| Author(s) | Citation |
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| de Jong BW, Shi S, Siewers V, Nielsen J | de Jong BW, et al. (2014) Improved production of fatty acid ethyl esters in Saccharomyces cerevisiae through up-regulation of the ethanol degradation pathway and expression of the heterologous phosphoketolase pathway. Microb Cell Fact 13(1):39
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| Nielsen MT, Nielsen JB, Anyaogu DC, Holm DK, Nielsen KF, Larsen TO, Mortensen UH | Nielsen MT, et al. (2013) Heterologous reconstitution of the intact geodin gene cluster in Aspergillus nidulans through a simple and versatile PCR based approach. PLoS One 8(8):e72871
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| Nielsen MT, Klejnstrup ML, Rohlfs M, Anyaogu DC, Nielsen JB, Gotfredsen CH, Andersen MR, Hansen BG, Mortensen UH, Larsen TO | Nielsen MT, et al. (2013) Aspergillus nidulans synthesize insect juvenile hormones upon expression of a heterologous regulatory protein and in response to grazing by Drosophila melanogaster larvae. PLoS One 8(8):e73369
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| Nielsen JB, Andersen MR, Mortensen UH | Nielsen JB, et al. (2013) Supercluster takes a walk on the wild side. Trends Microbiol 21(12):617-8
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| Kocharin K, Siewers V, Nielsen J | Kocharin K, et al. (2013) Improved polyhydroxybutyrate production by Saccharomyces cerevisiae through the use of the phosphoketolase pathway. Biotechnol Bioeng 110(8):2216-24
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| Knuf C, Nookaew I, Brown SH, McCulloch M, Berry A, Nielsen J | Knuf C, et al. (2013) Investigation of malic acid production in Aspergillus oryzae under nitrogen starvation conditions. Appl Environ Microbiol 79(19):6050-8
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| Caspeta L, Nielsen J | Caspeta L and Nielsen J (2013) Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels. Biotechnol J 8(5):534-44
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| Andersen MR, Nielsen JB, Klitgaard A, Petersen LM, Zachariasen M, Hansen TJ, Blicher LH, Gotfredsen CH, Larsen TO, Nielsen KF, Mortensen UH | Andersen MR, et al. (2013) Accurate prediction of secondary metabolite gene clusters in filamentous fungi. Proc Natl Acad Sci U S A 110(1):E99-107
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| Papini M, Nookaew I, Siewers V, Nielsen J | Papini M, et al. (2012) Physiological characterization of recombinant Saccharomyces cerevisiae expressing the Aspergillus nidulans phosphoketolase pathway: validation of activity through 13C-based metabolic flux analysis. Appl Microbiol Biotechnol 95(4):1001-10
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| Kristiansen A, Saunders AM, Hansen AA, Nielsen PH, Nielsen JL | Kristiansen A, et al. (2012) Community structure of bacteria and fungi in aerosols of a pig confinement building. FEMS Microbiol Ecol 80(2):390-401
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| Knuf C, Nielsen J | Knuf C and Nielsen J (2012) Aspergilli: systems biology and industrial applications. Biotechnol J 7(9):1147-55
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| Hansen BG, Mnich E, Nielsen KF, Nielsen JB, Nielsen MT, Mortensen UH, Larsen TO, Patil KR | Hansen BG, et al. (2012) Involvement of a natural fusion of a cytochrome P450 and a hydrolase in mycophenolic acid biosynthesis. Appl Environ Microbiol 78(14):4908-13
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| Andersen MR, Giese M, de Vries RP, Nielsen J | Andersen MR, et al. (2012) Mapping the polysaccharide degradation potential of Aspergillus niger. BMC Genomics 13:313
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| Vongsangnak W, Hansen K, Nielsen J | Vongsangnak W, et al. (2011) Integrated analysis of the global transcriptional response to alpha-amylase over-production by Aspergillus oryzae. Biotechnol Bioeng 108(5):1130-9
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| Nielsen ML, Nielsen JB, Rank C, Klejnstrup ML, Holm DM, Brogaard KH, Hansen BG, Frisvad JC, Larsen TO, Mortensen UH | Nielsen ML, et al. (2011) A genome-wide polyketide synthase deletion library uncovers novel genetic links to polyketides and meroterpenoids in Aspergillus nidulans. FEMS Microbiol Lett 321(2):157-66
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| Hansen BG, Salomonsen B, Nielsen MT, Nielsen JB, Hansen NB, Nielsen KF, Regueira TB, Nielsen J, Patil KR, Mortensen UH | Hansen BG, et al. (2011) Versatile enzyme expression and characterization system for Aspergillus nidulans, with the Penicillium brevicompactum polyketide synthase gene from the mycophenolic acid gene cluster as a test case. Appl Environ Microbiol 77(9):3044-51
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| Hansen BG, Genee HJ, Kaas CS, Nielsen JB, Regueira TB, Mortensen UH, Frisvad JC, Patil KR | Hansen BG, et al. (2011) A new class of IMP dehydrogenase with a role in self-resistance of mycophenolic acid producing fungi. BMC Microbiol 11:202
