Research papers in international journals with peer review
2012
L. Zihe; K.E.J. Tyo; J.L. Martinez; D. Petranovic; J. Nielsen (2012) Differential expression systems for production of recombinant proteins in Saccharomyces cerevisiae. Biotechnol. Bioeng., in press
W. Vongsangnak; L.F. Figueiredo; J. Förster; T. Weber; J. Thykaer; E. Stegmann; W. Wohlleben; J. Nielsen (2012) Genome-scale metabolic representation of Amycolatopsis balhamycina. Biotechnol. Bioeng., in press
J. Nielsen (2012) Translational and systems medicine. J. Int. Med. 271:108-110
A. Mardinoglu; J. Nielsen (2012) Systems medicine and metabolic modeling. J. Int. Med. 271:142-154
I.-K. Kim; A. Roldao; V. Siewers; J. Nielsen (2012) A system-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res., in press
B. de Jong; V. Siewers; J. Nielsen (2012) Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuels. Curr. Opion. Biotechnol. 23:1-7
2011
E. Larsson; V. Tremaroli; Y.S. Lee; O. Koren; I. Nookaew; A. Fricker; J. Nielsen; R. E. Ley; F. Bäckhed (2011) Analysis of the gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecoloty through MyD88. Gut, in press
M. Cvijovic; S. Bordel; J. Nielsen (2011) Mathematical models of cell factories: Moving towards the cores of industrial biotechnology. Microbiol. Biotechnol. 4:572-584
J. Zhang; S. Vaga; P. Chumnapuen; R. Kumar; G.N. Vemuri; R. Aebershold; J. Nielsen (2011) Mapping the interaction of Snf1 with Tor1 in Saccharomyces cerevisiae. Mol. Systems Biol., 7:545
P. Chumnapuen; C. Brackmann; S.K. Nandy; S. Chatzipapdopoulos; J. Nielsen; A. Enejder (2011) Lipid biosynthesis monitored at single cell level in Saccharomyces cerevisiae. Biotechnol. J. 6:1-8
L. Pedersen; K. Hansen; J. Nielsen; A. Eliasson Lantz; J. Thykaer (2011) Industrial glucoamylase fed-batch benefits from oxygen limitation and high osmolarity. Biotechnol. Bioeng., in press
T. Österlund; I. Nookaew; J. Nielsen (2011) Fifteen years of large scale metabolic modeling of yeast: Developments and impacts. Biotechnol. Adv., in press
J.S. Rokem; W. Vongsangnak; J. Nielsen (2011) Comparative metabolic capabilities for Micrococcus luteus NCTC 2665, the “Fleming” Strain, and Actinobacteria. Biotechnol. Bioeng. 108:2770-2775
K.-K. Hong; W. Vongsangnak; G.N. Vemuri; J. Nielsen (2011) Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. Proc. Nat. Acad. Sci. USA 108:12179-12184
M. Lindqvist; I. Nookaew; I. Brinkenberg; E. Samuelson; K. Thörn; J. Nielsen; A.M.Harandi (2011) Unraveling molecular signatures of immunostimulatory adjuvants in the female genital tract through systems biology. PLoS One 6:e20448
M.P. Piddocke; A. Fazio; W. Vongsangnak; M.L.Wong; H.P. Heldt-Hansen; C. Workman; J. Nielsen; L. Olsson (2011) Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using “-omics” techniques. Microbial Cell Factory 10:27
W.A. Rodriguez-Limas; K.E.J. Tyo; J. Nielsen; O.T. Ramirez; L.A. Palomares (2011)
Molecular and process design for rotavirus-like particle production in Saccharomyces cerevisiae. Microbial. Cell Factory10:33
K.M. Madsen; G.D.B.R.K. Udatha; S. Semba; J.M. Otero; P. Koetter; J. Nielsen; Y. Ebizuka; T. Kushiro; G. Panagiotou (2011)
Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyper-producers. PLoS One 6:e14763
F. H. Karlsson; I. Nookaew; D. Petranovic; J. Nielsen (2011)
Prospects for systems biology and modeling of the gut microbiome. Trends Biotechnol. 29:251-258
S. Shi; J.O. Valle-Rodriguez; V. Siewers; J. Nielsen (2011)
Prospects for microbial biodiesel production. Biotechnol. J. 6:277-285
A. Krivoruchko; V. Siewers; J. Nielsen (2011)
Opportunities for yeast metabolic engineering: Lessons from synthetic biology. Biotechnol. J. 6:262-276
M.R. Andersen; M.P- Salazar; ……; J. Nielsen; Scott Baker (2011)
Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res. 21:885-897
F.H. Karlsson; D.W.Ussery; J. Nielsen; I. Nookaew (2011) A closer look at Bacteroides: Phylogenetic relationship and genomic implications of a life in the human gut. Microb. Ecol.61:473-485
S.E. van Mulders; C. Stassen; L. Daenen; B. Devreese; V. Siewers; R.G.E. van Eijsden; J. Nielsen; F.R. Delvaux; R. Willaert (2011)
The influence of microgravity on invasive growth in Saccharomyces cerevisiae. Astrobiol. 11:45-55
B.G. Hansen; B. Salomonsen; M.T. Nielsen; N. B. Hansen; J.B. Nielsen; K.F. Nielsen; T.B. Reguira; J. Nielsen; K.R. Patil; U.H. Mortensen (2011)
A versatile gene expression and characterization system for Aspergillus: heterologous expression of the gene encoding the polyketide synthase from the mycophenolic acid gene cluster from Penicillium brevicompactum as a case study. Appl. Environ. Microbiol. 77:3044-3051
T.B. Reguira; K.R. Kildegaard; B.G. Hansen; U.H. Mortensen; C. Hertweck; J. Nielsen (2011)
Molecular basis for mycophenolic acid biosynthesis of Penicillium brevicompactum. Appl. Environ. Microbiol. 77:3035-3043
S. Pabinger; R. Rader; R. Agren; J. Nielsen; Z. Trajanoski (2011)
MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Systems Biol. 5:20
R. Olivares-Hernandez; S. Bordel; J. Nielsen (2011)
Codon usage variability determines the correlation betweem proteome and transcriptome fold changes. BMC Systems Biol. 5:33
R. Ruenwai; A. Neiss; K. Laoteng; W. Vongsangnak; A.B. Dalfard; S. Cheevadhanarak; D. Petranovic; J. Nielsen (2011)
Heterologous production of polyunsaturated fatty acids in Saccharomyces cerevisiae causes a global transcriptional response resulting in reduced proteasomal activity and increased oxidative stress. Biotechnol. J. 6:343-356
L. Albertsen; Y. Chen; L.S. Bach; S. Rattleff; J. Maury; S. Brix; J. Nielsen; U. Mortensen (2011)
Fusion of host and heterologous enzymes diverts flux towards sesquiterpene production in S. cerevisiae. Appl. Environ. Microbiol. 77:1033-1040
W. Vongsangnak; K. Hansen; J. Nielsen (2011)
Integrated analysis of the global transcriptional response to a-amylase over-production in Aspergillus oryzae. Biotechnol. Bioeng. 108:1130-1139
2010
J.M. Otero; W. Vongsangak; M.A.Asadollahi; R. Olivares-Hernandes; J.Maury; L.Farinelli; L.Barlocher; M.Østerås; M.Schalk; A. Clark; J. Nielsen (2010)
Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications. BMC Genomics 11:723
A.Canelas; N.Harrison; A.Fazio; J.Zhang; et al. ; J. Nielsen (2010)
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nature Comm., DOI:10:1038, 1-8
D. Petranovic; K. Tyo; G.N. Vemuri; J. Nielsen (2010)
Prospects of yeast systems biology for human health: integrating lipid, protein and energy metabolism. FEMS Yeast Res. 10:1046-1059
J. Zhang; G. Vemuri; J. Nielsen (2010)
Systems biology of energy homeostasis in yeast. Curr. Op. Microbiol. 13:382-388
J.M. Otero; M.A. Papadakis; D.B.R.K. Gupta Udatha; J. Nielsen; G. Panagiotou (2010)
Yeast biological networks unforld the interplay of antioxidants, genome and phenotype, and reveal a novel regulator of the oxidative stress response. PLoS One 5:e13606
S. Partow; V. Siewers; S. Bjørn; J. Nielsen; J. Maury (2010)
Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast 27:955-964
R. Olivares-Hernandez; H. Sunner; J. C. Frisvad; L. Olsson; J. Nielsen; G. Panagiotou (2010)
Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group. PLoS One 5:e12781
R. Olivares-Hernandez; R. Usaite; J. Nielsen (2010)
Integrative analysis using proteome and transcriptome data from yeast to unravel regulatory patterns at post-transcriptional level. Biotechnol. Bioeng. 107:865-87
M. Papini; I. Nookaew; G. Scalcinati; V. Siewers; J. Nielsen (2010)
Phosphoglycerate mutase knock-out mutant Saccharomyces cerevisiae: Physiological investigation and transcriptome analysis. Biotechnol. J. 5:1016-1027
I. Nookaew; B. G. Gabrielsson; A: Holmäng; A.-S. Sandberg; J. Nielsen (2010)
Identifying molecular effects of diet through systems biology: Influence of herring diet on sterol metabolism and protein turnover in mice. PLoS One 5:e12361
S. Bordel; R. Agren; J. Nielsen (2010)
Sampling the solution spaee in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS Comp. Biol. 6:e1000859
J. Zhang; L. Olsson; J. Nielsen (2010)
The β-subunits of the Snf1 kinase in Saccharomyces cerevisiae, Gal83 and Sip2, but not Sip1, are redundant in glucose derepression and regulation of sterol biosynthesis. Mol. Microbiol. 77:371-383
S. K. Nandy; P. Jouhten; J. Nielsen (2010)
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation. BMC Sys. Biol. 4:68
M. Cvijovic; R. Olivares-Hernandez; R. Agren; W. Vongsangnak; I. Nookaew; K. R. Patil; J. Nielsen (2010)
BioMet Toolbox: Genome-wide analysis of metabolism. Nuc. Acid Res. 38:W144-W149
J. Thykaer; J. Nielsen; W. Wohlleben; T. Weber; M. Gutknecht; A. E. Lantz; E. Stegmann (2010)
Increased glycopeptides production after overexpression of shikimate pathway genes being part of the balhimycin biosynthetic gene cluster. Met. Eng. 12:455-461
I. Rocha; P. M. P. Evangelista; P. Vilaça; S. Soares; J. P Pinto; J. Nielsen; K. R Patil; E. C. Ferreira; M. Rocha (2010)
OptFlux: an open-source software platform for in silico metabolic engineering. BMC Systems Biol., 4:45
V. Siewers; R. San-Bento; J. Nielsen (2010)
Implementation of communication-mediating domains for non-ribosomal peptide production in Saccharomyces cerevisiae. Biotechnol. Bioeng., 106:841-844
S. Bordel; J. Nielsen (2010)
Identification of flux control in metabolic networks using non-equilibrium thermodynamics. Met. Eng., 12:369-377
L. Liu; R. Agren; S. Bordel; J. Nielsen (2010)
Use of genome-scale metabolic models for understanding microbial physiology. FEBS Lett.584:2556-2564
K. Tyo; K. Kocharin; J. Nielsen (2010)
Toward Design-based Engineering of Industrial Microbes. Curr. Op. Microbiol. 13:1-10
J. M. Otero; J. Nielsen (2010)
Industrial Systems Biology. Biotechnol. Bioeng. 105:439-460
W. Vongsangnak; I. Nookaew; M. Salazar; J. Nielsen (2010)
Analysis of genome-wide co-expression and co-evolution of Aspergillus oryzae and Aspergillus niger. Omics 14:165-175
K. van Eunen; J. Bouwman; P. Daran-Lapujade; J. Postmus; A. B. Canelas; F. I. Mensonides; R. Orij; I. Tuzun; J. van den Brink; G. J. Smits; W. M. van Gulik; S. Brul; J. J. Heijnen; J. H. de Winde; M. J. Teixeira de Mattos; C. Kettner; J. Nielsen; H. V. Westerhoff; B. M. Bakker (2010)
Measuring enzyme activities under standardized in-vivo like conditions for systems biology. FEBS J. 277:749-760
M. A. Asadollahi; J. Maury; M. Schalk; A. Clark; J. Nielsen (2010)
Enhancement of farnesyl diphosphate pool as direct precursor of sesquiterpenes through metabolic engineering of the mevalonate pathway in Saccharomyces cerevisiae. Biotechnol. Bioeng., 106:86-96
2009
J. Nielsen (2009)
Systems biology of lipid metabolism: From yeast to human. FEBS Lett. 583:3905-3913
M. Salazar; W. Vongsangnak; G. Panagiotou; M. R. Andersen; J. Nielsen (2009)
Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Mol. Genet. Genom. 282:571-586
W. Vongsangnak; M. Salazar; K. Hansen; J. Nielsen (2009)
Genome-wide analysis of maltose utilization and regulation in aspergilla. Microbiol. 155:3893-3902
R. Usaite; M. C. Jewett; A. P. Oliveira; J. R. Yates III; L. Olsson; J. Nielsen (2009)
Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Mol. Sys. Biol. 5:319
V. Siewers; X. Chen; L. Huang; J. Zhang; J. Nielsen (2009)
Heterologous production of the non-ribosomal peptide LLD-ACV in Saccharomyces cerevisiae. Met. Eng. 11:391-397
D. B. Flagfeldt; V. Siewers; L. Huang; J. Nielsen (2009)
Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae. Yeast 26:545-551
S.Meijer; W.A.de Jongh; L. Olsson; J. Nielsen (2009)
Physiological characterization of acuB deletion in Aspergillus niger. Appl. Microbiol. Biotechnol. 84:157-167
D. Rossouw; R. Olivares-Hernandes; J. Nielsen; F.F. Bauer (2009)
A comparative ’omics’ approach to investigate differences in wine yeast physiology and metabolism during fermentation. Appl. Environ. Microbiol. 75:6600-6612
M. A. Asadollahi; J. Maury; K. R. Patil; M. Schalk; A. Clark; J. Nielsen (2009)
Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Met. Eng. 11;328-334
M. R. Andersen; L. Lehmann; J. Nielsen (2009)
Systemic analysis of the response of Aspergillus niger to ambient pH. Genome Biol. 10:R47
S. Meijer; M. L. Nielsen; L. Olsson; J. Nielsen (2009)
Gene deletion of cytosolic ATP:Citrate lyase leads to altered organic acid production in Aspergillus niger. J. Ind. Microbiol. Biotechnol. 36:1275-1280
G. Panagiotou; M. R. Andersen; T. Grotkjær; T. B. Regueira; J. Nielsen; L. Olsson (2009)
Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools. Appl. Environ, Microbiol. 75:2212-2220
G. Panagiotou; J. Nielsen (2009)
Nutritional systems biology: Definitions and approaches. Annual Rev. Nutr. 29:329-339
J. F. Moxley; M. C. Jewett; M. R. Antoniewicz; S. G. Villas-Boas; H. Alper; R. T. Wheeler; L. Tong; A. G. Hinnebusch; T. Ideker; J. Nielsen; G. Stephanopoulos (2009)
Linking transcriptional regulation and high resolution metabolic fluxes in yeast modulated by the global regulator Gcn4p. Proc. Nat. Acad. Sci.106:6477-6482
D. Cimini; K. R. Patil; C. Shiraldi; J. Nielsen (2009)
Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3. BMC Systems Biol. 3:17
S. Meijer; J. Otero; M. R. Andersen; L Olsson; J. Nielsen (2009)
Overexpression of isocitrate lyase – glyoxylate byplass influence on metabolism in Aspergillus niger. Metabolic Eng.11:107-116
T. S. Christensen; A. P. Olivaira; J. Nielsen (2009)
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae. BMC Systems Biol. 3:7
J. Thykaer; K. Rueksomtawin; H. Noorman; J. Nielsen (2009)
Disruption of the NADPH-dependent Glutamate Dehydrogenase Affects the Morphology of Two Industrial Strains of Penicillium chrysogenum. J. Biotechnol., 139:280-282
G. Hofmann; A. Diano; J. Nielsen (2009)
Recombinant bacterial haemoglobin alters metabolism of Aspergillus niger. Met. Eng. 11:8-12
M. R. Andersen; J. Nielsen (2008)
Current status of systems biology in Aspergilli. Fun. Gen. Biol., 46:S180-S190
P. M. Coutinho et al. (2009)
Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Asperpergillus niger and Aspergillus oryzae. Fungal Gen. Biol. 46:S161-S169
J. R. Wortman et al. (2008)
The 2008 update of the Aspergillus nidulans genome annotation: A community effort. Fungal Gen. Biol., 46:S2-S13
A. Diano; J. Peeters; J. Dynesen; J. Nielsen (2009)
Physiology of Aspergillus niger in oxygen-limited continuous cultures: Influence of aeration, carbon source concentration and dilution rate. Biotechnol. Bioeng. 103:956-965
2008
J. Maury; M. A. Asadollahi; K. Møller; M. Schalk; A. Clark; L. R. Formenti; J. Nielsen (2008)
Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae. FEBS Let. 582:4032-4038
M. Rocha; P. Maia; R. Mendes; J. P. Pinto; E. C. Ferreira; K. Patil; J. Nielsen; I. Rocha (2008)
Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics 9:499
Petranovic D, Nielsen J. (2008)
Can yeast systems biology contribute to the understanding of human disease?
