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Transcription shifts in gut bacteria shared between mothers and their infants.
Published in:
Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-04848-1
By:
- Vatanen, Tommi;
- Sakwinska, O.;
- Wilson, B.;
- Combremont, S.;
- Cutfield, W. S.;
- Chan, S. Y.;
- Godfrey, K. M.;
- NiPPeR Study Group;
- O'Sullivan, J. M.;
- Barton, Sheila J.;
- Cavanagh, Mary;
- Chong, Yap Seng;
- Costello, Paula;
- Cox, Vanessa;
- El-Heis, Sarah;
- Jagtap, Mrunalini;
- Lillycrop, Karen;
- Nield, Heidi;
- Satianegara, Gernalia;
- Silva-Zolezzi, Irma
Publication type:
Article
Sequence-structure-function relationships in the microbial protein universe.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37896-w
By:
- Koehler Leman, Julia;
- Szczerbiak, Pawel;
- Renfrew, P. Douglas;
- Gligorijevic, Vladimir;
- Berenberg, Daniel;
- Vatanen, Tommi;
- Taylor, Bryn C.;
- Chandler, Chris;
- Janssen, Stefan;
- Pataki, Andras;
- Carriero, Nick;
- Fisk, Ian;
- Xavier, Ramnik J.;
- Knight, Rob;
- Bonneau, Richard;
- Kosciolek, Tomasz
Publication type:
Article
Phages in the Gut Ecosystem.
Published in:
Frontiers in Cellular & Infection Microbiology, 2022, v. 11, p. 1, doi. 10.3389/fcimb.2021.822562
By:
- Zuppi, Michele;
- Hendrickson, Heather L.;
- O'Sullivan, Justin M.;
- Vatanen, Tommi
Publication type:
Article
Structure-based protein function prediction using graph convolutional networks.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23303-9
By:
- Gligorijević, Vladimir;
- Renfrew, P. Douglas;
- Kosciolek, Tomasz;
- Leman, Julia Koehler;
- Berenberg, Daniel;
- Vatanen, Tommi;
- Chandler, Chris;
- Taylor, Bryn C.;
- Fisk, Ian M.;
- Vlamakis, Hera;
- Xavier, Ramnik J.;
- Knight, Rob;
- Cho, Kyunghyun;
- Bonneau, Richard
Publication type:
Article
Gut microbiome shifts in people with type 1 diabetes are associated with glycaemic control: an INNODIA study.
Published in:
Diabetologia, 2024, v. 67, n. 9, p. 1930, doi. 10.1007/s00125-024-06192-7
By:
- Vatanen, Tommi;
- de Beaufort, Carine;
- Marcovecchio, M. Loredana;
- Overbergh, Lut;
- Brunak, Soren;
- Peakman, Mark;
- Mathieu, Chantal;
- Knip, Mikael
Publication type:
Article
Factors Associated With the Microbiome in Moderate–Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial.
Published in:
Frontiers in Cellular & Infection Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fcimb.2021.595323
By:
- Chong, Clara Yieh Lin;
- Vatanen, Tommi;
- Alexander, Tanith;
- Bloomfield, Frank H.;
- O'Sullivan, Justin M.
Publication type:
Article
An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09785-8
By:
- Cheng, Lu;
- Ramchandran, Siddharth;
- Vatanen, Tommi;
- Lietzén, Niina;
- Lahesmaa, Riitta;
- Vehtari, Aki;
- Lähdesmäki, Harri
Publication type:
Article
Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity.
Published in:
Microbiome, 2024, v. 12, n. 1, p. 1, doi. 10.1186/s40168-024-01833-w
By:
- Zuppi, Michele;
- Vatanen, Tommi;
- Wilson, Brooke C.;
- Golovina, Evgeniia;
- Portlock, Theo;
- Cutfield, Wayne S.;
- Vickers, Mark H.;
- O'Sullivan, Justin M.
Publication type:
Article
Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity.
Published in:
Microbiome, 2024, v. 12, p. 1, doi. 10.1186/s40168-024-01748-6
By:
- Behling, Anna H.;
- Wilson, Brooke C.;
- Ho, Daniel;
- Cutfield, Wayne S.;
- Vatanen, Tommi;
- O'Sullivan, Justin M.
Publication type:
Article
The microbial biogeography of the gastrointestinal tract of preterm and term lambs.
