1. 2014
  2. Published

    Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. / Raghavan, Maanasa; Skoglund, Pontus; Graf, Kelly E.; Metspalu, Mait; Albrechtsen, Anders; Moltke, Ida; Rasmussen, Simon; Stafford jr., Thomas; Orlando, Ludovic Antoine Alexandre; Metspalu, Ene; Karmin, Monika; Tambets, Kristiina; Rootsi, Siiri; Mägi, Reedik; Campos, Paula; Balanovska, Elena; Balanovsky, Oleg; Khusnutdinova, Elza; Litvinov, Sergey; Osipova, Ludmila P; Fedorova, Sardana A; Voevoda, Mikhail I; Degiorgio, Michael; Sicheritz-Pontén, Thomas; Brunak, Søren; Demeshchenko, Svetlana; Kivisild, Toomas; Villems, Richard; Nielsen, Rasmus; Jakobsson, Mattias; Willerslev, Eske.

    In: Nature, Vol. 505, No. 7481, 2014, p. 87–91.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  3. 2013
  4. Published
  5. Published

    Bacterial natural transformation by highly fragmented and damaged DNA.. / Overballe-Petersen, Søren; Harms, Klaus; Orlando, Ludovic Antoine Alexandre; Mayar, J. Victor Moreno; Rasmussen, Simon; Dahl, Tais Wittchen; Rosing, Minik Thorleif; Poole, Anthony M; Sicheritz-Pontén, Thomas; Brunak, Søren; Inselmann, Sabrina; de Vries, Johann; Wackernagel, Wilfried; Pybus, Oliver G; Nielsen, Rasmus; Johnsen, Pål Jarle; Nielsen, Kaare Magne; Willerslev, Eske.

    In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 110, No. 49, 2013, p. 19860-19865.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  6. E-pub ahead of print

    Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. / Kouskoumvekaki, Irene; Shublaq, Nour ; Brunak, Søren.

    In: Briefings in Bioinformatics, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  7. Published
  8. Published

    Metagenomic Analysis of the Human Gut Microbiome. / dos Santos, Marcelo Bertalan Quintanilha; Nielsen, Henrik Bjørn (Supervisor); Sicheritz-Pontén, Thomas (Main supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2013. 117 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2013

  9. Published

    Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. / Alsmark, Cecilia; Foster, Peter G; Sicheritz-Pontén, Thomas; Nakjang, Sirintra; Martin Embley, T; Hirt, Robert P.

    In: Genome Biology, Vol. 14, No. 2, 2013, p. R19.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  10. Published

    Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. / Steentoft, Catharina; Vakhrushev, Sergey; Joshi, Hiren Jitendra; Kong, Yun; Vester-Christensen, Malene B; Schjoldager, Katrine T-BG; Lavrsen, Kirstine; Dabelsteen, Sally Anne Malene; Pedersen, Nis Borbye; Marcos-Silva, Lara; Gupta, Ramneek; Paul Bennett, Eric; Mandel, Ulla; Brunak, Søren; Wandall, Hans H.; Levery, Steven Bruce; Clausen, Henrik.

    In: EMBO Journal, Vol. 32, No. 10, 2013, p. 1478-1488.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  11. Published
  12. Published

    Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.. / Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurélien; Zhang, Guojie; Froese, Duane; Albrechtsen, Anders; Stiller, Mathias; Schubert, Mikkel; Cappellini, Enrico; Petersen, Bent; Moltke, Ida; Johnson, Philip L F; Fumagalli, Matteo; Vilstrup, Julia T; Raghavan, Maanasa; Korneliussen, Thorfinn Sand; Malaspinas, Anna Sapfo; Vogt, Josef Korbinian; Szklarczyk, Damian; Kelstrup, Christian; Vinther, Jakob; Dolocan, Andrei; Stenderup, Jesper; Velazquez, Amhed M. V.; Cahill, James; Rasmussen, Morten; Wang, Xiaoli; Min, Jiumeng; Zazula, Grant D; Seguin-Orlando, Andaine; Mortensen, Cecilie; Magnussen, Kim; Thompson, John F; Weinstock, Jacobo; Gregersen, Magnus Kristian; Røed, Knut H; Eisenmann, Véra; Rubin, Carl J; Miller, Donald C; Antczak, Douglas F; Bertelsen, Mads; Brunak, Søren; Al-Rasheid, Khaled A S; Ryder, Oliver; Andersson, Leif; Mundy, John; Krogh, Anders; Gilbert, Marcus Thomas Pius; Kjær, Kurt H.; Sicheritz-Pontén, Thomas; Jensen, Lars Juhl; Olsen, Jesper; Hofreiter, Michael; Nielsen, Rasmus; Shapiro, Beth; Wang, Jun; Willerslev, Eske.