Trends Biotechnol. 2008 Nov;26(11):584-90.
M. J. Herrgård; N. et al.; J. Nielsen; D. B. Kell (2008)
A consensus yeast metabolic network obtained from a community approach to systems biology. Nature Biotechnol. 26:1155-1160
J. Højer-Pedersen; J. Smedsgaard; J. Nielsen (2008)
The yeast metabolome addressed by electrospray ionization mass spectrometry: Initiation of a mass spectral library and its application for metabolic footprinting by direct infusion mass spectrometry. Metabolomics, 4:393-405
I. Borodina; J. Siebring; J. Zhang; C. P. Smith; G. van Keulen; L. Dijkhuizen; J. Nielsen (2008)
Antibiotic overproduction in Streptomyces coelicolor A3(2) mediated by phosphofructokinase deletion. J. Biol. Chem. 283:25186-25199
F. Pizarro; M. C. Jewett; J. Nielsen; E. Agosin (2008)
Growth temperature exerts a differential physiological and transcriptional response in laboratory and wine strains of Saccharomyces cerevisiae. Appl. Environ. Microbiol., 74:6358-6368
I. Nookaew; M. C. Jewett; A. Meecha; C. Thammarongtham; K. Laoteng; S. Cheevadhanarak; J. Nielsen; S.Bhumiratana (2008)
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Sys. Biol. 2:71
S. Wattanachaisaereekul; A. E. Lantz; M. L. Nielsen; J. Nielsen (2008)
Production of the polyketide 6-MSA in yeast engineered for increased malonyl-CoA supply. Metabolic Eng. 10:246-254
A. Fazio; M. C. Jewett; P. Daran-Lapujade; R. Mustacchi; R. Usaite; J. Pronk; C. Workman; J. Nielsen (2008)
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design. BMC Genomics 9:341
W. Vongsangnak; P. Olsen; K. Hansen; S. Krogsgaard; J. Nielsen (2008)
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics 9:245
M. R. Andersen; W. Vongsangnak; G. Panagiotou; M. P. Salazar; L. Lehmann; J. Nielsen (2008)
A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species. Proc. Nat. Acad. Sci. 105:4387-4392
G. Panagiotou; M. R. Andersen; T. Grotkjær; T. B. Regueira; G. Hofmann; J. Nielsen; L. Olsson (2008)
Systems analysis unfolds the relationship between the phosphoketolase pathway and growth in Aspergillus nidulans. PLoS One 3:e2847
W. A. de Jongh; C. Bro; S. Ostergaard; B. Regenberg; L. Olsson; J. Nielsen (2008)
The roles of galactitol, galactose-1-phosphate and phosphoglucomutase in galactose-induced toxicity in Saccharomyces cerevisiae. Biotechnol. Bioeng. 101:317-326
H. David; I. Ozcelik; G. Hofmann; J. Nielsen (2008)
Analysis of Aspergillus nidulans metabolism at the genome-scale. BMC Genomics 9:163
J. Thykaer; K. Rueksomtawin; H. Noorman; J. Nielsen (2008)
NADPH-Dependent glutamate dehydrogenase in Penicillium chrysogenum is involved in regulation of β-lactam production. Microbiol. 154:1242-1250
A. P. Oliveira; K. Patil; J. Nielsen (2008)
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Systems Biol. 2:17
M. R. Andersen; M. L. Nielsen; J. Nielsen (2008)
Metabolic model integration of the bibliome, genome, metabolome and reactorme of Aspergillus niger. Mol. Systems Biol. 4:178
M. Asadollahi; J. Maury; K. Møller; K. F. Nielsen; M. Schalk; A. Clark; J. Nielsen (2008)
Production of plant sesquiterpenes in Saccharomyces cerevisiae: Effect of ERG9 repression on sesquiterpene biosynthesis. Biotechnol. Bioeng. 99:666-677
W. de Jongh; J. Nielsen (2007)
Enhanced citrate production through gene insertion in Aspergillus niger. Met. Eng. 10:87-96
R. Usaite; J. Wohlschlegel; J. D. Venable; S. K. Park;J. Nielsen; L. Olsson; John R. Yates III (2008)
Characterization of global yeast quantitative proteome data generated from the wild type and glucose repression Saccharomyces cerevisiae strains: the comparison of two quantitative algorithms. J. Proteom Res. 7:266-275
R. Usaite; J. Nielsen; L. Olsson (2008)
Physiological characterization of glucose repression in the strains with SNF1 and SNF4 genes deleted. J. Biotechnol. 133:73-81
V. Mapelli; L. Olsson; J. Nielsen (2008)
Metabolic footprinting in microbiology: methods and applications in functional genomics and biotechnology. Trends Biotechnol., in press
J. Nielsen; M. Jewett (2008)
Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res. 8:122-131
K. R. Kjeldsen; J. Nielsen (2008)
In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network. Biotechnol. Bioeng. 102:583-597
2007
M. J. van der Werf; R. Takors; J. Smedsgaard; J. Nielsen; T. Ferenci; J. C. Portais; C. Wittmann; M. Hooks; A. Tomassini; M. Oldiges; J. Fostel; U. Sauer (2007)
Standard reporting requirements for biological samples in metabolomics experiments: Microbial and in vitro biology experiments. Metabolomics 3:189-194
M. L. Nielsen; W. A. de Jongh; S. L. Meijer; J. Nielsen; U. Mortensen (2007)
Transient marker system for iterative gene targeting of a prototrophic fungus. Appl. Environ. Microbiol. 73:7240-7245
I. Nookaew; A. Meechai; C. Thammarongtham; K. Loateng; V. Ruanglek; S. Cheevadhanarak; J. Nielsen; S. Bhumiratana (2007)
Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks. Biotechnol. Bioeng. 97:1535-1549
S. Meier; G. Panagiotou; L. Olsson; J. Nielsen (2007)
Physiological characterization of xylose metabolism in Aspergillus niger under oxygen limited conditions. Biotechnol. Bioeng., in press
J. Thykaer; J. Nielsen (2007)
Evidence, through C13-labelling analysis, of phosphoketolase activity in fungi. Proc. Biochem. 42:1050-1055
T. Cakir; B. Kirdar; Z. I. Onsan; K. O. Ulgen; J. Nielsen (2007)
Effect of carbon source pertubations on transcriptional regulation of metabolic fluxes in Saccharomyces cierevisia. BMC Systems Biol. 1:18
K. Y. Arga; Z. I. Onsan; B. Kirdar; K. O. Ulgen; J. Nielsen (2007)
Understanding signaling in yeast: Insights from network analysis. Biotechnol. Bioeng. 97:1246-1258
C. J. Baxter; H. Redestig; N. Schauer; D.Repsilber; K. R. Patil; J. Nielsen; J. Selbig; J. Liu; A. R. Fernie; L. J. Sweetlove (2007)
The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Phys. 143:312-325
S. Wattanachaisaereekul; A. Eliasson Lantz; M. L. Nielsen; O. S. Andresson; J. Nielsen (2007)
Optimization of heterologous production of the polyketide 6-MSA in Saccharomyces cerevisiae. Biotechnol. Bioeng. 97:893 900
S. Mass; S. G. Villas-Boas; M. E. Hansen; M. Ålesson; J. Nielsen (2007)
A comparison of direct infusion MS and GC-MS for metabolic footprinting of yeast mutants. Biotechnol. Bioeng. 96:1014-1022
H. J. Pel et al. (2007)
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS513.88. Nature Biotech. 25:221-231
G. N. Vemuri; M. A. Eiteman; J. E. McEwen; L. Olsson; J. Nielsen (2007)
Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae. Proc. Nat. Acad. Sci.. 104:2402-2407
S. L. Westergaard; A. P. Oliveira; C. Bro; L. Olsson; J. Nielsen (2007)
A systems biology approach to study glucose repression in the yeast Saccharomyces cerevisiae. Biotechnol. Bioeng. 96:134-145
S. Rokem; A. Eliasson; J. Nielsen (2007)
Systems biology of secondary metabolism in microorganisms. Nat. Prod. Rep. 24:1262-1287
2006
T. Cakir; K. R. Patil; Z. I. Önsan; K. Ö. Ülgen; B. Kirdar; J. Nielsen (2006)
Integration of metabolome data with metabolic networks reveals reporter reactions. Mol. Systems Biol. 2:50
H. David; G. Hofmann; A. P. Oliveira; H. Jarmer; J. Nielsen (2006)
Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans. Genome Biol. 7:R108
B. Regenberg; T. Grotkjær; O. Winther; A. Fausbøll; M. Åkesson; C. Bro; L. K. Hansen; S. Brunak; J. Nielsen (2006)
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol. 7:R107
A. Diano; S. Bekker-Jensen; J. Dynesen; J. Nielsen (2006)
Polyol synthesis in Aspergillus niger: Influence of oxygen availability, carbon and nitrogen sources on the metabolism. Biotechnol. Bioeng. 94:899-908
R. Usaite; K. R. Patil; T. Grotkjær; J. Nielsen; B. Regenberg (2006)
Globl transcriptional and physiological responses of Saccharomyces cerevisiae to ammoniu, L-alanine or L-glutamine limitation. Appl. Environ. Microbiol. 72:6194-6203
V. Raghevendran; K. R. Patil; L. Olsson; J. Nielsen (2006)
Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae. J. Biol. Chem. 281:12308-12314
J. Mogensen; H. B. Nielsen; G. Hofmann; J. Nielsen (2006)
Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and DcreA mutant during growth on glucose and ethanol. Fung. Gen. Bio. 43:593-603
R. Mustachi; S. Hohmann; J. Nielsen (2006)
Yeast systems biology to unravel the network of life. Yeast 23:227-238
C. Bro; B. Regenberg; J. Förster; J. Nielsen (2006)
In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Met. Eng. 8:102-111
N. Eckert-Boulet; K. Larsson; B. Wu; P. Poulsen; B. Regenberg; J. Nielsen; M. Kielland-Brandt (2006)
Deletion of RTS1, encoding a regulatory subunit of protein phosphatase 2A, results in constitutive amino acid signaling via increased Stp1p processing. Eukaryotic Cell 5:174-179
T. Grotkjær; O. Winther; B. Regenberg; J. Nielsen; L. K. Hansen (2006)
Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm. Bioinformatics 22:58-67
M. C. Jewett; G. Hofmann; J. Nielsen (2006)
Fungal metabolite analysis in genomics and phenomics. Curr. Op. Biotechnol. 17:1-7
2005
S. G. Villas-Bôas; J. H. Pedersen; M. Åkesson; J. Smedsgaard; J. Nielsen (2005)
Global metabolite analysis of yeast: evaluation of sample preparation methods. Yeast 22:1155-1169
K. R. Patil; I. Rocha; J. Förster; J. Nielsen (2005)
Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6:308
T. Grotkjær; P. Christakopoulos; J. Nielsen ; L. Olsson (2005)
Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains. Met. Eng. 7:437-444
M. C. Jewett; A. P. Oliveira; K. R. Patil; J. Nielsen (2005)
The role of high-throughput transcriptome analysis in metabolic engineering. Biotechnol. Bioproc. Eng. 10:385-399
V. Raghevendran; J. Nielsen; L. Olsson (2005)
Teaching microbial physiology using glucose repression phenomenon in Baker’s yeast as an example. Biochem. Mol. Biol. Edu. 33:404-410
H. David; A. M. Krogh; C. Roca; M. Åkesson; J. Nielsen (2005)
CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose. Microbiol. 151:2209-2221
C. Bro; S. Knudsen; B. Regenberg; L. Olsson; J. Nielsen (2005)
Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: Example of transcript analysis as a tool in inverse metabolic engineering. Appl. Environ. Microbiol. 71:6465-6472
A. P. Oliveira; J. Nielsen; J. Förster (2005)
Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol. 5:39
I. Borodina; P. Krabben; J. Nielsen (2005)
Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res.15:820-829
T. Seker; K. Møller; J. Nielsen (2005)
Analysis of acyl CoA ester intermediates of the mevalonate pathway in Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 67:199-124
N. Eckert- Boulet; B. Regenberg; J. Nielsen (2005)
Grr1p is required for transcriptional indusction of amino acid permease genes and proper transcriptional regulation of genes in carbon metabolism of Saccharomyces cerevisiae. Curr. Genet. 47:139-149
S. G. Villas-Bôas; J. F. Moxley; M. Åkesson; G. Stephanopoulos; J. Nielsen (2005)
High-throughput metabolic state analysis: The missing link in integrated functional genomics of yeasts. Biochem. J. 388:669-677
S. G. Villas-Bôas; M. Åkesson; J. Nielsen (2005)
Biosynthesis of glyoxylate from glycine in Saccharomyces cerevisiae. FEMS Yeast Res. 5:703-709
I. Borodina, C. Schöller, A. Eliasson, J. Nielsen (2005)
Metabolic network analysis of Streptomyces tenebrarius, a Streptomyces with Entner-Doudoroff pathway. Appl. Environ. Microbiol. 71:2294-2302
K. R. Patil, J. Nielsen (2005)
Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Nat. Acad. Sci. 102:2685-2689
J. Smedsgaard, J. Nielsen (2005)
Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics. J. Exp. Bot. 56:273-286
G. Panagiotou, S. G. Villas-Boas, P. Christakopoulos, J. Nielsen, L. Olsson (2005)
Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. J. Biotechnol. 115:425-434
J. Nielsen; S. Oliver (2005)
The next wave in metabolome analysis. Trends Biotechnol. 23:544-546
S. G. Villas-Bôas; S. Mas; M. Åkesson; J. Smedsgaard; J. Nielsen (2005)
Mass spectrometry in metabolome analysis. Mass Spec. Rev. 24:613-646
I. Borodina; J. Nielsen (2005)
From genomes to in silico cells via metabolic networks. Curr. Op. Biotechnol. 16:1-6
2004
N. Gunnarson; P. Bruheim; J. Nielsen (2004)
Glucose metabolism in the antibiotic producing Actinomycete Nonomuiaea sp. Biotechnol. Bioeng. 88: 652-663
C. Cannizzaro; B. Christensen; J. Nielsen; U. von Stockar (2004)
Metabolic network analysis on Phaffia rhodozyma yeast using ¹³C-labeled glucose and gas chromatography-mass spectrometry. Met. Eng. 6:340-351
