Mani Arumugam - Publications

Affiliations: 
Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 
Website:
http://www.embl.de/research/units/scb/bork/members/index.php?s_personId=4432

32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, ... ... Arumugam M, et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. PMID 27409811 DOI: 10.1038/nature18646  0.72
2015 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Yvonne Voigt A, Vestergaard H, Hercog R, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26633628 DOI: 10.1038/nature15766  0.72
2015 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Yvonne Voigt A, Vestergaard H, Hercog R, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26618873 DOI: 10.1038/nature15766  0.72
2015 Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, ... ... Arumugam M, et al. A catalog of the mouse gut metagenome. Nature Biotechnology. PMID 26414350 DOI: 10.1038/nbt.3353  0.72
2015 Yu J, Feng Q, Wong SH, Zhang D, Liang QY, Qin Y, Tang L, Zhao H, Stenvang J, Li Y, Wang X, Xu X, Chen N, Wu WK, Al-Aama J, ... ... Arumugam M, et al. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut. PMID 26408641 DOI: 10.1136/gutjnl-2015-309800  0.72
2015 Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, Xia H, Xu X, Jie Z, Su L, Li X, Li X, Li J, Xiao L, ... ... Arumugam M, et al. Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nature Communications. 6: 6528. PMID 25758642 DOI: 10.1038/ncomms7528  0.72
2014 Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature Biotechnology. 32: 822-8. PMID 24997787 DOI: 10.1038/nbt.2939  0.72
2014 Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, et al. An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology. 32: 834-41. PMID 24997786 DOI: 10.1038/nbt.2942  0.72
2013 Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, et al. Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods. 10: 1196-9. PMID 24141494 DOI: 10.1038/nmeth.2693  0.72
2013 Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 500: 541-6. PMID 23985870 DOI: 10.1038/nature12506  0.72
2013 Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. Country-specific antibiotic use practices impact the human gut resistome. Genome Research. 23: 1163-9. PMID 23568836 DOI: 10.1101/gr.155465.113  0.72
2013 van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P. Consistent mutational paths predict eukaryotic thermostability. Bmc Evolutionary Biology. 13: 7. PMID 23305080 DOI: 10.1186/1471-2148-13-7  0.72
2013 Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P. Genomic variation landscape of the human gut microbiome. Nature. 493: 45-50. PMID 23222524 DOI: 10.1038/nature11711  0.72
2012 Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P. MOCAT: a metagenomics assembly and gene prediction toolkit. Plos One. 7: e47656. PMID 23082188 DOI: 10.1371/journal.pone.0047656  0.72
2012 Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P. Assessment of metagenomic assembly using simulated next generation sequencing data. Plos One. 7: e31386. PMID 22384016 DOI: 10.1371/journal.pone.0031386  0.72
2012 Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. The Isme Journal. 6: 1415-26. PMID 22258098 DOI: 10.1038/ismej.2011.212  0.72
2011 Amlacher S, Sarges P, Flemming D, van Noort V, Kunze R, Devos DP, Arumugam M, Bork P, Hurt E. Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell. 146: 277-89. PMID 21784248 DOI: 10.1016/j.cell.2011.06.039  0.72
2011 Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, ... ... Arumugam M, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29: 415-20. PMID 21552244 DOI: 10.1038/nbt.1823  0.72
2011 Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, et al. Enterotypes of the human gut microbiome. Nature. 473: 174-80. PMID 21508958 DOI: 10.1038/nature09944  0.72
2010 Harrington ED, Arumugam M, Raes J, Bork P, Relman DA. SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Bioinformatics (Oxford, England). 26: 2979-80. PMID 20966005 DOI: 10.1093/bioinformatics/btq564  0.72
2010 Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P. SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics (Oxford, England). 26: 2977-8. PMID 20959381 DOI: 10.1093/bioinformatics/btq536  0.72
2010 Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 464: 59-65. PMID 20203603 DOI: 10.1038/nature08821  0.72
2009 Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, et al. Transcriptome complexity in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1268-71. PMID 19965477 DOI: 10.1126/science.1176951  0.72
2009 Manikandan R, Thiagarajan R, Beulaja S, Chindhu S, Mariammal K, Sudhandiran G, Arumugam M. Anti-cataractogenic effect of curcumin and aminoguanidine against selenium-induced oxidative stress in the eye lens of Wistar rat pups: An in vitro study using isolated lens. Chemico-Biological Interactions. 181: 202-9. PMID 19481068 DOI: 10.1016/j.cbi.2009.05.011  0.01
2009 Lu DV, Brown RH, Arumugam M, Brent MR. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner. Bioinformatics (Oxford, England). 25: 1587-93. PMID 19414532 DOI: 10.1093/bioinformatics/btp273  0.72
2007 Keibler E, Arumugam M, Brent MR. The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs. Bioinformatics (Oxford, England). 23: 545-54. PMID 17237054 DOI: 10.1093/bioinformatics/btl659  0.72
2006 Arumugam M, Wei C, Brown RH, Brent MR. Pairagon+N-SCAN_EST: a model-based gene annotation pipeline. Genome Biology. 7: S5.1-10. PMID 16925839 DOI: 10.1186/gb-2006-7-s1-s5  0.72
2006 Giannakis M, Stappenbeck TS, Mills JC, Leip DG, Lovett M, Clifton SW, Ippolito JE, Glasscock JI, Arumugam M, Brent MR, Gordon JI. Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches. The Journal of Biological Chemistry. 281: 11292-300. PMID 16464855 DOI: 10.1074/jbc.M512118200  0.72
2005 Wei C, Lamesch P, Arumugam M, Rosenberg J, Hu P, Vidal M, Brent MR. Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions. Genome Research. 15: 577-82. PMID 15805498 DOI: 10.1101/gr.3329005  0.72
2004 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. PMID 15060008 DOI: 10.1101/gr.1959604  0.72
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Arumugam M, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/nature02426  0.72
2004 Arumugam M, Scott SD. EMPRR: A high-dimensional EM-based piecewise regression algorithm Proceedings of the 2004 International Conference On Machine Learning and Applications, Icmla '04. 264-271.  0.72
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