Falk Hildebrand, Toni I. Gossmann, Clémence Frioux, Ezgi Özkurt, Pernille Neve Myers, Pamela Ferretti, Michael Kuhn, Mohammad Bahram, Henrik Bjørn Nielsen, Peer Bork (2021) Dispersal strategies shape persistence and evolution of human gut bacteria, Cell Host & Microbe, doi:10.1016/j.chom.2021.05.008
Janne Marie Moll, Pernille Neve Myers, Chenchen Zhang, Carsten Eriksen, Johannes Wolf, K. Sofia Appelberg, Greger Lindberg, Martin Iain Bahl, Hui Zhao, Qiang Pan-Hammarström, Kaiye Cai, Huijue Jia, Stephan Borte, H. Bjørn Nielsen, Karsten Kristiansen, Susanne Brix, Lennart Hammarström (2021) Gut Microbiota Perturbation in IgA Deficiency Is Influenced by IgA-Autoantibody Status, Gastroenterology 160(7), doi:10.1053/j.gastro.2021.02.053
Jakob Nybo Nissen, Joachim Johansen, Rosa Lundbye Allesøe, Casper Kaae Sønderby, Jose Juan Almagro Armenteros, Christopher Heje Grønbech, Lars Juhl Jensen, Henrik Bjørn Nielsen, Thomas Nordahl Petersen, Ole Winther, Simon Rasmussen (2021) Improved metagenome binning and assembly using deep variational autoencoders, Nature Biotechnology 39(5), doi:10.1038/s41587-020-00777-4
Benjamin A. H. Jensen, Jacob B. Holm, Ida S. Larsen, Nicole von Burg, Stefanie Derer, Si B. Sonne, Simone I. Pærregaard, Mads V. Damgaard, Stine A. Indrelid, Aymeric Rivollier, Anne-Laure Agrinier, Karolina Sulek, Yke J. Arnoldussen, Even Fjære, André Marette, Inga L. Angell, Knut Rudi, Jonas T. Treebak, Lise Madsen, Caroline Piercey Åkesson, William Agace, Christian Sina, Charlotte R. Kleiveland, Karsten Kristiansen, Tor E. Lea (2021) Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism, Nature Communications 12(1), doi:10.1038/s41467-021-21408-9
Alexander Duscha, Barbara Gisevius, Sarah Hirschberg, Nissan Yissachar, Gabriele I. Stangl, Eva Eilers, Verian Bader, Stefanie Haase, Johannes Kaisler, Christina David, Ruth Schneider, Riccardo Troisi, Daniel Zent, Tobias Hegelmaier, Nikolaos Dokalis, Sara Gerstein, Sara Del Mare-Roumani, Sivan Amidror, Ori Staszewski, Gereon Poschmann, Kai Stühler, Frank Hirche, Andras Balogh, Stefan Kempa, Pascal Träger, Mario M. Zaiss, Jacob Bak Holm, Megan G. Massa, Henrik Bjørn Nielsen, Andreas Faissner, Carsten Lukas, Sören G. Gatermann, Markus Scholz, Horst Przuntek, Marco Prinz, Sofia K. Forslund, Konstanze F. Winklhofer, Dominik N. Müller, Ralf A. Linker, Ralf Gold, Aiden Haghikia (2020) Propionic Acid Shapes the Multiple Sclerosis Disease Course by an Immunomodulatory Mechanism, Cell 180(6), doi:10.1016/j.cell.2020.02.035
Kati Mokkala, Noora Houttu, Ella Koivuniemi, Nikolaj Sørensen, Henrik Bjørn Nielsen, Kirsi Laitinen (2020) GlycA, a novel marker for low grade inflammation, reflects gut microbiome diversity and is more accurate than high sensitive CRP in reflecting metabolomic profile, Metabolomics 16(7), doi:10.1007/s11306-020-01695-x