W. Prathumpai; S. J. Flitter; M. McIntyre; J. Nielsen (2004)
Lipase production by recombinant strains of Aspergillus niger expressing a lipase-encoding gene from Thermomyces lanuginosus. Appl. Microbiol. Biotechnol. 65:714-719
B. Regenberg; U. Krühne; M. Beyer; L. H. Pedersen; M. Simón; O. R.T. Thomas; J. Nielsen; T. Ahl (2004)
Use of laminar flow patterning for miniaturised biochemical assays. Lab. Chip 4:654-657
M. M. dos Santos; V. Raghevendran; P. Kötter; L. Olsson; J. Nielsen (2004)
Manipulation of the malic enzyme in Saccharomyces cerevisiae for increasing NADPH production capacity aerobically in different cellular compartments. Met. Eng. 6:352-363
T. Grotkjær; J. Nielsen (2004)
Enhancing yeast transcription analysis through integration of heterogeneous data. Cur. Genomics 5:673-686
V. Raghevendran; A. K. Gombert; B. Christensen; P. Kötter; J. Nielsen (2004)
Phenotypic characterization of glucose repression mutants of Saccharomyces cerevisiae using experiments with ¹³C-labelled glucose. Yeast 21:769-779
S. L. Westergaard; C. Bro; L. Olsson; J. Nielsen (2004)
Elucidation of the role of Grr1p on glucose sensing by Saccharomyces cerevisiae through genome-wide transcription analysis. FEMS Yeast Res. 5:193-204
N. Eckert-Boulet; P. S. Nielsen; C. Friis; M. M. dos Santos; J. Nielsen; M. C. Kielland-Brandt; B. Regenberg (2004)
Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp1p and Stp2p. Yeast 21: 635-648
N. Gunnarson; U. H. Mortensen; M. Sosio; J. Nielsen (2004)
Identification of the Entner-Doudoroff pathway in an antibiotic producing actinomycete species. Mol Microbiol 52: 895-902
G. G. Larsen; K. F. Appel; A.-M. Wolff, J. Nielsen; J. Arnau (2004)
Characterization of the Mucor circinelloides regulated promoter gpd1P and construction of a constitutive derivative. Curr. Genet. 45:225-234
M. Åkesson; J. Förster; J. Nielsen (2004)
Integration of gene expression data into genome-scale metabolic models. Met. Eng, 6:285-293
T. Grotkjær; M. Åkesson; B. Christensen; A. K. Gombert; J. Nielsen (2004)
Impact of transamination reactions and protein turnover on labeling dynamics in ¹³C-labelling experiments. Biotechnol. Bioeng. 86:209-216
K. Møller; C. Bro; R. B. Langkjær; J. Piskur; J. Nielsen; L. Olsson (2004)
Pyruvate decarboxylases from the petite-negative yeast Saccharomyces kluyveri. Mol. Genet. Genomics 270:558-568
C. Bro; J. Nielsen (2004)
Impact of ‘Ome’ analysis on inverse metabolic engineering. Met. Eng. 6:204-211
W. Prathumpai; M. McIntyre; J. Nielsen (2004)
The effect of CreA in glucose and xylose catabolism in Aspergillus nidulans. Appl. Microbiol. Biotechnol. 63:748-753
C. Bro; B. Regenberg; J. Nielsen (2004)
Genome-wide transcriptional response of a Saccharomyces cerevisiae strain with an altered redox metabolism. Biotechnol. Bioeng. 85:269-276
T. L. Lübbehüsen, V. G. Polo, S. Rossi, J. Nielsen, S. Moreno, M. McIntyre, J. Arnau (2004)
Protein kinase A is involved in the control of morphology and branching during aerobic growth in Mucor circinelloides. Microbiol. 150:143-150
T. L. Lübbehüsen, J. Nielsen, M. McIntyre (2004)
Aerobic and anaerobic ethanol production by Mucor circinelloides during submerged growth. Appl. Microbiol. Biotechnol. 63:543-548
K. Patil; M. Åkesson; J. Nielsen (2004)
Use of genome scale microbial models for metabolic enginereing. Curr. Op. Biotechnol. 15:64-69
2003
J. Nielsen (2003)
It is all about metabolic fluxes. J. Bacteriol., 185:7031-7035
S. G. Villas-Boas; D. G. Delicado; M. Åkesson; J. Nielsen (2003)
Simultaneous analysis of amino and nonamino organic acids as methyl chloroformate derivatives using gas chromatography-mass spectrometry. Anal. Biochem. 322:134-138
J. Dynesen; J. Nielsen (2003)
Branching is coordinated with mitosis in growing hyphae of Aspergillus nidulans. Fungal Gen. Biol. 40:15-24
I. Famili; J. Förster; J. Nielsen; B. Palsson (2003)
Saccharomyces cerevisiae phenotypes can be predicted using constraint based analysis of a genome-scale reconscructed metabolic network. Proc. Nat. Acad, Sci. 100:13134-13139
M. M. dos Santos; G. Thygesen; P. Kötter; L. Olsson; J. Nielsen (2003)
Aerobic physiology of redox-engineered Saccharomyces cerevisiae strains modified in the ammonium assimilation for increased NADPH availability. FEMS Yeast Res. 4:59-68
H. David; M. Åkesson; J. Nielsen (2003)
Reconstruction of the central carbon metabolism of Aspergillus niger. Eur. J. Biochem. 270: 4243-4253
W. Prathumpai; J. B. Gabelgaard; P. Wanchanthuek; P. J. I. van de Vondervoort; M. J. L. de Groot; M. McIntyre; J. Nielsen (2003)
Metabolic control analysis of xylose catabolism in Aspergillus. Biotechnol. Prog. 19:1136-1141
C. Bro; B. Regenberg; G. Lagniel; J. Labarre; M. Montero-Lomeli; J. Nielsen (2003)
Transcriptional, proteomics and metabolic response to lithium in galactose-grown yeast cells. J. Biol. Chem. 278:32141-32149
W. Prathumpai; M. McIntyre; J. Nielsen (2004)
The effect of CreA in glucose and xylose catabolism in Aspergillus nidulans. Appl. Microbiol. Biotechnol. 63:748-753
C. Roca; J. Nielsen; L. Olsson (2003)
Metabolic engineering of ammonium assimilation in xylose fermenting Saccharomyces cerevisiae improves ethanol production. Appl. Env. Microbiol. 69:4732-4736
T. L. Lübbehüsen; J. Nielsen; M. McIntyre (2003)
Morphology and physiology of the dimorphic fungus Mucor circinelloides (syn. M. racemosus) during anaerobic growth. Mycol. Res. 107:223-230
J. Förster; I. Famili; B. Ø. Palsson; J. Nielsen (2003)
Large-scale Evaluation of in silico Gene Deletions in Saccharomyces cerevisiae. Omics J. Integrative Biol. 7:193-202
M. M. dos Santos; A. K. Gombert; B. Christensen; L. Olsson; J. Nielsen (2003)
Identification of in vivo enzyme activities in the co-metabolism of glucose and acetate by Saccharomyces cerevisiae using ¹³C-labeled substrates. Eukar. Cell. 2:599-608
J. Dynesen; J. Nielsen (2003)
Surface hydrophobicity of Aspergillus nidulans conidiophores and its role in pellet formation. Biotechnol. Prog. 19:1049-1052
N. Gunnarsson; P. Bruheim; J. Nielsen (2003)
Production of the glycopeptide antibiotic A40926 by Nonomuria sp. ATCC 39727: influence of medium composition in batch fermentation. J. Ind. Microbiol. Biotechnol. 30:150-156
J. Robin; S. Bonneau; D. Schipper; H. Noorman; J. Nielsen (2003)
Influence of the adipate and dissolved oxygen concentrations on the b-lactams production during continuous cultivations of a Penicillium chrysogenum strain expressing the expandase gene from Streptomyces clavuligerus. Metabol. Eng. 5:42-48
T. L. Lübbehüsen; J. Nielsen; M. McIntyre (2003)
Characterization of the Mucor circinelloides life cycle by on-line image analysis. J. Appl. Microbiol. 95:1152-1160
J. Förster; I. Famili; P. Fu; B. Ø. Palsson; J. Nielsen (2003)
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13:244-253
J. Robin; P. Bruheim; M. L. Nielsen; H. Noorman; J. Nielsen (2003)
Continuous cultivations of Penicillium chrysogenum strain expressing the expandase gene from Streptomyces clavuligerus: Kinetics of adipoyl-7-aminodeacetoxycephalosporanic acid and by-product formation. Biotechnol. Bioeng. 83:361-368
J. Robin; G. Lettier; M. McIntyre; H. Noorman; J. Nielsen (2003)
Continuous cultivations of Penicillium chrysogenum strain expressing the expandase gene from Streptomyces clavuligerus: Growth yields and morphological characterisation. Biotechnol. Bioeng. 83:353-360
T. Christiansen; S. Michaelsen; M. Wümpelmann; J. Nielsen (2003)
Production of Savinase and population viability of Bacillus clausii during high cell density fed-batch cultivations. Biotechnol. Bioeng. 83:344-352
C. Müller; K. Hansen; P. Szabo; J. Nielsen (2003)
Effect of chitin synthesis on mycelial morphology and culture viscosity in Aspergillus oryzae. Biotechnol. Bioeng. 81:525-534
G. Hofmann; M. McIntyre; J. Nielsen (2003)
Fungal genomics beyond Saccharomyces cerevisiae. Curr. Op. Biotechnol. 14:226-231
J. Thykær; J. Nielsen (2003)
Metabolic engineering of b-lactam production. Metabolic Eng. 5:56-69
2002
M. D. W. Piper; P. Daran-Lapujade; C. Bro; B. Regenberg; S. Knudsen; J. Nielsen; J. T. Pronk (2002)
Reproducibility of oligonucleotide microarray transcriptome analysis: an interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 277:37001-37008
E. Jonsbu; M. McIntyre; J. Nielsen (2002)
The influence of carbon sources and morphology on nystatin production by Streptomyces noursei. J. Biotechnol. 95:133-144
B. Christensen; A. K. Gombert; J. Nielsen (2002)
Analysis of flux estimates based on ¹³C-labeling experiments. Eur. J. Biochem. 269:2795-2800
C. Müller; C. M. Hjort; K. Hansen; J. Nielsen (2002)
Altering the expression of two chitin synthase genes differentially affects the growth and morphology of Aspergillus oryzae. Microbiology 148:4025-4033
J. Zaldivar; A. Borges; B. Johansson; H. P. Smits; S. G. Villas-Boas; J. Nielsen; L. Olsson (2002)
Fermentation performance and intracellular metabolite patterns in laboratory and industrial xylose fermenting Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 59:436-442
J. Förster; A. K. Gombert; J. Nielsen (2002)
A functional genomics approach using metabolomics and in silico pathway analysis. Biotechnol. Bioengi 79:703-712
T. Christiansen; J. Nielsen (2002)
Production of extracellular protease and glucose uptake in Bacillus clausii in steady state and transient continuous cultures. J. Biotechnol. 97:265-273
K. Møller; C. Bro; J. Piskur; J. Nielsen; L. Olsson (2002)
Steady-state and transient-state analysis of aerobic fermentation in Saccharomyces kluyveri. FEMS Yeast Res. 2:233-244
N. B. S. Jensen; B. Christensen; J. Nielsen; J. Villadsen (2002)
The simultaneous biosynthesis and uptake of amino acids by Lactococcus lactis studied by ¹³C labelling experiments. Biotechnol. Bioeng. 78:11-16
J. Nielsen; L. Olsson (2002)
An expanded role for microbial physiology in metabolic engineering and functional genomics: Moving towards systems biology. FEMS Yeast Res. 2:175-181
A. G. Vara; A. Hochkoeppler; J. Nielsen; J. Villadsen (2002)
Production of teicoplanin by Actinoplanes teichomyceticus in continuous fermentation. Biotechnol. Bioeng. 77:589-598
C. Müller; M. McIntyre; K. Hansen; J. Nielsen (2002)
Metabolic engineering of the morphology of Aspergillus oryzae by altering chitin synthesis. Appl. Environ. Microbiol. 68:1827-1836
B. Christensen; J. Nielsen (2002)
Reciprocal ¹³C-labeling: A method for investigating the catabolism of co-substrates. Biotechnol. Prog. 18:163-166
T. Christiansen; J. Nielsen (2002)
Growth energetics of an alkaline serine protease producing strain of Bacillus clausii during continuous cultivation. Bioproc. Biosystems Eng. 24:329-339
M. McIntyre; J. Breum; J. Arnau; J. Nielsen (2002)
Growth physiology and dimorphism of Mucor circinelloides (syn. racemosus) during submerged batch cultivation. Appl. Microbiol. Biotechnol. 58:495-502
J. Thykaer; B. Christensen; J. Nielsen (2002)
Metabolic network analysis of an adipoyl-7-ADCA producing strain of Penicillium chrysogenum: Elucidation of adipate degradation. Metabolic Eng. 4:151-158
T. Christiansen; B. Christensen; J. Nielsen (2002)
Metabolic network analysis of Bacillus clausii on minimal and semi-rich medium using ¹³C-labeled glucose. Metabolic Eng. 4:159-169
2001
K. Møller; B. Christensen; J. Förster; J. Piskur; J. Nielsen; L. Olsson (2001)
Aerobic glucose metabolism of Saccharomyces kluyveri: Growth, metabolite production and quantification of metabolic fluxes. Biotechnol. Bioeng. 77:186-193
J. Robin; M. Jacobsen; M. Beyer; H. Noorman; J. Nielsen (2001)
Physiological characterisation of Penicillium chrysogenum strains expressing the expandase gene from Streptomyces clavuligerus during batch cultivations. Growth and adipoyl-7-ADCA production. Appl. Microbiol. Biotechnol. 57:357-362
T. C. Zangirolami; M. Carlsen; J. Nielsen; S. B. Jørgensen (2002)
Growth and enzyme production during continuous cultures of a high amylase-producing variant of Aspergillus oryzae. Brazilian J. Chem. Eng. 19:55-68
T. Agger; J. B. Petersen; S. M. O’Connor; R. L. Murphy; J. M. Kelly; J. Nielsen (2002)
Physiological characterisation of recombinant Aspergillus nidulans strains with different creA genotypes expressing A. oryzae a-amylase. J. Biotechnol. 92:279-285
M. Carlsen; J. Nielsen (2001)
Influence of carbon source on a-amylase production by Aspergillus oryzae. Appl. Microbiol. Biotechnol. 57:346-349
