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Gut Microbes Volume 13, 2021 - Issue 1

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Review

Harnessing machine learning for development of microbiome therapeutics

Laura E. McCoubreya UCL School of Pharmacy, University College London, London, UK

https://orcid.org/0000-0001-7773-6719 View further author information

Moe Elbadawia UCL School of Pharmacy, University College London, London, UK

https://orcid.org/0000-0003-1304-3686 View further author information

Mine Orlua UCL School of Pharmacy, University College London, London, UKView further author information

Simon Gaisforda UCL School of Pharmacy, University College London, London, UK;b FabRx Ltd., Ashford, Kent, UKView further author information

Abdul W. Basita UCL School of Pharmacy, University College London, London, UKCorrespondence[email protected]
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Article: 1872323 | Received 27 Nov 2020, Accepted 20 Dec 2020, Published online: 30 Jan 2021

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https://doi.org/10.1080/19490976.2021.1872323
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Huanqin Dai, Junjie Han, Tao Wang, Wen-Bing Yin, Yihua Chen & Hongwei Liu. (2023) Recent advances in gut microbiota-associated natural products: structures, bioactivities, and mechanisms. Natural Product Reports 40:6, pages 1078-1093.
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Mariia A. Beliaeva, Matthias Wilmanns & Michael Zimmermann. (2023) Decipher enzymes from human microbiota for drug discovery and development. Current Opinion in Structural Biology 80, pages 102567.
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Atheer Awad, Alvaro Goyanes, Abdul W. Basit, Ahmed S. Zidan, Changxue Xu, Wei Li, Roger J. Narayan & Roland K. Chen. (2023) A Review of State-of-the-Art on Enabling Additive Manufacturing Processes for Precision Medicine. Journal of Manufacturing Science and Engineering 145:1.
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Laura E. McCoubrey, Alessia Favaron, Atheer Awad, Mine Orlu, Simon Gaisford & Abdul W. Basit. (2023) Colonic drug delivery: Formulating the next generation of colon-targeted therapeutics. Journal of Controlled Release 353, pages 1107-1126.
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Maria Tcherni‐Buzzeo. (2022) Dietary interventions, the gut microbiome, and aggressive behavior: Review of research evidence and potential next steps. Aggressive Behavior 49:1, pages 15-32.
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Tamizhini Loganathan & George Priya Doss C. (2022) The influence of machine learning technologies in gut microbiome research and cancer studies - A review. Life Sciences 311, pages 121118.
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Animesh Acharjee, Utpreksha Singh, Saptamita Paul Choudhury & Georgios V. Gkoutos. (2022) The diagnostic potential and barriers of microbiome based therapeutics. Diagnosis 9:4, pages 411-420.
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Ricardo Hernández Medina, Svetlana Kutuzova, Knud Nor Nielsen, Joachim Johansen, Lars Hestbjerg Hansen, Mads Nielsen & Simon Rasmussen. (2022) Machine learning and deep learning applications in microbiome research. ISME Communications 2:1.
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Sean M Gibbons, Thomas Gurry, Johanna W Lampe, Anirikh Chakrabarti, Veerle Dam, Amandine Everard, Almudena Goas, Gabriele Gross, Michiel Kleerebezem, Jonathan Lane, Johanna Maukonen, Ana Lucia Barretto Penna, Bruno Pot, Ana M Valdes, Gemma Walton, Adrienne Weiss, Yoghatama Cindya Zanzer, Naomi V Venlet & Michela Miani. (2022) Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions. Advances in Nutrition 13:5, pages 1450-1461.
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Valeria M. Juarez, Alyssa N. Montalbine & Ankur Singh. (2022) Microbiome as an immune regulator in health, disease, and therapeutics. Advanced Drug Delivery Reviews 188, pages 114400.
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Timur Liwinski, Melina Heinemann & Christoph Schramm. (2022) The intestinal and biliary microbiome in autoimmune liver disease—current evidence and concepts. Seminars in Immunopathology 44:4, pages 485-507.
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Rachel Clifton, Emma M. Monaghan, Martin J. Green, Kevin J. Purdy & Laura E. Green. (2022) Differences in composition of interdigital skin microbiota predict sheep and feet that develop footrot. Scientific Reports 12:1.
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Renato Giliberti, Sara Cavaliere, Italia Elisa Mauriello, Danilo Ercolini & Edoardo Pasolli. (2022) Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa. PLOS Computational Biology 18:4, pages e1010066.
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Laura E. McCoubrey, Moe Elbadawi & Abdul W. Basit. (2022) Current clinical translation of microbiome medicines. Trends in Pharmacological Sciences 43:4, pages 281-292.
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Laura E. McCoubrey, Nidhi Seegobin, Moe Elbadawi, Yiling Hu, Mine Orlu, Simon Gaisford & Abdul W. Basit. (2022) Active Machine learning for formulation of precision probiotics. International Journal of Pharmaceutics 616, pages 121568.
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Wai Kit David Chee, Jing Wui Yeoh, Viet Linh Dao & Chueh Loo Poh. (2022) Thermogenetics: Applications come of age. Biotechnology Advances 55, pages 107907.
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Laura E. McCoubrey, Hannah Batchelor, Abdul W. Basit, Simon Gaisford & Mine Orlu. 2022. Biopharmaceutics. Biopharmaceutics 277 295 .

