Mani Arumugam

Mani Arumugam

ORCID: 0000-0002-0886-9101

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  1. Published

    A human gut microbial gene catalogue established by metagenomic sequencing

    MetaHIT Consortium, M. C., 2010, In: Nature. 464, 7285, p. 59-65 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  2. Published

    Prognostic performance of 7 biomarkers compared to liver biopsy in early alcohol-related liver disease

    Rasmussen, D. N., Thiele, M., Johansen, S., Kjærgaard, M., Lindvig, K. P., Israelsen, M., Antonsen, S., Detlefsen, S., Krag, A., Anastasiadou, E., Arumugam, M., Bork, P., Hansen, T., Hartoft, C., Israelsen, H., Karsdal, M., Legido-Quigley, C., Melberg, H. O., Trebicka, J., Mann, M. & 2 others, Matthijnssens, J. & MicrobLiver consortia, M. C., 2021, In: Journal of Hepatology. 75, 5, p. 1017-1025 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    Clostridium scindens secretome suppresses virulence gene expression of Clostridioides difficile in a bile acid-independent manner

    Saenz, C., Fang, Q., Gnanasekaran, Thiyagarajan, Trammell, Sam, Buijink, Jesse A., Pisano, P., Wierer, M., Moens, F., Lengger, B., Brejnrod, A. & Arumugam, Mani, 2023, In: Microbiology Spectrum. 11, 5, p. 1-18 e0393322.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration

    Saenz, C., Nigro, E., Gunalan, V. & Arumugam, Mani, 2022, In: Frontiers in Bioinformatics. 2, 15 p., 846922.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Circulating microbiome in blood of different circulatory compartments

    Schierwagen, R., Alvarez Silva, Maria Camila, Madsen, M. S. A., Kolbe, C. C., Meyer, C., Thomas, D., Uschner, F. E., Magdaleno, F., Jansen, C., Pohlmann, A., Praktiknjo, M., Hischebeth, G. T., Molitor, E., Latz, E., Lelouvier, B., Trebicka, J. & Arumugam, Mani, 2019, In: Gut. 68, 3, p. 578-580

    Research output: Contribution to journal › Letter › Research › peer-review

  6. Published

    Trust is good, control is better: technical considerations in blood microbiome analysis

    Schierwagen, R., Alvarez Silva, Maria Camila, Servant, F., Trebicka, J., Lelouvier, B. & Arumugam, Mani, 2020, In: Gut. 69, 7, p. 1362-1363

    Research output: Contribution to journal › Letter › Research › peer-review

  7. Published

    Genomic variation landscape of the human gut microbiome

    Schloissnig, S., Arumugam, Mani, Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., Kota, K., Sunyaev, S. R., Weinstock, G. M. & Bork, P., 2013, In: Nature. 493, 7430, p. 45-50 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Metagenomic species profiling using universal phylogenetic marker genes

    Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., Rasmussen, S., Brunak, S., Pedersen, O. B., Guarner, F., de Vos, W. M., Wang, J., Li, J., Doré, J., Ehrlich, S. D., Stamatakis, A. & 1 others, Bork, P., 2013, In: Nature Methods. 10, 12, p. 1196-1199 4 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Complete Genome Sequences of emm111 Type Streptococcus pyogenes Strain GUR, with Antitumor Activity, and Its Derivative Strain GURSA1 with an Inactivated emm Gene

    Suvorova, M. A., Tsapieva, A. N., Bak, Emilie Glad, Chereshnev, V. A., Kiseleva, E. P., Suvorov, A. N. & Arumugam, Mani, 21 Sep 2017, In: Genome Announcements. 5, 38, 2 p., e00939-17.

