Search Results - "Sicheritz‐Pontén, Thomas"

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 by Roager, Henrik Munch, Vogt, Josef K, Kristensen, Mette, Hansen, Lea Benedicte S, Ibrügger, Sabine, Mærkedahl, Rasmus B, Bahl, Martin Iain, Lind, Mads Vendelbo, Nielsen, Rikke L, Frøkiær, Hanne, Gøbel, Rikke Juul, Landberg, Rikard, Ross, Alastair B, Brix, Susanne, Holck, Jesper, Meyer, Anne S, Sparholt, Morten H, Christensen, Anders F, Carvalho, Vera, Hartmann, Bolette, Holst, Jens Juul, Rumessen, Jüri Johannes, Linneberg, Allan, Sicheritz-Pontén, Thomas, Dalgaard, Marlene D, Blennow, Andreas, Frandsen, Henrik Lauritz, Villas-Bôas, Silas, Kristiansen, Karsten, Vestergaard, Henrik, Hansen, Torben, Ekstrøm, Claus T, Ritz, Christian, Nielsen, Henrik Bjørn, Pedersen, Oluf Borbye, Gupta, Ramneek, Lauritzen, Lotte, Licht, Tine Rask

“…To investigate whether a whole grain diet alters the gut microbiome and insulin sensitivity, as well as biomarkers of metabolic health and gut functionality…”
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The microbiome of New World vultures by Roggenbuck, Michael, Bærholm Schnell, Ida, Blom, Nikolaj, Bælum, Jacob, Bertelsen, Mads Frost, Sicheritz-Pontén, Thomas, Sørensen, Søren Johannes, Gilbert, M. Thomas P., Graves, Gary R., Hansen, Lars H

“…Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report…”
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Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data by Al-Nakeeb, Kosai, Petersen, Thomas Nordahl, Sicheritz-Pontén, Thomas

“…Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin…”
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Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence by Blom, Nikolaj, Sicheritz-Pontén, Thomas, Gupta, Ramneek, Gammeltoft, Steen, Brunak, Søren

“…Post‐translational modifications (PTMs) occur on almost all proteins analyzed to date. The function of a modified protein is often strongly affected by these…”
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Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat by Zepeda Mendoza, M. Lisandra, Xiong, Zijun, Escalera-Zamudio, Marina, Runge, Anne Kathrine, Thézé, Julien, Streicker, Daniel, Frank, Hannah K., Loza-Rubio, Elizabeth, Liu, Shengmao, Ryder, Oliver A., Samaniego Castruita, Jose Alfredo, Katzourakis, Aris, Pacheco, George, Taboada, Blanca, Löber, Ulrike, Pybus, Oliver G., Li, Yang, Rojas-Anaya, Edith, Bohmann, Kristine, Carmona Baez, Aldo, Arias, Carlos F., Liu, Shiping, Greenwood, Alex D., Bertelsen, Mads F., White, Nicole E., Bunce, Michael, Zhang, Guojie, Sicheritz-Pontén, Thomas, Gilbert, M. P. Thomas

“…Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat…”
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Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut by Roager, Henrik M., Hansen, Lea B. S., Bahl, Martin I., Frandsen, Henrik L., Carvalho, Vera, Gøbel, Rikke J., Dalgaard, Marlene D., Plichta, Damian R., Sparholt, Morten H., Vestergaard, Henrik, Hansen, Torben, Sicheritz-Pontén, Thomas, Nielsen, H. Bjørn, Pedersen, Oluf, Lauritzen, Lotte, Kristensen, Mette, Gupta, Ramneek, Licht, Tine R.

“…Little is known about how colonic transit time relates to human colonic metabolism and its importance for host health, although a firm stool consistency, a…”
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Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing by Mak, Sarah Siu Tze, Gopalakrishnan, Shyam, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel-Holger S, Kuderna, Lukas F K, Zhang, Wenwei, Fu, Shujin, Vieira, Filipe G, Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, Gilbert, M Thomas P

“…Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been…”
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Diverse Prophage Elements of Salmonella enterica Serovars Show Potential Roles in Bacterial Pathogenicity by Andrews, Kirstie, Landeryou, Toby, Sicheritz-Pontén, Thomas, Nale, Janet Yakubu

