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2014 (2) 2013 (6) 2012 (2) 2011 (2) 2010 (5) 2009 (5) 2008 and before (24)

2014

    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; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD Nat Biotechnol
    Nature Biotechnology. 2014 Jul 6., 2014
    PubMed
    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    Bjørn Nielsen H, 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, MetaHIT Consortium, Pierre Renault, Thomas Sicheritz-Ponten, Peer Bork, Jun Wang, Søren Brunak & S Dusko Ehrlich
    Nature Biotechnology. 2014 Jul 6., 2014
    PubMed

2013

    Metagenomic species profiling using universal phylogenetic marker genes.
    Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P
    Nature Methods 10(12):1196-9 doi:10.1038/nmeth.2693, 2013
    PubMed
    Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes.
    Barah P, Jayavelu ND, Rasmussen S, Nielsen HB, Mundy J, Bones AM
    BMC Genomics 14:722 doi:10.1186/1471-2164-14-722, 2013
    PubMed
    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
    TIMP1 overexpression mediates resistance of MCF-7 human breast cancer cells to fulvestrant and down-regulates progesterone receptor expression.
    Bjerre C, Vinther L, Belling KC, Würtz SO, Yadav R, Lademann U, Rigina O, Do KN, Ditzel HJ, Lykkesfeldt AE, Wang J, Nielsen HB, Brünner N, Gupta R, Schrohl AS, Stenvang J
    Tumour Biology. 34(6):3839-51 doi:10.1007/s13277-013-0969-7, 2013
    PubMed
    Transcriptome profiling of mice testes following low dose irradiation
    Belling KC, Tanaka M, Dalgaard MD, Nielsen JE, Nielsen HB, Brunak S, Almstrup K, Leffers H
    Reproductive Biology and Endocrinology 2013, 2013
    Relevant URL
    Transcriptome responses to combinations of stresses in Arabidopsis.
    Rasmussen S, Barah P, Suarez-Rodriguez MC, Bressendorff S, Friis P, Costantino P, Bones AM, Nielsen HB, Mundy J
    Plant Physiology 161(4):1783-94 doi:10.1104/pp.112.210773, 2013
    PubMed

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
    The chemical interactome space between the human host and the genetically defined gut metabotypes
    Jacobsen UP, Nielsen HB, Hildebrand F, Raes J, Sicheritz-Ponten T, Kouskoumvekaki I, Panagiotou G
    The ISME Journal advance online publication, 22 November 2012; doi:10.1038/ismej.2012.141, 2012
    Relevant URL

2011

    FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data
    Manijak MP, Nielsen HB
    BMC Res Notes 4:181 doi:10.1186/1756-0500-4-181, 2011
    PubMed
    Enterotypes of the human gut microbiome
    Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M\'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P
    Nature 473(7346):174-80 doi:10.1038/nature09944, 2011
    PubMed

2010

    Lazarus1, a DUF300 protein, contributes to programmed cell death associated with Arabidopsis acd11 and the hypersensitive response
    Malinovsky FG, Brodersen P, Fiil BK, McKinney LV, Thorgrimsen S, Beck M, Nielsen HB, Pietra S, Zipfel C, Robatzek S, Petersen M, Hofius D, Mundy J
    PLoS ONE 5(9):e12586 doi:10.1371/journal.pone.0012586, 2010
    PubMed
    Transcriptome differentiation along the dorso-ventral axis in laser-captured microdissected rat hippocampal granular cell layer
    Christensen T, Bisgaard CF, Nielsen HB, Wiborg O
    Neuroscience 170(3):731-41 doi:10.1016/j.neuroscience.2010.07.016, 2010
    PubMed
    Autoimmunity in Arabidopsis acd11 Is Mediated by Epigenetic Regulation of an Immune Receptor
    Palma K, Thorgrimsen S, Malinovsky FG, Fiil BK, Nielsen HB, Brodersen P, Hofius D, Petersen M, Mundy J
    PLoS Pathog. 6(10):e1001137 doi:10.1371/journal.ppat.1001137, 2010
    PubMed
    Read article
    Transcriptomes of the desiccation- tolerant resurrection plant Craterostigma plantagineum
    Rodriguez MC, Edsgärd D, Hussain SS, Alquezar D, Rasmussen M, Gilbert T, Nielsen HB, Bartels D, Mundy J
    Plant J. 63(2):212-28 doi:10.1111/j.1365-313X.2010.04243.x, 2010
    PubMed
    A human gut microbial gene catalogue established by metagenomic sequencing
    Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich DS & Wang J
    Nature 464(7285):59-65 doi:10.1038/nature08821, 2010
    PubMed
    Nature frontpage