    Research output: Contribution to journal › Journal article › Research

  10. Published

    The intestinal microbiome is a co-determinant of the postprandial plasma glucose response

    Søndertoft, N. B., Vogt, J. K., Arumugam, Mani, Kristensen, M., Gøbel, R. J., Fan, Yong, Lyu, Liwei, Bahl, M. I., Eriksen, C., Ängquist, Lars, Frøkiær, Hanne, Hansen, T. H., Brix, Susanne, Nielsen, H. B., Hansen, Torben, Vestergaard, H., Gupta, R., Licht, T. R., Lauritzen, Lotte & Pedersen, Oluf Borbye, 2020, In: P L o S One. 15, 9, 23 p., e0238648.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. E-pub ahead of print

    Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases

    Thiele, M., Villesen, I. F., Niu, L., Johansen, S., Sulek, K., Nishijima, S., Espen, L. V., Keller, M., Israelsen, M., Suvitaival, T., Zawadzki, A. D., Juel, H. B., Brol, M. J., Stinson, S. E., Huang, Y., Silva, M. C. A., Kuhn, M., Anastasiadou, E., Leeming, D. J., Karsdal, M. & 12 others, Matthijnssens, J., Arumugam, Mani, Dalgaard, L. T., Legido-Quigley, C., Mann, Matthias, Trebicka, J., Bork, P., Jensen, Lars Juhl, Hansen, Torben, Krag, A., MicrobLiver Consortium, M. C. & GALAXY Consortium, G. C., 2024, (E-pub ahead of print) In: Journal of Hepatology.

    Research output: Contribution to journal › Review › Research › peer-review

  12. Published

    Sphingolipids Are Depleted in Alcohol-Related Liver Fibrosis

    Thiele, M., Suvitaival, T., Trošt, K., Kim, M., de Zawadzki, A., Kjaergaard, M., Rasmussen, D. N., Lindvig, K. P., Israelsen, M., Detlefsen, S., Andersen, P., Juel, H. B., Nielsen, T., Georgiou, S., Filippa, V., Kuhn, M., Nishijima, S., Moitinho-Silva, L., Rossing, P., Trebicka, J. & 14 others, Anastasiadou, E., Bork, P., Hansen, T., Legido-Quigley, C., Krag, A., Mann, M., Matthijnssens, J., Arumugam, Mani, Henrar, R., Israelsen, H., Karsdal, M., Melberg, H. O., MicrobLiver Consortium, M. C. & GALAXY Consortium, G. C., 2023, In: Gastroenterology. 164, 7, p. 1248-1260

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation (Nature Medicine, (2019), 25, 4, (667-678), 10.1038/s41591-019-0405-7)

    Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., Gandini, S., Serrano, D., Tarallo, S., Francavilla, A., Gallo, G., Trompetto, M., Ferrero, G., Mizutani, S., Shiroma, H., Shiba, S. & 19 others, Shibata, T., Yachida, S., Yamada, T., Wirbel, J., Schrotz-King, P., Ulrich, C. M., Brenner, H., Arumugam, Mani, Bork, P., Zeller, G., Cordero, F., Dias-Neto, E., Setubal, J. C., Tett, A., Pardini, B., Rescigno, M., Waldron, L., Naccarati, A. & Segata, N., 1 Dec 2019, In: Nature Medicine. 25, 12, p. 1948 1 p.

    Research output: Contribution to journal › Comment/debate › Research › peer-review

  14. Published

    Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

    Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., Gandini, S., Serrano, D., Tarallo, S., Francavilla, A., Gallo, G., Trompetto, M., Ferrero, G., Mizutani, S., Shiroma, H., Shiba, S. & 19 others, Shibata, T., Yachida, S., Yamada, T., Wirbel, J., Schrotz-King, P., Ulrich, C. M., Brenner, H., Arumugam, Mani, Bork, P., Zeller, G., Cordero, F., Dias-Neto, E., Setubal, J. C., Tett, A., Pardini, B., Rescigno, M., Waldron, L., Naccarati, A. & Segata, N., 2019, In: Nature Medicine. 25, 4, p. 667-678 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure

    Trebicka, J., Bork, P., Krag, A. & Arumugam, Mani, 2021, In: Nature Reviews Gastroenterology & Hepatology. 18, p. 167-180 14 p.

    Research output: Contribution to journal › Review › Research › peer-review

  16. Published

    Variation in Bile Microbiome by the Etiology of Cholestatic Liver Disease

    Tyc, O., Jansen, C., Schierwagen, R., Uschner, F. E., Israelsen, M., Klein, S., Ortiz, C., Strassburg, C. P., Zeuzem, S., Gu, W., Torres, S., Praktiknjo, M., Kersting, S., Langheinrich, M., Nattermann, J., Servant, F., Arumugam, M., Krag, A., Lelouvier, B., Weismueller, T. J. & 1 others, Trebicka, J., 2020, In: Liver Transplantation. 26, 12, p. 1652-1657 6 p.

