Publications

Reverse chronological listing of our publications. Authors from group are underlined, and group-led articles (first or last author from the group) are marked with §.

  1. Goedel C, Kunkel B, Kashani A, et al. “Perturbation of gut microbiota decreases susceptibility but does not modulate ongoing autoimmune neurological disease.” Journal of Neuroinflammation, 17, 79 (2020).
  2. §Kashani A, Brejnrod AD, Jin C, et al. “Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob mice.” Animal microbiome, 1, 11 (2019).
  3. Bolyen E, Rideout JR, Dillon MR, et al. “Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.” Nature biotechnology, 37, 852-7 (2019).
  4. §Schierwagen R*, Alvarez-Silva C*, Servant F, et al. “Trust is good, control is better: Technical considerations in blood microbiome analysis.” Gut, doi:10.1136/gutjnl-2019-319123 (2019).
  5. § Wirbel J*, Pyl PT*, Zych K, Kartal E, et al. “Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.” Nature medicine, 25, 679-89 (2019).
  6. Thomas AM, Manghi P, Asnicar F, Pasolli E, et al. “Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.” Nature medicine, 25, 667-78 (2019).
  7. § Alvarez-Silva C*, Schierwagen R*, Pohlmann A, Magdaleno F, et al. “Compartmentalization of immune response and microbial translocation in decompensated cirrhosis.” Frontiers in Immunology, doi:10.3389/fimmu.2019.00069 (2019).
  8. Poupeau A, Garde C, Sulek K, et al. “Genes controlling the activation of natural killer lymphocytes are epigenetically remodeled in intestinal cells from germ-free mice.” FASEB Journal, doi:10.1096/fj.201800787R (2018).
  9. § Palleja A*, Mikkelsen KH*, Forslund SK*, et al. “Recovery of gut microbiota of healthy adults following antibiotic exposure.” Nature microbiology 3, 1255-65 (2018).
  10. § Schierwagen R*, Alvarez-Silva C*, Madsen MSA, et al. “Circulating microbiome in blood of different circulatory compartments.” Gut, doi:10.1136/gutjnl-2018-316227 (2018).
  11. Madsen BM, Trebicka J, Thiele M, Israelsen M, Arumugam M, Havelund T, Krag A. “Antifibrotic and molecular aspects of rifaximin in alcoholic liver disease: study protocol for a randomized controlled trial.” Trials 19, 143 (2018).
  12. Costea P, Hildebrand F, Arumugam M, Backhed F, et al. “Enterotypes in the landscape of gut microbial community composition.” Nature microbiology 3, 8-16 (2018).
  13. § Suvorova MA, Tsapieva AN, Bak EG, Chereshnev VA, Kiseleva EP, Suvorov AN, Arumugam M. “Complete genome sequences of emm111 type Streptococcus pyogenes strain GUR, with antitumor activity, and its derivative strain GURSA1 with an inactivated emm gene.” Genome Announcements 5, e00939-17 (2017).
  14. Xiao L, Sonne SB, Feng Q, Chen N, et al. “High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice.” Microbiome 5, 43 (2017).
  15. § Yu J, Feng Q, Wong SH, Zhang D, et al. “Metagenomic analysis of fecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer.” Gut 66, 70-78 (2017).
  16. Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, et al. “Human gut microbes impact host serum metabolome and insulin sensitivity.” Nature 535, 376-381 (2016).
  17. § Palleja A, Kashani A, Allin K, Nielsen T, et al. “Roux-en-Y gastric bypass surgery of morbidly obese patients shows swift and persistent changes of the individual gut microbiota.” Genome Medicine 8:67 (2016).
  18. Bag S, Saha B, Mehta O, Anbumani D, et al. “An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples.” Scientific Reports 31, 26775 (2016).
  19. Forslund K, Hildebrand F, Nielsen T, Falony G, et al. “Disentangling disease- and drug signatures of the human gut microbiome: the case of type 2 diabetes mellitus.” Nature 528, 262-6 (2015).
  20. Xiao L, Feng Q, Liang S, Sonne SB, et al. “A Catalogue of the Mouse Gut Metagenome.” Nature Biotechnology 33, 1103-8 (2015).
  21. Feng Q, Liang S, Jia H, Stadlmayr A, et al. “Gut microbiome development along the colorectal adenoma-carcinoma sequence.” Nature Communications 6, 6528 (2015).
  22. Li J, Jia H, Cai X, Zhong H, et al. “An integrated reference gene catalog of the human gut microbiome.” Nature Biotechnology 32, 834-41 (2014).
