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2013
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. 2013, 2013 |
PubMed
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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 Biol. 2013, 2013 |
PubMed
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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 |
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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 Physiol. 2013 Apr;161(4):1783-94. doi: 10.1104/pp.112.210773. Epub 2013 Feb 27., 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. 2012 Sep 28;13:514. doi: 10.1186/1471-2164-13-514., 2012 |
PubMed
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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 |
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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. June 11, 2011 |
PubMed
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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, May 12, 2011 |
PubMed
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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. 2010 Sep 7;5(9):e12586, 2010 |
PubMed
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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, October 27, 2010 |
PubMed
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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, 2010 |
PubMed
Read article
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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
The Plant Journal, 2010 |
PubMed
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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, Volume 464 Number 7285 pp7-132, 2010 |
PubMed
Nature frontpage
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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
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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, 2009 |
PubMed
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The transcriptionally active regions in the genome of Bacillus subtilis
Rasmussen S, Nielsen HB, Jarmer H
Mol Micro 73: 1043-57, 2009 |
PubMed
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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, 2009 |
PubMed
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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 |
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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, 2008 Sep;148(1):212-22. Epub 2008 Jul 3, 2008 |
PubMed
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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 Physiol. 2008 Jul 3, 2008 |
PubMed
Relevant URL
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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 2008 (16):2214-21, 2008 |
PubMed
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2007
Probe Selection for DNA Microarrays using OligoWiz
Wernersson R, Juncker AS, Nielsen HB
Nature Protocols, vol. 2, no. 11, p. 2677-91, 2007 |
PubMed
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Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes
Nielsen HB, Mundy J, Willenbrock H
PLoS ONE. Aug 1;2:e676, 2007 |
PubMed
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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 |
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Improving comparability between microarray probe signals by thermodynamic intensity correction
Bruun GM, Wernersson R, Juncker AS, Willenbrock H, Nielsen HB
Nucleic Acids Research, doi:10.1093/nar/gkl1098, 2007 |
PubMed
Web
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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
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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
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Distinct developmental defense activations in barley embryos identified by transcriptome profiling
Nielsen ME, Lok F, Nielsen HB
Plant molecular biology, 61, 589-601, 2006 |
PubMed
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Crosstalk
Mundy J, Nielsen HB, Brodersen P
Trends plant Sci, 11, 63-64, 2006 |
PubMed
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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, 1191-201, 2005 |
PubMed
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OligoWiz 2.0 - Integrating sequence feature annotation into the design of microarray probes
Wernersson R, Nielsen HB
Nucleic Acids, 33, 611-5, 2005 |
PubMed
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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
EMBO Journal, 24, 2579-89, 2005 |
PubMed
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Implementation of a gene expression index cal-culation method based on the PDNN model
Nielsen HB, Gautier L, Knudsen S
Bioinformatics, 1;21, 687-8, 2005 |
PubMed
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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
Journal of Cell Science, 117, 4807-4818, 2004 |
PubMed
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Implementation of a gene expression index calculatation method based on the PDNN model
Bjørn Nielsen H, Gautier L, Knudsen S
Bioinformatics, 1;21, 687-8, 2004 |
PubMed
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2003
Microarray Data Analysis
Nielsen HB
Ph.D. thesis, 2003 |
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Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
Nielsen HB, Wernersson R, Knudsen S
Nucleic Acids Res.,31, 3491-6, 2003 |
PubMed
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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, research0048.1-0048.16, 2002 |
PubMed
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Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays
Nielsen HB, Knudsen S
Bioinformatics, 18, 321-322, 2002 |
PubMed
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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 Molecular Biology (2000) 44: 463–476, 2000 |
PubMed
Relevant URL
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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 (2000) Dec;44(6):799, 2000 |
PubMed
Relevant URL
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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, 1111-1120, 2000 |
PubMed
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This file was last modified Friday 31st 2013f May 2013 08:37:15 GMT |
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