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Jens Nielsen - Publications

Affiliations: 
Department of Biology and Biological Engineering Chalmers University of Technology, Sweden 
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Year Citation  Score
2024 Chen Y, Gustafsson J, Yang J, Nielsen J, Kerkhoven EJ. Single-cell omics analysis with genome-scale metabolic modeling. Current Opinion in Biotechnology. 86: 103078. PMID 38359604 DOI: 10.1016/j.copbio.2024.103078  0.311
2024 Chen Y, Gustafsson J, Tafur Rangel A, Anton M, Domenzain I, Kittikunapong C, Li F, Yuan L, Nielsen J, Kerkhoven EJ. Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0. Nature Protocols. PMID 38238583 DOI: 10.1038/s41596-023-00931-7  0.312
2023 Yang H, Li X, Jin H, Turkez H, Ozturk G, Doganay HL, Zhang C, Nielsen J, Uhlén M, Borén J, Mardinoglu A. Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators. Free Radical Biology & Medicine. 204: 347-358. PMID 37245532 DOI: 10.1016/j.freeradbiomed.2023.05.013  0.301
2023 Qin N, Li L, Ji X, Pereira R, Chen Y, Yin S, Li C, Wan X, Qiu D, Jiang J, Luo H, Zhang Y, Dong G, Zhang Y, Shi S, ... ... Nielsen J, et al. Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast. Cell. PMID 36758548 DOI: 10.1016/j.cell.2023.01.014  0.323
2022 Luo H, Li P, Ji B, Nielsen J. Modeling the metabolic dynamics at the genome-scale by optimized yield analysis. Metabolic Engineering. 75: 119-130. PMID 36503050 DOI: 10.1016/j.ymben.2022.12.001  0.317
2022 Cao X, Yu W, Chen Y, Yang S, Zhao ZK, Nielsen J, Luan H, Zhou YJ. Engineering yeast for high-level production of diterpenoid sclareol. Metabolic Engineering. PMID 36371032 DOI: 10.1016/j.ymben.2022.11.002  0.355
2022 Lu H, Kerkhoven EJ, Nielsen J. A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species. Biomolecules. 12. PMID 36358981 DOI: 10.3390/biom12111632  0.306
2022 Yu T, Liu Q, Wang X, Liu X, Chen Y, Nielsen J. Metabolic reconfiguration enables synthetic reductive metabolism in yeast. Nature Metabolism. PMID 36302903 DOI: 10.1038/s42255-022-00654-1  0.314
2022 Ishchuk OP, Domenzain I, Sánchez BJ, Muñiz-Paredes F, Martínez JL, Nielsen J, Petranovic D. Genome-scale modeling drives 70-fold improvement of intracellular heme production in . Proceedings of the National Academy of Sciences of the United States of America. 119: e2108245119. PMID 35858410 DOI: 10.1073/pnas.2108245119  0.318
2022 Domenzain I, Sánchez B, Anton M, Kerkhoven EJ, Millán-Oropeza A, Henry C, Siewers V, Morrissey JP, Sonnenschein N, Nielsen J. Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0. Nature Communications. 13: 3766. PMID 35773252 DOI: 10.1038/s41467-022-31421-1  0.335
2022 Chen Y, Li F, Nielsen J. Genome-scale modeling of yeast metabolism: retrospectives and perspectives. Fems Yeast Research. PMID 35094064 DOI: 10.1093/femsyr/foac003  0.33
2020 Hellgren J, Godina A, Nielsen J, Siewers V. Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products. Metabolic Engineering. 62: 150-160. PMID 32911054 DOI: 10.1016/J.Ymben.2020.09.003  0.386
2020 Hu Y, Zhu Z, Gradischnig D, Winkler M, Nielsen J, Siewers V. Engineering carboxylic acid reductase for selective synthesis of medium-chain fatty alcohols in yeast. Proceedings of the National Academy of Sciences of the United States of America. PMID 32873649 DOI: 10.1073/Pnas.2010521117  0.361
2020 Hou J, Nielsen J. Editorial: yeast synthetic biology. Fems Yeast Research. 20. PMID 32854113 DOI: 10.1093/Femsyr/Foaa049  0.326
2020 Björkeroth J, Campbell K, Malina C, Yu R, Di Bartolomeo F, Nielsen J. Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media. Proceedings of the National Academy of Sciences of the United States of America. PMID 32817546 DOI: 10.1073/Pnas.1921890117  0.349
2020 Van Olden CC, Van de Laar AW, Meijnikman AS, Aydin O, Van Olst N, Hoozemans JB, De Brauw LM, Bruin SC, Acherman Y, Verheij J, Pyykkö JE, Hagedoorn M, Sanderman R, Bosma NC, Tremaroli V, ... ... Nielsen J, et al. A Systems Biology approach to understand gut microbiota and host metabolism in morbid obesity: design of the BARIA Longitudinal Cohort Study. Journal of Internal Medicine. PMID 32640105 DOI: 10.1111/Joim.13157  0.308
2020 Babaei M, Borja Zamfir GM, Chen X, Bjerre Christensen H, Kristensen M, Nielsen J, Borodina I. Metabolic engineering of Saccharomyces cerevisiae for rosmarinic acid production. Acs Synthetic Biology. PMID 32589831 DOI: 10.1021/Acssynbio.0C00048  0.343
2020 Nilsson A, Haanstra JR, Engqvist M, Gerding A, Bakker BM, Klingmüller U, Teusink B, Nielsen J. Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis. Proceedings of the National Academy of Sciences of the United States of America. PMID 32341162 DOI: 10.1073/Pnas.1919250117  0.337
2020 Zhang C, Bjornson E, Arif M, Tebani A, Lovric A, Benfeitas R, Ozcan M, Juszczak K, Kim W, Kim JT, Bidkhori G, Ståhlman M, Bergh PO, Adiels M, Turkez H, ... ... Nielsen J, et al. The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alc33oholic fatty liver disease. Molecular Systems Biology. 16: e9495. PMID 32337855 DOI: 10.15252/Msb.209495  0.363
2020 Yu R, Campbell K, Pereira R, Björkeroth J, Qi Q, Vorontsov E, Sihlbom C, Nielsen J. Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast. Nature Communications. 11: 1881. PMID 32312967 DOI: 10.1038/S41467-020-15749-0  0.386
2020 Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Nielsen J, et al. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. 38: 504. PMID 32265554 DOI: 10.1038/S41587-020-0477-4  0.52
2020 Robinson JL, Kocabaş P, Wang H, Cholley PE, Cook D, Nilsson A, Anton M, Ferreira R, Domenzain I, Billa V, Limeta A, Hedin A, Gustafsson J, Kerkhoven EJ, Svensson LT, ... ... Nielsen J, et al. An atlas of human metabolism. Science Signaling. 13. PMID 32209698 DOI: 10.1126/Scisignal.Aaz1482  0.522
2020 Lam S, Doran S, Yuksel HH, Altay O, Turkez H, Nielsen J, Boren J, Uhlen M, Mardinoglu A. Addressing the heterogeneity in liver diseases using biological networks. Briefings in Bioinformatics. PMID 32201876 DOI: 10.1093/Bib/Bbaa002  0.337
2020 Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Nielsen J, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. PMID 32123384 DOI: 10.1038/S41587-020-0446-Y  0.533
2020 Gutierrez JM, Feizi A, Li S, Kallehauge TB, Hefzi H, Grav LM, Ley D, Baycin Hizal D, Betenbaugh MJ, Voldborg B, Faustrup Kildegaard H, Min Lee G, Palsson BO, Nielsen J, Lewis NE. Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion. Nature Communications. 11: 68. PMID 31896772 DOI: 10.1038/S41467-019-13867-Y  0.529
2020 Anton M, Cholley P, Robinson JL, Huang S, Svensson LT, Nielsen J. Metabolic Atlas – a website for exploration and visualization of metabolic networks F1000research. 9. DOI: 10.7490/F1000Research.1117998.1  0.333
2020 Cook D, Nielsen J, Braun E. A systems medicine-based approach for finding metabolic targets applied to primary basal-like breast cancer. Journal of Clinical Oncology. 38. DOI: 10.1200/Jco.2020.38.15_Suppl.E12590  0.324
