Knuuttila and Christophe Roos},
	year         = 2005,
	month        = {September},
	journal      = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
	volume       = 2,
	number       = 3,
	pages        = {203--216},
	doi          = {10.1109/TCBB.2005.32},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2005-TCBB–Kaski-AC.pdf},
	note         = {Special Issue on Machine Learning for Bioinformatics -- Part 2},
	keywords     = {datascience}
}
@techreport{Sinkkonen05tr,
	title        = {Associative Clustering (AC): Technical Details},
	author       = {Janne Sinkkonen and Samuel Kaski and Janne Nikkil{\"a} and Leo Lahti},
	year         = 2005,
	month        = {April},
	address      = {Espoo, Finland},
	number       = {A84},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2005-TechRep-Sinkkonen-ACtechdetails.pdf},
	note         = {Publications in Computer and Information Science},
	institution  = {Helsinki University of Technology},
	keywords     = {datascience}
}
@incollection{Sinkkonen04ecml,
	title        = {Associative Clustering},
	author       = {Janne Sinkkonen and Janne Nikkil\"{a} and Leo Lahti and Samuel Kaski},
	year         = 2004,
	booktitle    = {Proceedings of the ECML'04, 15th European Conference on Machine Learning},
	publisher    = {Springer},
	address      = {Berlin},
	pages        = {396--406},
	url          = {http://www.cis.hut.fi/projects/mi/abstracts/ecml04.html},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2004-ECML-Sinkkonen-AC.pdf},
	category     = {abstract},
	editor       = {Boulicaut and Esposito and Giannotti and Pedreschi},
	keywords     = {datascience}
}
@mastersthesis{Lahti03,
	title        = {Comparative functional genome analysis using associative clustering},
	author       = {Lahti, Leo},
	year         = 2003,
	month        = 12,
	url          = {https://github.com/antagomir/thesis/tree/master/msc03},
	url          = {https://github.com/antagomir/thesis/blob/master/msc03/dtyo.pdf},
	category     = {thesis},
	note         = {(in Finnish)},
	school       = {Helsinki University of Technology},
	language     = {Finnish},
	keywords     = {thesis}
}
@techreport{Sinkkonen03tr,
	title        = {Associative Clustering by Maximizing a {B}ayes Factor},
	author       = {Janne Sinkkonen and Janne Nikkil\"{a} and Leo Lahti and Samuel Kaski},
	year         = 2003,
	month        = 6,
	address      = {Espoo, Finland},
	number       = {A68},
	url          = {https://github.com/openresearchlabs/openresearchlabs.github.io/blob/master/content/publication_resources/papers/2003-TechRep-Sinkkonen-ACBayesFactor.pdf},
	institution  = {Helsinki University of Technology and Laboratory of Computer and Information Science},
	keywords     = {bioscience}
}
@misc{Lahti2002,
	title        = {Itsesimilaaristen joukkojen Hausdorffin dimension määrittäminen},
	author       = {Leo Lahti},
	year         = 2002,
	url          = {https://github.com/antagomir/thesis/tree/master/hausdorff02},
	category     = {thesis},
	note         = {Special assignment in Mathematics (in Finnish)},
	keywords     = {thesis},
	language     = {Finnish}
}
@misc{Lahti2001,
	title        = {Julian joukko iteraatioden valuma-altaan reunana},
	author       = {Leo Lahti},
	year         = 2001,
	url          = {https://github.com/antagomir/thesis/tree/master/julia01},
	category     = {thesis},
	note         = {Special assignment in Mathematics (in Finnish)},
	keywords     = {thesis},
	language     = {Finnish}
}
@misc{Lahti10blog,
	title        = {opencomp blog},
	author       = {Leo Lahti},
	url          = {http://antagomir.wordpress.com/},
	category     = {blog},
	keywords     = {blog}
}
@misc{Lahti11-louhos,
	title        = {Louhos blog},
	author       = {Leo Lahti and Joona Lehtomäki and Juuso Parkkinen and others},
	url          = {http://louhos.github.io/},
	note         = {Open government data analytics blog (in Finnish)},
	keywords     = {blog}
}
@misc{Lahti13-ropengov,
	title        = {rOpenGov blog},
	author       = {Leo Lahti and Joona Lehtomäki and Markus Kainu and Juuso Parkkinen and others},
	url          = {http://ropengov.github.io/},
	note         = {Open government data analytics blog},
	keywords     = {blog}
}