Tobias Hegelmaier, Marco Lebbing, Alexander Duscha, Laura Tomaske, Lars Tönges, Jacob Bak Holm, Henrik Bjørn Nielsen, Sören G. Gatermann, Horst Przuntek, Aiden Haghikia (2020) Interventional Influence of the Intestinal Microbiome Through Dietary Intervention and Bowel Cleansing Might Improve Motor Symptoms in Parkinson’s Disease, Cells 9(2), doi:10.3390/cells9020376
Henrik Munch Roager, Josef K Vogt, Mette Kristensen, Lea Benedicte S Hansen, Sabine Ibrügger, Rasmus B Mærkedahl, Martin Iain Bahl, Mads Vendelbo Lind, Rikke L Nielsen, Hanne Frøkiær, Rikke Juul Gøbel, Rikard Landberg, Alastair B Ross, Susanne Brix, Jesper Holck, Anne S Meyer, Morten H Sparholt, Anders F Christensen, Vera Carvalho, Bolette Hartmann, Jens Juul Holst, Jüri Johannes Rumessen, Allan Linneberg, Thomas Sicheritz-Pontén, Marlene D Dalgaard, Andreas Blennow, Henrik Lauritz Frandsen, Silas Villas-Bôas, Karsten Kristiansen, Henrik Vestergaard, Torben Hansen, Claus T Ekstrøm, Christian Ritz, Henrik Bjørn Nielsen, Oluf Borbye Pedersen, Ramneek Gupta, Lotte Lauritzen, Tine Rask Licht (2019) Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial, Gut 68(1), doi:10.1136/gutjnl-2017-314786
Brynjulf Mortensen, Clodagh Murphy, John O’Grady, Mary Lucey, Gafer Elsafi, Lillian Barry, Vibeke Westphal, Anja Wellejus, Oksana Lukjancenko, Aron C. Eklund, Henrik Bjørn Nielsen, Adam Baker, Anders Damholt, Johan E.T. van Hylckama Vlieg, Fergus Shanahan, Martin Buckley (2019) Bifidobacterium breve Bif195 Protects Against Small-Intestinal Damage Caused by Acetylsalicylic Acid in Healthy Volunteers, Gastroenterology 157(3), doi:10.1053/j.gastro.2019.05.008
Mette Simone Aae Madsen, Jacob Bak Holm, Albert Pallejà, Pernille Wismann, Katrine Fabricius, Kristoffer Rigbolt, Martin Mikkelsen, Morten Sommer, Jacob Jelsing, Henrik Bjørn Nielsen, Niels Vrang, Henrik H. Hansen (2019) Metabolic and gut microbiome changes following GLP-1 or dual GLP-1/GLP-2 receptor agonist treatment in diet-induced obese mice, Scientific Reports 9(1), doi:10.1038/s41598-019-52103-x
Mads F. Hjorth, Trine Blædel, Line Q. Bendtsen, Janne K. Lorenzen, Jacob B. Holm, Pia Kiilerich, Henrik M. Roager, Karsten Kristiansen, Lesli H. Larsen, Arne Astrup (2019) Prevotella-to-Bacteroides ratio predicts body weight and fat loss success on 24-week diets varying in macronutrient composition and dietary fiber: results from a post-hoc analysis, International Journal of Obesity 43(1), doi:10.1038/s41366-018-0093-2
Melissa R. Ingala, Daniel J. Becker, Jacob Bak Holm, Karsten Kristiansen, Nancy B. Simmons (2019) Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats, Ecology and Evolution 9(11), doi:10.1002/ece3.5228
Ida Søgaard Larsen, Andreas Mæchel Fritzen, Christian Strini Carl, Marianne Agerholm, Mads Thue Fejerskov Damgaard, Jacob Bak Holm, André Marette, Peter Nordkild, Bente Kiens, Karsten Kristiansen, Jan Wehkamp, Benjamin Anderschou Holbech Jensen (2019) Human Paneth cell α-defensin-5 treatment reverses dyslipidemia and improves glucoregulatory capacity in diet-induced obese mice, American Journal of Physiology-Endocrinology and Metabolism 317(1), doi:10.1152/ajpendo.00019.2019