2019 Borja GM, Rodriguez A, Campbell K, Borodina I, Chen Y, Nielsen J. Metabolic engineering and transcriptomic analysis of Saccharomyces cerevisiae producing p-coumaric acid from xylose. Microbial Cell Factories. 18: 191. PMID 31690329 DOI: 10.1186/S12934-019-1244-4  0.339
2019 Yu R, Nielsen J. Big data in yeast systems biology. Fems Yeast Research. PMID 31603503 DOI: 10.1093/Femsyr/Foz070  0.377
2019 Ferreira R, Skrekas C, Hedin A, Sánchez BJ, Siewers V, Nielsen J, David F. Model-assisted fine-tuning of central carbon metabolism in yeast through dCas9-based regulation. Acs Synthetic Biology. PMID 31577419 DOI: 10.1021/acssynbio.9b00258  0.329
2019 Pereira R, Wei Y, Mohamed E, Radi M, Malina C, Herrgård MJ, Feist AM, Nielsen J, Chen Y. Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae. Metabolic Engineering. PMID 31550508 DOI: 10.1016/J.Ymben.2019.09.008  0.323
2019 Tiukova IA, Prigent S, Nielsen J, Sandgren M, Kerkhoven EJ. Genome-scale model of Rhodotorula toruloides metabolism. Biotechnology and Bioengineering. 116: 3396-3408. PMID 31502665 DOI: 10.1002/Bit.27162  0.418
2019 Lu H, Li F, Sánchez BJ, Zhu Z, Li G, Domenzain I, Marcišauskas S, Anton PM, Lappa D, Lieven C, Beber ME, Sonnenschein N, Kerkhoven EJ, Nielsen J. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications. 10: 3586. PMID 31395883 DOI: 10.1038/S41467-019-11581-3  0.422
2019 Dabirian Y, Gonçalves Teixeira P, Nielsen J, Siewers V, David F. FadR-based biosensor assisted screening for genes enhancing fatty acyl-CoA pools in Saccharomyces cerevisiae. Acs Synthetic Biology. PMID 31314504 DOI: 10.1021/Acssynbio.9B00118  0.349
2019 Tiukova IA, Brandenburg J, Blomqvist J, Sampels S, Mikkelsen N, Skaugen M, Arntzen MØ, Nielsen J, Sandgren M, Kerkhoven EJ. Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production. Biotechnology For Biofuels. 12: 137. PMID 31171938 DOI: 10.1186/S13068-019-1478-8  0.385
2019 Hu Y, Zhu Z, Nielsen J, Siewers V. Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals. Open Biology. 9: 190049. PMID 31088249 DOI: 10.1098/Rsob.190049  0.367
2019 Nielsen JC, Prigent S, Grijseels S, Workman M, Ji B, Nielsen J. Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi. Msystems. 4. PMID 31020039 DOI: 10.1128/mSystems.00012-19  0.318
2019 Wang G, Björk SM, Huang M, Liu Q, Campbell K, Nielsen J, Joensson HN, Petranovic D. RNAi expression tuning, microfluidic screening, and genome recombineering for improved protein production in . Proceedings of the National Academy of Sciences of the United States of America. PMID 31000602 DOI: 10.1073/Pnas.1820561116  0.352
2019 Pereira R, Vilaça P, Maia P, Nielsen J, Rocha I. TDPS - Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategies. Acs Synthetic Biology. PMID 30925047 DOI: 10.1021/Acssynbio.8B00248  0.386
2019 Li X, Chen Y, Nielsen J. Harnessing xylose pathways for biofuels production. Current Opinion in Biotechnology. 57: 56-65. PMID 30785001 DOI: 10.1016/j.copbio.2019.01.006  0.304
2019 Bauer J, Brambilla L, Duboc P, Francois JM, Gancedo C, Giuseppin ML, Heijnen JJ, Hoare M, Lange HC, Madden EA, Niederberger P, Nielsen J, Parrou JL, Petit T, Porro D, et al. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme and Microbial Technology. 26: 706-714. PMID 10862876 DOI: 10.1016/S0141-0229(00)00162-9  0.336
2018 Bidkhori G, Benfeitas R, Klevstig M, Zhang C, Nielsen J, Uhlen M, Boren J, Mardinoglu A. Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes. Proceedings of the National Academy of Sciences of the United States of America. 115: E11874-E11883. PMID 30482855 DOI: 10.1073/Pnas.1807305115  0.356
2018 Huang M, Wang G, Qin J, Petranovic D, Nielsen J. Engineering the protein secretory pathway of enables improved protein production. Proceedings of the National Academy of Sciences of the United States of America. PMID 30397111 DOI: 10.1073/Pnas.1809921115  0.345
2018 Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. Plos Computational Biology. 14: e1006541. PMID 30335785 DOI: 10.1371/Journal.Pcbi.1006541  0.352
2018 Yu T, Zhou YJ, Huang M, Liu Q, Pereira R, David F, Nielsen J. Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis. Cell. PMID 30100189 DOI: 10.1016/J.Cell.2018.07.013  0.441
2018 Dai Z, Huang M, Chen Y, Siewers V, Nielsen J. Global rewiring of cellular metabolism renders Saccharomyces cerevisiae Crabtree negative. Nature Communications. 9: 3059. PMID 30076310 DOI: 10.1038/s41467-018-05409-9  0.311
2018 Yu T, Zhou YJ, Wenning L, Liu Q, Krivoruchko A, Siewers V, Nielsen J, David F. Author Correction: Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals. Nature Communications. 9: 16220. PMID 30004090 DOI: 10.1038/Ncomms16220  0.342
2018 Teixeira PG, David F, Siewers V, Nielsen J. Engineering lipid droplet assembly mechanisms for improved triacylglycerol accumulation in Saccharomyces cerevisiae. Fems Yeast Research. 18. PMID 29897501 DOI: 10.1093/Femsyr/Foy060  0.387
2018 Ferreira R, Teixeira PG, Gossing M, David F, Siewers V, Nielsen J. Metabolic engineering of for overproduction of triacylglycerols. Metabolic Engineering Communications. 6: 22-27. PMID 29896445 DOI: 10.1016/J.Meteno.2018.01.002  0.418
2018 Rola-Łuszczak M, Materniak-Kornas M, Pluta A, Podgórska K, Nielsen J, Stadejek T, Kuźmak J. Transcriptional profiles of PBMCs from pigs infected with three genetically diverse porcine reproductive and respiratory syndrome virus strains. Molecular Biology Reports. 45: 675-688. PMID 29882085 DOI: 10.1007/S11033-018-4204-X  0.315
2018 Prigent S, Nielsen JC, Frisvad JC, Nielsen J. Reconstruction of 24 Penicillium genome-scale metabolic models shows diversity based on their secondary metabolism. Biotechnology and Bioengineering. 115: 2604-2612. PMID 29873086 DOI: 10.1002/bit.26739  0.305
2018 Maury J, Kannan S, Jensen NB, Öberg FK, Kildegaard KR, Forster J, Nielsen J, Workman CT, Borodina I. Glucose-Dependent Promoters for Dynamic Regulation of Metabolic Pathways. Frontiers in Bioengineering and Biotechnology. 6: 63. PMID 29872655 DOI: 10.3389/Fbioe.2018.00063  0.699
2018 Bao J, Huang M, Petranovic D, Nielsen J. Balanced trafficking between the ER and the Golgi apparatus increases protein secretion in yeast. Amb Express. 8: 37. PMID 29532188 DOI: 10.1186/S13568-018-0571-X  0.314
2018 Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, ... ... Nielsen J, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology. PMID 29457794 DOI: 10.1038/Nbt.4072  0.569
2018 Mardinoglu A, Wu H, Bjornson E, Zhang C, Hakkarainen A, Räsänen SM, Lee S, Mancina RM, Bergentall M, Pietiläinen KH, Söderlund S, Matikainen N, Ståhlman M, Bergh PO, Adiels M, ... ... Nielsen J, et al. An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans. Cell Metabolism. PMID 29456073 DOI: 10.1016/J.Cmet.2018.01.005  0.312
2018 Ferreira R, Teixeira PG, Siewers V, Nielsen J. Redirection of lipid flux toward phospholipids in yeast increases fatty acid turnover and secretion. Proceedings of the National Academy of Sciences of the United States of America. PMID 29358378 DOI: 10.1073/Pnas.1715282115  0.384
2018 Bergenholm D, Gossing M, Wei Y, Siewers V, Nielsen J. Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids. Biotechnology and Bioengineering. PMID 29313898 DOI: 10.1002/Bit.26518  0.302