E. Jonsbu; B. Christensen; J. Nielsen (2001)
Changes in in vivo fluxes through central metabolic pathways during production of nystatin by Streptomyces noursei in batch culture. Appl. Microbiol. Biotechnol. 56:93-100
B. Christensen; T. Christiansen; A. K. Gombert; J. Thykær; J. Nielsen (2001)
A simple and robust method for estimation of the flux through the pentose phosphate pathway in micro-organisms. Biotechnol. Bioeng. 74:517-523
K. Møller; L. D. Tidemand; J. R. Winther; L. Olsson; J. Piskur; J. Nielsen (2001)
Production of a heterologous proteinase A by Saccharomyces kluyveri. Appl. Microbiol. Biotechnol. 57:216-219
T. L. Nissen; M. Anderlund; M. C. Kielland-Brandt; J. Nielsen; J. Villadsen (2001)
Expression of a cytoplasmic transhydrogenase in Saccharomyces cerevisiae results in formation of 2-oxoglutarate due to depletion of the NADPH pool. Yeast 18:19-32
S. Ostergaard; K. O. Walløe; C. S. G. Gomes; L. Olsson; J. Nielsen (2001)
The impact of GAL6, GAL80, and MIG1 on glucose control of the GAL system in Saccharomyces cerevisiae. FEMS Yeast Research. 1:47-55
S. Ostergaard; L. Olsson; J. Nielsen (2001)
In vivo dynamics of galactose metabolism in Saccharomyces cerevisiae: Metabolic fluxes and metabolite levels. Biotechnol. Bioeng. 73:412-425
A. K. Gombert; M. M. dos Santos; B. Christensen; J. Nielsen (2001)
Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae at different conditions of glucose repression. J. Bacteriol. 183:1441-1451
M. McIntyre; J. Dynesen; J. Nielsen (2001)
Morphological characaterization of Aspergillus nidulans: Growth, septation and fragmentation. Microbiol. 147:239-246
E. Jonsbu; T. Elingsen; J. Nielsen (2001)
Effects of nitrogen sources on cell growth and production of nystatin by Streptomyces noursei J. Antibiot. 53:1354-1362
S. Ostergaard; L. Olsson; M. Johnston; J. Nielsen (2000)
Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network. Nature Biotechnol. 18:1283-1286
T. Agger; A. Spohr; J. Nielsen (2001)
a-Amylase production in high cell density submerged cultivations of Aspergillus oryzae and Aspergillus nidulans. Appl. Microbiol. Biotechnol. 55:81-84
J. Zaldivar; J. Nielsen; L. Olsson (2001)
Metabolic engineering of biocatalysts for fuel ethanol production. Appl. Microbiol. Biotechnol. 56:17-34
J. Nielsen (2001)
Metabolic engineering. Appl. Microbiol. Biotechnol. 55:263-283
2000
L. F. Bautista; M. Hentzer; A. Santerre Henriksen; A. Aleksenko; J. Nielsen (2000)
Antisense silencing of the creA gene in Aspergillus nidulans. Appl. Environ. Microbiol. 66:4579-4581
H. Aae Theilgaard; M. van den Berg; C. Mulder; R. A. L. Bovenberg; J. Nielsen (2000)
Quantitative analysis of Penicillium chrysogenum Wis54-1255 transformants over-expressed in the penicillin biosynthetic genes. Biotechnol. Bioeng. 72:379-388
H. P. Smits; J. Hauf; S. Müller; T. J. Hobley; F. K. Zimmermann; B. Hahn-Hägerdal; J. Nielsen; L. Olsson (2000)
Simultaneous over-expression of enzymes of the lower part of glycolysis can enhance the fermentative capacity of Saccharomyces cerevisiae. Yeast 16:1325-1334
J. Nielsen (2000)
The role of metabolic engineering in the improvement of industrial processes. Thai J. Biotechnol. 2:14-25
B. Christensen; J. Thykær; J. Nielsen (2000)
Metabolic characterization of high and low yielding strains of Penicillium chrysogenum. Appl. Microbiol. Biotechnol. 54:212-217
B. Christensen; J. Nielsen (2000)
Metabolic network analysis on Penicillium chrysogenum using 13C-labelled glucose. Biotechnol. Bioeng. 68:652-659
T. C. Zangirolami; M. Carlsen; J. Nielsen; S. B. Jørgensen (2000)
Selection and characterization of a high a-amylase-producing variant in glucose-limited continuous cultures of Aspergillus oryzae. Myc. Res. 104:1241-1249
J. P. van Dijken et al. (2000)
An inter-laboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enz. Microb. Technol. 26:706-714
A. Heydorn; B. O. Pedersen; J. Ø. Duus, S. Bergmann; T. Suhr-Jessen; J. Nielsen (2000)
Biosynthetic studies of the glycopeptide teicoplanin by 1H and 13C NMR. J. Biol. Chem. 275:6201-6206
T. L. Nissen; M. C. Kielland-Brandt; J. Nielsen; J. Villadsen (2000)
Optimisation of ethanol production in Sacchaoromyces cerevisiae by metabolic engineering of the ammonia assimilation. Metabol. Eng. 2:69-77
T. L. Nissen; C. W. Hamann; M. C. Kielland-Brandt; J. Nielsen; J. Villadsen (2000)
Anaerobic and batch cultivations of Saccharomyces cerevisiae mutants impaired in glycerol synthesis. Yeast 16:463-474
L. Olsson; J. Nielsen (2000)
The role of metabolic engineering in the improvement of Saccharomyces cerevisiae: Utilization of industrial media. Enz. Microbiol. Technol. 26:785-792
H. Pedersen; C. Hjort; J. Nielsen (2000)
Cloning and characterization of oah, the gene encoding oxaloacetate hydrolase from Aspergillus niger. Mol. Gen. Genetics. 263:281-286
S. Ostergaard; C. Roca; B. Rønnow; J. Nielsen; L. Olsson (2000)
Physiological studies in aerobic batch cultivations of Saccharomyces cerevisiae strains harbouring the MEL1 gene. Biotechnol. Bioeng. 68:252-259
H. Pedersen; M. Beyer; J. Nielsen (2000)
Glucoamylase production in batch, chemostat and fed-batch cultivations by an industrial strain of Aspergillus niger. Appl. Microbiol. Biotechnol. 53:272-277
H. Pedersen; B. Christensen; C. Hjort; J. Nielsen (2000)
Construction and characterization of an oxalic acid non-producing strain of Aspergillus niger. Metabol. Eng. 2:34-41
C. Müller; A. Spohr; J. Nielsen (2000)
Role of substrate concentration on mitosis and hyphal extension of Aspergillus. Biotechnol. Bioeng. 67:390-397
T. Agger; J. Nielsen (1999)
Genetically structured modelling of protein production in filamentous fungi. Biotechnol. Bioeng. 66:164-170
H. Pedersen; J. Nielsen (2000)
The influence of nitrogen sources on the a-amylase productivity of Aspergillus oryzae in continuous culture. Appl. Microb. Biotechnol. 53:278-281
A. K. Gombert; J. Nielsen (2000)
Mathematical modelling of metabolism. Curr. Opinion Biotechnol. 11:180-186
S. Ostergaard; L. Olsson; J. Nielsen (2000)
Metabolic engineering of Saccharomyces cerevisiae. Microb. Mol. Biol. Rev. 64:34-50
1999
B. Rønnow; L. Olsson; J. Nielsen; J. D. Mikkelsen (1999)
Derepression of galactose metabolism in melibiase producing baker’s and distillers’ yeast J. Biotechnol. 72:213-228
A. Santerre Henriksen; M. Carlsen; H. de Bang; J. Nielsen (1999)
Kinetics of a-amylase secretion in Aspergillus oryzae. Biotechnol. Bioeng. 65:76-82
B. Christensen; J. Nielsen (1999)
Isotopomer analysis using GC-MS. Metabol. Eng. 1:282-290
K. Schmidt; L. C. Nørregaard; B. Pedersen; A. Meissner; J. Ø. Duus; J. Nielsen; J. Villadsen (1999)
Quantification of intracellular metabolic fluxes from fractional enrichment measurements and isotopomer analysis of ¹³C labelled biomass components. Metabol. Eng. 1:166-179
M. Anderlund; T. L. Nissen; J. Nielsen; J. Villadsen; J. Rydström; B. Hahn-Hägerdal; M. C. Kielland-Brandt (1999)
Expression of the E. coli pntA and pntB genes encoding nicotinamide nucleotide transhydrogenase in Saccharomyces cerevisiae and its effect on product formation during anaerobic glucose fermentation. Appl. Environ. Microbiol. 65:2333-2340
C. J. L. Klein; J. J. Rasmussen; B. Rønnow; L. Olsson; J. Nielsen (1999)
Investigation of the impact of MIG1 and MIG2 on the phyiology of Saccharomyces cerevisiae. J. Biotechnol. 68:197-212
H. Aae. Theilgaard; J. Nielsen (1999)
Metabolic control analysis of the penicillin biosynthetic pathway: The influence of the LLD-ACV:bisACV ratio on the flux control. Antonie van Leeuvenhoek 75:145-154
A. Heydorn; T. Suhr-Jessen; J. Nielsen (1999)
Growth and production kinetics of a teicoplanin producing strain of Actinoplanes teicomyceticus. J. Antibio. 52:40-44
T. Christiansen; A. Spohr; J. Nielsen (1999)
On-line study of growth kinetics of single hyphae of Aspergillus oryzae in a flow-through cell. Biotechnol. Bioeng. 63:147-153
A. L. Santerre Henriksen; S. Even; C. Müller; P. J. Punt; C. A. M. J. J. van den Hondel; J. Nielsen (1999)
Study of the glucoamylase promoter in Aspergillus niger using green fluorescence protein. Microbiol. 145:729-734
H. Pedersen; M. Carlsen; J. Nielsen (1999)
Identification of enzymes and quantification of metabolic fluxes in the wild type and in a recombinant strain of Aspergillus oryzae strain. Appl. Environ. Microbiol. 65:11-19
A. Aleksenko; W. Liu; Z. Gojkovic; J. Nielsen; J. Piskur (1999)
Structural and transcriptional analysis of the pyrABCN, pyrC, and PyrF genes in Aspergillus nidulans and the evolutionary origin of fungal dihydroorotases. Mol. Microbiol. 33:599-611
1998
S. Ostergaard; H. B. Aa. Theilgaard; J. Nielsen (1998)
Identification and purification of O-acetyl-L-serine sulfhydrylase in Penicillium chrysogenum. Appl. Microbiol. Biotechnol. 50:663-668
J. Dynesen; H. P. Smits; L. Olsson; J. Nielsen (1998)
Carbon catabolite repression of invertase during batch cultivations of Saccharomyces cerevisiae: The role of glucose, fructose, and mannose. Appl. Microbiol. Biotechnol. 50:579-582
C. M. Henriksen; J. Nielsen; J. Villadsen (1998)
Modelling of the protonophoric uncoupling by phenoxyacetic acid of the plasma membrane of Penicillium chrysogenum. Biotechnol. Bioeng. 60:761-767
C. M. Henriksen; J. Nielsen; J. Villadsen (1998)
High exogeneous concentrations of phenoxyacetic acid are crucial for a high penicillin V productivity in Penicillium chrysogenum. Microbiol. 144:2001-2006
C. J. L. Klein; L. Olsson; J. Nielsen (1998)
Nitrogen-limited continuous cultivations as a tool to quantify glucose control in Saccharomyces cerevisiae. Enz. Microbial. Technol. 23:91-100
J. Holmalahti; O. Raatikainen; A. von Wright; H. Laatsch; A. Spohr; O. K. Lyngberg; J. Nielsen (1998)
Production of dihydroabikoviromycin by Streptomyces anulatus. Production parameters and chemical characterization of genotoxicity. J. Appl. Microbiol. 85:61-68
H. P. Smits; A. Cohen; T. Buttler; J. Nielsen; L. Olsson (1998)
Clean-up and analysis of sugar phosphates in biological extracts by using solid phase extraction and anion-exchange chromatography with pulsed amperometric detection. Anal. Biochem. 261:36-42
C. K. Klein; L. Olsson; B. Rønnow; J. D. Mikkelsen; J. Nielsen (1998)
Glucose and maltose metabolism in MIG1-disrupted and MAL-constitutive strains of Saccharomyces cerevisiae. Food Technol. Biotechnol. 35:287-292
K. Schmidt; J. Nielsen; J. Villadsen (1999)
Quantitative analysis of metabolic fluxes in E. coli, using 2 dimensional NMR spectroscopy and complete isotopomer models. J. Biotechnol. 71:175-190
A. B. Spohr; C. Dam Mikkelsen; M. Carlsen; J. Nielsen; J. Villadsen (1998)
On-line study of fungal morphology during submerged growth in a small flow-through cell. Biotechnol. Bioeng. 58:541-553
C. M. Henriksen; J. Nielsen; J. Villadsen (1997)
Influence of dissolved oxygen concentration on the penicillin biosynthetic pathway in steady state cultures of Penicillium chrysogenum. Biotechnol. Prog. 13:776-782
T. Agger; A. B. Spohr; M. Carlsen; J. Nielsen (1998)
Growth and product formation of Aspergillus oryzae during submerged cultivations: Verification of a morphologically structured model using fluorescent probes. Biotechnol. Bioeng. 57:321-329
K Schmidt; A. Marx; A. A. de Graaf; W. Wiechert; H. Sahm; J. Nielsen; J. Villadsen (1998)
¹³C Tracer experiments and metabolite balancing for metabolic flux analysis: Comparing two approaches. Biotechnol. Bioeng. 58:254-257
H. B. Aa. Theilgaard; C. M. Henriksen; K. Kristiansen; J. Nielsen (1997)
Purification and characterization of d-(L-a-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS) from Penicillium chrysogenum. Biochem. J. 327:185-191
A. Spohr; M. Carlsen; J. Nielsen; J. Villadsen (1998)
a-Amylase production in recombinant Aspergillus oryzae during fed-batch and continuous cultivations. J. Ferment. Bioeng. 86:49-56
J. Nielsen (1998)
Metabolic Engineering: Techniques for analysis of targets for genetic manipulations. Biotechnol. Bioeng. 58:125-132
J. Nielsen (1998)
The role of metabolic engineering in the production of secondary metabolites. Curr. Opion Microbiol. 1:330-336
C. M. Henriksen; J. Nielsen; J. Villadsen (1998)
Cyclization of a-aminoadipic acid into the d-lactam 6-oxo-piperidine-2-carboxylic acid by Penicillium chrysogenum. J. Antibio. 51:99-106
L. Olsson; U. Schulze; J. Nielsen (1998)
On-line bioprocess monitoring - an academic discipline or an industrial tool? Trends Anal. Chem. 17:88-95