Anne-Marie Lundsgaard, Jacob B. Holm, Kim A. Sjøberg, Kirstine N. Bojsen-Møller, Lene S. Myrmel, Even Fjære, Benjamin A.H. Jensen, Trine S. Nicolaisen, Janne R. Hingst, Sine L. Hansen, Sophia Doll, Philip E. Geyer, Atul S. Deshmukh, Jens J. Holst, Lise Madsen, Karsten Kristiansen, Jørgen F.P. Wojtaszewski, Erik A. Richter, Bente Kiens (2019) Mechanisms Preserving Insulin Action during High Dietary Fat Intake, Cell Metabolism 29(1), doi:10.1016/j.cmet.2018.08.022
Albert Palleja, Kristian H. Mikkelsen, Sofia K. Forslund, Alireza Kashani, Kristine H. Allin, Trine Nielsen, Tue H. Hansen, Suisha Liang, Qiang Feng, Chenchen Zhang, Paul Theodor Pyl, Luis Pedro Coelho, Huanming Yang, Jian Wang, Athanasios Typas, Morten F. Nielsen, Henrik Bjorn Nielsen, Peer Bork, Jun Wang, Tina Vilsbøll, Torben Hansen, Filip K. Knop, Manimozhiyan Arumugam, Oluf Pedersen (2018) Recovery of gut microbiota of healthy adults following antibiotic exposure, Nature Microbiology 3(11), doi:10.1038/s41564-018-0257-9
Lea B. S. Hansen, Henrik M. Roager, Nadja B. Søndertoft, Rikke J. Gøbel, Mette Kristensen, Mireia Vallès-Colomer, Sara Vieira-Silva, Sabine Ibrügger, Mads V. Lind, Rasmus B. Mærkedahl, Martin I. Bahl, Mia L. Madsen, Jesper Havelund, Gwen Falony, Inge Tetens, Trine Nielsen, Kristine H. Allin, Henrik L. Frandsen, Bolette Hartmann, Jens Juul Holst, Morten H. Sparholt, Jesper Holck, Andreas Blennow, Janne Marie Moll, Anne S. Meyer, Camilla Hoppe, Jørgen H. Poulsen, Vera Carvalho, Domenico Sagnelli, Marlene D. Dalgaard, Anders F. Christensen, Magnus Christian Lydolph, Alastair B. Ross, Silas Villas-Bôas, Susanne Brix, Thomas Sicheritz-Pontén, Karsten Buschard, Allan Linneberg, Jüri J. Rumessen, Claus T. Ekstrøm, Christian Ritz, Karsten Kristiansen, H. Bjørn Nielsen, Henrik Vestergaard, Nils J. Færgeman, Jeroen Raes, Hanne Frøkiær, Torben Hansen, Lotte Lauritzen, Ramneek Gupta, Tine Rask Licht, Oluf Pedersen (2018) A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults, Nature Communications 9(1), doi:10.1038/s41467-018-07019-x
Helle Krogh Pedersen, Sofia K. Forslund, Valborg Gudmundsdottir, Anders Østergaard Petersen, Falk Hildebrand, Tuulia Hyötyläinen, Trine Nielsen, Torben Hansen, Peer Bork, S. Dusko Ehrlich, Søren Brunak, Matej Oresic, Oluf Pedersen, Henrik Bjørn Nielsen (2018) A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links, Nature Protocols 13(12), doi:10.1038/s41596-018-0064-z
Line Quist Bendtsen, Trine Blædel, Jacob Bak Holm, Janne Kunchel Lorenzen, Alicja Budek Mark, Pia Kiilerich, Karsten Kristiansen, Arne Astrup, Lesli Hingstrup Larsen (2018) High intake of dairy during energy restriction does not affect energy balance or the intestinal microflora compared with low dairy intake in overweight individuals in a randomized controlled trial, Applied Physiology, Nutrition, and Metabolism 43(1), doi:10.1139/apnm-2017-0234