    In: Nature, Vol. 499, 2013, p. 74-78.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  13. Published

    Richness of human gut microbiome correlates with metabolic markers.. / Le Chatelier, Emmanuelle; Nielsen, Trine; Qin, Junjie; Prifti, Edi; Hildebrand, Falk; Falony, Gwen; Almeida, Mathieu; Arumugam, Manimozhiyan; Batto, Jean-Michel; Kennedy, Sean; Leonard, Pierre; Li, Junhua; Burgdorf, Kristoffer; Grarup, Niels; Jørgensen, Torben; Brandslund, Ivan; Nielsen, Henrik Bjørn; Juncker, Agnieszka; dos Santos, Marcelo Bertalan Quintanilha; Levenez, Florence; Pons, Nicolas; Rasmussen, Simon; Sunagawa, Shinichi; Tap, Julien; Tims, Sebastian; Zoetendal, Erwin G; Brunak, Søren; Clément, Karine; Doré, Joël; Kleerebezem, Michiel; Kristiansen, Karsten; Renault, Pierre; Sicheritz-Pontén, Thomas; de Vos, Willem M.; Zucker, Jean-Daniel; Raes, Jeroen; Hansen, Torben; Bork, Peer; Wang, Jun; Ehrlich, S Dusko; Pedersen, Oluf.

    In: Nature, Vol. 500, No. 7464, 2013, p. 541-546.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  14. Published

    Targeted Metabolic Engineering Guided by Computational Analysis of Single-Nucleotide Polymorphisms (SNPs). / Udatha, D B R K Gupta; Rasmussen, Simon; Sicheritz-Pontén, Thomas; Panagiotou, Gianni.

    Systems Metabolic Engineering : Methods and Protocols. Springer, 2013. p. 409-428 (Methods in Molecular Biology, Vol. 985).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2013

  15. Published
  16. 2012
  17. Published

    A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). / Hildebrand, Falk; Ebersbach, Tine; Nielsen, Henrik Bjørn; Li, Xiaoping; Sonne, Si Brask; dos Santos, Marcelo Bertalan Quintanilha; Dimitrov, Peter; Madsen, Lise; Qin, Junjie; Wang, Jun; Raes, Jeroen; Kristiansen, Karsten; Licht, Tine Rask.

    In: B M C Genomics, Vol. 13, No. 514, 2012.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  18. Published

    Analysis of cytotoxic T cell epitopes in relation to cancer. / Stranzl, Thomas; Brunak, Søren (Main supervisor); Larsen, Mette Voldby (Supervisor).

    Kgs. Lyngby : Technical University of Denmark, 2012. 97 p.

    Publication: ResearchPh.D. thesis – Annual report year: 2012

  19. Published
  20. Published

    Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures. / Krysiak-Baltyn, Konrad; Toppari, J.; Skakkebaek, N. E.; Jensen, Thomas Skøt; Virtanen, H. E.; Schramm, K.‐W.; Shen, Hao; Vartiainen, T.; Kiviranta, H.; Taboureau, Olivier ; Audouze, Karine Marie Laure; Brunak, S.; Main, K. M.