C. Klein; L. Olsson; J. Nielsen (1998)
Glucose control in Saccharomyces cerevisiae.The role of MIG1on metabolic functions. Microbiol 144:13-24
1997
L. Olsson; M. E. Larsen; B. Rønnow; J. D. Mikkelsen; J. Nielsen (1997)
Silencing MIG1 in Saccharomyces cerevisiae: Effects of Antisense MIG1 Expression and MIG1 Gene Disruption. Appl. Environ. Microbiol. 63:2366-2371
L. Olsson; J. Nielsen (1997)
On-line and in-situ monitoring of biomass in submerged cultivations. Trends Biotechnol 15:517-522
J. Nielsen (1996)
Modelling the morphology of filamentous microorganisms. Trends Biotechnol. 14:438-443
A. B. Spohr; M. Carlsen; J. Nielsen; J. Villadsen (1997)
Morphological characterization of recombinant strains of Aspergillus oryzae producing a-amylase during batch cultivations. Biotechnol. Letters 19:257-261
P. Krabben; J. Nielsen; M. L. Michelsen (1997)
Analysis of single hyphal growth and fragmentation in submerged cultures using a population model. Chem. Eng. Sci. 52:2641-2652
M. Carlsen; K. V. Jocumsen; C. Emborg; J. Nielsen (1997)
Modeling the growth and proteinase A production in continuous cultures of recombinant Saccharomyces cerevisiae. Biotechnol. Bioeng. 55:447-454
P. de N. Pissarra; J. Nielsen (1997)
Thermodynamics of metabolic pathways for penicillin production: Analysis of thermodynamic feasibility and free energy changes during fed-batch cultivations. Biotechnol. Prog. 13:156-165
T. C. Zangirolami; C. L. Johansen; J. Nielsen; S. B. Jørgensen (1997)
Simulation of penicillin production in fed-batch cultivations using a morphologically structured model. Biotechnol. Bioeng. 56:593-604
K. Schmidt; M. Carlsen; J. Nielsen; J. Villadsen (1997)
Modelling isotopmer distributions in biochemical networks Using isotopomer mapping matrices. Biotechnol. Bioeng. 55:831-840
T. L. Nissen; U. Schulze; J. Nielsen; J. Villadsen (1997)
Flux distributions in anaerobic, glucose limited continuous cultures of Saccharomyces cerevisiae. Microbiology 143:203-218
J. Nielsen (1997)
Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates. Biochem. J. 321:133-138
1996
C. J. L. Klein, L. Olsson, B. Rønnow, J. D. Mikkelsen, J. Nielsen (1996)
Alleviation of glucose repression on maltose metabolism by MIG1 disruption in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 62:4441-4449
J. Nielsen; H. S. Jørgensen (1996)
Kinetic model for the penicillin biosynthetic pathway in Penicillium chrysogenum. Control Eng. Prac.4:765-771
U. Schulze; G. Liden; J. Nielsen; J. Villadsen (1996)
Physiological effects of nitrogen starvation in an anaerobic batch culture of Saccharomyces cerevisiae. Microbiology 142:2299-2310
P. de N. Pissarra; J. Nielsen; M. J. Bazin (1996)
Pathway kinetics and metabolic control analysis of a high-yielding strain of Penicillium chrysogenum during fed-batch cultivations. Biotechnol. Bioeng. 51:168-176
Rong Wei Min; J. Nielsen; J. Villadsen (1996)
On-line monitoring of glucose and penicillin by Sequential Injection Analysis. Anal. Chim. Acta 320:199-205
M. Carlsen; J. Nielsen; J. Villadsen (1996)
Growth and a-amylase production of Aspergillus oryzae during continuous cultivations.J. Biotechnol. 45:81-93
C. M. Henriksen; S. S. Holm; H. S. Jørgensen; J. Nielsen; J. Villadsen (1997)
Kinetic studies of the carboxylation of 6-amino-penicillanic acid to 8-hydroxy-penillic acid, Proc. Biochem. 32:85-91
L. H. Christensen; J. Marcher; U. Schulze; M. Carlsen; R. W. Min; J. Nielsen; J. Villadsen (1996)
Semi-on-line analysis for fast and precise monitoring of bioreaction processes. Biotechnol. Bioeng. 52:237-247
C. M. Henriksen; L. H. Christensen; J. Nielsen; J. Villadsen (1996)
Growth energetics and metabolic fluxes in continuous cultures of Penicillium chrysogenum, J. Biotechnol. 45:149-164
M. Carlsen; A. B. Spohr; J. Nielsen; J. Villadsen (1996)
Morphology and physiology of an a-amylase producing strain of Aspergillus oryzae during batch cultivations, Biotechnol. Bioeng. 49:266-276
M. Carlsen; J. Nielsen; J. Villadsen (1996)
Kinetic studies of acid-inactivation of a-amylase from Aspergillus oryzae. Chem. Eng. Sci. 51:37-43
1995
Rong Wei Min; M. Carlsen; J. Nielsen; J. Villadsen (1995)
Measurements of a-amylase activity by Sequential Injection Analysis. Biotechnol. Techn. 9:765-768
M. A. Hjortso; J. Nielsen (1995)
Population balance models of autonomous microbial oscillations. J. Biotechnol. 42:255-269
L. H. Christensen; C. M. Henriksen; J. Nielsen; J. Villadsen; M. Egel-Mitani (1995)
Continuous cultivation of P. chrysogenum. Growth on glucose and penicillin production. J. Biotechnol. 42:95-107
Rong Wei Min; J. Nielsen; J. Villadsen (1995)
Simultaneous monitoring of glucose, lactic acid and penicillin by Sequential Injection Analysis. Anal. Chim. Acta 312:149-156
R. Lejeune; J. Nielsen; G. Baron (1995)
Influence of pH on the morphology of Trichoderma reesei QM 9414 in submerged cultures. Biotechnol. Lett. 17:341-344
L. H. Christensen; U. Schulze; J. Nielsen; J. Villadsen (1995)
Acoustic gas analysis for fast and precise monitoring of bioreactors, Chem. Eng. Sci. 50:2101-2110
R. Lejeune; J. Nielsen; G. Baron (1995)
Morphology of Trichoderma reesei QM 9414 in submerged cultures, Biotechnol. Bioeng. 47:609-615
J. Nielsen; H. S. Jørgensen (1995)
Metabolic control analysis of the penicillin biosynthetic pathway in a high yielding strain of Penicillium chrysogenum, Biotechnol. Prog. 11:299-305
R. Mørkeberg; M. Carlsen; J. Nielsen (1995)
Induction and repression of a-amylase production in recombinant and wild-type strains of Aspergillus oryzae, Microbiol. 141:2449-2454
H. Jørgensen; J. Nielsen; J. Villadsen; H. Mølgaard (1995)
Metabolic flux distributions in Penicillium chrysogenum during fed-batch cultivations. Biotechnol. Bioeng. 46:117-131
J. Nielsen; C. L. Johansen; M. Jacobsen; P. Krabben; J. Villadsen (1995)
Pellet formation and fragmentation in submerged cultures of Penicillium chrysogenum and its relation to penicillin production, Biotechnol. Prog. 11:93-98
J. Nielsen; P. Krabben (1995)
Hyphal growth and fragmentation of P. chrysogenum in submerged cultures.Biotechnol. Bioeng. 46:588-598
H. Jørgensen; J. Nielsen; J. Villadsen; H. Mølgaard (1995)
Analysis of the penicillin V biosynthesis during fed-batch cultivations with a high yielding strain of Penicillium chrysogenum, Appl. Microbiol. Biotechnol. 43:123-130
1994
M. Carlsen; J. Marcher; J. Nielsen (1994)
An improved FIA-system for measuring a-amylase in cultivation media, Biotechnol. Tech. 8:479-482
J. Nielsen; C. L. Johansen; J. Villadsen (1994)
Culture fluorescence measurements during batch and fed-batch cultivations with Penicillium chrysogenum. J. Biotechnol 38:51-62
M. A. Hjortso; J. Nielsen (1994)
A conceptual model of autonomous oscillations in microbial cultures. Chem. Eng. Sci. 49:1083-1095
L. H. Christensen; J. Nielsen; J. Villadsen (1994)
Degradation of penicillin V in fermentation media. Biotechnol. Bioeng. 44:165-169
L. H. Christensen; G. Mandrup; J. Nielsen; J. Villadsen (1994)
A robust LC method for studying the penicillin fermentation. Anal. Chim. Acta 296:51-62
S. Benthin; U. Schulze; J. Nielsen; J. Villadsen (1994)
Growth energetics of Lactococcus cremoris FD1 during energy-, carbon- and nitrogen limitation in steady state and transient cultures.Chem. Eng. Sci. 49:589-610
A. G. Pedersen; H. Andersen; J. Nielsen; J. Villadsen (1994)
A novel technique based on 85Kr for quantification of gas-liquid mass transfer in bioreactors.Chem.Eng. Sci. 49:803-810
A. G. Pedersen; M. Bundgaard-Nielsen; J. Nielsen; J. Villadsen (1994)
Characterization of mixing in stirred tank bioreactors equipped with Rushton turbines. Biotechnol. Bioeng. 44:1013-1017
S. Benthin; J. Nielsen; J. Villadsen (1994)
Galactose expulsion during lactose metabolism in Lactococcus lactis subsp. cremoris FD1 due to dephosphorylation of intracellular galactose-6-phosphate.Appl. Environ. Microbiol. 60:1254-1259
1993
S. Benthin; J. Nielsen; J. Villadsen (1993)
Two uptake systems for fructose in Lactococcus lactis subsp. cremoris FD1 produce glucolytic and gluconeogenic fructose phosphates and induce oscillations of growth and lactic acid formation. Appl. Environ. Microbiol. 59:3206-3211
J. Nielsen (1993)
Simulation of bioreactions. Comp. Chem. Eng. 18:S615-S620
S. Benthin; J. Nielsen; J. Villadsen (1993)
Transport of sugars via two anomer-specific sites on mannose-phosphotransferase system in Lactococcus cremoris : In vivo study of mechanism, kinetics and adaption. Biotechnol. Bioeng. 42:440-448
M. Carlsen; H. Meier; F. Lantreibecq; C. Johansen; R. W. Min; J. Nielsen (1993)
On-line monitoring of penicillin V during penicillin fermentations : A comparison of two different methods based on FIA. Anal. Chim. Acta 279:51-58
M. Carlsen; L. H. Christensen; J. Nielsen (1993)
Flow-injection analysis for measurement of penicillin V in fermentation samples. Anal. Chim. Acta 274:117-123
J. Nielsen (1993)
A simple morphologically structured model describing the growth of filamentous microorganisms. Biotechnol. Bioeng. 41:715-727
A. G. Pedersen; M. Bundgaard; O. Hassager; J. Nielsen; J. Villadsen (1993)
Rheological characterization of media containing Penicillium chrysogenum. Biotechnol. Bioeng. 41:162-164
1992
K. Strudsholm; J. Nielsen; C. Emborg (1992)
Product formation during batch fermentation with recombinant Escherichia coli containing a runaway plasmid. Bioprocess Eng. 8:173-181
C. L. Johansen; L. H. Christensen; J. Villadsen; J. Nielsen (1992)
Monitoring and control of fed-batch penicillin fermentation. Comp. Chem. Eng. 16:S297-S304
J. Nielsen; J. Villadsen (1992)
Modelling of microbial kinetics. Chem. Eng. Sci. 47:4225-4270
J. Nielsen (1992)
On-line monitoring of microbial processes by flow injection analysis. Proc. Control Qual. 2:371-384
S. Benthin; J. Nielsen; J. Villadsen (1992)
Anomeric specificity of glucose uptake systems in Lactococcus cremoris, Escherichia coli and Saccharomyces cerevisiae: Mechanisms, kinetics and implications. Biotechnol. Bioeng. 40:137-146
S. Benthin; J. Nielsen; J. Villadsen (1992)
Flow Injection Analysis of micromolar concentrations of glucose and lactate in fermentation media. Anal. Chim. Acta 261:145-153
1991
L. H. Christensen; J. Nielsen; J. Villadsen (1991)
Delay and dispersion in an in-situ membrane probe for bioreactors. Chem. Eng. Sci. 46:3304-3307
L. H. Christensen; J. Nielsen; J. Villadsen (1991)
Monitoring of substrates and products during fed-batch penicillin fermentations on complex media. Anal. Chim. Acta 249:123-136
S. Benthin; J. Nielsen; J. Villadsen (1991)
Characterisation and application of precise and robust flow injection analyzers for on-line measurement during fermentations. Anal. Chim. Acta 247:45-50
J. Nielsen; A. G. Pedersen; K. Strudsholm; J. Villadsen (1991)
Modelling fermentations with recombinant microorganisms : Formulation of a structured model. Biotechnol. Bioeng. 37:802-808
K. Nikolajsen; J. Nielsen; J. Villadsen (1991)
Structured modelling of a microbial system 3. Growth on mixed substrates. Biotechnol. Bioeng. 38:24-29
J. Nielsen; K. Nikolajsen; J. Villadsen (1991)
Structured modelling of a microbial system 2. Experimental verification of a structured lactic acid fermentation model. Biotechnol. Bioeng. 38:11-23
J. Nielsen; K. Nikolajsen; J. Villadsen (1991)
Structured modelling of a microbial system 1. A theoretical study of the lactic acid fermentation. Biotechnol. Bioeng. 38:1-10
S. Benthin; J. Nielsen; J. Villadsen (1991)
A simple and reliable method for the determination of cellular RNA content. Biotechnol. Techn.. 5:39-42
1990
G. Wehnert; K.-D. Anders; C. Bittner; R. Kammeyer; U. Hübner; J. Nielsen; T. Scheper (1990)
Ein kombinierter Fluoreszenz-/Streulichtsensor und dessen Einsatz zur Prozessbeobachtung in der Biotechnologie. Chem.-Ing.-Tech. 62:211-212
J. Nielsen; K. Nikolajsen; S. Benthin; J. Villadsen (1990)
Application of flow-injection analysis in the on-line monitoring of sugars, lactic acid, protein, and biomass during lactic acid fermentations. Anal. Chim. Acta 237:165-175
1989
J. Nielsen; C. Emborg; K. Halberg; J. Villadsen (1989)
Compartment model concept used in the design of fermentation with recombinant microorganisms Biotechnol. Bioeng. 34:478-486
J. Nielsen; K. Nikolajsen; J. Villadsen (1989)
FIA for on-line monitoring of important lactic acid fermentation variables. Biotechnol. Bioeng. 33:1127-1134