2018 Huang M, Joensson HN, Nielsen J. High-Throughput Microfluidics for the Screening of Yeast Libraries. Methods in Molecular Biology (Clifton, N.J.). 1671: 307-317. PMID 29170967 DOI: 10.1007/978-1-4939-7295-1_19  0.348
2018 Zhou YJ, Kerkhoven EJ, Nielsen J. Barriers and opportunities in bio-based production of hydrocarbons Nature Energy. 3: 925-935. DOI: 10.1038/S41560-018-0197-X  0.321
2017 Nilsson A, Nielsen J, Palsson BO. Metabolic Models of Protein Allocation Call for the Kinetome. Cell Systems. 5: 538-541. PMID 29284126 DOI: 10.1016/J.Cels.2017.11.013  0.447
2017 Zhou YJ, Hu Y, Zhu Z, Siewers V, Nielsen J. Dynamic engineering of 1-alkenes biosynthesis and secretion in yeast. Acs Synthetic Biology. PMID 29284088 DOI: 10.1021/Acssynbio.7B00338  0.378
2017 Zhao X, Nielsen J. Metabolic engineering frontiers emerging with advanced tools and methodologies. Biotechnology Advances. PMID 29107149 DOI: 10.1016/J.Biotechadv.2017.10.007  0.339
2017 Rodriguez A, Chen Y, Khoomrung S, Özdemir E, Borodina I, Nielsen J. Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains. Metabolic Engineering. PMID 29101089 DOI: 10.1016/J.Ymben.2017.10.013  0.396
2017 Huang M, Bao J, Hallström BM, Petranovic D, Nielsen J. Efficient protein production by yeast requires global tuning of metabolism. Nature Communications. 8: 1131. PMID 29070809 DOI: 10.1038/S41467-017-00999-2  0.39
2017 Nielsen JC, Nielsen J. Development of fungal cell factories for the production of secondary metabolites: Linking genomics and metabolism. Synthetic and Systems Biotechnology. 2: 5-12. PMID 29062956 DOI: 10.1016/j.synbio.2017.02.002  0.312
2017 Zhu Z, Zhou YJ, Kang MK, Krivoruchko A, Buijs NA, Nielsen J. Enabling the synthesis of medium chain alkanes and 1-alkenes in yeast. Metabolic Engineering. PMID 28939277 DOI: 10.1016/J.Ymben.2017.09.007  0.316
2017 Liu G, Chen Y, Færgeman NJ, Nielsen J. Elimination of the last reactions in ergosterol biosynthesis alters the resistance of Saccharomyces cerevisiae to multiple stresses. Fems Yeast Research. 17. PMID 28910986 DOI: 10.1093/Femsyr/Fox063  0.301
2017 Gong Z, Nielsen J, Zhou YJ. Engineering robustness of microbial cell factories. Biotechnology Journal. PMID 28857502 DOI: 10.1002/Biot.201700014  0.389
2017 Sánchez BJ, Zhang C, Nilsson A, Lahtvee PJ, Kerkhoven EJ, Nielsen J. Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints. Molecular Systems Biology. 13: 935. PMID 28779005 DOI: 10.15252/Msb.20167411  0.434
2017 Cook DJ, Nielsen J. Genome-scale metabolic models applied to human health and disease. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 28644920 DOI: 10.1002/Wsbm.1393  0.372
2017 Kerkhoven EJ, Kim YM, Wei S, Nicora CD, Fillmore TL, Purvine SO, Webb-Robertson BJ, Smith RD, Baker SE, Metz TO, Nielsen J. Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica. Mbio. 8. PMID 28634240 DOI: 10.1128/Mbio.00857-17  0.362
2017 Rodriguez A, Strucko T, Stahlhut SG, Kristensen M, Svenssen DK, Forster J, Nielsen J, Borodina I. Metabolic engineering of yeast for fermentative production of flavonoids. Bioresource Technology. PMID 28634125 DOI: 10.1016/J.Biortech.2017.06.043  0.707
2017 Yu T, Zhou YJ, Wenning L, Liu Q, Krivoruchko A, Siewers V, Nielsen J, David F. Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals. Nature Communications. 8: 15587. PMID 28548095 DOI: 10.1038/Ncomms15587  0.377
2017 Hu Y, Zhou YJ, Bao J, Huang L, Nielsen J, Krivoruchko A. Metabolic engineering of Saccharomyces cerevisiae for production of germacrene A, a precursor of beta-elemene. Journal of Industrial Microbiology & Biotechnology. PMID 28547322 DOI: 10.1007/S10295-017-1934-Z  0.338
2017 Nielsen J, Archer J, Essack M, Bajic VB, Gojobori T, Mijakovic I. Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity. Applied Microbiology and Biotechnology. PMID 28528426 DOI: 10.1007/S00253-017-8310-9  0.312
2017 Kang MK, Zhou YJ, Buijs NA, Nielsen J. Functional screening of aldehyde decarbonylases for long-chain alkane production by Saccharomyces cerevisiae. Microbial Cell Factories. 16: 74. PMID 28464872 DOI: 10.1186/S12934-017-0683-Z  0.314
2017 Chen Y, Wang Y, Nielsen J. Systematic inference of functional phosphorylation events in yeast metabolism. Bioinformatics (Oxford, England). PMID 28334215 DOI: 10.1093/Bioinformatics/Btx110  0.32
2017 Teixeira PG, Ferreira R, Zhou YJ, Siewers V, Nielsen J. Dynamic regulation of fatty acid pools for improved production of fatty alcohols in Saccharomyces cerevisiae. Microbial Cell Factories. 16: 45. PMID 28298234 DOI: 10.1186/S12934-017-0663-3  0.322
2017 Mardinoglu A, Bjornson E, Zhang C, Klevstig M, Söderlund S, Ståhlman M, Adiels M, Hakkarainen A, Lundbom N, Kilicarslan M, Hallström BM, Lundbom J, Vergès B, Barrett PH, Watts GF, ... ... Nielsen J, et al. Personal model-assisted identification of NAD(+) and glutathione metabolism as intervention target in NAFLD. Molecular Systems Biology. 13: 916. PMID 28254760 DOI: 10.15252/Msb.20167422  0.346
2017 Robinson JL, Nielsen J. Anticancer drug discovery through genome-scale metabolic modeling Current Opinion in Systems Biology. 4: 1-8. DOI: 10.1016/J.Coisb.2017.05.007  0.372
2016 Martínez JL, Meza E, Petranovic D, Nielsen J. The impact of respiration and oxidative stress response on recombinant α-amylase production by. Metabolic Engineering Communications. 3: 205-210. PMID 29468124 DOI: 10.1016/J.Meteno.2016.06.003  0.342
2016 Pereira R, Nielsen J, Rocha I. Improving the flux distributions simulated with genome-scale metabolic models of. Metabolic Engineering Communications. 3: 153-163. PMID 29468121 DOI: 10.1016/j.meteno.2016.05.002  0.303
2016 Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J. Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. Npj Systems Biology and Applications. 2: 16005. PMID 28725468 DOI: 10.1038/npjsba.2016.5  0.315
2016 Sweetlove LJ, Nielsen J, Fernie AR. Engineering central metabolism - a grand challenge for plant biologists. The Plant Journal : For Cell and Molecular Biology. PMID 28004455 DOI: 10.1111/tpj.13464  0.309
2016 Casey JR, Mardinoglu A, Nielsen J, Karl DM. Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus. Msystems. 1. PMID 27868089 DOI: 10.1128/mSystems.00065-16  0.376
2016 Li M, Schneider K, Kristensen M, Borodina I, Nielsen J. Engineering yeast for high-level production of stilbenoid antioxidants. Scientific Reports. 6: 36827. PMID 27833117 DOI: 10.1038/Srep36827  0.378
2016 Zhou YJ, Buijs NA, Zhu Z, Gómez DO, Boonsombuti A, Siewers V, Nielsen J. Harnessing yeast peroxisomes for biosynthesis of fatty acid-derived biofuels and chemicals with relieved side-pathway competition. Journal of the American Chemical Society. PMID 27753483 DOI: 10.1021/Jacs.6B07394  0.362
2016 Grijseels S, Nielsen JC, Randelovic M, Nielsen J, Nielsen KF, Workman M, Frisvad JC. Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites. Scientific Reports. 6: 35112-35112. PMID 27739446 DOI: 10.1038/Srep35112  0.348