    In: International Journal of Andrology, Vol. 35, No. 3, 2012, p. 294-302.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  21. Published

    Bacterial adaptive response to changing herbicide discharge rates in the streambed sediments impacted by a landfill. / Pazarbasi, Meric Batioglu; Bælum, Jacob; Pilloni, Giovanni; Larentis, Micheal; Jacobsen, Carsten S.; Lueders, Tillmann; Hansen, Lars H.; Aamand, Jens .

    2012. Poster session presented at 14th International Symposium on Microbial Ecology, Copenhagen, Denmark.

    Publication: Research - peer-reviewPoster – Annual report year: 2012

  22. Published

    Choosing the right platform for the right product: Sustainable production of chemicals in microbial cell factories. / Herrgard, Markus.

    2012. Abstract from Chemical engineering at the Life science interface conference, Sheffield, United Kingdom.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2012

  23. Published

    Common and Distant Structural Characteristics of Feruloyl Esterase Families from Aspergillus oryzae. / Udatha, D. B. R. K. Gupta; Mapelli, Valeria; Panagiotou, Gianni; Olsson, Lisbeth.

    In: P L o S One, Vol. 7, No. 6, 2012, p. e39473.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  24. Published

    From Genome Sequence to Taxonomy - A Skeptic’s View. / Özen, Asli Ismihan; Vesth, Tammi Camilla; Ussery, David.

    The Prokaryotes. ed. / Rosenberg E.2012 : Springer, 2012.

    Publication: Research - peer-reviewBook chapter – Annual report year: 2012

  25. Published

    Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development. / Hansen, Kasper Lage; Greenway, Steven C.; Rosenfeld, Jill A.; Wakimoto, Hiroko; Gorham, Joshua M.; Segrè, Ayellet V.; Roberts, Amy E.; Smoot, Leslie B.; Pu, William T.; C. Pereira, Alexandre; Mesquita, Sonia M.; Tommerup, Niels; Brunak, Søren; Ballif, Blake C.; Shaffer, Lisa G.; Donahoe, Patricia K.; Daly, Mark J.; Seidman, Jonathan G.; Seidman, Christine E.; Larsen, Lars.

    In: National Academy of Sciences. Proceedings, Vol. 109, No. 35, 2012, p. 14035-14040.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  26. Published

    How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases. / Udatha, D. B. R. K. Gupta; Sugaya, Nobuyoshi; Olsson, Lisbeth; Panagiotou, Gianni.

    In: Scientific Reports, Vol. 2, 2012.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  27. Published

    Hyperactivity of the Ero1α Oxidase Elicits Endoplasmic Reticulum Stress but No Broad Antioxidant Response. / Hansen, Henning Gram; Schmidt, Jonas Damgard; Soltoft, Cecilie Lutzen; Ramming, Thomas; Geertz-Hansen, Henrik Marcus; Christensen, Brian; Sorensen, Esben Skipper; Juncker, Agnieszka; Appenzeller-Herzog, Christian; Ellgaard, Lars.

    In: Journal of Biological Chemistry, Vol. 287, No. 47, 2012, p. 39513-39523.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  28. Published

    Knowledge engineering for health: A new discipline required to bridge the “ICT gap” between research and healthcare. / Beck, Tim; Gollapudi, Sirisha; Brunak, Søren; Graf, Norbert; Lemke, Heinz U.; Dash, Debasis; Buchan, Iain; Díaz, Carlos; Sanz, Ferran; Brookes, Anthony J.

    In: Human Mutation, Vol. 33, No. 5, 2012, p. 797-802.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  29. Published
  30. Published

    Mining electronic health records: towards better research applications and clinical care.. / Jensen, Peter B; Jensen, Lars Juhl; Brunak, Søren.

    In: Nature Reviews. Genetics, Vol. 13, No. 6, 2012, p. 395-405.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  31. Published

    Modeling of Phenoxy Acid Herbicide Mineralization and Growth of Microbial Degraders in 15 Soils Monitored by Quantitative Real-Time PCR of the Functional tfdA Gene. / Bælum, Jacob; Prestat, Emmanuel; David, Maude M.; Strobel, Bjarne W.; Jacobsen, Carsten Suhr.