1988
K. Nikolajsen; J. Nielsen; J. Villadsen (1988)
In-line flow injection analysis for monitoring lactic acid fermentations. Anal. Chim. Acta 214:137-145
Commentaries and Short Papers
J. Nielsen; J. Keasling (2011) Synergies between synthetic biology and metabolic engineering. Nature Biotechnol. 29:693-695
J. Nielsen (2011) Chimeric Synthetic Pathways. Nature Chem. Biol. 7:195-196
J. Nielsen (2011) Transcriptional control of metabolic fluxes. Mol. Systems Biol. 7:478
J. Nielsen; M. Vidal (2010)
Systems biology of microorganisms. Current Opp. Microbiol. 13:335-336
J. Nielsen (2009)
Quantification of flux control in metabolic pathways, Biotechnol. Bioeng. 104: 1-2
J. Nielsen (2008)
Vintage paper Introduction. Biotechnol. Bioeng. 103:1
G. Vemuri; J. Nielsen (2008)
Systems biology: Is the hope worth the hype. SIM News 58:178-188
J. Nielsen (2007)
Principles of optimal metabolic network operation. Mol. Sys. Biol. 3:126
J. M. Otero; L. Olsson; J. Nielsen (2007)
Industrial biotech meets systems biology. Genetic Eng. News 1:28-31
J. Thykaer; B. Christensen; J. Nielsen (2001)
The application of metabolic network analysis in metabolic engineering. BIOforum International 5:228-231
B. Hahn-Hägerdal; K. van Dam; I. Spencer-Martins; J. Nielsen (1998)
Le dédale du métabolisme. Biofutur 184:81-82
Books
J. Nielsen; M. Jewett (2008)
Metabolomics. Topics in Current Genetics, Vol. 18, Springer Verlag, Heidelberg (editor and co-author of 2 chapters)
S. G. Villas-Boas; U. Roessner; M. A. E. Hansen; J. Smedsgaard; J. Nielsen (2007)
Metabolome Analysis. An Introduction, Wiley, Hoboken
J. Nielsen (2006) (editor)
Frontiers in Biotechnology. Advances in Biochemical Engineering/Biotechnology, Vol. 100, Springer Verlag, Heidelberg
J. Nielsen; J. Villadsen; G. Liden (2003)
Bioreaction Engineering Principles, 2. ed., Kluywer Plenum, New York
J. Nielsen (2001) (editor)
Metabolic Engineering. Advances in Biochemical Engineering/Biotechnology, Vol. 73, Springer Verlag, Heidelberg
G. Stephanopoulos; A. Aristodou; J. Nielsen (1998)
Metabolic Engineering. Academic Press, San Diego
J. Nielsen (1997)
Physiological Engineering Aspects of Penicillium chrysogenum. World Scientific Publishing Co., Singapore
J. Nielsen; J. Villadsen (1994)
Bioreaction Engineering Principles. Plenum Press, New York
M. Y. Andersen et al. (1991)
Bioreaktionsteknik. Metoder til fortolkning af data fra bioreaktorer. Akademiet for Tekniske Videnskaber, Lyngby
Contribution in Books
M. Papini; M. Salazar; J. Nielsen (2010) Systems Biology of Industrial Microorganisms. Adv. Biochem. Eng./Biotechnol. 120:51-99
K. R. Patil; P. M. Bapat; J. Nielsen (2010)
Structure and flux analysis of metabolic networks. Pp. 17.1-17.18. In: The Metabolic Pathway Engineering Handbook. Ed. C. D. Smolke. CRC Press, Boca Raton, USA
J. Nielsen (2010)
Developing appropriate hosts for metabolic engineering. Pp. V.1-V.8. In: The Metabolic Pathway Engineering Handbook. Ed. C. D. Smolke. CRC Press, Boca Raton, USA
I. Borodina; A. Eliasson; J. Nielsen (2010)
Metabolic Engineering of Streptomyces. Pp. 24.1-24.30. In: The Metabolic Pathway Engineering Handbook. Ed. C. D. Smolke. CRC Press, Boca Raton, USA
M. R. Andersen; K. Rucksomtawin; G. Hofmann; J. Nielsen (2010)
Metabolic Engineering of filamentous fungi. Pp. 25.1-25.30. In: The Metabolic Pathway Engineering Handbook. Ed. C. D. Smolke. CRC Press, Boca Raton, USA
J. M. Otero; J. Nielsen (2010)
Industrial Systems Biology. Pp. 79-148. In: Industrial Biotechnology. Eds. W. Soetaert and E. J. Vandamme. Wiley VCH, Weinheim, Germany
V. Siewers; U. H. Mortensen; J. Nielsen (2010)
Genetic engineering tools for Saccharomyces cerevisiae. Pp. 287-301. In: Manual of Industrial Microbiology and Biotechnology (3.ed). Eds. R. H. Baltz, A. L. Demain and J. E. Davies. ASM Press, Washington, USA
G. Vemuri; J. Nielsen (2009)
Yeast as a prototype for systems biology. Pp. 287-354. In: Systems biology and synthetic biology. Eds. P. Fu and S. Panke, Wiley, Hoboken, USA
W. Vongsangnak; J. Nielsen (2009)
Bioinformatics and systems biology of Aspergillus. Pp. 61-84. In: Aspergillus. Molecular Biology and Genomics. Eds. M. Machida and K. Gomi. Caister Academic Press, UK
M. C. Jewett; M. A. E. Hansen; J. Nielsen (2008)
Data acquisition, analysis, and mining: Integrative tools for discerning metabolic function in Saccharomyces cerevisiae. Pp. 159-188. In: Metabolomics. Topics in Current Genetics. Eds. J. Nielsen and M. C. Jewett, Vol. 18, Springer Verlag, Heidelberg
M. C. Jewett; J. Nielsen (2008)
The role of Metabolomics in systems biology. Pp. 1-10. In: Metabolomics. Topics in Current Genetics. Eds. J. Nielsen and M. C. Jewett, Vol. 18, Springer Verlag, Heidelberg
A. P. Oliveira; M. C. Jewett; J. Nielsen (2007)
From gene expression to metabolic fluxes, Pp. 37-66. In: Introduction to Systems Biology. Ed. S. Choi, Humana Press, Totowa, USA
W. de Jongh, J. Nielsen (2007)
Filamentous fungi as cell factories for metabolite production, Pp. 163-182. In: Food Mycology. A multifaceted approach to fungi and food. Ed. J. Dijksterhuis, R. A. Samson, CRC Press, Boca Raton, USA
I. Rocha; J. Förster, J. Nielsen (2007)
Design and application of genome-scale reconstructed metabolic models, Pp. 409-431. In: Methods in Molecular Biology, Vol. 416: Gene Essentiality. Ed. S. Y. Gerdes, A. L. Osterman, Humana Press Inc., Totowa, USA
J. Nielsen (2006)
Fermentation Kinetics. pp. 69-120. Chap. 4. In: Fermentation Microbiology and Biotechnology. Eds. E. M. T. El-Mansi, C. F. A. Bryce, A. L. Demain, A. R. Allman, Taylor and Francis, London
J. Nielsen (2006)
Microbial Process Kinetics. pp. 155-180, Chap. 6. In: Basic Biotechnology. 3. Edition. Eds. C. Ratledge, B. Kristiansen, Cambridge University Press, Cambridge
J. Højer-Pedersen; J. Smedsgaard; J. Nielsen (2006)
Elucidating the mode-of-action of compounds from metabolite profiling studies, Pp. 103-130. In: Systems Biological Approaches in Infectious Diseases. Progress in Drug Research Vol. 64. Ed. H. I. Boshoff, C. E. Barry III, Birkhäuser, Berlin
J. Maury, M. A. Asadollahi, K. Møller, A. Clark, J. Nielsen (2005)
Microbial isoprenoid production: An example of green chemistry through metabolic engineering. Adv. Biochem. Eng./Biotechnol. 100:19-51
H. David, J. Nielsen (2005)
Modelling of fungal metabolism. Pp. 195-214. In: Metabolome Analysis. Strategies for Systems Biology. Ed. S. Vaidyanathan, G. G. Harrigan, R. Goodacre, Springer, New York
J. Nielsen, A. Eliasson (2005)
From glucose to antibiotics: What controls the fluxes? pp. 195-214. In: Biocombinatorial Approaches for Drug Finding. Ed. W. Wohlleben, T. Spelling, B. Müller-Tiemann, Springer, Heidelberg
N. Gunnarsson, A. Eliasson, J. Nielsen (2004)
Control of fluxes towards antibiotics and the role of primary metabolism in production of antibiotics. Adv. Biochem. Eng./Biotechnol. 88:137-178
A. Gombert; J. Nielsen (2003)
Quantification of metabolic fluxes. In: Encyclopaedia of Life Sciences. Nature Publishing Group, London (www.els.net)
C. Bro; B. Regenberg; J. Nielsen (2003)
Yeast Functional Genomics and Metabolic Engineering; Past, present and future. pp. 331-360. In: Functional Genetics of Industrial Yeast. Ed. H. de Winde, Springer, Heidelberg
M. M. dos Santos; M. Åkesson; J. Nielsen (2003)
Metabolic Flux Analysis in the post genomics area. pp. 89-105. In: Metabolic Engineering in the Post Genomic Era . Eds. B. Kholodenko; H. Westerhoff, Horizon Scientific Press, Norfolk
J. Nielsen (2002)
Metabolic Engineering. pp. 391-406. In: Encyclopedia of Physical Science and Technology, Vol. 9. Academic Press, San Diego
M. McIntyre; C. Müller; J. Dynesen; J. Nielsen (2001)
Metabolic engineering of the morphology of Aspergillus. Adv. Biochem. Eng./Biotechnol. 73:103-128
S. Ostergaard; L. Olsson; J. Nielsen (2001)
Metabolic Pathway Analysis of Saccharomyces cerevisiae. pp. 75-85. In: Applied Microbiology. Focus on Biotechnology Vol. 2. Eds. M. Hofman, P. Thonart, Kluwer Academic Publishers, Dordrecht
T. Agger; J. Nielsen (2001)
Mathematical modelling of microbial processes – Motivation and means. pp. 61-75. In: Engineering and Manufacturing for Biotechnology. Eds. M. Hofman, P. Thonart, Kluwer Academic Publishers, Dordrecht
J. Nielsen (2001)
Metabolic Turnover. In: Encyclopaedia of Life Sciences. Nature Publishing Group, London (www.els.net)
J. Nielsen (2001)
Microbial Process Kinetics. pp. 127-149, Chap. 6. In: Basic Biotechnology. 2. Edition. Eds. C. Ratledge, B. Kristiansen, Cambridge University Press, Cambridge
B. Christensen; J. Nielsen (1999)
Metabolic network analysis – powerful tool in metabolic engineering. Adv. Biochem. Eng./Biotechnol. 66:209-231
J. Nielsen (1999)
Fermentation kinetics. pp. 69-119, Chap. 4. In: Modern Concepts in Fermentation Biotechnology. Eds. M. El-Mansi, Bryce, Taylor and Francis, London
J. Nielsen (1999)
Fermentation monitoring, design and optimization. pp. 1147-1157. In: The Encyclopedia of Bioprocess Technology: Fermentation, Biocatalysis & Bioseparations. Eds. M. C. Flickinger; S. W. Drew, John Wiley & Sons
A. B. Spohr, T. Agger; M. Carlsen; J. Nielsen (1998)
Quantitative morphology of filamentous microorganisms. pp. 373-410, Chap. 14. In: Digital analysis of Microbes. Eds. M. H. F. Wilkinson; F. Schut, John Wiley & Sons
P. Krabben; J. Nielsen (1998)
Modeling the mycelium morphology of Penicillium species in submerged cultures. Adv. Biochem. Eng./Biotechnol. 60:125-152
J. Nielsen; M. Carlsen (1996)
Fungal Pellets. pp. 273-293, Chap. 13. In: Immobilised living cell systems: Modelling and experimental methods. Eds. G. Baron, R. Willaert; L. De Backer, John Wiley & Sons, Chichester
J. Nielsen; J. Villadsen (1993)
Bioreactors : Description and modelling. pp. 77-104, Chap. 5 in Biotechnology Vol. 3 (2. ed.). Eds. H.-J. Rehm; G. Reed (volume editor G. Stephanopoulos), VCR Verlag
J. Nielsen (1992)
Modelling the growth of filamentous fungi. Adv. Biochem. Eng./Biotechnol. 46:187-223
Papers in Conference Proceedings
J. Nielsen (1998)
Mathematical modelling of biochemical pathways. BioThermoKinetics in the post genomic era. Proc. 8’th BTK Meeting, Fiskebäckskil, Sweden
H. Aae Theilgaard; J. Nielsen (1998)
The influence of the LLD-ACV:bisACV ration on a MCA of the penicillin biosynthetic pathway in Penicillium chrysogenum. BioThermoKinetics in the post genomic era. Proc. 8’th BTK Meeting, Fiskebäckskil, Sweden
S. Østergaard; L. Olsson; J. Nielsen (1998)
Metabolic control analysis of the Leloir pathway in Saccharomyces cerevisiae. BioThermoKinetics in the post genomic era. Proc. 8’th BTK Meeting, Fiskebäckskil, Sweden
J. Nielsen; I. Spencer Martins (1997)
Metabolic Engineering. Proc. European Cell Factory Conference, Lund, Sweden
D. L. Bogle et al. (1996)
Process synthesis, design and simulation of integrated biochemical processes. Proc. V’th World Congress on Chemical Engineering, San Diego, USA
P. de N. Pissarra; J. Nielsen (1996)
Kinetic and thermodynamic analysis of the penicillin biosynthetic pathway. Proc. V’th World Congress on Chemical Engineering, San Diego, USA
U. Schulze; T. L. Nissen; J. Nielsen; J. Villadsen (1996)
Application of Metabolic Flux Analysis in physiological studies. Proc. V’th World Congress on Chemical Engineering, San Diego, USA
J. Nielsen (1995)
Metabolic control analysis of the penicillin biosynthetic pathway. Proc. National Biotechnology and Bioengineering Conference, Ixtapa, Mexico
K. Schmidt: P. N. Pissarra; J. Nielsen (1995)
The evolutionary strategy: A simple and straightforward optimization algorithm for parameter estimation in structured biochemical models. Proc. Nordic Matlab Conference ‘95, Stockholm
P. N. Pissarra; M. J. Bazin; K. Schmidt; J. Nielsen (1995)
A user-friendly and interactive methodology for simulation and non-linear parameter estimation of biotechnological process models using SIMULINK. Proc. Nordic Matlab Conference ‘95, Stockholm
J. Nielsen; H. Jørgensen (1995)
A kinetic model for the penicillin biosynthetic pathway in Penicillium chrysogenum. pp. 136-141. In Proc. Computer Application in Biotechnology 6, Garmisch-Partenkirchen
G. Lidén; U. Schulze; J. Nielsen; J. Villadsen (1995)
On the optimization of ethanol production in nitrogen limited yeast fermentations. In Proc. VII’th European Congress on Biotechnology, Nice
J. Nielsen (1994)
Physiological aspects of Penicillium chrysogenum. pp. 15-18. Proc. Modelling of filamentousfungi, Otocek.