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| Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE | Andersen MR, et al. (2011) Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res 21(6):885-97
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| Vongsangnak W, Hansen K, Nielsen J | Vongsangnak W, et al. (2010) Integrated analysis of the global transcriptional response to alpha-amylase over-production by Aspergillus oryzae. Biotechnol Bioeng
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| Vongsangnak W, Nookaew I, Salazar M, Nielsen J | Vongsangnak W, et al. (2010) Analysis of genome-wide coexpression and coevolution of Aspergillus oryzae and Aspergillus niger. OMICS 14(2):165-75
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| Vongsangnak W, Salazar M, Hansen K, Nielsen J | Vongsangnak W, et al. (2009) Genome-wide analysis of maltose utilization and regulation in aspergilli. Microbiology 155(Pt 12):3893-902
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| Siewers V, Chen X, Huang L, Zhang J, Nielsen J | Siewers V, et al. (2009) Heterologous production of non-ribosomal peptide LLD-ACV in Saccharomyces cerevisiae. Metab Eng 11(6):391-7
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| Salazar M, Vongsangnak W, Panagiotou G, Andersen MR, Nielsen J | Salazar M, et al. (2009) Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Mol Genet Genomics 282(6):571-86
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| Panagiotou G, Andersen MR, Grotkjaer T, Regueira TB, Nielsen J, Olsson L | Panagiotou G, et al. (2009) Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools. Appl Environ Microbiol 75(7):2212-20
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| Meijer S, de Jongh WA, Olsson L, Nielsen J | Meijer S, et al. (2009) Physiological characterisation of acuB deletion in Aspergillus niger. Appl Microbiol Biotechnol 84(1):157-67
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| Hofmann G, Diano A, Nielsen J | Hofmann G, et al. (2009) Recombinant bacterial hemoglobin alters metabolism of Aspergillus niger. Metab Eng 11(1):8-12
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| Coutinho PM, Andersen MR, Kolenova K, vanKuyk PA, Benoit I, Gruben BS, Trejo-Aguilar B, Visser H, van Solingen P, Pakula T, Seiboth B, Battaglia E, Aguilar-Osorio G, de Jong JF, Ohm RA, Aguilar M, Henrissat B, Nielsen J, Stalbrand H, de Vries RP | Coutinho PM, et al. (2009) Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genet Biol 46 Suppl 1:S161-S169
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| Andersen MR, Lehmann L, Nielsen J | Andersen MR, et al. (2009) Systemic analysis of the response of Aspergillus niger to ambient pH. Genome Biol 10(5):R47
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| Wattanachaisaereekul S, Lantz AE, Nielsen ML, Nielsen J | Wattanachaisaereekul S, et al. (2008) Production of the polyketide 6-MSA in yeast engineered for increased malonyl-CoA supply. Metab Eng 10(5):246-54
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| Vongsangnak W, Olsen P, Hansen K, Krogsgaard S, Nielsen J | Vongsangnak W, et al. (2008) Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics 9:245
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| Panagiotou G, Andersen MR, Grotkjaer T, Regueira TB, Hofmann G, Nielsen J, Olsson L | Panagiotou G, et al. (2008) Systems analysis unfolds the relationship between the phosphoketolase pathway and growth in Aspergillus nidulans. PLoS One 3(12):e3847
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| Nielsen JB, Nielsen ML, Mortensen UH | Nielsen JB, et al. (2008) Transient disruption of non-homologous end-joining facilitates targeted genome manipulations in the filamentous fungus Aspergillus nidulans. Fungal Genet Biol 45(3):165-70
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| David H, Ozcelik IS, Hofmann G, Nielsen J | David H, et al. (2008) Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics 9:163
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| Andersen MR, Nielsen ML, Nielsen J | Andersen MR, et al. (2008) Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol 4:178
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| Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J | Andersen MR, et al. (2008) A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A 105(11):4387-92
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| Wattanachaisaereekul S, Lantz AE, Nielsen ML, Andresson OS, Nielsen J | Wattanachaisaereekul S, et al. (2007) Optimization of heterologous production of the polyketide 6-MSA in Saccharomyces cerevisiae. Biotechnol Bioeng 97(4):893-900
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| Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H | Pel HJ, et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25(2):221-31