“…Nontyphoidal salmonellosis is an important foodborne and zoonotic infection that causes significant global public health concern. Diverse serovars are…”
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High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach by Mollerup, Sarah, Asplund, Maria, Friis-Nielsen, Jens, Kjartansdóttir, Kristín Rós, Fridholm, Helena, Hansen, Thomas Arn, Herrera, José Alejandro Romero, Barnes, Christopher James, Jensen, Randi Holm, Richter, Stine Raith, Nielsen, Ida Broman, Pietroni, Carlotta, Alquezar-Planas, David E, Rey-Iglesia, Alba, Olsen, Pernille V S, Rajpert-De Meyts, Ewa, Groth-Pedersen, Line, von Buchwald, Christian, Jensen, David H, Gniadecki, Robert, Høgdall, Estrid, Langhoff, Jill Levin, Pete, Imre, Vereczkey, Ildikó, Baranyai, Zsolt, Dybkaer, Karen, Johnsen, Hans Erik, Steiniche, Torben, Hokland, Peter, Rosenberg, Jacob, Baandrup, Ulrik, Sicheritz-Pontén, Thomas, Willerslev, Eske, Brunak, Søren, Lund, Ole, Mourier, Tobias, Vinner, Lasse, Izarzugaza, Jose M G, Nielsen, Lars Peter, Hansen, Anders Johannes

“…Abstract Background Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer…”
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Phage Therapy: Insights from the Past, the Great Need of the Present, and Glimpses into the Future by Clokie, Martha R J, Sicheritz-Pontén, Thomas E

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Single‐tube library preparation for degraded DNA by Carøe, Christian, Gopalakrishnan, Shyam, Vinner, Lasse, Mak, Sarah S. T., Sinding, Mikkel Holger S., Samaniego, José A., Wales, Nathan, Sicheritz‐Pontén, Thomas, Gilbert, M. Thomas P., Johnston, Susan

“…In recent years, massive parallel sequencing has revolutionised the study of degraded DNA, thus enabling the field of ancient DNA to evolve into that of…”
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Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira by Palomo, Alejandro, Pedersen, Anders G., Fowler, S. Jane, Dechesne, Arnaud, Sicheritz-Pontén, Thomas, Smets, Barth F.

“…The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate oxidation, and their co-occurrence with canonical β-proteobacterial ammonia…”
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Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers by Friis-Nielsen, Jens, Kjartansdóttir, Kristín Rós, Mollerup, Sarah, Asplund, Maria, Mourier, Tobias, Jensen, Randi Holm, Hansen, Thomas Arn, Rey-Iglesia, Alba, Richter, Stine Raith, Nielsen, Ida Broman, Alquezar-Planas, David E, Olsen, Pernille V S, Vinner, Lasse, Fridholm, Helena, Nielsen, Lars Peter, Willerslev, Eske, Sicheritz-Pontén, Thomas, Lund, Ole, Hansen, Anders Johannes, Izarzugaza, Jose M G, Brunak, Søren

“…Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease…”
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Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago by Rasmussen, Simon, Allentoft, Morten Erik, Nielsen, Kasper, Orlando, Ludovic, Sikora, Martin, Sjögren, Karl-Göran, Pedersen, Anders Gorm, Schubert, Mikkel, Van Dam, Alex, Kapel, Christian Moliin Outzen, Nielsen, Henrik Bjørn, Brunak, Søren, Avetisyan, Pavel, Epimakhov, Andrey, Khalyapin, Mikhail Viktorovich, Gnuni, Artak, Kriiska, Aivar, Lasak, Irena, Metspalu, Mait, Moiseyev, Vyacheslav, Gromov, Andrei, Pokutta, Dalia, Saag, Lehti, Varul, Liivi, Yepiskoposyan, Levon, Sicheritz-Pontén, Thomas, Foley, Robert A., Lahr, Marta Mirazón, Nielsen, Rasmus, Kristiansen, Kristian, Willerslev, Eske

“…The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it…”
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Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria by LARSEN, Mette V, COSENTINO, Salvatore, LUND, Ole, RASMUSSEN, Simon, FRIIS, Carsten, HASMAN, Henrik, LYKKE MARVIG, Rasmus, JELSBAK, Lars, SICHERITZ-PONTEN, Thomas, USSERY, David W, AARESTRUP, Frank M