    Research output: Contribution to journal › Letter › Research

  17. Published

    A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog

    Van Espen, L., Bak, E. G., Beller, L., Close, L., Deboutte, W., Juel, H. B., Nielsen, T., Sinar, D., De Coninck, L., Frithioff-Bøjsøe, C., Fonvig, C. E., Jacobsen, S., Kjærgaard, M., Thiele, M., Fullam, A., Kuhn, M., Holm, J. C., Bork, P., Krag, A., Hansen, T. & 2 others, Arumugam, Mani & Matthijnssens, J., 2021, In: mSystems. 6, 5, 20 p., e00382-21.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. Published

    Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions

    Wei, C., Lamesch, P., Arumugam, Mani, Rosenberg, J., Hu, P., Vidal, M. & Brent, M. R., 2005, In: Genome Research. 15, 4, p. 577-82 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  19. Published

    Genetic studies of abdominal MRI data identify genes regulating hepcidin as major determinants of liver iron concentration

    Wilman, H. R., Parisinos, C. A., Atabaki-Pasdar, N., Kelly, M., Thomas, E. L., Neubauer, S., Jennison, C., Ehrhardt, B., Baum, P., Schoelsch, C., Freijer, J., Grempler, R., Graefe-Mody, U., Hennige, A., Dings, C., Lehr, T., Scherer, N., Sihinecich, I., Pattou, F., Raverdi, V. & 31 others, Caiazzo, R., Torres, F., Verkindt, H., Mari, A., Tura, A., Giorgino, T., Bizzotto, Froguel, P., Brorsson, C., Brunak, Søren, De Masi, F., Pedersen, H., Banasik, Karina, Thomas, Cecilia Engel, Lundgaard, Agnete Troen, Nielsen, A., Mazzoni, G., Karaderi, Tugce, Rasmussen, Simon, Johansen, Joachim, Allesøe, R., Arumugam, Mani, Allin, K., Hansen, Torben, Hansen, T., Jonsson, Anna Elisabet, Pedersen, Oluf Borbye, Dutta, A., Vogt, J., drb459, drb459 & IMI-DIRECT consortium, I. C., 2019, In: Journal of Hepatology. 71, 3, p. 594-602 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

    Wirbel, J., Pyl, P. T., Kartal, E., Zych, K., Kashani, A., Milanese, A., Fleck, J. S., Voigt, A. Y., Palleja, A., Ponnudurai, R., Sunagawa, S., Coelho, L. P., Schrotz-King, P., Vogtmann, E., Habermann, N., Niméus, E., Thomas, A. M., Manghi, P., Gandini, S., Serrano, D. & 15 others, Mizutani, S., Shiroma, H., Shiba, S., Shibata, T., Yachida, S., Yamada, T., Waldron, L., Naccarati, A., Segata, N., Sinha, R., Ulrich, C. M., Brenner, H., Arumugam, Mani, Bork, P. & Zeller, G., 2019, In: Nature Medicine. 25, 4, p. 679-689 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing

    Wu, J. Q., Shteynberg, D., Arumugam, Mani, Gibbs, R. A. & Brent, M. R., 2004, In: Genome Research. 14, 4, p. 665-71 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

    Xiao, L., Sonne, S. B., Feng, Q., Chen, N., Xia, Z., Li, X., Fang, Z., Zhang, D., Fjære, E., Midtbø, L. K., Derrien, M., Hugenholtz, F., Tang, L., Li, J., Zhang, J., Liu, C., Hao, Q., Vogel, U. B., Mortensen, A., Kleerebezem, M. & 8 others, Licht, T. R., Yang, H., Wang, J., Li, Y., Arumugam, Mani, Wang, J., Madsen, L. & Kristiansen, Karsten, 8 Apr 2017, In: Microbiome. 5, 12 p., 43.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    A catalog of the mouse gut metagenome: [incl. Author Correction]