2009

    Transcriptomic variation in a coral reveals pathways of clonal organisation
    Line K Bay, Bjørn Nielsen H, Hanne Jarmer, Francois Seneca, Madeleine J H van Oppe
    Marine Genomics, 2009
    Read abstract
    Impaired uptake and/or utilisation of leucine is suppressed by the SPT15-300 allele of the TATA binding protein gene.
    Baerends RJ, Qiu JL, Rasmussen S, Nielsen HB, Brandt A
    Appl. Environ. Microbiol. 75(19):6055-61 doi:10.1128/AEM.00989-09, 2009
    PubMed
    The transcriptionally active regions in the genome of Bacillus subtilis
    Rasmussen S, Nielsen HB, Jarmer H
    Mol. Microbiol. 73(6):1043-57 doi:10.1111/j.1365-2958.2009.06830.x, 2009
    PubMed
    Controlled indole-3-acetaldoxime production through ethanol-induced expression of CYP79B2
    Mikkelsen MD, Fuller VL, Hansen BG, Nafisi M, Olsen CE, Nielsen HB, Halkier BA
    Planta 229(6):1209-17 doi:10.1007/s00425-009-0907-5, 2009
    PubMed
    Microarray analysis reveals transcriptional plasticity in the reef building coral Acropora millepora
    Bay LK, Ulstrup KE, Nielsen HB, Jarmer H, Goffard N, Willis BL, Miller DJ, van Oppen MJH
    Molecular Ecology; doi: 10.1111/j.1365-294X.2009.04257.x, 2009

2008

    Arabidopsis mitogen-activated protein kinase kinases MKK1 and MKK2 have overlapping functions in defense signaling mediated by MEKK1, MPK4, and MKS1
    Qiu JL, Zhou L, Yun BW, Nielsen HB, Fiil BK, Petersen K, Mackinlay J, Loake GJ, Mundy J, Morris PC
    Plant Physiology. 148(1):212-22 doi:10.1104/pp.108.120006, 2008
    PubMed
    Arabidopsis MAP Kinase Kinases MKK1 and MKK2 have overlapping functions in defense signalling mediated by MEKK1, MPK4 and MKS1.
    Qiu J, Nielsen HB, Fiil BK, Petersen K, MacKinlay J, Loake G, Mundy J, Morris PC
    Plant Physiology. 148(1):212-22 doi:10.1104/pp.108.120006, 2008
    PubMed
    Relevant URL
    Arabidopsis MAP Kinase 4 regulates gene expression via transcription factor release in the nucleus
    Qiu J, Fiil BK, Petersen K, Nielsen HB, Botanga CJ, Thorgrimsen S, Lichota J, Brodersen P, Grasser KD, Mattsson O, Glazebrook J, Mundy J, Petersen M
    The EMBO Journal . 27(16):2214-21 doi:10.1038/emboj.2008.147, 2008
    PubMed
    Relevant URL

2007

    Probe Selection for DNA Microarrays using OligoWiz
    Wernersson R, Juncker AS, Nielsen HB
    Nat Protoc 2(11):2677-91, 2007
    PubMed
    Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes
    Nielsen HB, Mundy J, Willenbrock H
    PLoS ONE 2(7):e676, 2007
    PubMed
    Analysis of cell death inducing compounds
    Spicker JS, Pedersen HT, Nielsen HB, Brunak S
    Archives of Toxicology, DOI 10.1007/s00204-007-0207-4, 2007
    Improving comparability between microarray probe signals by thermodynamic intensity correction
    Bruun GM, Wernersson R, Juncker AS, Willenbrock H, Nielsen HB
    Nucleic Acids Res. 35(7):e48, 2007
    PubMed
    Web