Mads T.F. Damgaard, Simone I. Pærregaard, Ida Søgaard, Marianne Agerholm, Joseph N. Paulson, Jonas T. Treebak, Christian Sina, Jacob B. Holm, Karsten Kristiansen, Benjamin A.H. Jensen (2018) Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat, The Journal of Nutritional Biochemistry 54, doi:10.1016/j.jnutbio.2017.09.026
Anders Hay-Schmidt, Olivia T Ejlstrup Finkielman, Benjamin A H Jensen, Christine F Høgsbro, Jacob Bak Holm, Kristoffer Haurum Johansen, Tina Kold Jensen, Anderson Martino Andrade, Shanna H Swan, Carl-Gustaf Bornehag, Søren Brunak, Bernard Jegou, Karsten Kristiansen, David Møbjerg Kristensen (2017) Prenatal exposure to paracetamol/acetaminophen and precursor aniline impairs masculinisation of male brain and behaviour, Reproduction 154(2), doi:10.1530/REP-17-0165
Daniel Sorobetea, Jacob Bak Holm, Henrietta Henningsson, Karsten Kristiansen, Marcus Svensson-Frej (2017) Acute infection with the intestinal parasite Trichuris muris has long-term consequences on mucosal mast cell homeostasis and epithelial integrity, European Journal of Immunology 47(2), doi:10.1002/eji.201646738
Helle Krogh Pedersen, Valborg Gudmundsdottir, Henrik Bjørn Nielsen, Tuulia Hyotylainen, Trine Nielsen, Benjamin A. H. Jensen, Kristoffer Forslund, Falk Hildebrand, Edi Prifti, Gwen Falony, Emmanuelle Le Chatelier, Florence Levenez, Joel Doré, Ismo Mattila, Damian R. Plichta, Päivi Pöhö, Lars I. Hellgren, Manimozhiyan Arumugam, Shinichi Sunagawa, Sara Vieira-Silva, Torben Jørgensen, Jacob Bak Holm, Kajetan Trošt, MetaHIT Consortium, Karsten Kristiansen, Susanne Brix, Jeroen Raes, Jun Wang, Torben Hansen, Peer Bork, Søren Brunak, Matej Oresic, S. Dusko Ehrlich, Oluf Pedersen (2016) Human gut microbes impact host serum metabolome and insulin sensitivity, Nature 535(7612), doi:10.1038/nature18646
Patricio Jeraldo, Alvaro Hernandez, Henrik B. Nielsen, Xianfeng Chen, Bryan A. White, Nigel Goldenfeld, Heidi Nelson, David Alhquist, Lisa Boardman, Nicholas Chia (2016) Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data, Frontiers in Microbiology 7, doi:10.3389/fmicb.2016.00783
Ilias Lagkouvardos, Rüdiger Pukall, Birte Abt, Bärbel U. Foesel, Jan P. Meier-Kolthoff, Neeraj Kumar, Anne Bresciani, Inés Martínez, Sarah Just, Caroline Ziegler, Sandrine Brugiroux, Debora Garzetti, Mareike Wenning, Thi P. N. Bui, Jun Wang, Floor Hugenholtz, Caroline M. Plugge, Daniel A. Peterson, Mathias W. Hornef, John F. Baines, Hauke Smidt, Jens Walter, Karsten Kristiansen, Henrik B. Nielsen, Dirk Haller, Jörg Overmann, Bärbel Stecher, Thomas Clavel (2016) The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota, Nature Microbiology 1(10), doi:10.1038/nmicrobiol.2016.131
