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2017
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Have CT, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Løngren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Pontén T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sørensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Børglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH
Nature, 2017 |
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2016
The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota
Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, Bresciani A, Martínez I, Just S, Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui TPN, Wang J, Hugenholtz F, Plugge CM, Peterson DA, Hornef MW, Baines JF, Smidt H, Walter J, Kristiansen K, Nielsen HB, Haller D, Overmann J, Stecher B, Clavel T
Nature Microbiology, 2016 |
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2015
Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale
Schierup M, Villsen P, Wang J, Xu X, Li N, Kristiansen K, Krogh A, Sørensen TIA, Hansen T, Pedersen O, Brunak S, Gupta R, Rasmussen S, Lund O, Bolund L, Børglum AD, Eiberg H, Flindt EN, Xu R, Sun J, Liu H, Jiang H, Wang O, Cheng X, Demontis D, Besenbacher S, Mailund T, Friborg RM, Pedersen CNS, Liu S, Huang S, Rao J, Ye W, Chang Y, Li S, Guo X, Cao H, Ye C, Maretty L, Sibbesen JA, Albrechtsen A, Bork-Jensen J, Have CT, Izarzugaza JMG, Belling K, Yadav R, Grove J, Als TD, Lescal F
GigaScience, 2015 |
PubMed
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The elusive endogenous adipogenic PPARy agonists: Lining up the suspects
Hallenborg P, Petersen RK, Kouskoumvekaki I, Newman JW, Madsen L, Kristiansen K
Prog Lipid Res. 2015 Dec 15. pii: S0163-7827(15)30012-6. doi: 10.1016/j.plipres.2015.11.002, 2015 |
PubMed
ScienceDirect
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Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O
Nature, 2015 |
PubMed
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Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago
Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CMO, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E
Cell, 2015 |
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A catalog of the mouse gut metagenome
Xiao L, Feng Q, Licht TR, Dworzynski P, Nielsen HB, Arumugam M, Wang J, Madsen L, Kristiansen K
Nature Biotechnology, 2015 |
PubMed
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Population genomics of Bronze Age Eurasia
Allentoft ME, Sikora M, Sjögren KG, Rasmussen S, Rasmussen M, Stenderup J, Damgaard PB, Schroeder H, Ahlström T, Vinner L, Malaspinas AS, Margaryan A, Higham T, Chivall D, Lynnerup N, Harvig L, Baron J, Della Casa P, D?browski P, Duffy PR, Ebel AV, Epimakhov A, Frei K, Furmanek M, Gralak T, Gromov A, Gronkiewicz S, Grupe G, Hajdu T, Jarysz R, Khartanovich V, Khokhlov A, Kiss V, Kolá? J, Kriiska A, Lasak I, Longhi C, McGlynn G, Merkevicius A, Merkyte I, Metspalu M, Mkrtchyan R, Moiseyev V, Paja L, Pálfi G, Pokutta D, Pospieszny ?, Price TD, Saag L, Sablin M, Shishlina N, Smr?ka V, Soenov VI, Szeverényi V, Tóth G, Trifanova SV, Varul L, Vicze M, Yepiskoposyan L, Zhitenev V, Orlando L, Sicheritz-Pontén T, Brunak S, Nielsen R, Kristiansen K, Willerslev E
Nature, 2015 |
PubMed
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Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling
Basse AL, Dixen K, Yadav R, Tygesen MP, Qvortrup K, Kristiansen K, Quistorff B, Gupta R, Wang J, Hansen JB
BMC Genomics, 2015 |
PubMed
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Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios
Besenbacher S, Liu S, Izarzugaza JM, Grove J, Belling KC, Bork-Jensen J, Huang S, Als TD, Li S, Yadav R, Rubio-García A, Lescai F, Demontis D, Rao J, Ye W, Mailund T, Friborg RM, Pedersen CN, Xu R, Sun J, Liu H, Wang O, Cheng X, Flores D, Rydza E, Rapacki K, Damm Sørensen J, Chmura P, Westergaard D, Dworzynski P, Sørensen TI, Lund O, Hansen T, Xu X, Li N, Bolund L, Pedersen O, Eiberg H, Krogh A, Børglum AD, Brunak S, Kristiansen K, Schierup MH, Wang J, Gupta R, Villesen P, Rasmussen S
Nature Communications, 2015 |
PubMed
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2014
Transcriptome profiling of brown adipose tissue during cold exposure reveals extensive regulation of glucose metabolism.