2016 Tippmann S, Anfelt J, David F, Rand JM, Siewers V, Uhlén M, Nielsen J, Hudson EP. Affibody scaffolds improve sesquiterpene production in Saccharomyces cerevisiae. Acs Synthetic Biology. PMID 27560952 DOI: 10.1021/Acssynbio.6B00109  0.353
2016 Gatto F, Schulze A, Nielsen J. Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics. Cell Reports. PMID 27396332 DOI: 10.1016/J.Celrep.2016.06.038  0.327
2016 Zhou YJ, Buijs NA, Zhu Z, Qin J, Siewers V, Nielsen J. Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories. Nature Communications. 7: 11709. PMID 27222209 DOI: 10.1038/Ncomms11709  0.351
2016 Gatto F, Volpi N, Nilsson H, Nookaew I, Maruzzo M, Roma A, Johansson ME, Stierner U, Lundstam S, Basso U, Nielsen J. Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma. Cell Reports. PMID 27184840 DOI: 10.1016/J.Celrep.2016.04.056  0.32
2016 Kildegaard KR, Jensen NB, Schneider K, Czarnotta E, Özdemir E, Klein T, Maury J, Ebert BE, Christensen HB, Chen Y, Kim IK, Herrgård MJ, Blank LM, Forster J, Nielsen J, et al. Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway. Microbial Cell Factories. 15: 53. PMID 26980206 DOI: 10.1186/S12934-016-0451-5  0.669
2016 Nielsen J, Keasling JD. Engineering Cellular Metabolism. Cell. 164: 1185-97. PMID 26967285 DOI: 10.1016/J.Cell.2016.02.004  0.404
2016 Maury J, Germann SM, Baallal Jacobsen SA, Jensen NB, Kildegaard KR, Herrgård MJ, Schneider K, Koza A, Forster J, Nielsen J, Borodina I. EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae. Plos One. 11: e0150394. PMID 26934490 DOI: 10.1371/Journal.Pone.0150394  0.722
2016 David F, Nielsen J, Siewers V. Flux Control at the Malonyl-CoA Node through Hierarchical Dynamic Pathway Regulation in Saccharomyces cerevisiae. Acs Synthetic Biology. 5: 224-33. PMID 26750662 DOI: 10.1021/acssynbio.5b00161  0.304
2016 Martínez JL, Petranovic D, Nielsen J. Heme metabolism in stress regulation and protein production: from Cinderella to a key player. Bioengineered. 0. PMID 26731643 DOI: 10.1080/21655979.2015.1126016  0.372
2016 de Jong BW, Shi S, Valle-Rodríguez JO, Siewers V, Nielsen J. Metabolic pathway engineering for fatty acid ethyl ester production in Saccharomyces cerevisiae using stable chromosomal integration Journal of Industrial Microbiology and Biotechnology. 42: 477-486. PMID 25422103 DOI: 10.1007/S10295-014-1540-2  0.403
2016 Uhlén M, Hallström BM, Lindskog C, Mardinoglu A, Pontén F, Nielsen J. Transcriptomics resources of human tissues and organs Molecular Systems Biology. 12. DOI: 10.15252/Msb.20155865  0.3
2015 Ghaffari P, Mardinoglu A, Nielsen J. Cancer Metabolism: A Modeling Perspective Frontiers in Physiology. 6: 382-382. PMID 26733270 DOI: 10.3389/Fphys.2015.00382  0.372
2015 Shi S, Ji H, Siewers V, Nielsen J. Improved production of fatty acids by Saccharomyces cerevisiae through screening a cDNA library from the oleaginous yeast Yarrowia lipolytica. Fems Yeast Research. PMID 26658002 DOI: 10.1093/Femsyr/Fov108  0.351
2015 Irani ZA, Kerkhoven E, Shojaosadati SA, Nielsen J. Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins. Biotechnology and Bioengineering. PMID 26480251 DOI: 10.1002/Bit.25863  0.354
2015 Mardinoglu A, Shoaie S, Bergentall M, Ghaffari P, Zhang C, Larsson E, Bäckhed F, Nielsen J. The gut microbiota modulates host amino acid and glutathione metabolism in mice. Molecular Systems Biology. 11: 834. PMID 26475342 DOI: 10.15252/Msb.20156487  0.359
2015 Anfelt J, Kaczmarzyk D, Shabestary K, Renberg B, Rockberg J, Nielsen J, Uhlén M, Hudson EP. Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol production. Microbial Cell Factories. 14: 167. PMID 26474754 DOI: 10.1186/S12934-015-0355-9  0.394
2015 Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, ... ... Nielsen J, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284 DOI: 10.15252/Msb.20156157  0.45
2015 Mardinoglu A, Heiker JT, Gärtner D, Björnson E, Schön MR, Flehmig G, Klöting N, Krohn K, Fasshauer M, Stumvoll M, Nielsen J, Blüher M. Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue. Scientific Reports. 5: 14841. PMID 26434764 DOI: 10.1038/Srep14841  0.33
2015 Fletcher E, Feizi A, Kim S, Siewers V, Nielsen J. RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH. Microbial Cell Factories. 14: 143. PMID 26376644 DOI: 10.1186/S12934-015-0331-4  0.307
2015 Qin J, Zhou YJ, Krivoruchko A, Huang M, Liu L, Khoomrung S, Siewers V, Jiang B, Nielsen J. Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine. Nature Communications. 6: 8224. PMID 26345617 DOI: 10.1038/Ncomms9224  0.39
2015 Li M, Kildegaard KR, Chen Y, Rodriguez A, Borodina I, Nielsen J. De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae. Metabolic Engineering. 32: 1-11. PMID 26344106 DOI: 10.1016/J.Ymben.2015.08.007  0.385
2015 Nielsen J. BIOENGINEERING. Yeast cell factories on the horizon. Science (New York, N.Y.). 349: 1050-1. PMID 26339012 DOI: 10.1126/Science.Aad2081  0.37
2015 Rodriguez A, Kildegaard KR, Li M, Borodina I, Nielsen J. Establishment of a yeast platform strain for production of p-coumaric acid through metabolic engineering of aromatic amino acid biosynthesis. Metabolic Engineering. 31: 181-8. PMID 26292030 DOI: 10.1016/J.Ymben.2015.08.003  0.358
2015 Huang M, Bai Y, Sjostrom SL, Hallström BM, Liu Z, Petranovic D, Uhlén M, Joensson HN, Andersson-Svahn H, Nielsen J. Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast. Proceedings of the National Academy of Sciences of the United States of America. 112: E4689-96. PMID 26261321 DOI: 10.1073/Pnas.1506460112  0.367
2015 Zhang Y, Liu G, Engqvist MK, Krivoruchko A, Hallström BM, Chen Y, Siewers V, Nielsen J. Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain. Microbial Cell Factories. 14: 116. PMID 26253003 DOI: 10.1186/S12934-015-0305-6  0.385
2015 Shoaie S, Ghaffari P, Kovatcheva-Datchary P, Mardinoglu A, Sen P, Pujos-Guillot E, de Wouters T, Juste C, Rizkalla S, Chilloux J, Hoyles L, Nicholson JK, Dore J, Dumas ME, ... ... Nielsen J, et al. Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome. Cell Metabolism. 22: 320-31. PMID 26244934 DOI: 10.1016/J.Cmet.2015.07.001  0.329
2015 Sánchez BJ, Nielsen J. Genome scale models of yeast: towards standardized evaluation and consistent omic integration. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 26079294 DOI: 10.1039/C5Ib00083A  0.393
2015 López J, Essus K, Kim IK, Pereira R, Herzog J, Siewers V, Nielsen J, Agosin E. Production of β-ionone by combined expression of carotenogenic and plant CCD1 genes in Saccharomyces cerevisiae. Microbial Cell Factories. 14: 84. PMID 26063466 DOI: 10.1186/S12934-015-0273-X  0.345
2015 Gatto F, Miess H, Schulze A, Nielsen J. Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism. Scientific Reports. 5: 10738. PMID 26040780 DOI: 10.1038/Srep10738  0.42
2015 Tymoshenko S, Oppenheim RD, Agren R, Nielsen J, Soldati-Favre D, Hatzimanikatis V. Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. Plos Computational Biology. 11: e1004261. PMID 26001086 DOI: 10.1371/Journal.Pcbi.1004261  0.447