Damian Rafal Plichta, Agnieszka Sierakowska Juncker, Marcelo Bertalan, Elizabeth Rettedal, Laurent Gautier, Encarna Varela, Chaysavanh Manichanh, Charlène Fouqueray, Florence Levenez, Trine Nielsen, Joël Doré, Ana Manuel Dantas Machado, Mari Cristina Rodriguez de Evgrafov, Torben Hansen, Torben Jørgensen, Peer Bork, Francisco Guarner, Oluf Pedersen, Morten O. A. Sommer, S. Dusko Ehrlich, Thomas Sicheritz-Pontén, Søren Brunak, H. Bjørn Nielsen (2016) Transcriptional interactions suggest niche segregation among microorganisms in the human gut, Nature Microbiology 1(11), doi:10.1038/nmicrobiol.2016.152
Henrik M. Roager, Lea B. S. Hansen, Martin I. Bahl, Henrik L. Frandsen, Vera Carvalho, Rikke J. Gøbel, Marlene D. Dalgaard, Damian R. Plichta, Morten H. Sparholt, Henrik Vestergaard, Torben Hansen, Thomas Sicheritz-Pontén, H. Bjørn Nielsen, Oluf Pedersen, Lotte Lauritzen, Mette Kristensen, Ramneek Gupta, Tine R. Licht (2016) Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut, Nature Microbiology 1(9), doi:10.1038/nmicrobiol.2016.93
Trine Blædel, Jacob B. Holm, Ulrik K. Sundekilde, Mette S. Schmedes, Anne L. Hess, Janne K. Lorenzen, Karsten Kristiansen, Trine K. Dalsgaard, Arne Astrup, Lesli H. Larsen (2016) A randomised, controlled, crossover study of the effect of diet on angiopoietin-like protein 4 (ANGPTL4) through modification of the gut microbiome, Journal of Nutritional Science 5, doi:10.1017/jns.2016.38
Jacob Bak Holm, Alexander Rønnevik, Hanne Sørup Tastesen, Even Fjære, Kristin Røen Fauske, Ulrike Liisberg, Lise Madsen, Karsten Kristiansen, Bjørn Liaset (2016) Diet-induced obesity, energy metabolism and gut microbiota in C57BL/6J mice fed Western diets based on lean seafood or lean meat mixtures, The Journal of Nutritional Biochemistry 31, doi:10.1016/j.jnutbio.2015.12.017
Jacob Bak Holm, Severine Mazaud-Guittot, Niels Banhos Danneskiold-Samsøe, Clementine Chalmey, Benjamin Jensen, Mette Marie Nørregård, Cecilie Hurup Hansen, Bjarne Styrishave, Terje Svingen, Anne Marie Vinggaard, Holger Martin Koch, Josephine Bowles, Peter Koopman, Bernard Jégou, Karsten Kristiansen, David Møbjerg Kristensen (2016) Intrauterine Exposure to Paracetamol and Aniline Impairs Female Reproductive Development by Reducing Follicle Reserves and Fertility, Toxicological Sciences 150(1), doi:10.1093/toxsci/kfv332
Benjamin A.H. Jensen, Thomas S. Nielsen, Andreas M. Fritzen, Jacob B. Holm, Even Fjære, Annette K. Serup, Kamil Borkowski, Steve Risis, Simone I. Pærregaard, Ida Søgaard, Audrey Poupeau, Michelle Poulsen, Tao Ma, Christian Sina, Bente Kiens, Lise Madsen, Karsten Kristiansen, Jonas T. Treebak (2016) Dietary fat drives whole-body insulin resistance and promotes intestinal inflammation independent of body weight gain, Metabolism 65(12), doi:10.1016/j.metabol.2016.09.002
Ulrike Liisberg, Lene Secher Myrmel, Even Fjære, Alexander K. Rønnevik, Susanne Bjelland, Kristin Røen Fauske, Jacob Bak Holm, Astrid Linde Basse, Jacob B. Hansen, Bjørn Liaset, Karsten Kristiansen, Lise Madsen (2016) The protein source determines the potential of high protein diets to attenuate obesity development in C57BL/6J mice, Adipocyte 5(2), doi:10.1080/21623945.2015.1122855