M. Carlsen; A. Spohr; R. Mørkeberg; J. Nielsen; J. Villadsen (1994)
Growth and protein formation of recombinant Aspergillus: Utility of morphological characterization by image analysis. pp. 197-202. In Proc. Advances in Bioprocess Engineering, Cuernavaca. Kluwer Academic Publishers
J. Nielsen (1994)
Physiological Engineering - Towards a new science. pp. 30-38. In Proc. The 1994 IChemE Research Event, London, Vol. I
A. G. Pedersen; J. Nielsen; J. Villadsen (1993)
Characterization of bioreactors using isotope techniques. pp. 931-934. In Progress in Biotechnology, Vol. 9. Proc. VI'th European Congress on Biotechnology, Florence. Elsevier
S. Frandsen; J. Nielsen; J. Villadsen (1993)
Dynamics of Saccharomyces cerevisiae in continuous culture. pp. 887-890. In Progress in Biotechnology, Vol. 9. Proc. VI'th European Congress on Biotechnology, Florence. Elsevier
S. Frandsen; J. Nielsen; J. Villadsen (1993)
Application of regimen analysis of yeast fermentation for down-scaling. pp. 171-179. Proc. Bioreactor Performance, eds. U. Mortensen; H. J. Noorman, Elsingore
J. Nielsen (1993)
Modelling the morphology of filamentous fungi. pp. 131-142. Proc. Bioreactor Performance, eds. U. Mortensen; H. J. Noorman, Elsingore
H. S. Jørgensen; H. Møllgaard; J. Nielsen; J. Villadsen (1993)
Identification of rate controlling enzymes in the metabolic pathway of penicillin in a high yielding strain of P. chrysogenum. pp. 251-254. In Computer Applications in Fermentation Technology. Modelling and Control of Biotechnological Processes, eds. M. N. Karim; G. Stephanopoulos, Pergamon Press
J. Nielsen (1993)
Modelling of filamentous microorganisms. pp. 45-52. In Computer Applications in Fermentation Technology. Modelling and Control of Biotechnological Processes, eds. M. N. Karim; G. Stephanopoulos, Pergamon Press
S. Benthin; J. Nielsen; J. Villadsen (1992)
Transmembrane transport systems, studied on actively growing cells. pp. 351-355. In Harnessing Biotechnology for the 21st Century (Proc. IX'th International Biotechnology Symposium, Crystal City), eds. M. R. Ladisch; A. Rose,
J. Nielsen (1991)
Application of structured fermentation models. pp. 843-848. Proc. European Simulation Multiconference, Copenhagen
J. Villadsen; J. Nielsen (1990)
Modelling of fermentation kinetics. pp. 259-266. Proc. V'th European Congress on Biotechnology, Lyngby
J. Nielsen; K. Nikolajsen; J. Villadsen (1989)
Computer controlled system for on-line monitoring of a fermentation process. pp. 53-57. In Computer Applications in Fermentation Technology. Modelling and Control of Biotechnological Processes, eds. N. M. Fish; R. I. Fox; N. F. Thornhill, Elsevier Applied Science, London
Other Publications
J. Højer-Pedersen; J. Smedsgaard; J. Nielsen (2006)
Metabolomet: Et indirekte produkt af genomet. Dansk Kemi 3:18-20
M. R. Andersen; M. L. Nielsen; J. Nielsen (2006)
Genomet – systembiologiens rygrad. Dansk Kemi 3:15-17
C. Bro; B. Regenberg; J. Nielsen (2001)
DNA Arrays. Dansk Kemi 1:18-20
J. Nielsen (1999)
Functional genomics og dens rolle i udviklingen af fremtidige bioteknologiske processer. Dansk Kemi 1:20-27
B. Christensen; J. Nielsen (1999)
Metabolsk flux analyse – en kvantitativ beskrivelse af mikroorganismers primære metabolisme. Dansk Kemi 1:16-18
T. Agger; J. Nielsen (1999)
Optimering af enzymproduktion med skimmelsvampe. Dansk Kemi 1:14-15
U. Schulze; J. Nielsen (1997)
Massachusetts Institute of Technology. Dansk Kemi
J. Nielsen (1995)
Penicillinets historie. Dansk Kemi 12:24-28
J. Nielsen (1995)
Doktorafhandling om industriel penicillinproduktion. Dansk Kemi 11:20-23
J. Nielsen; A. G. Pedersen; M. Bundgaard-Nielsen; H. Andersen (1994)
Anvendelse af radioaktive isotoper til karakterisering af bioreaktorer. Dansk Kemi 4:28-31
J. Nielsen (1993)
Physiological Engineering. Dansk Kemi 11:14-17
J. Nielsen; J. Gram; L. Foldager (1990)
Bioreaktionsteknik: Kendte metoder anvendt på nye processer. Dansk Kemi 12:430-431
J. Nielsen (1990)
On-line måling af biomasse i bioreaktorer. Dansk Kemi 8:260-265
J. Nielsen (1990)
Post doc på Universität Hannover. Dansk Kemi 5:178-179
List of Presentations
Invited conference presentations
- Modelling of fermentation kinetics, European Congress on Biotechnology 5, Lyngby (1990)
- Modelling of the lactic acid fermentation, European Congress on Biotechnology 5, Lyngby (1990)
- Modelling of fermentation processes, European Simulation Multiconference, Copenhagen (1991)
- On-line monitoring of microbial processes, FACSS, Anaheim, California (1991)
- Modelling the growth of filamentous microorganisms, IFAC/ICCAFT, Keystone, Colorado (1992)
- On-line monitoring of fermentation processes, Bioreactor Performance, Annual Conference of a Nordic Industrial programme, Stockholm, Sweden (1992)
- On-line måling af bioprocesser, 2. Danske Symposium i Analytisk Kemi, Lyngby, Denmark (1992)
- On-line monitoring of penicillin fermentations, AnaBiotec'92, Noordwijkerhout, Holland (1992)
- Modelling the morphology of filamentous fungi, Bioreactor Performance, Elsingore, Denmark (1993)
- Simulation of bioreactions, ESCAPE-3, Graz, Austria (1993)
- Pellet formation, Process Integration in Biochemical Engineering, European Science Foundation Workshop, Sitges, Spain (1993)
- Physiological Engineering - Towards a new science, The 1994 IChemE Research Event, London (1994)
- Modelling the growth and product formation of Penicillium chrysogenum, IUMS Congresses '94, Prague (1994)
- Mathematical models: An excellent tool in physiological studies of filamentous fungi, International conference on Modelling of filamentous fungi, Otocek, Slovenien (1994)
- In-situ and on-line analysis of cultivation processes, International seminar on Analyses in biomass conversion to ethanol, Lund, Sweden (1994)
- A kinetic model for the penicillin biosynthetic pathway in Penicillium chrysogenum, 6’th International conference on Computer Application in Biotechnology, Garmisch-Partenkirchen, Germany (1995)
- Modelling the growth of filamentous fungi, National Biotechnology and Bioengineering Conference, Ixtapa, Mexico (1995)
- Metabolic Control Analysis of the penicillin biosynthetic pathway, National Biotechnology and Bioengineering Conference, Ixtapa, Mexico (1995)
- Metabolic Control Analysis of the penicillin biosynthetic pathway, Pacifichem’95, Honolulu, USA (1995)
- Fungal Morphology. Measurements and modelling, 6th Netherlands Biotechnology Congress, Amsterdam, The Netherlands (1996)
- Metabolic Flux Analysis of filamentous fungi, DECHEMA Jahrestagungen’96, Wiesbaden, Germany (1996)
- Metabolic Engineering: The analysis part, rDNA Biotechnology: Focus on Metabolic Engineering, Engineering Foundation, Danvers, USA (1996)
- What can we learn from metabolic flux analysis, VW-symposium on Metabolic fluxes, Hannover, Germany (1997)
- Metabolic engineering, Danish Biotechnology Conference III, Vejle, Denmark (1997)
- Metabolic control analysis of the penicillin biosynthetic pathway based on a kinetic model and on a thermokinetic description of reaction rates, ESF Conference on Control of Metabolic Flux, Giens, France (1997)
- Physiological Engineering, European Congress on Biotechnology 8, Budapest, Hungary (1997)
- Mathematical modelling of biochemical pathways, 8’th BTK meeting, Fiskebäckskil, Sweden (1998)
- Enzyme production by Aspergillus, SGM meeting, Norwich, UK (1998)
- Metabolic engineering of Saccharomyces cerevisiae for the improvement of industrial processes, Yeast as a cell factory, Vlaardingen, The Netherlands (1998)
- The role of mathematical models in kinetic studies of hyphal growth, Analysis of microbial cells at the single cell level, Como, Italy (1999)
- The role of mathematical models in microbial physiology, Annual Meeting of Swedish Society of Microbiology, Lund, Sweden (1999)
- Modeling of cellular processes, European Congress on Biotechnology 9, Brussels, Belgium (1999)
- The application of mathematical models in molecular physiology, European Congress on Biotechnology 9, Brussels, Belgium (1999)
- Metabolic engineering of Saccharomyces cerevisiae for the improvement of ethanol production, IEA Bioenergy Workshop, Itala Game Reserve, South Africa (1999)
- Yeast mixed sugar metabolism, Cell Factory Area. Grand Finale, Graz, Austria (1999)
- The role of metabolic engineering in the improvement of industrial processes, APBioChEC’99, Phuket, Thailand (1999)
- Transgenic microorganisms and industrial strain enhancement, Perspectives and limitations of biotechnology in developing countries, San José, Costa Rica (2000)
- Metabolic engineering of enzyme production by filamentous fungi, 4th International Congress on Biochemical Engineering, Stuttgart, Germany (2000)
- Metabolic Engineering of Saccharomyces cerevisiae, XIII SINAFERM, Teresopolis, Brasilien (2000)
- Metabolome analysis: A powerful tool in metabolic engineering and functional genomics, Metabolic Engineering III, Colorado Springs, USA (2000)
- Metabolome analysis: A powerful tool in functional genomics, WFCS Symposium on Genomics, Wageningen, The Netherlands (2000)
- Genome wide expression monitoring of metabolically engineered strains of S. cerevisiae with improved ethanol yield, PacificChem2000, Honolulu, USA
- Metabolome analysis: A powerful tool in metabolic engineering and functional genomics, MTBio Workshop, Dresden, Germany (2001)
- The role of functional genomics in metabolic engineering, SIM Annual Meeting, St. Louis, USA (2001)
- Metabolic engineering for improved b-lactam production, Recent Advances in Fermentation Technology IV, Long Beach, USA (2001)
- The role of yeast in modern biotechnology, International Specialized Symposium on Yeast 2002, Pilansberg, South Africa (2002)
- Metabolic engineering and functional genomics: Moving towards systems biology, SGM Annual Meeting, Warwick, UK (2002)
- Impact of Systems Biology on Modern Biotechnology, Danish Biotechnology Conference VIII, Vejle, Denmark (2002)
- Metabolic engineering for improvement of b-lactam production, Genetics of Industrial Microorganisms 2002, South Korea (2002)
- Carbon metabolism in Aspergillus and Penicillium, International Mycology Congress 7, Oslo, Norway (2002)
- From the Genome to the Fluxome: A Metabolic Engineering challenge, ASM Annual Meeting, Washington DC, USA (2003)
- Systems Biology of glucose repression in S. cerevisiae,Yeast Genetics and Molecular Biology, Gothenburg, Sweden (2003)
- From Genomics to Industrial Bioprocesses: A Metabolic Engineering challenge, European Congress on Biotechnology 11, Basel, Switzerland (2003)
- Systems Biology of S. cerevisiae, First International Workshop on Yeast Systems Biology, St. Louis, USA (2003)
- From Glucose to Antibiotics – what controls the flux, Ernst Schering Foundation Research Workshop, Berlin, Germany (2004)
- Systems Biology of S. cerevisiae, South Africa Microbial Society’s annual meeting, Stellenbosch, South Africa (2004)
- Aspergillus – the Ultimate Cell Factory for Production of Chemicals, European Congress on Fungal Genetics 7, Copenhagen, Denmark (2004)
- Microorganisms – the Chemical Factories of the Future, ETIF Conference, Lund, Sweden (2004)
- Grøn Kemi, Konference om Ansvarlig Bioteknologi, Copenhagen, Denmark (2004)
- Integration of Metabolic Models and Ome Data: Lessons from S. cerevisiae, ASM Conference on Integration of Metabolism and Genomics, Montreal, Canada (2004)
- Green Chemistry – the New S-curve in Biotechnology, 35th R3 Nordic Symposium and Exibition, Elsingore, Denmark (2004)
- Metabolic Engineering, European Symposium on Biochemical Engineering Science 5, Stuttgart, Germany (2004)
- Metabolic Engineering: Impacts of Functional Genomics, Metabolic Engineering V, Lake Tahoe, USA (2004)
- From gene expression to metabolic fluxes, International Congress on Systems Biology 2004, Heidelberg, Germany (2004)
- Integration of the metabolism of S. coelicolor through genome-scale modelling, Streptomyces Dissemination Meeting, University of Surrey, UK (2005)
- Design af cellefabrikker til production af nye levnedsmiddelingredienser, LMC Congress, Lyngby, Denmark (2005)
- White Biotechnology: From gene expression to metabolic fluxes, DECHEMA Bioperspectives, Wiesbaden, Germany (2005)
- Identification of global regulatory structures in cellular metabolism, Biochemical Engineering XIV, Harrison Hot Springs, Canada (2005)
- Genome-scale models of fungi, 13th International Meeting on Microbial Genomes (2005)
- The role of chemical engineering in modern biotechnology, CHEMPOR 2005, Braga, Portugal (2005)
- Systems biology of the yeast Saccharomyces cerevisiae, The Norwegian Biochemical Society, 42. Contact Meeting, Storefjell, Norway (2006)
- Model driven data integration in yeast systems biology, Genomes to Systems Conference 2006, Manchester, UK (2006)
- Systems Biology of Industrial Microbes, American Society for Microbiology 106th General Meeting, Orlando, USA (2006)
- Impacts of systems biology on industrial biotechnology, Danish Conference on Molecular Biology and Biotechnology, Munkebjerg, Denmark (2006)
- Reporter features: A tool for mapping of global control in metabolism through model driven analysis of ome data, ISSY25 Systems Biology of Yeasts – from Models to Applications, Helsinki, Finland (2006)
- Yeast as a versatile cell factory, Genetics of Industrial Microorganisms, Prague, Czech Republic (2006)
- Metabolism of Aspergillus: Lessons from Genomics, Society for Industrial Microbiology Annual Meeting, Baltimore, USA (2006)
- Production of engineered haemoglobin from yeast, International Visions on Blood Substitutes, Parma, Italy (2006)
- Systems biology of lipid metabolism in Saccharomyces cerevisiae: Mapping of global regulatory structures, Keystone conference on Bioactive Lipids, Taos, New Mexico, USA (2007)
- Yeast as a versatile chemical factory, ASM Annual Meeting, Toronto, Canada (2007)