Published in:
Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-66056-z
By:
- Chong, Clara Yieh Lin;
- Vatanen, Tommi;
- Oliver, Mark;
- Bloomfield, Frank H.;
- O'Sullivan, Justin M.
Publication type:
Article
Higher circulating EGF levels associate with a decreased risk of IgE sensitization in young children.
Published in:
Pediatric Allergy & Immunology, 2022, v. 33, n. 1, p. 1, doi. 10.1111/pai.13613
By:
- Reinert‐Hartwall, Linnea;
- Siljander, Heli;
- Härkönen, Taina;
- Vatanen, Tommi;
- Ilonen, Jorma;
- Niemelä, Onni;
- Luopajärvi, Kristiina;
- Dorshakova, Natalya;
- Mokurov, Sergei;
- Peet, Aleksandr;
- Tillmann, Vallo;
- Uibo, Raivo;
- Knip, Mikael;
- Vaarala, Outi;
- Honkanen, Jarno;
- Genuneit, Jon
Publication type:
Article
The Super-Donor Phenomenon in Fecal Microbiota Transplantation.
Published in:
Frontiers in Cellular & Infection Microbiology, 2019, v. 9, p. N.PAG, doi. 10.3389/fcimb.2019.00002
By:
- Wilson, Brooke C.;
- Vatanen, Tommi;
- Cutfield, Wayne S.;
- O'Sullivan, Justin M.
Publication type:
Article
High-throughput automated microfluidic sample preparation for accurate microbial genomics.
Published in:
Nature Communications, 2017, v. 8, n. 1, p. 13919, doi. 10.1038/ncomms13919
By:
- Kim, Soohong;
- De Jonghe, Joachim;
- Kulesa, Anthony B.;
- Feldman, David;
- Vatanen, Tommi;
- Bhattacharyya, Roby P.;
- Berdy, Brittany;
- Gomez, James;
- Nolan, Jill;
- Epstein, Slava;
- Blainey, Paul C.
Publication type:
Article
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.
Published in:
Science Translational Medicine, 2016, v. 8, n. 343, p. 1, doi. 10.1126/scitranslmed.aad0917
By:
- Yassour, Moran;
- Vatanen, Tommi;
- Siljander, Heli;
- Hämäläinen, Anu-Maaria;
- Härkönen, Taina;
- Ryhänen, Samppa J.;
- Franzosa, Eric A.;
- Vlamakis, Hera;
- Huttenhower, Curtis;
- Gevers, Dirk;
- Lander, Eric S.;
- Knip, Mikael;
- Xavier, Ramnik J.
Publication type:
Article
High prevalence of undiagnosed comorbidities among adolescents with obesity.
Published in:
Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-76921-6
By:
- Leong, Karen S. W.;
- Jayasinghe, Thilini N.;
- Wilson, Brooke C.;
- Derraik, José G. B.;
- Albert, Benjamin B.;
- Chiavaroli, Valentina;
- Svirskis, Darren M.;
- Beck, Kathryn L.;
- Conlon, Cathryn A.;
- Jiang, Yannan;
- Schierding, William;
- Vatanen, Tommi;
- Holland, David J.;
- O'Sullivan, Justin M.;
- Cutfield, Wayne S.
Publication type:
Article
Desacetyl-α-MSH and α-MSH have sex specific interactions with diet to influence mouse gut morphology, metabolites and microbiota.
Published in:
Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-75786-z
By:
- Sun, Bo;
- Vatanen, Tommi;
- Jayasinghe, Thilini N.;
- McKenzie, Elizabeth;
- Murphy, Rinki;
- O'Sullivan, Justin M.
Publication type:
Article
Effects of Fecal Microbiome Transfer in Adolescents With Obesity: The Gut Bugs Randomized Controlled Trial.
Published in:
JAMA Network Open, 2020, v. 3, n. 12, p. e2030415, doi. 10.1001/jamanetworkopen.2020.30415
By:
- Leong, Karen S. W.;
- Jayasinghe, Thilini N.;
- Wilson, Brooke C.;
- Derraik, José G. B.;
- Albert, Benjamin B.;
- Chiavaroli, Valentina;
- Svirskis, Darren M.;
- Beck, Kathryn L.;
- Conlon, Cathryn A.;
- Jiang, Yannan;
- Schierding, William;
- Vatanen, Tommi;
- Holland, David J.;
- O'Sullivan, Justin M.;
- Cutfield, Wayne S.