Katarzyna M. Luda, Thorsten Joeris, Emma K. Persson, Aymeric Rivollier, Mimoza Demiri, Katarzyna M. Sitnik, Lieneke Pool, Jacob B. Holm, Felipe Melo-Gonzalez, Lisa Richter, Bart N. Lambrecht, Karsten Kristiansen, Mark A. Travis, Marcus Svensson-Frej, Knut Kotarsky, William W. Agace (2016) IRF8 Transcription-Factor-Dependent Classical Dendritic Cells Are Essential for Intestinal T Cell Homeostasis, Immunity 44(4), doi:10.1016/j.immuni.2016.02.008
Lee O'Brien Andersen, Ida Bonde, Henrik Bjørn Nielsen, Christen Rune Stensvold (2015) A retrospective metagenomics approach to studying Blastocystis, FEMS Microbiology Ecology 91(7), doi:10.1093/femsec/fiv072
Kristoffer Forslund, Falk Hildebrand, Trine Nielsen, Gwen Falony, Emmanuelle Le Chatelier, Shinichi Sunagawa, Edi Prifti, Sara Vieira-Silva, Valborg Gudmundsdottir, Helle Krogh Pedersen, Manimozhiyan Arumugam, Karsten Kristiansen, Anita Yvonne Voigt, Henrik Vestergaard, Rajna Hercog, Paul Igor Costea, Jens Roat Kultima, Junhua Li, Torben Jørgensen, Florence Levenez, Joël Dore, H. Bjørn Nielsen, Søren Brunak, Jeroen Raes, Torben Hansen, Jun Wang, S. Dusko Ehrlich, Peer Bork, Oluf Pedersen (2015) Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota, Nature 528(7581), doi:10.1038/nature15766
Liang Xiao, Qiang Feng, Suisha Liang, Si Brask Sonne, Zhongkui Xia, Xinmin Qiu, Xiaoping Li, Hua Long, Jianfeng Zhang, Dongya Zhang, Chuan Liu, Zhiwei Fang, Joyce Chou, Jacob Glanville, Qin Hao, Dorota Kotowska, Camilla Colding, Tine Rask Licht, Donghai Wu, Jun Yu, Joseph Jao Yiu Sung, Qiaoyi Liang, Junhua Li, Huijue Jia, Zhou Lan, Valentina Tremaroli, Piotr Dworzynski, H Bjørn Nielsen, Fredrik Bäckhed, Joël Doré, Emmanuelle Le Chatelier, S Dusko Ehrlich, John C Lin, Manimozhiyan Arumugam, Jun Wang, Lise Madsen, Karsten Kristiansen (2015) A catalog of the mouse gut metagenome, Nature Biotechnology 33(10), doi:10.1038/nbt.3353
Jacob Bak Holm, Clementine Chalmey, Hendrik Modick, Lars Skovgaard Jensen, Georg Dierkes, Tobias Weiss, Benjamin Anderschou Holbech Jensen, Mette Marie Nørregård, Kamil Borkowski, Bjarne Styrishave, Holger Martin Koch, Severine Mazaud-Guittot, Bernard Jegou, Karsten Kristiansen, David Møbjerg Kristensen (2015) Aniline Is Rapidly Converted Into Paracetamol Impairing Male Reproductive Development, Toxicological Sciences 148(1), doi:10.1093/toxsci/kfv179
Jacob Bak Holm, Daniel Sorobetea, Pia Kiilerich, Yuliaxis Ramayo-Caldas, Jordi Estellé, Tao Ma, Lise Madsen, Karsten Kristiansen, Marcus Svensson-Frej (2015) Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli, PLOS ONE 10(5), doi:10.1371/journal.pone.0125495
I. H. Lambert, D. M. Kristensen, J. B. Holm, O. H. Mortensen (2015) Physiological role of taurine - from organism to organelle, Acta Physiologica 213(1), doi:10.1111/apha.12365