“…OA  Article Usage Stats Services JCM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+…”
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A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults by Hansen, Lea B. S., Roager, Henrik M., Søndertoft, Nadja B., Gøbel, Rikke J., Kristensen, Mette, Vallès-Colomer, Mireia, Vieira-Silva, Sara, Ibrügger, Sabine, Lind, Mads V., Mærkedahl, Rasmus B., Bahl, Martin I., Madsen, Mia L., Havelund, Jesper, Falony, Gwen, Tetens, Inge, Nielsen, Trine, Allin, Kristine H., Frandsen, Henrik L., Hartmann, Bolette, Holst, Jens Juul, Sparholt, Morten H., Holck, Jesper, Blennow, Andreas, Moll, Janne Marie, Meyer, Anne S., Hoppe, Camilla, Poulsen, Jørgen H., Carvalho, Vera, Sagnelli, Domenico, Dalgaard, Marlene D., Christensen, Anders F., Lydolph, Magnus Christian, Ross, Alastair B., Villas-Bôas, Silas, Brix, Susanne, Sicheritz-Pontén, Thomas, Buschard, Karsten, Linneberg, Allan, Rumessen, Jüri J., Ekstrøm, Claus T., Ritz, Christian, Kristiansen, Karsten, Nielsen, H. Bjørn, Vestergaard, Henrik, Færgeman, Nils J., Raes, Jeroen, Frøkiær, Hanne, Hansen, Torben, Lauritzen, Lotte, Gupta, Ramneek, Licht, Tine Rask, Pedersen, Oluf

“…Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, the effects of reducing gluten-rich food items…”
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Benchmarking of methods for genomic taxonomy by Larsen, Mette V, Cosentino, Salvatore, Lukjancenko, Oksana, Saputra, Dhany, Rasmussen, Simon, Hasman, Henrik, Sicheritz-Pontén, Thomas, Aarestrup, Frank M, Ussery, David W, Lund, Ole

“…One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. The…”
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Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum) by Sánchez‐Barreiro, Fátima, Gopalakrishnan, Shyam, Ramos‐Madrigal, Jazmín, Westbury, Michael V., Manuel, Marc, Margaryan, Ashot, Ciucani, Marta M., Vieira, Filipe G., Patramanis, Yannis, Kalthoff, Daniela C., Timmons, Zena, Sicheritz‐Pontén, Thomas, Dalén, Love, Ryder, Oliver A., Zhang, Guojie, Marquès‐Bonet, Tomás, Moodley, Yoshan, Gilbert, M. Thomas P.

“…Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a…”
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Arctic-adapted dogs emerged at the Pleistocene-Holocene transition by Sinding, Mikkel-Holger S, Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, de Manuel, Marc, Pitulko, Vladimir V, Kuderna, Lukas, Feuerborn, Tatiana R, Frantz, Laurent A F, Vieira, Filipe G, Niemann, Jonas, Samaniego Castruita, Jose A, Carøe, Christian, Andersen-Ranberg, Emilie U, Jordan, Peter D, Pavlova, Elena Y, Nikolskiy, Pavel A, Kasparov, Aleksei K, Ivanova, Varvara V, Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jørgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalén, Love, Larson, Greger, Petersen, Bent, Sicheritz-Pontén, Thomas, Bachmann, Lutz, Wiig, Øystein, Marques-Bonet, Tomas, Hansen, Anders J, Gilbert, M Thomas P

“…Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We…”
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Ancient human genome sequence of an extinct Palaeo-Eskimo by Wang, Jun, Willerslev, Eske, Rasmussen, Morten, Li, Yingrui, Lindgreen, Stinus, Pedersen, Jakob Skou, Albrechtsen, Anders, Moltke, Ida, Metspalu, Mait, Metspalu, Ene, Kivisild, Toomas, Gupta, Ramneek, Bertalan, Marcelo, Nielsen, Kasper, Gilbert, M. Thomas P, Wang, Yong, Raghavan, Maanasa, Campos, Paula F, Kamp, Hanne Munkholm, Wilson, Andrew S, Gledhill, Andrew, Tridico, Silvana, Bunce, Michael, Lorenzen, Eline D, Binladen, Jonas, Guo, Xiaosen, Zhao, Jing, Zhang, Xiuqing, Zhang, Hao, Li, Zhuo, Chen, Minfeng, Orlando, Ludovic, Kristiansen, Karsten, Bak, Mads, Tommerup, Niels, Bendixen, Christian, Pierre, Tracey L, Grønnow, Bjarne, Meldgaard, Morten, Andreasen, Claus, Fedorova, Sardana A, Osipova, Ludmila P, Higham, Thomas F. G, Ramsey, Christopher Bronk, Hansen, Thomas v. O, Nielsen, Finn C, Crawford, Michael H, Brunak, Søren, Sicheritz-Pontén, Thomas, Villems, Richard, Nielsen, Rasmus, Krogh, Anders

“…We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from…”
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