2015 Väremo L, Scheele C, Broholm C, Mardinoglu A, Kampf C, Asplund A, Nookaew I, Uhlén M, Pedersen BK, Nielsen J. Proteome- and transcriptome-driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes. Cell Reports. 11: 921-33. PMID 25937284 DOI: 10.1016/J.Celrep.2015.04.010  0.398
2015 Nicastro R, Tripodi F, Guzzi C, Reghellin V, Khoomrung S, Capusoni C, Compagno C, Airoldi C, Nielsen J, Alberghina L, Coccetti P. Enhanced amino acid utilization sustains growth of cells lacking Snf1/AMPK. Biochimica Et Biophysica Acta. 1853: 1615-25. PMID 25841981 DOI: 10.1016/J.Bbamcr.2015.03.014  0.39
2015 Pronk JT, Lee SY, Lievense J, Pierce J, Palsson B, Uhlen M, Nielsen J. How to set up collaborations between academia and industrial biotech companies. Nature Biotechnology. 33: 237-40. PMID 25748909 DOI: 10.1038/Nbt.3171  0.4
2015 Zhang C, Ji B, Mardinoglu A, Nielsen J, Hua Q. Logical transformation of genome-scale metabolic models for gene level applications and analysis. Bioinformatics (Oxford, England). PMID 25735769 DOI: 10.1093/Bioinformatics/Btv134  0.359
2015 Jullesson D, David F, Pfleger B, Nielsen J. Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals. Biotechnology Advances. PMID 25728067 DOI: 10.1016/J.Biotechadv.2015.02.011  0.38
2015 Pfleger BF, Gossing M, Nielsen J. Metabolic engineering strategies for microbial synthesis of oleochemicals. Metabolic Engineering. 29: 1-11. PMID 25662836 DOI: 10.1016/J.Ymben.2015.01.009  0.388
2015 Ghaffari P, Mardinoglu A, Asplund A, Shoaie S, Kampf C, Uhlen M, Nielsen J. Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling Scientific Reports. 5: 8183-8183. PMID 25640694 DOI: 10.1038/Srep08183  0.336
2015 Buijs NA, Zhou YJ, Siewers V, Nielsen J. Long‐chain alkane production by the yeast Saccharomyces cerevisiae Biotechnology and Bioengineering. 112: 1275-1279. PMID 25545362 DOI: 10.1002/Bit.25522  0.342
2015 Krivoruchko A, Nielsen J. Production of natural products through metabolic engineering of Saccharomyces cerevisiae. Current Opinion in Biotechnology. 35: 7-15. PMID 25544013 DOI: 10.1016/j.copbio.2014.12.004  0.322
2015 Krivoruchko A, Zhang Y, Siewers V, Chen Y, Nielsen J. Microbial acetyl-CoA metabolism and metabolic engineering. Metabolic Engineering. 28: 28-42. PMID 25485951 DOI: 10.1016/j.ymben.2014.11.009  0.327
2015 Borodina I, Kildegaard KR, Jensen NB, Blicher TH, Maury J, Sherstyk S, Schneider K, Lamosa P, Herrgård MJ, Rosenstand I, Öberg F, Forster J, Nielsen J. Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine. Metabolic Engineering. 27: 57-64. PMID 25447643 DOI: 10.1016/J.Ymben.2014.10.003  0.695
2015 Martínez JL, Liu L, Petranovic D, Nielsen J. Engineering the oxygen sensing regulation results in an enhanced recombinant human hemoglobin production by Saccharomyces cerevisiae. Biotechnology and Bioengineering. 112: 181-8. PMID 25082441 DOI: 10.1002/Bit.25347  0.362
2015 Kildegaard KR, Wang Z, Chen Y, Nielsen J, Borodina I. Production of 3-hydroxypropionic acid from glucose and xylose by metabolically engineered Saccharomyces cerevisiae Metabolic Engineering Communications. 2: 132-136. DOI: 10.1016/J.Meteno.2015.10.001  0.386
2014 Aspuria PJ, Lunt SY, Väremo L, Vergnes L, Gozo M, Beach JA, Salumbides B, Reue K, Wiedemeyer WR, Nielsen J, Karlan BY, Orsulic S. Succinate dehydrogenase inhibition leads to epithelial-mesenchymal transition and reprogrammed carbon metabolism. Cancer & Metabolism. 2: 21. PMID 25671108 DOI: 10.1186/2049-3002-2-21  0.372
2014 Chen Y, Zhou YJ, Siewers V, Nielsen J. Enabling Technologies to Advance Microbial Isoprenoid Production Advances in Biochemical Engineering \/ Biotechnology. 148: 143-160. PMID 25549781 DOI: 10.1007/10_2014_284  0.351
2014 Nielsen J. Synthetic biology for engineering acetyl coenzyme A metabolism in yeast. Mbio. 5: e02153. PMID 25370498 DOI: 10.1128/mBio.02153-14  0.307
2014 Caspeta L, Chen Y, Ghiaci P, Feizi A, Buskov S, Hallström BM, Petranovic D, Nielsen J. Altered sterol composition renders yeast thermotolerant Science. 346: 75-78. PMID 25278608 DOI: 10.1126/Science.1258137  0.365
2014 Kildegaard KR, Hallström BM, Blicher TH, Sonnenschein N, Jensen NB, Sherstyk S, Harrison SJ, Maury J, Herrgård MJ, Juncker AS, Forster J, Nielsen J, Borodina I. Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance. Metabolic Engineering. 26: 57-66. PMID 25263954 DOI: 10.1016/J.Ymben.2014.09.004  0.691
2014 Fahnøe U, Pedersen AG, Risager PC, Nielsen J, Belsham GJ, Höper D, Beer M, Rasmussen TB. Rescue of the highly virulent classical swine fever virus strain "Koslov" from cloned cDNA and first insights into genome variations relevant for virulence Virology. 468: 379-387. PMID 25240324 DOI: 10.1016/J.Virol.2014.08.021  0.306
2014 Zhou YJ, Buijs NA, Siewers V, Nielsen J. Fatty Acid-Derived Biofuels and Chemicals Production in Saccharomyces cerevisiae Frontiers in Bioengineering and Biotechnology. 2: 32-32. PMID 25225637 DOI: 10.3389/Fbioe.2014.00032  0.37
2014 Kampf C, Mardinoglu A, Fagerberg L, Hallström BM, Danielsson A, Nielsen J, Pontén F, Uhlen M. Defining the human gallbladder proteome by transcriptomics and affinity proteomics. Proteomics. 14: 2498-2507. PMID 25175928 DOI: 10.1002/Pmic.201400201  0.334
2014 Kerkhoven EJ, Lahtvee P, Nielsen J. Applications of computational modeling in metabolic engineering of yeast Fems Yeast Research. 15: 1-13. PMID 25156867 DOI: 10.1111/1567-1364.12199  0.423
2014 Liu Z, Liu L, Österlund T, Hou J, Huang M, Fagerberg L, Petranovic D, Uhlén M, Nielsen J. Improved production of a heterologous amylase in Saccharomyces cerevisiae by inverse metabolic engineering. Applied and Environmental Microbiology. 80: 5542-50. PMID 24973076 DOI: 10.1128/Aem.00712-14  0.409
2014 Liu L, Feizi A, Österlund T, Hjort C, Nielsen J. Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae Bmc Systems Biology. 8: 73-73. PMID 24961398 DOI: 10.1186/1752-0509-8-73  0.332
2014 Tyo KE, Liu Z, Magnusson Y, Petranovic D, Nielsen J. Impact of protein uptake and degradation on recombinant protein secretion in yeast. Applied Microbiology and Biotechnology. 98: 7149-59. PMID 24816620 DOI: 10.1007/S00253-014-5783-7  0.319
2014 Shi S, Chen Y, Siewers V, Nielsen J. Improving Production of Malonyl Coenzyme A-Derived Metabolites by Abolishing Snf1-Dependent Regulation of Acc1 Mbio. 5. PMID 24803522 DOI: 10.1128/Mbio.01130-14  0.372
2014 Shi S, Valle-Rodríguez JO, Siewers V, Nielsen J. Engineering of chromosomal wax ester synthase integrated Saccharomyces cerevisiae mutants for improved biosynthesis of fatty acid ethyl esters Biotechnology and Bioengineering. 111: 1740-1747. PMID 24752598 DOI: 10.1002/Bit.25234  0.401
2014 Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M. Kinetic models in industrial biotechnology - Improving cell factory performance. Metabolic Engineering. 24: 38-60. PMID 24747045 DOI: 10.1016/J.Ymben.2014.03.007  0.325
2014 Nielsen J, Fussenegger M, Keasling J, Lee SY, Liao JC, Prather K, Palsson B. Engineering synergy in biotechnology. Nature Chemical Biology. 10: 319-22. PMID 24743245 DOI: 10.1038/Nchembio.1519  0.491
2014 El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH, Nielsen J. Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction Bmc Systems Biology. 8: 41-41. PMID 24708835 DOI: 10.1186/1752-0509-8-41  0.374