Publication type:
Article
Differences in Compositions of Gut Bacterial Populations and Bacteriophages in 5–11 Year-Olds Born Preterm Compared to Full Term.
Published in:
Frontiers in Cellular & Infection Microbiology, 2020, v. 10, p. 1, doi. 10.3389/fcimb.2020.00276
By:
- Jayasinghe, Thilini N.;
- Vatanen, Tommi;
- Chiavaroli, Valentina;
- Jayan, Sachin;
- McKenzie, Elizabeth J.;
- Adriaenssens, Evelien;
- Derraik, José G. B.;
- Ekblad, Cameron;
- Schierding, William;
- Battin, Malcolm R.;
- Thorstensen, Eric B.;
- Cameron-Smith, David;
- Forbes-Blom, Elizabeth;
- Hofman, Paul L.;
- Roy, Nicole C.;
- Tannock, Gerald W.;
- Vickers, Mark H.;
- Cutfield, Wayne S.;
- O'Sullivan, Justin M.
Publication type:
Article
Experimental design and quantitative analysis of microbial community multiomics.
Published in:
Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1359-z
By:
- Mallick, Himel;
- Siyuan Ma;
- Franzosa, Eric A.;
- Vatanen, Tommi;
- Morgan, Xochitl C.;
- Huttenhower, Curtis
Publication type:
Article
Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.
Published in:
Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0331-y
By:
- Shaw, Kelly A.;
- Bertha, Madeline;
- Hofmekler, Tatyana;
- Chopra, Pankaj;
- Vatanen, Tommi;
- Srivatsa, Abhiram;
- Prince, Jarod;
- Kumar, Archana;
- Sauer, Cary;
- Zwick, Michael E.;
- Satten, Glen A.;
- Kostic, Aleksandar D.;
- Mulle, Jennifer G.;
- Xavier, Ramnik J.;
- Kugathasan, Subra
Publication type:
Article
The influence of a short-term gluten-free diet on the human gut microbiome.
Published in:
Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0295-y
By:
- Bonder, Marc Jan;
- Tigchelaar, Ettje F.;
- Xianghang Cai;
- Trynka, Gosia;
- Cenit, Maria C.;
- Hrdlickova, Barbara;
- Huanzi Zhong;
- Vatanen, Tommi;
- Gevers, Dirk;
- Wijmenga, Cisca;
- Yang Wang;
- Zhernakova, Alexandra
Publication type:
Article
Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity.
Published in:
Microbiome, 2021, v. 9, n. 1, p. 1, doi. 10.1186/s40168-021-01060-7
By:
- Wilson, Brooke C.;
- Vatanen, Tommi;
- Jayasinghe, Thilini N.;
- Leong, Karen S. W.;
- Derraik, José G. B.;
- Albert, Benjamin B.;
- Chiavaroli, Valentina;
- Svirskis, Darren M.;
- Beck, Kathryn L.;
- Conlon, Cathryn A.;
- Jiang, Yannan;
- Schierding, William;
- Holland, David J.;
- Cutfield, Wayne S.;
- O'Sullivan, Justin M.
Publication type:
Article
Randomised Double-Blind Placebo-Controlled Trial of Inulin with Metronidazole in Non-Alcoholic Fatty Liver Disease (NAFLD).
Published in:
Nutrients, 2020, v. 12, n. 4, p. 937, doi. 10.3390/nu12040937
By:
- Chong, Clara Yieh Lin;
- Orr, David;
- Plank, Lindsay D.;
- Vatanen, Tommi;
- O'Sullivan, Justin M.;
- Murphy, Rinki
Publication type:
Article
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.
Published in:
Genome Medicine, 2017, v. 9, p. 1, doi. 10.1186/s13073-017-0490-5
By:
- Hall, Andrew Brantley;
- Yassour, Moran;
- Sauk, Jenny;
- Garner, Ashley;
- Xiaofang Jiang;
- Arthur, Timothy;
- Lagoudas, Georgia K.;
- Vatanen, Tommi;
- Fornelos, Nadine;
- Wilson, Robin;
- Bertha, Madeline;
- Cohen, Melissa;
- Garber, John;
- Khalili, Hamed;
- Gevers, Dirk;
- Ananthakrishnan, Ashwin N.;
- Kugathasan, Subra;
- Lander, Eric S.;
- Blainey, Paul;
- Vlamakis, Hera
Publication type:
Article

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