    In: Applied and Environmental Microbiology, Vol. 78, No. 15, 2012, p. 5305-5312.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  32. Published
  33. Published

    Scale-free behaviour of amino acid pair interactions in folded proteins. / Petersen, Steffen B. ; Neves-Petersen, Maria Teresa; Mortensen, Rasmus J. ; Henriksen, Svend B. ; Geertz-Hansen, Henrik Marcus.

    In: P L o S One, Vol. 7, No. 7, 2012, p. e41322-e41322.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  34. Published

    The impact of network biology in pharmacology and toxicology. / Panagiotou, Gianni; Taboureau, Olivier .

    In: S A R and Q S A R in Environmental Research, Vol. 23, No. 3-4, Sp. Iss. SI, 2012, p. 221-235.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  35. Published

    Toxicogenomics Investigation Under the eTOX Project. / Taboureau, Olivier ; Hersey, Anne; Audouze, Karine Marie Laure; Gautier, Laurent; Jacobsen, Ulrik Plesner; Akhtar, Ruth; Atkinson, Francis; Overington, John P.; Brunak, Søren.

    In: Journal of Pharmacogenomics & Pharmacoproteomics, 2012.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  36. Published

    Uncovering the Molecular Machinery of the Human Spindle-An Integration of Wet and Dry Systems Biology. / Rojas, Ana M.; Santamaria, Anna; Malik, Rainer; Jensen, Thomas Skot; Korner, Roman; Morilla, Ian; de Juan, David; Krallinger, Martin; Hansen, Daniel Aaen; Hoffmann, Robert Daniel; Lees, Jonathan; Reid, Adam; Yeats, Corin; Wehner, Anja; Elowe, Sabine; Clegg, Andrew B.; Brunak, Soren; Nigg, Erich A.; Orengo, Christine; Valencia, Alfonso; Ranea, Juan A. G.

    In: P L o S One, Vol. 7, No. 3, 2012, p. e31813.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  37. Published

    Wide Distribution of Closely Related, Antibiotic-Producing Arthrobacter Strains throughout the Arctic Ocean. / Wietz, Matthias; Månsson, Maria; Bowman, Jeff S.; Blom, Nikolaj; Ng, Yin; Gram, Lone.

    In: Applied and Environmental Microbiology, Vol. 78, No. 6, 2012, p. 2039-2042.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  38. 2011
  39. Published

    An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. / Rasmussen, Morten; Guo, Xiaosen; Wang, Yong; Lohmueller, Kirk E.; Rasmussen, Simon; Albrechtsen, Anders; Skotte, Line; Lindgreen, Stinus; Metspalu, Mait; Jombart, Thibaut; Kivisild, Toomas; Zhai, Weiwei; Eriksson, Anders; Manica, Andrea; Orlando, Ludovic; De La Vega, Francisco M.; Tridico, Silvana; Metspalu, Ene; Nielsen, Kasper; Ávila-Arcos, María C.; Moreno-Mayar, J. Víctor; Muller, Craig; Dortch, Joe; Gilbert, M. Thomas P.; Lund, Ole; Wesolowska, Agata; Karmin, Monika; Weinert, Lucy A.; Wang, Bo; Li, Jun; Tai, Shuaishuai; Xiao, Fei; Hanihara, Tsunehiko; van Driem, George; Jha, Aashish R.; Ricaut, François-Xavier; de Knijff, Peter; Migliano, Andrea B; Gallego Romero, Irene; Kristiansen, Karsten; Lambert, David M.; Brunak, Søren; Forster, Peter; Brinkmann, Bernd; Nehlich, Olaf; Bunce, Michael; Richards, Michael; Gupta, Ramneek; Bustamante, Carlos D.; Krogh, Anders; Foley, Robert A.; Lahr, Marta M.; Balloux, Francois; Sicheritz-Pontén, Thomas; Villems, Richard; Nielsen, Rasmus; Wang, Jun; Willerslev, Eske.

