• Pfeil J, Siptroth J, Pospisil H, Frohme M, Hufert FT, Moskalenko O, Yateem M, Nechyporenko A. Classification of Microbiome Data from Type 2 Diabetes Mellitus Individuals with Deep Learning Image Recognition. Big Data and Cognitive Computing. 2023; 7(1):51. https://doi.org/10.3390/bdcc7010051
  • Frontiers in Genetics volume – Research Topic: Microbiome and Machine Learning (2022) – 10 articles published. Microbiome and Machine Learning | Frontiers Research Topic (frontiersin.org)
  • Moreno-Indias I., Zomer AL,  Gómez-Cabrero D,  Claesson MJ on behalf of ML4Microbiome (2022) Editorial: Microbiome and Machine Learning Research Topic. Front. Microbiol., Sec. Evolutionary and Genomic Microbiology. https://doi.org/10.3389/fmicb.2022.964921
  • Cekikj Miodrag, Jakimovska Özdemir, Milena Kalajdzhiski, Slobodan Özcan, Orhan Sezerman, Osman Uğur (2022) Understanding the Role of the Microbiome in Cancer Diagnostics and Therapeutics by Creating and Utilizing ML Models. Appl. Sci.12(9), 4094; https://doi.org/10.3390/app12094094
  • Vilne Baiba, Ķibilds Juris, Siksna Inese, Lazda Ilva, Valciņa Olga, Krūmiņa Angelika (2022) Could Artificial Intelligence/Machine Learning and Inclusion of Diet-Gut Microbiome Interactions Improve Disease Risk Prediction? Case Study: Coronary Artery Disease. Frontiers in Microbiology, 13. doi:10.3389/fmicb.2022.627892 
  • Ibrahimi, E., Elbere, I., Berland, M., & D’Elia, D. (2022) Report of the ML4Microbiome workshop 2021 – Statistical and Machine Learning Techniques for Microbiome Data Analysis. EMBnet.journal, 27, e1012. doi:https://doi.org/10.14806/ej.27.0.1012
  • Rosario D, Bidkhori G, Lee S, Bedarf J, Hildebrand F, Le Chatelier E, Uhlen M, Ehrlich SD, Proctor G, Wüllner U, Mardinoglu A, Shoaie S. Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson’s disease. Cell Rep. 2021 Mar 2;34(9):108807. doi: 10.1016/j.celrep.2021.108807. PMID: 33657381.
  • Gholamreza Bidkhori, Sunjae Lee, Lindsey A. Edwards, Emmanuelle Le Chatelier, Mathieu Almeida, Bouchra Ezzamouri, Florian Plaza Onate, Nicolas Ponte, Debbie L. Shawcross, Gordon Proctor, Lars Nielsen, Jens Nielsen, Mathias Uhlen, Stanislav Dusko Ehrlich, Saeed Shoaie (2021)The Reactobiome Unravels a New Paradigm in Human Gut Microbiome Metabolism, bioRxiv 2021
  • Shoaie S, Lee S, Almeida M, et al. (2021) Global and temporal state of the human gut microbiome in health and disease. Research Square. doi:10.21203/rs.3.rs-339282/v1
  • Marcos-Zambrano LJ, Karaduzovic-Hadziabdic K, Loncar Turukalo T, Przymus P, Trajkovik V, Aasmets O, Berland M, Gruca A, Hasic J, Hron K, Klammsteiner T, Kolev M, Lahti L, Lopes MB, Moreno V, Naskinova I, Org E, Paciência I, Papoutsoglou G, Shigdel R, Stres B, Vilne B, Yousef M, Zdravevski E, Tsamardinos I, Carrillo de Santa Pau E, Claesson MJ, Moreno-Indias I, Truu J. Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. Front Microbiol. 2021 Feb 19;12:634511. doi: 10.3389/fmicb.2021.634511. PMID: 33737920; PMCID: PMC7962872.
  • Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, Bakir-Gungor B, Santa Pau EC, D’Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes MB, Marcos-Zambrano LJ, Marques C, Mason M, May P, Pašić L, Pio G, Pongor S, Promponas VJ, Przymus P, Saez-Rodriguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truică CO, Vilne B, Vlachakis D, Yilmaz E, Zeller G, Zomer AL, Gómez-Cabrero D, Claesson MJ. Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Front Microbiol. 2021 Feb 22;12:635781. doi: 10.3389/fmicb.2021.635781. PMID: 33692771; PMCID: PMC7937616.
  • Tonkovic P, Kalajdziski S, Zdravevski E, Lameski P, Corizzo R, Pires IM, Garcia NM, Loncar-Turukalo T, Trajkovik V. Literature on Applied Machine Learning in Metagenomic Classification: A Scoping Review. Biology (Basel). 2020 Dec 9;9(12):453. doi: 10.3390/biology9120453. PMID: 33316921; PMCID: PMC7763105.