2014 Borodina I, Nielsen J. Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals. Biotechnology Journal. 9: 609-620. PMID 24677744 DOI: 10.1002/Biot.201300445  0.4
2014 Martínez JL, Bordel S, Hong KK, Nielsen J. Gcn4p and the Crabtree effect of yeast: drawing the causal model of the Crabtree effect in Saccharomyces cerevisiae and explaining evolutionary trade-offs of adaptation to galactose through systems biology. Fems Yeast Research. 14: 654-62. PMID 24655306 DOI: 10.1111/1567-1364.12153  0.328
2014 Agren R, Mardinoglu A, Asplund A, Kampf C, Uhlen M, Nielsen J. Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling Molecular Systems Biology. 10: 721-721. PMID 24646661 DOI: 10.1002/Msb.145122  0.307
2014 Chumnanpuen P, Hansen MAE, Smedsgaard J, Nielsen J. Dynamic Metabolic Footprinting Reveals the Key Components of Metabolic Network in Yeast Saccharomyces cerevisiae. Comparative and Functional Genomics. 2014: 894296-894296. PMID 24616891 DOI: 10.1155/2014/894296  0.388
2014 Mardinoglu A, Agren R, Kampf C, Asplund A, Uhlen M, Nielsen J. Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease Nature Communications. 5: 3083-3083. PMID 24419221 DOI: 10.1038/Ncomms4083  0.323
2014 Ledesma-Amaro R, Kerkhoven EJ, Revuelta JL, Nielsen J. Genome Scale Metabolic Modeling of the Riboflavin Overproducer Ashbya gossypii Biotechnology and Bioengineering. 111: 1191-1199. PMID 24374726 DOI: 10.1002/Bit.25167  0.432
2014 Sjostrom SL, Bai Y, Huang M, Liu Z, Nielsen J, Joensson HN, Svahn HA. High-throughput screening for industrial enzyme production hosts by droplet microfluidics Lab On a Chip. 14: 806-813. PMID 24366236 DOI: 10.1039/C3Lc51202A  0.347
2014 Liu L, Martínez JL, Liu Z, Petranovic D, Nielsen J. Balanced globin protein expression and heme biosynthesis improve production of human hemoglobin in Saccharomyces cerevisiae. Metabolic Engineering. 21: 9-16. PMID 24188961 DOI: 10.1016/J.Ymben.2013.10.010  0.36
2014 Jensen NB, Strucko T, Kildegaard KR, David F, Maury J, Mortensen UH, Forster J, Nielsen J, Borodina I. EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae. Fems Yeast Research. 14: 238-48. PMID 24151867 DOI: 10.1111/1567-1364.12118  0.676
2014 Huang M, Bao J, Nielsen J. Biopharmaceutical protein production by Saccharomyces cerevisiae: current state and future prospects Pharmaceutical Bioprocessing. 2: 167-182. DOI: 10.4155/Pbp.14.8  0.331
2014 Tippmann S, Khoomrung S, Siewers V, Nielsen J. Metabolic Engineering of Saccharomyces cerevisiae for Isoprenoid Production New Biotechnology. 31. DOI: 10.1016/J.Nbt.2014.05.2032  0.382
2014 Prado AR, Kildegaard K, Li M, Borodina I, Nielsen J. Development of a yeast cell factory for production of aromatic products New Biotechnology. 31: 130. DOI: 10.1016/J.Nbt.2014.05.1934  0.302
2014 Mardinoglu A, Uhlen M, Nielsen J. The use of Genome-scale metabolic models for drug target and biomarker identification New Biotechnology. 31: 49. DOI: 10.1016/J.Nbt.2014.05.1724  0.332
2014 Valle-Rodríguez JO, Shi S, Siewers V, Nielsen J. Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid ethyl esters, an advanced biofuel, by eliminating non-essential fatty acid utilization pathways Applied Energy. 115: 226-232. DOI: 10.1016/J.Apenergy.2013.10.003  0.388
2013 Jewett MC, Workman CT, Nookaew I, Pizarro FA, Agosin E, Hellgren LI, Nielsen J. Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae. G3 (Bethesda, Md.). 3: 1979-95. PMID 24062529 DOI: 10.1534/G3.113.006601  0.382
2013 Anfelt J, Hallström B, Nielsen J, Uhlén M, Hudson EP. Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803. Applied and Environmental Microbiology. 79: 7419-27. PMID 24056459 DOI: 10.1128/Aem.02694-13  0.383
2013 Shoaie S, Karlsson F, Mardinoglu A, Nookaew I, Bordel S, Nielsen J. Understanding the interactions between bacteria in the human gut through metabolic modeling Scientific Reports. 3: 2532-2532. PMID 23982459 DOI: 10.1038/Srep02532  0.341
2013 Petelenz-Kurdziel E, Kuehn C, Nordlander B, Klein D, Hong KK, Jacobson T, Dahl P, Schaber J, Nielsen J, Hohmann S, Klipp E. Quantitative analysis of glycerol accumulation, glycolysis and growth under hyper osmotic stress. Plos Computational Biology. 9: e1003084. PMID 23762021 DOI: 10.1371/journal.pcbi.1003084  0.334
2013 Krivoruchko A, Serrano-Amatriain C, Chen Y, Siewers V, Nielsen J. Improving biobutanol production in engineered Saccharomyces cerevisiae by manipulation of acetyl-CoA metabolism. Journal of Industrial Microbiology & Biotechnology. 40: 1051-6. PMID 23760499 DOI: 10.1007/s10295-013-1296-0  0.303
2013 Feizi A, Österlund T, Petranovic D, Bordel S, Nielsen J. Genome-Scale Modeling of the Protein Secretory Machinery in Yeast Plos One. 8. PMID 23667601 DOI: 10.1371/Journal.Pone.0063284  0.311
2013 Österlund T, Nookaew I, Bordel S, Nielsen J. Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling Bmc Systems Biology. 7: 36-36. PMID 23631471 DOI: 10.1186/1752-0509-7-36  0.466
2013 Buijs NA, Siewers V, Nielsen J. Advanced biofuel production by the yeast Saccharomyces cerevisiae Current Opinion in Chemical Biology. 17: 480-488. PMID 23628723 DOI: 10.1016/J.Cbpa.2013.03.036  0.328
2013 Mardinoglu A, Gatto F, Nielsen J. Genome-scale modeling of human metabolism - a systems biology approach. Biotechnology Journal. 8: 985-96. PMID 23613448 DOI: 10.1002/biot.201200275  0.333
2013 Nielsen J, Larsson C, Maris Av, Pronk J. Metabolic engineering of yeast for production of fuels and chemicals Current Opinion in Biotechnology. 24: 398-404. PMID 23611565 DOI: 10.1016/J.Copbio.2013.03.023  0.401
2013 Agren R, Otero JM, Nielsen J. Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production. Journal of Industrial Microbiology & Biotechnology. 40: 735-47. PMID 23608777 DOI: 10.1007/s10295-013-1269-3  0.34
2013 Caspeta L, Nielsen J. Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels. Biotechnology Journal. 8: 534-44. PMID 23576362 DOI: 10.1002/biot.201200345  0.33
2013 Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. Plos Computational Biology. 9: e1002980. PMID 23555215 DOI: 10.1371/journal.pcbi.1002980  0.35
2013 Mardinoglu A, Agren R, Kampf C, Asplund A, Nookaew I, Jacobson P, Walley AJ, Froguel P, Carlsson LM, Uhlen M, Nielsen J. Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Molecular Systems Biology. 9: 649. PMID 23511207 DOI: 10.1038/Msb.2013.5  0.398
2013 Borgos SEF, Bordel S, Sletta H, Ertesvåg H, Jakobsen ØM, Bruheim P, Ellingsen TE, Nielsen J, Valla S. Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling Bmc Systems Biology. 7: 19-19. PMID 23497367 DOI: 10.1186/1752-0509-7-19  0.436
2013 Kocharin K, Siewers V, Nielsen J. Improved polyhydroxybutyrate production by Saccharomyces cerevisiae through the use of the phosphoketolase pathway. Biotechnology and Bioengineering. 110: 2216-24. PMID 23456608 DOI: 10.1002/bit.24888  0.334
2013 Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, ... ... Nielsen J, et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 31: 419-25. PMID 23455439 DOI: 10.1038/Nbt.2488  0.376