  23. Nielsen HB, Almeida M, Juncker AS, Rasmussen S, et al. “Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.” Nature Biotechnology 32, 822-28 (2014).
  24. Emanuelli B, Vienberg S, Smyth G, Cheng C, et al. “Interplay between FGF21 and Insulin Action in the Liver for the Regulation of Metabolism.” Journal of Clinical Investigation 124, 515-27 (2014).
  25. Sunagawa S, Mende D, Zeller G, Izquierdo-Carrasco F, et al. “Metagenomic species profiling using universal phylogenetic marker genes.” Nature Methods 10, 1196-9 (2013).
  26. Le Chatelier E, Nielsen T, Qin J, Prifti E, et al. “Richness of human gut microbial communities correlates with metabolic markers.” Nature 500, 541-6 (2013).
  27. Forslund K, Sunagawa S, Kultima JR, Mende D, Arumugam M, Typas A and Bork, P. “Country-specific antibiotic use practices impact the human gut resistome.” Genome Research 23, 1163-9 (2013).
  28. van Noort V, Bradatsch B, Arumugam M, Amlacher S, et al. “Consistent mutational paths predict eukaryotic thermostability.” BMC evolutionary biology 13, 7 (2013).
  29. Schloissnig S*, Arumugam M*, Sunagawa S*, Mitreva M, et al.  “Genomic variation landscape of the human gut microbiome.” Nature 493, 45-50 (2013).
  30. Kultima JR, Sunagawa S, Li J, Chen W, et al. “MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit.” PLoS One 7, e47656 (2012).
  31. Mende DR, Waller A, Sunagawa S, Jaervelin AI, Chan MM, Arumugam M, Raes J, and Bork P. “Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data.”  PLoS One 7, e31386 (2012).
  32. Zoetendal EG, Raes J, van den Bogert B, Arumugam M, et al. “The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.” ISME Journal 6, 1415-26 (2012).
  33. Amlacher S, Sarges P, Flemming D, van Noort V, et al. “Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing a Eukaryotic Thermophile.”  Cell 146, 277-289 (2011).
  34. Arumugam M*, Raes J*, Pelletier E, Le Paslier D, et al. “Enterotypes of the human gut microbiome.” Nature 473, 174-180 (2011).
  35. Yilmaz P, Kottmann R, Field D, Knight R, et al. “Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.” Nature Biotechnology 29, 415-420 (2011).
  36. Harrington ED, Arumugam M, Raes J, Bork P and Relman DA. “SmashCell: A software framework for the analysis of single-cell amplified genome sequences.”  Bioinformatics 26, 2979-80 (2010).
  37. Arumugam M, Harrington ED, Foerstner KU, Raes J and Bork P. “SmashCommunity: A metagenomic annotation and analysis tool.”  Bioinformatics 26, 2977-78 (2010).
  38. Qin J, Li R, Raes M, Arumugam M, et al. “A human gut microbial gene catalogue established by metagenomic sequencing.”  Nature 464, 59-65 (2010).
  39. Güell M, van Noort V, Yus E, Chen W, et al. “Transcriptome complexity in a genome-reduced bacterium.” Science 326, 1268-71 (2009).
  40. Lu DV, Brown RH, Arumugam M and Brent MR. “Pairagon: a highly accurate, HMM-based cDNA-to- genome aligner.” Bioinformatics 25, 1587-93 (2009).
  41. Keibler E, Arumugam M and Brent MR. “The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs.”  Bioinformatics 23, 545-54 (2007).
  42. Arumugam M, Wei C, Brown RH and Brent MR. “Pairagon+NSCAN_EST: a model-based gene annotation pipeline.” Genome Biology 7 Suppl 1, 1-10 (2006).
  43. Giannakis M, Stappenbeck TS, Mills JC, Leip DG, et al. “Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches.” J. Biological Chemistry 281, 11292-300 (2006).
  44. Wei C, Lamesch P, Arumugam M, Rosenberg J, et al. “Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions.” Genome Research 15, 577-82 (2005).
  45. Wu JQ, Shteynberg D, Arumugam M, Gibbs RA, Brent MR. “Identification  of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing.” Genome Research 14, 665-71 (2004).
  46. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, et al. “Genome sequence of the Brown Norway rat yields insights into mammalian evolution.”  Nature 428, 493-521 (2004).
  47. Arumugam M and Scott SD. “EMPRR: A high-dimensional EM-based piecewise regression algorithm.” International Conference on Machine Learning and Applications, Proceedings, 264-271 (2004).