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 §.
- § 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, doi:10.1038/s41591-019-0406-6 (2019).
- 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, doi:10.1038/s41591-019-0405-7 (2019).
- § 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).
- 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).
- § Palleja A*, Mikkelsen KH*, Forslund SK*, et al. “Recovery of gut microbiota of healthy adults following antibiotic exposure.”
Nature microbiology 3, 1255-65 (2018).
- § 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).
- 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).
- 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).
- § 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).
- 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).
- § 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).
- 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).
- § 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).
- 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).
- 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).
- Xiao L, Feng Q, Liang S,
Sonne SB, et al. “A Catalogue of the Mouse Gut Metagenome.” Nature Biotechnology
33, 1103-8 (2015).
- Feng Q, Liang S, Jia H,
Stadlmayr A, et al. “Gut microbiome development along the colorectal
adenoma-carcinoma sequence.” Nature Communications 6, 6528 (2015).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- van Noort V, Bradatsch B, Arumugam M, Amlacher
S, et al. “Consistent mutational paths predict eukaryotic
thermostability.” BMC evolutionary biology 13, 7 (2013).
- Schloissnig S*, Arumugam M*, Sunagawa S*, Mitreva M, et al. “Genomic variation landscape of
the human gut microbiome.” Nature 493, 45-50 (2013).
- Kultima JR, Sunagawa S, Li J, Chen W, et al.
“MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit.” PLoS One 7,
e47656 (2012).
- 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).
- 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).
- 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).
- Arumugam M*, Raes J*, Pelletier E, Le Paslier D, et
al. “Enterotypes of the human gut microbiome.” Nature 473, 174-180
(2011).
- 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).
- 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).
- Arumugam M, Harrington ED, Foerstner KU, Raes J and Bork P. “SmashCommunity: A
metagenomic annotation and analysis tool.” Bioinformatics 26, 2977-78
(2010).
- 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).
- Güell M, van Noort V,
Yus E, Chen W, et al. “Transcriptome complexity in a genome-reduced
bacterium.” Science 326, 1268-71 (2009).
- Lu DV, Brown RH, Arumugam M and
Brent MR. “Pairagon: a highly accurate, HMM-based cDNA-to- genome aligner.” Bioinformatics
25, 1587-93 (2009).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).