Junhua Li, Huijue Jia, Xianghang Cai, Huanzi Zhong, Qiang Feng, Shinichi Sunagawa, Manimozhiyan Arumugam, Jens Roat Kultima, Edi Prifti, Trine Nielsen, Agnieszka Sierakowska Juncker, Chaysavanh Manichanh, Bing Chen, Wenwei Zhang, Florence Levenez, Juan Wang, Xun Xu, Liang Xiao, Suisha Liang, Dongya Zhang, Zhaoxi Zhang, Weineng Chen, Hailong Zhao, Jumana Yousuf Al-Aama, Sherif Edris, Huanming Yang, Jian Wang, Torben Hansen, Henrik Bjørn Nielsen, Søren Brunak, Karsten Kristiansen, Francisco Guarner, Oluf Pedersen, Joel Doré, S Dusko Ehrlich, Peer Bork, Jun Wang (2014) An integrated catalog of reference genes in the human gut microbiome, Nature Biotechnology 32(8), doi:10.1038/nbt.2942
H Bjørn Nielsen, Mathieu Almeida, Agnieszka Sierakowska Juncker, Simon Rasmussen, Junhua Li, Shinichi Sunagawa, Damian R Plichta, Laurent Gautier, Anders G Pedersen, Emmanuelle Le Chatelier, Eric Pelletier, Ida Bonde, Trine Nielsen, Chaysavanh Manichanh, Manimozhiyan Arumugam, Jean-Michel Batto, Marcelo B Quintanilha dos Santos, Nikolaj Blom, Natalia Borruel, Kristoffer S Burgdorf, Fouad Boumezbeur, Francesc Casellas, Joël Doré, Piotr Dworzynski, Francisco Guarner, Torben Hansen, Falk Hildebrand, Rolf S Kaas, Sean Kennedy, Karsten Kristiansen, Jens Roat Kultima, Pierre Léonard, Florence Levenez, Ole Lund, Bouziane Moumen, Denis Le Paslier, Nicolas Pons, Oluf Pedersen, Edi Prifti, Junjie Qin, Jeroen Raes, Søren Sørensen, Julien Tap, Sebastian Tims, David W Ussery, Takuji Yamada, Pierre Renault, Thomas Sicheritz-Ponten, Peer Bork, Jun Wang, Søren Brunak, S Dusko Ehrlich (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes, Nature Biotechnology 32(8), doi:10.1038/nbt.2939
Ulrik Plesner Jacobsen, Henrik Bjørn Nielsen, Falk Hildebrand, Jeroen Raes, Thomas Sicheritz-Ponten, Irene Kouskoumvekaki, Gianni Panagiotou (2013) The chemical interactome space between the human host and the genetically defined gut metabotypes, The ISME Journal 7(4), doi:10.1038/ismej.2012.141
Emmanuelle Le Chatelier, Trine Nielsen, Junjie Qin, Edi Prifti, Falk Hildebrand, Gwen Falony, Mathieu Almeida, Manimozhiyan Arumugam, Jean-Michel Batto, Sean Kennedy, Pierre Leonard, Junhua Li, Kristoffer Burgdorf, Niels Grarup, Torben Jørgensen, Ivan Brandslund, Henrik Bjørn Nielsen, Agnieszka S. Juncker, Marcelo Bertalan, Florence Levenez, Nicolas Pons, Simon Rasmussen, Shinichi Sunagawa, Julien Tap, Sebastian Tims, Erwin G. Zoetendal, Søren Brunak, Karine Clément, Joël Doré, Michiel Kleerebezem, Karsten Kristiansen, Pierre Renault, Thomas Sicheritz-Ponten, Willem M. de Vos, Jean-Daniel Zucker, Jeroen Raes, Torben Hansen, Peer Bork, Jun Wang, S. Dusko Ehrlich, Oluf Pedersen (2013) Richness of human gut microbiome correlates with metabolic markers, Nature 500(7464), doi:10.1038/nature12506
Shinichi Sunagawa, Daniel R Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A Berger, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap, Henrik Bjørn Nielsen, Simon Rasmussen, Søren Brunak, Oluf Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros Stamatakis, Peer Bork (2013) Metagenomic species profiling using universal phylogenetic marker genes, Nature Methods 10(12), doi:10.1038/nmeth.2693