- Integrated analysis of yeast metabolism, ASM Annual Meeting, Toronto, Canada (2007)
- Systems biology of the cell factory Aspergillus niger, International Conference on Biorefinery, Beijing, China (2007)
- The role of chemical engineering in modern biotechnology, European Congress on Chemical Engineering 6, Copenhagen, Denmark (2007)
- Integrated analysis of yeast metabolism, FOSBE2007, Stuttgart, Germany (2007)
- Integrated analysis of yeast metabolism, 9th Functional Genomics Conference: Synthetic Biology, Gothenburg, Sweden
- Systems biology of the cell factory Aspergillus niger, RAFT VII, St. Petersburg, Florida, USA (2007)
- Systems Biology as a driver for industrial biotechnology, 2008 BERN meeting, University College London, UK (2008)
- Comparative metabolic analysis of Aspergilli at the genome level, European Conference on Fungal Genetics 9, Edinburgh, UK (2008)
- The role of Snf1/AMPK on regulation of lipid metabolism: Lessons from yeast, Danish Conference on Molecular Biology and Biotechnology II, Munkebjerg, Denmark (2008)
- Modeling of microbial metabolic networks, Tutzing Symposium 2008, Tutzing, Germany (2008)
- Systems Biology of the cell factories A. niger and A. oryzae, FEBS2008, Athens, Greece (2008)
- Systems Biology of the yeast Saccharomyces cerevisiae, International Congress on Genetics 2008, Berlin, Germany (2008)
- Systems Biology of lipid and energy metabolism in yeast, International Conference on Yeast, Kiev, Ukraine (2008)
- Industrial systems biology: Yeast and Aspergilli as cell factories for sustainable production of chemicals, International Conference on Systems Biology 2008, Gothenburg, Sweden (2008)
- Production of fine chemicals by yeast and Aspergilli, International Biotechnology Symposium 2008, Dalian, China (2008)
- Integrated analysis of yeast metabolism, 61st Annual Symposium on Cancer Research: Systems Biology of Cancer, Houston, USA (2008)
- The metabolic networks of Aspergilliı, Asperfest, Asilomar, USA (2009)
- Metabolism of Aspergilli at the genome level, 25th Fungal Genetics Conference, Asilomar, USA (2009)
- Systems biology of lipid metabolism: Mapping of global regulatory structures, 9th Yeast Lipid Conference, Berlin, Germany (2009)
- Integrated analysis of metabolism; From yeast to human, Nobel Symposium on Systems Biology, Stockholm, Sweden (2009)
- Industrial Systems Biology: Identification of metabolic engineering targets using metabolic networks, Foundation of Engineering in Systems Biology 2009, Denver, USA (2009)
- From omics data to phenotype through integrative systems biology, ISSY 27, Paris, France (2009)
- Systems biology of metabolism: From yeast to mammals, European Congress on Biotechnology 14, Barcelona, Spain (2009)
- Yeast Metabolomics, Metabolomics Conference, University of Copenhagen, Copenhagen, Denmark (2009)
- Prospects of Systems Biology for advancing our understanding of global regulation of metabolism, Annual INRA Conference, Genoscope, France (2010)
- Genome-Scale Modeling of Fungi: Expansion from Metabolism to Protein Production, PYFF4, Rotterdam, The Netherlands (2010)
- Yeast as a Platform Cell Factory for the Production of Fuels and Chemicals, MEVIII, Jeju Island, South Korea (2010)
- Metabolism of Filamentous Fungi at the Genome Level, FEBS2010, Gothenburg, Sweden (2010)
- Insight into Metabolic Diseases through Systems Biology, 8th Aegian Conference on Pathways, Networks and Systems, Rhodes, Greece (2010)
- Genome-Scale Metabolic Models: The Core of Industrial Systems Biology, Industrial Systems Biology 2010, Gothenburg, Sweden (2010)
- Yeast as a platform cell factory for production of fuels and chemicals. International Biotechnology Symposium 2010, Rimini, Italy (2010)
- Yeast as a platform cell factory. Power of Microbes in Industry and Environment 2010, Island Krk, Croatia (2010)
- The application of genome-scale metabolic models in industrial biotechnology, ICSB2010, Edinburgh, UK (2010)
- Synthetic biology and industrial biotechnology, Green Chem Conference, Lund, Sweden (2010)
- Development of yeast as a platform cell factory, 3rd International Conference on Biomolecular Engineering, San Fransisco, USA (2011)
- Engineering of the Biocatalyst in Biorefineries, 3rd International Symposium for Innovation Bioproduction Kobe, Kobe, Japan (2011)
- The Art of Making Yeast to Produce Biodiesel, Chalmers Energy Conference 2011, Gothenburg, Sweden (2011)
- Yeast as Platform Cell Factories in Future Biorefineries, AAAS Annual Symposium 2011, Washington, USA (2011)
- Yeast as Platform Cell Factories in Future Biorefineries, Asian Congress on Biotechnologyn 2011, Shanghai, China (2011)
- Nutritional Systems Biology, Experimental Biology 2011, Washington, USA (2011)
- Yeast as Platform Cell Factories in Future Biorefineries, Danish Conference on Biotechnology 6, Munkebjerg, Denmark (2011)
- Towards The Human Metabolic Atlas, 8th Key Symposium, Stockholm, Sweden (2011)
- Application of Genome Scale Metabolic Models in Industrial Biotechnology, 1st COBRA Conference, Reykavik, Iceland (2011)
- Metabolic Engineering, Synthetic Biology, Systems Biology, … what is the role of Biochemical Engineering, Biochemical and Biomolecular Engineering XVII, Seattle, USA (2011)
Invited seminar presentations (not complete)
- Design of an on-line monitoring system for lactic acid fermentations, Ciba Geigy, Basel, Switzerland (1987)
- Automation of laboratory fermentors, Technical University of Denmark, Lyngby (1987)
- On-line monitoring of lactic acid fermentation, Department of Chemical Engineering, Caltech, Pasedena, California (1988)
- Application of FIA for on-line monitoring of fermentation processes, Technion, Lund, Sweden (1988)
- Structured modelling of microbial systems, Technical University of Denmark, Lyngby (1989)
- Experimentally verification of fermentation models, University of Lund, Sweden (1990)
- Structural models for fermentation processes, Departmental seminar, Institut für Biotechnologie,Technische Universität Graz, Austria (1990)
- Modelling and on-line monitoring of fermentation processes, Departmental seminar, Institut für Technische Chemie, Universität Hannover, Germany (1990)
- Verification of structured models for fermentation processes, Departmental seminar, Kemisk Reaktionsteknik, Chalmars Tekniska Högskola, Gothenburg, Sweden (1991)
- Modelling of filamentous microorganisms, Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan (1992)
- On-line monitoring and modelling of microbial processes, Departmental seminar, Department of Biochemical Engineering, Indian Institute of Technology, New Delhi (1992)
- Growth of filamentous fungi - An engineers perspective, Seminar at University of Manchester, Manchester (1992)
- On-line monitoring of filamentous fungi fermentations, Meeting of EFB Working Party on "Measurement and Control", Florence (1993)
- Modelling of filamentous growth, Meeting of DECHEMA Working Party on "Messung und Regelung in Biotechnologie", Frankfurt (1993)
- Industriel anvendelse af skimmelsvampe, Dansk Ingeniørforening, Copenhagen (1994)
- Metabolic flux analysis of the penicillin fermentation, Institute of Chemical Metalurgy, Chinese Academy of Science, Beijing (1994)
- Mathematical models - An excellent tool in physiological studies of filamentous fungi, Department of Chemical Engineering, University of Minnesota, Minneapolis (1994)
- Physiological Engineering of filamentous fungi, Departmental Seminar, Department of Chemical Engineering, MIT, Cambridge (1994)
- Physiological Engineering. The integration of microbial physiology and chemical engineering, Department of Chemical Engineering, MIT, Cambridge, USA (1996)
- Modelling the growth of filamentous microorganisms, Departmental seminar, Department of Chemical Engineering, Tufts University, Medford, USA (1996)
- Modelling the growth of filamentous microorganisms, Departmental seminar, Department of Chemical and Biochemical Engineering, University of Western Ontario, London, Canada (1996)
- Modelling the growth of filamentous fungi, Department of Chemical Engineering, MIT, Cambridge (1996)
- Metabolic Engineering, University of Shandong, Jinan (1996)
- Metabolic flux analysis of filamentous fungi, BASF, Ludwigshafen (1996)
- Metabolic Flux Analysis, Departmental seminar, Department of Chemical Engineering, Xinghua University, Beijing, China (1996)
- Biochemical analysis of the penicillin biosynthetic pathway, Departmental Seminar, Department of Microbiology, Technical University of Denmark, Lyngby, Denmark (1997)
- Biochemical characterization of the penicillin biosynthetic pathway, Departmental Seminar, Institut für Biotechnologie, ETH, Zürich, Switzerland (1997)
- Metabolic engineering. Methods and applications, Institute seminar, Institut für Biotechnologie, Forschungszentrum Jülich, Germany (1998)
- Enzyme production by Aspergillus. Biochemical engineering methods for fundamental research and process optimisation, Seminar, Carlsberg Laboratory, Copenhagen, Denmark (1999)
- Metabolomics, Seminar, Biologisk Selskab, Copenhagen, Denmark (2000)
- Metabolic Engineering and Functional Genomics, Seminar, Novo Nordisk, Bagsværd, Denmark (2000)
- Metabolic Engineering and Functional Genomics, Seminar, Chr. Hansen, Hørsholm, Denmark (2000)
- Metabolic Engineering and Functional Genomics, Bjerrum-Brøndsted-Lang lecture, Carlsberg Laboratory, Denmark (2000)
- Metabolic engineering of Penicillium chrysogenum for improved b-lactam production, Seminar, Microbia, Cambridge, USA (2001)
- Analysis of metabolism: Control of fluxes, Seminar, BASF, Ludwigshafen, Germany (2001)
- The role of Functional Genomics in Metabolic Engineering, Seminar, EPFL, Lausanne, Switzerland (2001)
- Metabolomics, Seminar, Genomics in Food Science, KVL, Denmark (2002)
- From quantitative physiology to metabolic engineering and systems biology, Sunner Memorial Lecture, Lund University, Lund, Sweden (2002)
- Hough Memorial Lecture, University of Birmingham, Birmingham, UK (2004)
- Metabolic engineering: Impacts of functional genomics, Seconda Università degli Studi di Napoli, Naples, Italy (2005)
- Linking the transcriptome and the metabolome through genome-scale metabolic models, University Milano-Bicocca, Milan, Italy (2005)
- Systems Biology: Current status and future challenges, NTNU, Trondheim, Norway (2005)
- Systems Biology of Yeasts: Impacts on Metabolic Engineering and Basic Sciences, The National Hellenic Research Foundation, Athens, Greece (2006)
- Impacts of systems biology on biotech process based on yeast, Merck, West Point, USA (2006)
- The role of metabolic engineering in the improvement of industrial processes, BIOTEC, Bangkok, Thailand (2006)
- Yeast systems biology: A vehicle for medical and biotechnological research, Department of Chemical and Biological Engineering. Chalmers University of Technology, Gothenburg, Sweden (2007)
- Yeast as a model organism for studying nutragenomic, Department of Systems Biology, ETH Zürich, Switzerland (2007)
- Systems Biology and Synthetic Biology, Beijing University of Chemical Technology, Beijing, China (2007)
- Systems Biology of lipid metabolism in yeast, Department of Biotechnology, University of Graz, Austria (2008)
- Systems Biology as a driver for industrial biotechnology, Department of Chemical Engineering, Catholic University of Chile, Santiago, Chile (2008)
- Systems Biology of Lipid Metabolismı, Departmental Seminar, Institute for Molecular Biosciences, Universität Graz, Austria (2008)
- Industrial systems biology: Yeast and Aspergillus as cell factories for sustainable production of chemicals, Sandoz, Kundl, Austria (2008)
- Industrial Systems Biology: Yeast and Filamentous Fungi as Cell Factories for Sustainable Production of Chemicals, Departmental Seminar, Department of Chemical Engineering, Rice University, Houston, Texas, USA (2008)
- Yeast systems biology: Does this have any medical relevance?, Wallenberg Laboratory, Sahlgrenska Academy, Gothenburg, Sweden (2008)
- Industrial systems biology, Amyris, Berkeley, USA (2009)
- Understanding the function of biological networks through systems biology, Faculty of Science and Mathematics, University of Zagreb, Zagreb, Croatia (2009)
- Systems biology of metabolism: From yeast to mammals, Department of Bioengineering, UC San Diego, California, USA (2009)
- Industrial systems biology, Genomatica, San Diego, USA (2009)
- Industrial systems biology: Yeast and Aspergilli as cell factories for sustainable production of chemicals. CJ Company, Seoul, South Korea (2010)
- Engineering the metabolism of yeast cell factories, Novo Nordisk Foundation, Denmark (2010)
- Development of yeast as a platform cell factory for production of fuels and chemicals through industrial systems biology, Tufts University, Boston, USA (2010)
- Impact of systems biology on synthetic biology, Yale University, New Haven, USA (2010)
- Yeast Systems Biology, Carlsberg Laboratory, Copenhagen, Denmark (2010)
- Biorefinery. Cell Factory Design and Implementation, World Council of Industrial Biotechnology meeting, Beijing, China (2010)
- Development of Yeast as a Platform Cell Factory, Joint Bioenergy Institute, Berkeley, USA (2011)
- Insights into Metabolic Diseases through Systems Biology, SomaLogic, Boulder, USA (2011)
- Systems Biology: Integrated Analysis of Human Metabolism through the Human Metabolic Atlas, Rigshospitalet, Copenhagen, Denmark (2011)
- Yeast as a Cell Factory Platform for Production of Fuels and Chemicals, University of Umeå, Umeå, Sweden (2011)
- Biochemical Engineering as the Foundation of Systems Biology, Synthetic Biology and Metabolic Engineering, Seminar in connection with Prof. Reuss, University of Stuttgart, Germany (2011)
- Systems Biology, Synthetic Biology and Metabolic Engineering of Yeast, Genomatica, San Diego, USA (2011)
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