2013 Liu Z, Hou J, Martínez JL, Petranovic D, Nielsen J. Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae. Applied Microbiology and Biotechnology. 97: 8955-62. PMID 23392765 DOI: 10.1007/S00253-013-4715-2  0.353
2013 Otero JM, Cimini D, Patil KR, Poulsen SG, Olsson L, Nielsen J. Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory. Plos One. 8: e54144. PMID 23349810 DOI: 10.1371/Journal.Pone.0054144  0.458
2013 Chen Y, Daviet L, Schalk M, Siewers V, Nielsen J. Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism Metabolic Engineering. 15: 48-54. PMID 23164578 DOI: 10.1016/J.Ymben.2012.11.002  0.373
2013 Garcia-Albornoz MA, Nielsen J. Application of genome-scale metabolic models in metabolic engineering Industrial Biotechnology. 9: 203-214. DOI: 10.1089/Ind.2013.0011  0.411
2012 Partow S, Siewers V, Daviet L, Schalk M, Nielsen J. Reconstruction and Evaluation of the Synthetic Bacterial MEP Pathway in Saccharomyces cerevisiae Plos One. 7. PMID 23285068 DOI: 10.1371/Journal.Pone.0052498  0.385
2012 Michener JK, Nielsen J, Smolke CD. Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases. Proceedings of the National Academy of Sciences of the United States of America. 109: 19504-9. PMID 23129650 DOI: 10.1073/Pnas.1212287109  0.322
2012 Papini M, Nookaew I, Uhlén M, Nielsen J. Scheffersomyces stipitis : a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae Microbial Cell Factories. 11: 136-136. PMID 23043429 DOI: 10.1186/1475-2859-11-136  0.395
2012 Kocharin K, Chen Y, Siewers V, Nielsen J. Engineering of acetyl-CoA metabolism for the improved production of polyhydroxybutyrate in Saccharomyces cerevisiae. Amb Express. 2: 52. PMID 23009357 DOI: 10.1186/2191-0855-2-52  0.33
2012 Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlén M, Nielsen J. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae Nucleic Acids Research. 40: 10084-10097. PMID 22965124 DOI: 10.1093/Nar/Gks804  0.307
2012 Scalcinati G, Partow S, Siewers V, Schalk M, Daviet L, Nielsen J. Combined metabolic engineering of precursor and co-factor supply to increase α-santalene production by Saccharomyces cerevisiae Microbial Cell Factories. 11: 117-117. PMID 22938570 DOI: 10.1186/1475-2859-11-117  0.399
2012 Knuf C, Nielsen J. Aspergilli: systems biology and industrial applications. Biotechnology Journal. 7: 1147-55. PMID 22890866 DOI: 10.1002/biot.201200169  0.307
2012 Agren R, Bordel S, Mardinoglu A, Pornputtapong N, Nookaew I, Nielsen J. Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. Plos Computational Biology. 8: e1002518. PMID 22615553 DOI: 10.1371/Journal.Pcbi.1002518  0.387
2012 Hou J, Tyo KE, Liu Z, Petranovic D, Nielsen J. Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae. Fems Yeast Research. 12: 491-510. PMID 22533807 DOI: 10.1111/J.1567-1364.2012.00810.X  0.387
2012 Martínez JL, Liu L, Petranovic D, Nielsen J. Pharmaceutical protein production by yeast: towards production of human blood proteins by microbial fermentation. Current Opinion in Biotechnology. 23: 965-71. PMID 22503236 DOI: 10.1016/J.Copbio.2012.03.011  0.35
2012 Scalcinati G, Otero JM, Van Vleet JR, Jeffries TW, Olsson L, Nielsen J. Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption. Fems Yeast Research. 12: 582-97. PMID 22487265 DOI: 10.1111/J.1567-1364.2012.00808.X  0.44
2012 Caspeta L, Shoaie S, Agren R, Nookaew I, Nielsen J. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. Bmc Systems Biology. 6: 24. PMID 22472172 DOI: 10.1186/1752-0509-6-24  0.324
2012 Nijkamp JF, van den Broek M, Datema E, de Kok S, Bosman L, Luttik MA, Daran-Lapujade P, Vongsangnak W, Nielsen J, Heijne WH, Klaassen P, Paddon CJ, Platt D, Kötter P, van Ham RC, et al. De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microbial Cell Factories. 11: 36. PMID 22448915 DOI: 10.1186/1475-2859-11-36  0.351
2012 Tyo KEJ, Liu Z, Petranovic D, Nielsen J. Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress Bmc Biology. 10: 16-16. PMID 22380681 DOI: 10.1186/1741-7007-10-16  0.335
2012 Papini M, Nookaew I, Siewers V, Nielsen J. Physiological characterization of recombinant Saccharomyces cerevisiae expressing the Aspergillus nidulans phosphoketolase pathway: validation of activity through 13C-based metabolic flux analysis. Applied Microbiology and Biotechnology. 95: 1001-10. PMID 22367611 DOI: 10.1007/s00253-012-3936-0  0.358
2012 Shi S, Valle-Rodríguez JO, Khoomrung S, Siewers V, Nielsen J. Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production Biotechnology For Biofuels. 5: 7-7. PMID 22364438 DOI: 10.1186/1754-6834-5-7  0.361
2012 Scalcinati G, Knuf C, Partow S, Chen Y, Maury J, Schalk M, Daviet L, Nielsen J, Siewers V. Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode. Metabolic Engineering. 14: 91-103. PMID 22330799 DOI: 10.1016/J.Ymben.2012.01.007  0.389
2012 Vongsangnak W, Figueiredo LF, Förster J, Weber T, Thykaer J, Stegmann E, Wohlleben W, Nielsen J. Genome-scale metabolic representation of Amycolatopsis balhimycina. Biotechnology and Bioengineering. 109: 1798-807. PMID 22252737 DOI: 10.1002/Bit.24436  0.738
2012 Nielsen J, Pronk JT. Metabolic engineering, synthetic biology and systems biology. Fems Yeast Research. 12: 103-103. PMID 22188459 DOI: 10.1111/J.1567-1364.2011.00783.X  0.318
2012 Liu Z, Tyo KE, Martínez JL, Petranovic D, Nielsen J. Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae. Biotechnology and Bioengineering. 109: 1259-68. PMID 22179756 DOI: 10.1002/Bit.24409  0.328
2012 Jensen NB, Maury J, Oberg F, Kildegaard KR, Forster J, Nielsen J, Borodina I. Metabolic engineering of Saccharomyces cerevisiae for optimizing 3HP production New Biotechnology. 29. DOI: 10.1016/J.Nbt.2012.08.170  0.7
2011 Zhang J, Vaga S, Chumnanpuen P, Kumar R, Vemuri GN, Aebersold R, Nielsen J. Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae. Molecular Systems Biology. 7: 545. PMID 22068328 DOI: 10.1038/Msb.2011.80  0.384
2011 Nookaew I, Olivares-Hernández R, Bhumiratana S, Nielsen J. Genome-scale metabolic models of Saccharomyces cerevisiae. Methods in Molecular Biology (Clifton, N.J.). 759: 445-63. PMID 21863502 DOI: 10.1007/978-1-61779-173-4_25  0.409
2011 Osterlund T, Nookaew I, Nielsen J. Fifteen years of large scale metabolic modeling of yeast: developments and impacts. Biotechnology Advances. 30: 979-88. PMID 21846501 DOI: 10.1016/j.biotechadv.2011.07.021  0.348
2011 Nielsen J, Keasling JD. Synergies between synthetic biology and metabolic engineering. Nature Biotechnology. 29: 693-5. PMID 21822239 DOI: 10.1038/Nbt.1937  0.353
2011 Rokem JS, Vongsangnak W, Nielsen J. Comparative metabolic capabilities for Micrococcus luteus NCTC 2665, the "Fleming" strain, and actinobacteria. Biotechnology and Bioengineering. 108: 2770-5. PMID 21618466 DOI: 10.1002/Bit.23212  0.423
2011 Rodríguez-Limas WA, Tyo KE, Nielsen J, Ramírez OT, Palomares LA. Molecular and process design for rotavirus-like particle production in Saccharomyces cerevisiae. Microbial Cell Factories. 10: 33. PMID 21569612 DOI: 10.1186/1475-2859-10-33  0.329