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| Nielsen ML, Albertsen L, Lettier G, Nielsen JB, Mortensen UH | Nielsen ML, et al. (2006) Efficient PCR-based gene targeting with a recyclable marker for Aspergillus nidulans. Fungal Genet Biol 43(1):54-64
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| Mogensen J, Nielsen HB, Hofmann G, Nielsen J | Mogensen J, et al. (2006) Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol. Fungal Genet Biol 43(8):593-603
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| David H, Hofmann G, Oliveira AP, Jarmer H, Nielsen J | David H, et al. (2006) Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans. Genome Biol 7(11):R108
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| David H, Krogh AM, Roca C, Akesson M, Nielsen J | David H, et al. (2005) CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose. Microbiology 151(Pt 7):2209-21
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| Prathumpai W, McIntyre M, Nielsen J | Prathumpai W, et al. (2004) The effect of CreA in glucose and xylose catabolism in Aspergillus nidulans. Appl Microbiol Biotechnol 63(6):748-53
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| Prathumpai W, Gabelgaard JB, Wanchanthuek P, van de Vondervoort PJ, de Groot MJ, McIntyre M, Nielsen J | Prathumpai W, et al. (2003) Metabolic control analysis of xylose catabolism in Aspergillus. Biotechnol Prog 19(4):1136-41
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| Muller C, Hansen K, Szabo P, Nielsen J | Muller C, et al. (2003) Effect of deletion of chitin synthase genes on mycelial morphology and culture viscosity in Aspergillus oryzae. Biotechnol Bioeng 81(5):525-34
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| Dynesen J, Nielsen J | Dynesen J and Nielsen J (2003) Surface hydrophobicity of Aspergillus nidulans conidiospores and its role in pellet formation. Biotechnol Prog 19(3):1049-52
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| Dynesen J, Nielsen J | Dynesen J and Nielsen J (2003) Branching is coordinated with mitosis in growing hyphae of Aspergillus nidulans. Fungal Genet Biol 40(1):15-24
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| Muller C, McIntyre M, Hansen K, Nielsen J | Muller C, et al. (2002) Metabolic engineering of the morphology of Aspergillus oryzae by altering chitin synthesis. Appl Environ Microbiol 68(4):1827-36
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| Muller C, Hjort CM, Hansen K, Nielsen J | Muller C, et al. (2002) Altering the expression of two chitin synthase genes differentially affects the growth and morphology of Aspergillus oryzae. Microbiology 148(Pt 12):4025-33
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| Agger T, Petersen JB, O'Connor SM, Murphy RL, Kelly JM, Nielsen J | Agger T, et al. (2002) Physiological characterisation of recombinant Aspergillus nidulans strains with different creA genotypes expressing A. oryzae alpha-amylase. J Biotechnol 92(3):279-85
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| McIntyre M, Dynesen J, Nielsen J | McIntyre M, et al. (2001) Morphological characterization of Aspergillus nidulans: growth, septation and fragmentation. Microbiology 147(Pt 1):239-46
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| Carlsen M, Nielsen J | Carlsen M and Nielsen J (2001) Influence of carbon source on alpha-amylase production by Aspergillus oryzae. Appl Microbiol Biotechnol 57(3):346-9
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| Agger T, Spohr AB, Nielsen J | Agger T, et al. (2001) alpha-Amylase production in high cell density submerged cultivation of Aspergillus oryzae and A. nidulans. Appl Microbiol Biotechnol 55(1):81-4
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| Pedersen H, Beyer M, Nielsen J | Pedersen H, et al. (2000) Glucoamylase production in batch, chemostat and fed-batch cultivations by an industrial strain of Aspergillus niger. Appl Microbiol Biotechnol 53(3):272-7
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| Bautista LF, Aleksenko A, Hentzer M, Santerre-Henriksen A, Nielsen J | Bautista LF, et al. (2000) Antisense silencing of the creA gene in Aspergillus nidulans. Appl Environ Microbiol 66(10):4579-81
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| Aleksenko A, Liu W, Gojkovic Z, Nielsen J, Piskur J | Aleksenko A, et al. (1999) Structural and transcriptional analysis of the pyrABCN, pyrD and pyrF genes in Aspergillus nidulans and the evolutionary origin of fungal dihydroorotases. Mol Microbiol 33(3):599-611
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| Agger T, Nielsen J | Agger T and Nielsen J (1999) Genetically structured modeling of protein production in filamentous fungi. Biotechnol Bioeng 66(3):164-70
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| Kelly R, Register E, Hsu MJ, Kurtz M, Nielsen J | Kelly R, et al. (1996) Isolation of a gene involved in 1,3-beta-glucan synthesis in Aspergillus nidulans and purification of the corresponding protein. J Bacteriol 178(15):4381-91
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