2006

    Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4
    Brodersen P, Petersen M, Nielsen HB, Zhu S, Newman MA, Shokat KM, Rietz S, Parker J, Mundy J
    Plant J. 47(4):532-46, 2006
    PubMed
    Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol
    Mogensen J, Nielsen HB, Hofmann G, Nielsen J
    Fungal Genet. Biol. 43(8):593-603, 2006
    PubMed
    Distinct developmental defense activations in barley embryos identified by transcriptome profiling
    Nielsen ME, Lok F, Nielsen HB
    Plant Mol. Biol. 61:589-601, 2006
    PubMed
    Crosstalk
    Mundy J, Nielsen HB, Brodersen P
    Trends Plant Sci. 11(2):63-4, 2006
    PubMed

2005

    New weakly expressed cell cycle-regulated genes in yeast
    Hansen B, Schmidt P, Fausboll A, de Lichtenberg U, Wernersson R, Skøt Jensen T, Nielsen HB, Knudsen S, Brunak S
    Yeast 22(15):1191-201, 2005
    PubMed
    OligoWiz 2.0 - Integrating sequence feature annotation into the design of microarray probes
    Wernersson R, Nielsen HB
    The EMBO Journal . 24(14):2579-89, 2005
    PubMed
    The MAP kinase substrate MKS1 is a regulator of plant defense responses
    Andreasson E, Jenkins T, Brodersen P, Thorgrimsen S, Petersen NH, Zhu S, Qiu JL, Micheelsen P, Rocher A, Petersen M, Newman MA, Nielsen HB, Hirt H, Somssich I, Mattsson O, Mundy J
    The EMBO Journal . 24(14):2579-89, 2005
    PubMed
    Implementation of a gene expression index cal-culation method based on the PDNN model
    Nielsen HB, Gautier L, Knudsen S
    Bioinformatics 21(5):687-8, 2005
    PubMed

2004

    Arabidopsis VARIEGATED 3encodes a chloroplasttargeted, zinc-finger protein required for chloroplast and palisade cell development
    Næsted H, Holm A, Jenkins T, Bjørn Nielsen H, Harris CA, Beale MH, Andersen M, Mant A, Scheller H, Camara B, Mattsson O, Mundy J
    J. Cell. Sci. 117:4807-18, 2004
    PubMed
    Implementation of a gene expression index calculatation method based on the PDNN model
    Bjørn Nielsen H, Gautier L, Knudsen S
    Bioinformatics 21(5):687-8, 2004
    PubMed

2003

    Microarray Data Analysis
    Nielsen HB
    Ph.D. thesis, 2003
    Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
    Nielsen HB, Wernersson R, Knudsen S
    Nucleic Acids Res. 31(13):3491-6, 2003
    PubMed

2002

    A new non-linear normalization method for reducing variability in DNA microarray experiments
    Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielsen HB, Saxild HH, Nielsen C, Brunak S, Knudsen S
    Genome Biol. 3(9):research0048, 2002
    PubMed
    Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays
    Nielsen HB, Knudsen S
    Bioinformatics 18(2):321-2, 2002
    PubMed

2000

    Caleosins: Ca2+-binding proteins associated with lipid bodies
    Næsted H, Frandsen GI, Jauh G, Hernandez-Pinzon I, Nielsen HB, Murphy DJ, Rogers JC, Mundy J
    Plant Mol. Biol. 44(4):463-76, 2000
    PubMed
    Relevant URL
    Promiscuous and specific phospholipid binding by domains in ZAC, a membrane-associated Arabidopsis protein with an ARF GAP zinc finger and a C2 domain
    Jensen RB, Lykke-Andersen K, Frandsen GI, Nielsen HB, Haseloff J, Jespersen HM, Mundy J, Skriver K
    Plant Mol. Biol. 44(6):799-814, 2000
    PubMed
    Relevant URL
    Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired Resistance
    Petersen M, Brodersen P, Naested H, Andreasson E, Lindhart U, Johansen B, Nielsen HB, Lacy M, Austin MJ, Parker JE, Sharma SB, Klessig DF, Martienssen R, Mattsson O, Jensen AB, Mundy J
    Cell 103(7):1111-20, 2000
    PubMed

2014 (2) 2013 (6) 2012 (2) 2011 (2) 2010 (5) 2009 (5) 2008 and before (24)