    Xiao, L., Feng, Q., Liang, S., Sonne, S. B., Xia, Z., Qiu, X., Li, X., Long, H., Zhang, J., Zhang, D., Liu, C., Fang, Z., Chou, J., Glanville, J., Hao, Q., Kotowska, D. E., Colding, C. S., Licht, T. R., Wu, D., Yu, J. & 17 others, Sung, J. J. Y., Liang, Q., Li, J., Jia, H., Lan, Z., Tremaroli, V., Dworzynski, P., Nielsen, H. B., Bäckhed, G. F., Dore, J., Le Chatelier, E., Ehrlich, S. D., Lin, J. C., Arumugam, Mani, Wang, J., Madsen, L. & Kristiansen, Karsten, 2015, In: Nature Biotechnology. 33, 10, p. 1103-1108 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

    Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

    Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L., Gilbert, J. A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G., Vaughan, R., Hunter, C., Park, J., Morrison, N., Rocca-Serra, P., Sterk, P., Arumugam, M., Bailey, M., Baumgartner, L., Birren, B. W. & 78 others, Blaser, M. J., Bonazzi, V., Booth, T., Bork, P., Bushman, F. D., Buttigieg, P. L., Chain, P. S. G., Charlson, E., Costello, E. K., Huot-Creasy, H., Dawyndt, P., DeSantis, T., Fierer, N., Fuhrman, J. A., Gallery, R. E., Gevers, D., Gibbs, R. A., San Gil, I., Gonzalez, A., Gordon, J. I., Guralnick, R., Hankeln, W., Highlander, S., Hugenholtz, P., Jansson, J., Kau, A. L., Kelley, S. T., Kennedy, J., Knights, D., Koren, O., Kuczynski, J., Kyrpides, N., Larsen, R., Lauber, C. L., Legg, T., Ley, R. E., Lozupone, C. A., Ludwig, W., Lyons, D., Maguire, E., Methé, B. A., Meyer, F., Muegge, B., Nakielny, S., Nelson, K. E., Nemergut, D., Neufeld, J. D., Newbold, L. K., Oliver, A. E., Pace, N. R., Palanisamy, G., Peplies, J., Petrosino, J., Proctor, L., Pruesse, E., Quast, C., Raes, J., Ratnasingham, S., Ravel, J., Relman, D. A., Assunta-Sansone, S., Schloss, P. D., Schriml, L., Sinha, R., Smith, M. I., Sodergren, E., Spo, A., Stombaugh, J., Tiedje, J. M., Ward, D. V., Weinstock, G. M., Wendel, D., White, O., Whiteley, A., Wilke, A., Wortman, J. R., Yatsunenko, T. & Glöckner, F. O., 2011, In: Nature Biotechnology. 29, 5, p. 415-20 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

    Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

    Yu, J., Feng, Q., Wong, S. H., Zhang, D., Liang, Q. Y., Qin, Y., Tang, L., Zhao, H., Stenvang, J., Li, Y., Wang, X., Xu, X., Chen, N., Wu, W. K. K., Al-Aama, J., Nielsen, H. J., Kiilerich, P., Jensen, B. A. H., Yau, T. O., Lan, Z. & 19 others, Jia, H., Li, J., Xiao, L., Lam, T. Y. T., Ng, S. C., Cheng, A. S., Wong, V. W., Chan, F. K. L., Xu, X., Yang, H., Madsen, L., Datz, C., Tilg, H., Wang, J., Brünner, N., Kristiansen, Karsten, Arumugam, Mani, Sung, J. J. & Wang, J., 2017, In: Gut. 66, p. 70-78 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  26. Published

    The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

    Zoetendal, E. G., Raes, J., van den Bogert, B., Arumugam, Mani, Booijink, C. C. G. M., Troost, F. J., Bork, P., Wels, M., de Vos, W. M. & Kleerebezem, M., 2012, In: I S M E Journal. 6, 7, p. 1415-26 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  27. Consistent mutational paths predict eukaryotic thermostability

    van Noort, V., Bradatsch, B., Arumugam, Mani, Amlacher, S., Bange, G., Creevey, C., Falk, S., Mende, D. R., Sinning, I., Hurt, E. & Bork, P., 2013, In: B M C Evolutionary Biology. 13, p. 7

    Research output: Contribution to journal › Journal article › Research › peer-review

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