Francesca K. H. Gavins, Christine M. Madla, Sarah J. Trenfield, Laura E. McCoubrey, Abdul W. Basit & Mark McAllister. 2022. Biopharmaceutics. Biopharmaceutics 165 188 .

Ting-Wei Kao & Chin-Chou Huang. (2022) Inflammatory Burden and Immunomodulative Therapeutics of Cardiovascular Diseases. International Journal of Molecular Sciences 23:2, pages 804.
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Francesca K.H. Gavins, Zihao Fu, Moe Elbadawi, Abdul W. Basit, Miguel R.D. Rodrigues & Mine Orlu. (2022) Machine learning predicts the effect of food on orally administered medicines. International Journal of Pharmaceutics 611, pages 121329.
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Laura E. McCoubrey, Simon Gaisford, Mine Orlu & Abdul W. Basit. (2022) Predicting drug-microbiome interactions with machine learning. Biotechnology Advances 54, pages 107797.
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Enriqueta Garcia-Gutierrez & Lizbeth Sayavedra. 2022. Comprehensive Gut Microbiota. Comprehensive Gut Microbiota 69 83 .

Carlos Sabater, Inés Calvete-Torre, Mar Villamiel, F. Javier Moreno, Abelardo Margolles & Lorena Ruiz. (2021) Vegetable waste and by-products to feed a healthy gut microbiota: Current evidence, machine learning and computational tools to design novel microbiome-targeted foods. Trends in Food Science & Technology 118, pages 399-417.
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Jonas Ghyselinck, Lynn Verstrepen, Frédéric Moens, Pieter Van Den Abbeele, Arnout Bruggeman, Jawal Said, Barry Smith, Lynne Ann Barker, Caroline Jordan, Valentina Leta, K. Ray Chaudhuri, Abdul W. Basit & Simon Gaisford. (2021) Influence of probiotic bacteria on gut microbiota composition and gut wall function in an in-vitro model in patients with Parkinson's disease. International Journal of Pharmaceutics: X 3, pages 100087.
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Laura E. McCoubrey, Stavriani Thomaidou, Moe Elbadawi, Simon Gaisford, Mine Orlu & Abdul W. Basit. (2021) Machine Learning Predicts Drug Metabolism and Bioaccumulation by Intestinal Microbiota. Pharmaceutics 13:12, pages 2001.
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Atheer Awad, Sarah J. Trenfield, Thomas D. Pollard, Jun Jie Ong, Moe Elbadawi, Laura E. McCoubrey, Alvaro Goyanes, Simon Gaisford & Abdul W. Basit. (2021) Connected healthcare: Improving patient care using digital health technologies. Advanced Drug Delivery Reviews 178, pages 113958.
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Moe Elbadawi, Laura E. McCoubrey, Francesca K.H. Gavins, Jun J. Ong, Alvaro Goyanes, Simon Gaisford & Abdul W. Basit. (2021) Disrupting 3D printing of medicines with machine learning. Trends in Pharmacological Sciences 42:9, pages 745-757.
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Jun Jie Ong, Thomas D. Pollard, Alvaro Goyanes, Simon Gaisford, Mohammed Elbadawi & Abdul W. Basit. (2021) Optical biosensors - Illuminating the path to personalized drug dosing. Biosensors and Bioelectronics 188, pages 113331.
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Moe Elbadawi, Laura E. McCoubrey, Francesca K.H. Gavins, Jun Jie Ong, Alvaro Goyanes, Simon Gaisford & Abdul W. Basit. (2021) Harnessing artificial intelligence for the next generation of 3D printed medicines. Advanced Drug Delivery Reviews 175, pages 113805.
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Laura E. McCoubrey, Moe Elbadawi, Mine Orlu, Simon Gaisford & Abdul W. Basit. (2021) Machine Learning Uncovers Adverse Drug Effects on Intestinal Bacteria. Pharmaceutics 13:7, pages 1026.
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Zahari Vinarov, Mohammad Abdallah, José A.G. Agundez, Karel Allegaert, Abdul W. Basit, Marlies Braeckmans, Jens Ceulemans, Maura Corsetti, Brendan T. Griffin, Michael Grimm, Daniel Keszthelyi, Mirko Koziolek, Christine M. Madla, Christophe Matthys, Laura E. McCoubrey, Amitava Mitra, Christos Reppas, Jef Stappaerts, Nele Steenackers, Natalie L. Trevaskis, Tim Vanuytsel, Maria Vertzoni, Werner Weitschies, Clive Wilson & Patrick Augustijns. (2021) Impact of gastrointestinal tract variability on oral drug absorption and pharmacokinetics: An UNGAP review. European Journal of Pharmaceutical Sciences 162, pages 105812.
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Vipul Yadav, Yang Mai, Laura E. McCoubrey, Yasufumi Wada, Motoyasu Tomioka, Satofumi Kawata, Shrikant Charde & Abdul W. Basit. (2021) 5-Aminolevulinic Acid as a Novel Therapeutic for Inflammatory Bowel Disease. Biomedicines 9:5, pages 578.
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Carlos Sabater, Lorena Ruiz & Abelardo Margolles. (2021) A Machine Learning Approach to Study Glycosidase Activities from Bifidobacterium. Microorganisms 9:5, pages 1034.
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Matthew B. Biggs, Kelly Craig, Esther Gachango, David Ingham & Mathias Twizeyimana. (2021) Genomics- and Machine Learning-Accelerated Discovery of Biocontrol Bacteria. Phytobiomes Journal 5:4, pages 452-463.
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