CFB - Metagenomic Systems Biology

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  1. 2013
  2. Published

    A conceptual model linking functional gene expression and reductive dechlorination rates of chlorinated ethenes in clay rich groundwater sediment. / Bælum, Jacob; Chambon, Julie Claire Claudia; Scheutz, Charlotte; Binning, Philip John; Laier, Troels; Bjerg, Poul Løgstrup; Jacobsen, Carsten.

    In: Water Research, Vol. 47, No. 7, 2013, p. 2467-2478.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  3. Published

    ChemProt-2.0: visual navigation in a disease chemical biology database. / Kjærulff, Sonny Kim; Wich, Louis; Kringelum, Jens Vindahl; Jacobsen, Ulrik Plesner; Kouskoumvekaki, Irene; Audouze, Karine Marie Laure; Lund, Ole; Brunak, Søren; Oprea, Tudor; Taboureau, Olivier .

    In: Nucleic Acids Research, Vol. 41, No. D1, 2013, p. D464-D469.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  4. Published

    Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer.. / Edsgard, Stefan Daniel; Dalgaard, Marlene Danner; Weinhold, Nils; Wesolowska, Agata; Rajpert-De Meyts, Ewa; Ottesen, Anne Marie; Juul, Anders; Skakkebæk, Niels Erik; Jensen, Thomas Skøt; Gupta, Ramneek; Leffers, Henrik; Brunak, Søren.

    In: Frontiers in Endocrinology, Vol. 4, 2013.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  5. Published

    Reply to 'Mining electronic health records: an additional perspective'. / Jensen, Peter B.; Jensen, Lars J.; Brunak, Søren.

    In: Nature Reviews. Genetics, Vol. 14, No. 1, 2013, p. -.

    Publication: Research - peer-review › Journal article – Annual report year: 2013

  6. 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.

    In: Systems Metabolic Engineering : Methods and Protocols. Springer Science+Business Media B.V., 2013. (Methods in Molecular Biology, Vol. 985).

    Publication: Research - peer-review › Book chapter – Annual report year: 2013

  7. Published

    The chemical interactome space between the human host and the genetically defined gut metabotypes. / Jacobsen, Ulrik Plesner; Nielsen, Henrik Bjørn; Hildebrand, Falk; Raes, Jeroen; Sicheritz-Pontén, Thomas; Kouskoumvekaki, Irene; Panagiotou, Gianni.

    In: I S M E Journal, Vol. 7, 2013, p. 730-742.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  8. 2012
  9. 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-review › Journal article – Annual report year: 2012

  10. Published

    Analyzing the genomic variation of microbial cell factories in the era of “New Biotechnology”. / Herrgard, Markus; Panagiotou, Gianni.

    In: Computational and Structural Biotechnology Journal, Vol. 3, No. 4, 2012.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  11. 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-review › Journal article – Annual report year: 2012

  12. 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-review › Poster – Annual report year: 2012

  13. 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-review › Conference abstract for conference – Annual report year: 2012

  14. 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-review › Journal article – Annual report year: 2012

  15. Published

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

    In: The Prokaryotes. ed. / Rosenberg E.2012 : Springer Berlin Heidelberg, 2012.

    Publication: Research - peer-review › Book chapter – Annual report year: 2012

  16. 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-review › Journal article – Annual report year: 2012

  17. 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-review › Journal article – Annual report year: 2012

  18. 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-review › Journal article – Annual report year: 2012

  19. 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-review › Journal article – Annual report year: 2012

  20. Published

    Mapping the genome of Plasmodium falciparum on the drug-like chemical space reveals novel anti-malarial targets and potential drug leads. / Jensen, Kasper; Plichta, Damian Rafal; Panagiotou, Gianni; Kouskoumvekaki, Irene.

    In: Molecular BioSystems, Vol. 8, No. 6, 2012, p. 1678-1685.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  21. 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-review › Journal article – Annual report year: 2012

  22. 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-review › Journal article – Annual report year: 2012

  23. Published

    Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria. / Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon; Rundsten, Carsten Friis; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W.; Aarestrup, Frank M.; Lund, Ole.

    In: Journal of Clinical Microbiology, Vol. 50, No. 4, 2012, p. 1355-1361.

    Publication: Research - peer-review › Journal article – Annual report year: 2012

  24. 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-review › Journal article – Annual report year: 2012

  25. 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-review › Journal article – Annual report year: 2012

  26. 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-review › Journal article – Annual report year: 2012

  27. 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-review › Journal article – Annual report year: 2012

  28. 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-review › Journal article – Annual report year: 2012

  29. 2011
  30. 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-review › Journal article – Annual report year: 2011

  31. 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-review › Journal article – Annual report year: 2011

  32. 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-review › Journal article – Annual report year: 2011

  33. 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-review › Journal article – Annual report year: 2011

  34. 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: Research › Conference abstract in journal – Annual report year: 2011

  35. 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-review › Journal article – Annual report year: 2011

  36. 2000
  37. Published

    The biologist and the computer. / Brunak, Søren.

    In: Trends in Genetics, Vol. 16, No. 12, 2000.

    Publication: Research - peer-review › Review – Annual report year: 2000

  38. 1995
  39. Published

    How many protein fold classes are to be found?. / Lindgård, Per-Anker; Bohr, Henrik; Bohr, Jakob; Brunak, Søren.

    In: Protein folds: A distance based approach. ed. / H. Bohr; S. Brunak. Boca Raton, FL : CRC Press, 1995. p. 98-102.

    Publication: Research › Book chapter – Annual report year: 1995

  40. Published

    Patterns of Protein Conformations. / Bohr, Henrik; Brunak, Søren.

    In: The Pattern Book: Fractals, Art, and Nature. ed. / Clifford A. Pickover. World Scientific, 1995. p. 6-9.

    Publication: Research - peer-review › Book chapter – Annual report year: 1995

  41. Published

    Resonator Driven Protein Folding: The Implication of Topology for Protein Structure and Folding. / Bohr, Jakob; Bohr, Henrik; Brunak, Søren.

    In: Protein Folds: A Distance-Based Approach. ed. / Henrik Bohr; Søren Brunak. CRC Press, 1995. p. 243-252.

    Publication: Research - peer-review › Book chapter – Annual report year: 1995

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