Jacob Bak Holm, Ryszard Grygorczyk, Ian Henry Lambert (2013) Volume-sensitive release of organic osmolytes in the human lung epithelial cell line A549: role of the 5-lipoxygenase, American Journal of Physiology-Cell Physiology 305(1), doi:10.1152/ajpcell.00412.2012
Falk Hildebrand, Tine Ebersbach, Henrik Nielsen, Xiaoping Li, Si Sonne, Marcelo Bertalan, Peter Dimitrov, Lise Madsen, Junjie Qin, Jun Wang, Jeroen Raes, Karsten Kristiansen, Tine Licht (2012) A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens), BMC Genomics 13(1), doi:10.1186/1471-2164-13-514
Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Bruls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel, Francesc Casellas, Leyden Fernandez, Laurent Gautier, Torben Hansen, Masahira Hattori, Tetsuya Hayashi, Michiel Kleerebezem, Ken Kurokawa, Marion Leclerc, Florence Levenez, Chaysavanh Manichanh, H. Bjørn Nielsen, Trine Nielsen, Nicolas Pons, Julie Poulain, Junjie Qin, Thomas Sicheritz-Ponten, Sebastian Tims, David Torrents, Edgardo Ugarte, Erwin G. Zoetendal, Jun Wang, Francisco Guarner, Oluf Pedersen, Willem M. de Vos, Søren Brunak, Joel Doré, Jean Weissenbach, S. Dusko Ehrlich, Peer Bork (2011) Enterotypes of the human gut microbiome, Nature 473(7346), doi:10.1038/nature09944
Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, Nicolas Pons, Florence Levenez, Takuji Yamada, Daniel R. Mende, Junhua Li, Junming Xu, Shaochuan Li, Dongfang Li, Jianjun Cao, Bo Wang, Huiqing Liang, Huisong Zheng, Yinlong Xie, Julien Tap, Patricia Lepage, Marcelo Bertalan, Jean-Michel Batto, Torben Hansen, Denis Le Paslier, Allan Linneberg, H. Bjørn Nielsen, Eric Pelletier, Pierre Renault, Thomas Sicheritz-Ponten, Keith Turner, Hongmei Zhu, Chang Yu, Shengting Li, Min Jian, Yan Zhou, Yingrui Li, Xiuqing Zhang, Songgang Li, Nan Qin, Huanming Yang, Jian Wang, Søren Brunak, Joel Doré, Francisco Guarner, Karsten Kristiansen, Oluf Pedersen, Julian Parkhill, Jean Weissenbach, Peer Bork, S. Dusko Ehrlich, Jun Wang (2010) A human gut microbial gene catalogue established by metagenomic sequencing, Nature 464(7285), doi:10.1038/nature08821
S. Dusko Ehrlich (2010) Metagenomics of the intestinal microbiota: potential applications, Gastroentérologie Clinique et Biologique 34, doi:10.1016/S0399-8320(10)70017-8
Hanne S. Tastesen, Jacob B. Holm, Jacob Møller, Kristian A. Poulsen, Charlotte Møller, Stefan Stürup, Else K. Hoffmann, Ian H. Lambert (2010) Pinpointing Differences in Cisplatin-induced Apoptosis in Adherent and Non-adherent Cancer Cells, Cellular Physiology and Biochemistry 26(6), doi:10.1159/000323990
Simon Rasmussen, Henrik Bjørn Nielsen, Hanne Jarmer (2009) The transcriptionally active regions in the genome of Bacillus subtilis, Molecular Microbiology 73(6), doi:10.1111/j.1365-2958.2009.06830.x
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