Hao Q, Yadav R, Basse AL, Petersen S, Sonne SB, Rasmussen S, Zhu Q, Lu Z, Wang J, Audouze K, Gupta R, Madsen L, Kristiansen K, Hansen JB
The American Journal of Physiology - Endocrinology and Metabolism, 2014 |
PubMed
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Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
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, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD, MetaHIT Consortium
Nature Biotechnology. 2014 Jul 6., 2014 |
PubMed
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Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis.
Wesolowska A, Bahl MI, Carvalho V, Kristiansen K, Sicheritz-Pontén T, Gupta R, Licht TR
Microbiome. 2014 Jun 5;2:19, 2014 |
PubMed
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Identification of odorant-receptor interactions by global mapping of the human odorome.
Audouze K, Tromelin A, Le Bon AM, Belloir C, Petersen RK, Kristiansen K, Brunak S, Taboureau O
PLoS One. 2014 Apr 2;9(4):e93037., 2014 |
PubMed
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2013
Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes
Lohmueller KE, Sparsø T, Li Q, Andersson E, Korneliussen T, Albrechtsen A, Banasik K, Grarup N, Hallgrimsdottir I, Kiil K, Kilpeläinen TO, Krarup NT, Pers TH, Sanchez G, Hu Y, DeGiorgio M, Jørgensen T, Sandbæk A, Lauritzen T, Brunak S, Kristiansen K, Li Y, Hansen T, Wang J, Nielsen R, Pedersen O
AJHG, The American Journal of Human Genetics - Cell, 2013 |
PubMed
AJHG
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Richness of human gut microbiome correlates with metabolic markers.
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, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O, Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Maguin E, Haimet F, Winogradski Y, Cultrone A, Leclerc M, Juste C, Blottière H, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K, Parkhill J, Antolin M, Manichanh C, Casellas F, Boruel N, Varela E, Torrejon A, Guarner F, Denariaz G, Derrien M, van Hylckama Vlieg JE, Veiga P, Oozeer R, Knol J, Rescigno M, Brechot C, M\\\'Rini C, Mérieux A, Yamada T
Nature 500(7464):541-6 doi:10.1038/nature12506, 2013 |
PubMed
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Discovery of a Novel Selective PPAR Ligand with Partial Agonist Binding Properties by Integrated in Silico in Vitro Work Flow
Kouskoumvekaki I, Petersen RK, Fratev F, Taboureau O, Nielsen TE, Oprea TI, Sonne S, Flindt E, Jónsdóttir SO, Kristiansen K
Journal of Chemical Information and Modeling 53(4):923-37 doi:10.1021/ci3006148, 2013 |
PubMed
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2012
A comparative analysis of the intestinal metagenomes present in guinea pigs
Hildebrand F, Ebersbach T, Nielsen HB, Li X, Sonne SB, Bertalan M, Dimitrov P, Madsen L, Qin J, Wang J, Raes J, Kristiansen K, Licht TR
BMC Genomics 13:514 doi:10.1186/1471-2164-13-514, 2012 |
PubMed
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2011
An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgren S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega F, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MA, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijf P, Migliano AB, Gallego-Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sichertitz-Pontén T, Villems R, Nielsen R, Jun W, Willerslev E
Science 334(6052):94-8 doi:10.1126/science.1211177, 2011 |
PubMed
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2010
Pharmacophore-driven identification of PPARã agonists from natural sources
Petersen RK, Christensen KB, Assimopoulou AN, Fretté X, Papageorgiou VP, Kristiansen K, Kouskoumvekaki I
J. Comput. Aided Mol. Des. 25(2):107-16 doi:10.1007/s10822-010-9398-5, 2010 |
PubMed
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2005
The 3\' region of human papillomavirus type 16 early mRNAs decrease expression
Vinther J, Rosenstierne MW, Kristiansen K, Norrild B
BMC Infect. Dis. 5:83, 2005 |
PubMed
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