    In: Science, Vol. 334, No. 6052, 2011, p. 94-98.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  40. Published

    Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia. / Wesolowska, Agata; Dalgaard, M. D.; Borst, L.; Gautier, Laurent; Bak, M.; Weinhold, Nils; Nielsen, B. F.; Helt, L. R.; Audouze, Karine Marie Laure; Nersting, J; Tommerup, N.; Brunak, Søren; Sicheritz-Pontén, Thomas; Leffers, H.; Schmiegelow, K.; Gupta, Ramneek.

    In: Leukemia, Vol. 25, 2011, p. 1001-1006.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  41. Published

    Enterotypes of the human gut microbiome. / Arumugam, Manimozhiyan; Raes, Jeroen; Pelletier, Eric; Le Paslier, Denis; Yamada, Takuji; Mende, Daniel R.; Fernandes, Gabriel R.; Tap, Julien; Bruls, Thomas; Batto, Jean-Michel; dos Santos, Marcelo Bertalan Quintanilha; Borruel, Natalia; Casellas, Francesc; Fernandez, Leyden; Gautier, Laurent; Hansen, Torben; Hattori, Masahira; Hayashi, Tetsuya; Kleerebezem, Michiel; Kurokawa, Ken; Leclerc, Marion; Levenez, Florence; Manichanh, Chaysavanh; Nielsen, Henrik Bjørn; Nielsen, Trine; Pons, Nicolas; Poulain, Julie; Qin, Junjie; Sicheritz-Pontén, Thomas; Tims, Sebastian; Torrents, David; Ugarte, Edgardo; Zoetendal, Erwin G.; Wang, Jun; Guarner, Francisco; Pedersen, Oluf; de Vos, Willem M.; Brunak, Søren; Doré, Joel; Antolín, María; Artiguenave, François; Blottiere, Hervé M.; Almeida, Mathieu; Brechot, Christian; Cara, Carlos; Chervaux, Christian; Cultrone, Antonella; Delorme, Christine; Denariaz, Gérard; Dervyn, Rozenn; Foerstner, Konrad U.; Friss, Carsten; van de Guchte, Maarten; Guedon, Eric; Haimet, Florence; Huber, Wolfgang; van Hylckama-Vlieg, Johan; Jamet, Alexandre; Juste, Catherine; Kaci, Ghalia; Knol, Jan; Lakhdari, Omar; Layec, Severine; Le Roux, Karine; Maguin, Emmanuelle; Mérieux, Alexandre; Melo Minardi, Raquel; M'rini, Christine; Muller, Jean; Oozeer, Raish; Parkhill, Julian; Renault, Pierre; Rescigno, Maria; Sanchez, Nicolas; Sunagawa, Shinichi; Torrejon, Antonio; Turner, Keith; Vandemeulebrouck, Gaetana; Varela, Encarna; Winogradsky, Yohanan; Zeller, Georg; Weissenbach, Jean; Ehrlich, S. Dusko; Bork, Peer.

    In: Nature, Vol. 473, No. 7346, 2011, p. 174-180.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  42. Published

    Genome sequences of two stress-tolerant Campylobacter jejuni poultry strains, 305 and DFVF1099.. / Takamiya, Monica; Özen, Asli Ismihan; Rasmussen, Morten; Alter, Thomas; Gilbert, Tom; Ussery, David; Knøchel, S.

    In: Journal of Bacteriology, Vol. 193, No. 19, 2011, p. 5546-5547.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  43. Published

    Metatranscriptomics of the human gut microbiome. / Sicheritz-Pontén, Thomas (Invited author).

    In: Genome Biology (Online Edition), Vol. 12 Suppl 1, 2011, p. I15.

    Publication: ResearchConference abstract in journal – Annual report year: 2011

  44. Published

    Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease. / Jensen, Majken Karoline; Pers, Tune Hannes; Dworzynski, Piotr; Girman, Cynthia J.; Brunak, Søren; Rimm, Eric B.

    In: Circulation: Cardiovascular Genetics, Vol. 4, No. 5, 2011, p. 549-U159.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

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