2011 Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, ... ... Nielsen JB, ... ... Nielsen J, et al. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Research. 21: 885-97. PMID 21543515 DOI: 10.1101/Gr.112169.110  0.373
2011 Piddocke MP, Fazio A, Vongsangnak W, Wong ML, Heldt-Hansen HP, Workman C, Nielsen J, Olsson L. Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using "-omics" techniques. Microbial Cell Factories. 10: 27. PMID 21513553 DOI: 10.1186/1475-2859-10-27  0.389
2011 Vongsangnak W, Hansen K, Nielsen J. Integrated analysis of the global transcriptional response to α‐amylase over‐production by Aspergillus oryzae Biotechnology and Bioengineering. 108: 1130-1139. PMID 21449027 DOI: 10.1002/Bit.23033  0.4
2011 Madsen KM, Udatha GD, Semba S, Otero JM, Koetter P, Nielsen J, Ebizuka Y, Kushiro T, Panagiotou G. Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyper-producers. Plos One. 6: e14763. PMID 21445244 DOI: 10.1371/Journal.Pone.0014763  0.652
2011 Hansen BG, Salomonsen B, Nielsen MT, Nielsen JB, Hansen NB, Nielsen KF, Regueira TB, Nielsen J, Patil KR, Mortensen UH. Versatile enzyme expression and characterization system for Aspergillus nidulans, with the Penicillium brevicompactum polyketide synthase gene from the mycophenolic acid gene cluster as a test case. Applied and Environmental Microbiology. 77: 3044-51. PMID 21398493 DOI: 10.1128/Aem.01768-10  0.347
2011 Regueira TB, Kildegaard KR, Hansen BG, Mortensen UH, Hertweck C, Nielsen J. Molecular basis for mycophenolic acid biosynthesis in Penicillium brevicompactum. Applied and Environmental Microbiology. 77: 3035-43. PMID 21398490 DOI: 10.1128/Aem.03015-10  0.359
2011 Cvijovic M, Bordel S, Nielsen J. Mathematical models of cell factories: moving towards the core of industrial biotechnology. Microbial Biotechnology. 4: 572-584. PMID 21375719 DOI: 10.1111/J.1751-7915.2010.00233.X  0.355
2011 Van Mulders SE, Stassen C, Daenen L, Devreese B, Siewers V, van Eijsden RG, Nielsen J, Delvaux FR, Willaert R. The influence of microgravity on invasive growth in Saccharomyces cerevisiae. Astrobiology. 11: 45-55. PMID 21345087 DOI: 10.1089/Ast.2010.0518  0.306
2011 Krivoruchko A, Siewers V, Nielsen J. Opportunities for yeast metabolic engineering: Lessons from synthetic biology. Biotechnology Journal. 6: 262-76. PMID 21328545 DOI: 10.1002/Biot.201000308  0.384
2011 Shi S, Valle-Rodríguez JO, Siewers V, Nielsen J. Prospects for microbial biodiesel production Biotechnology Journal. 6: 277-285. PMID 21328544 DOI: 10.1002/Biot.201000117  0.313
2011 Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z. MEMOSys: Bioinformatics platform for genome-scale metabolic models. Bmc Systems Biology. 5: 20. PMID 21276275 DOI: 10.1186/1752-0509-5-20  0.372
2011 Karlsson FH, Ussery DW, Nielsen J, Nookaew I. A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut. Microbial Ecology. 61: 473-85. PMID 21222211 DOI: 10.1007/S00248-010-9796-1  0.316
2011 Ruenwai R, Neiss A, Laoteng K, Vongsangnak W, Dalfard AB, Cheevadhanarak S, Petranovic D, Nielsen J. Heterologous production of polyunsaturated fatty acids in Saccharomyces cerevisiae causes a global transcriptional response resulting in reduced proteasomal activity and increased oxidative stress. Biotechnology Journal. 6: 343-56. PMID 21184438 DOI: 10.1002/Biot.201000316  0.338
2011 Albertsen L, Chen Y, Bach LS, Rattleff S, Maury J, Brix S, Nielsen J, Mortensen UH. Diversion of Flux toward Sesquiterpene Production in Saccharomyces cerevisiae by Fusion of Host and Heterologous Enzymes Applied and Environmental Microbiology. 77: 1033-1040. PMID 21148687 DOI: 10.1128/Aem.01361-10  0.401
2010 Canelas AB, Harrison N, Fazio A, Zhang J, Pitkänen JP, van den Brink J, Bakker BM, Bogner L, Bouwman J, Castrillo JI, Cankorur A, Chumnanpuen P, Daran-Lapujade P, Dikicioglu D, van Eunen K, ... ... Nielsen J, et al. Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nature Communications. 1: 145. PMID 21266995 DOI: 10.1038/Ncomms1150  0.39
2010 Otero JM, Vongsangnak W, Asadollahi MA, Olivares-Hernandes R, Maury J, Farinelli L, Barlocher L, Østerås M, Schalk M, Clark A, Nielsen J. Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications Bmc Genomics. 11: 723-723. PMID 21176163 DOI: 10.1186/1471-2164-11-723  0.416
2010 Otero JM, Papadakis MA, Udatha DB, Nielsen J, Panagiotou G. Yeast biological networks unfold the interplay of antioxidants, genome and phenotype, and reveal a novel regulator of the oxidative stress response. Plos One. 5: e13606. PMID 21049050 DOI: 10.1371/Journal.Pone.0013606  0.606
2010 Olivares-Hernández R, Sunner H, Frisvad JC, Olsson L, Nielsen J, Panagiotou G. Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group. Plos One. 5: e12781. PMID 20877647 DOI: 10.1371/Journal.Pone.0012781  0.579
2010 Bordel S, Agren R, Nielsen J. Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes Plos Computational Biology. 6: 16. PMID 20657658 DOI: 10.1371/Journal.Pcbi.1000859  0.42
2010 Olivares-Hernández R, Usaite R, Nielsen J. Integrative Analysis Using Proteome and Transcriptome Data From Yeast to Unravel Regulatory Patterns at Post-Transcriptional Level Biotechnology and Bioengineering. 107: 865-875. PMID 20635383 DOI: 10.1002/Bit.22868  0.306
2010 Partow S, Siewers V, Bjørn S, Nielsen J, Maury J. Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae Yeast. 27: 955-964. PMID 20625983 DOI: 10.1002/Yea.1806  0.317
2010 Thykaer J, Nielsen J, Wohlleben W, Weber T, Gutknecht M, Lantz AE, Stegmann E. Increased glycopeptide production after overexpression of shikimate pathway genes being part of the balhimycin biosynthetic gene cluster. Metabolic Engineering. 12: 455-461. PMID 20570618 DOI: 10.1016/J.Ymben.2010.05.001  0.359
2010 Cvijovic M, Olivares-Hernández R, Agren R, Dahr N, Vongsangnak W, Nookaew I, Patil KR, Nielsen J. BioMet Toolbox: genome-wide analysis of metabolism Nucleic Acids Research. 38: 144-149. PMID 20483918 DOI: 10.1093/Nar/Gkq404  0.43
2010 Liu L, Agren R, Bordel S, Nielsen J. Use of genome-scale metabolic models for understanding microbial physiology. Febs Letters. 584: 2556-2564. PMID 20420838 DOI: 10.1016/J.Febslet.2010.04.052  0.398
2010 Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M. OptFlux: an open-source software platform for in silico metabolic engineering. Bmc Systems Biology. 4: 45. PMID 20403172 DOI: 10.1186/1752-0509-4-45  0.351
2010 Bordel S, Nielsen J. Identification of flux control in metabolic networks using non-equilibrium thermodynamics. Metabolic Engineering. 12: 369-77. PMID 20302968 DOI: 10.1016/j.ymben.2010.03.001  0.325
2010 Tyo KEJ, Kocharin K, Nielsen J. Toward design-based engineering of industrial microbes Current Opinion in Microbiology. 13: 255-262. PMID 20226723 DOI: 10.1016/J.Mib.2010.02.001  0.315
2010 Asadollahi MA, Maury J, Schalk M, Clark A, Nielsen J. Enhancement of farnesyl diphosphate pool as direct precursor of sesquiterpenes through metabolic engineering of the mevalonate pathway in Saccharomyces cerevisiae Biotechnology and Bioengineering. 106: 86-96. PMID 20091767 DOI: 10.1002/Bit.22668  0.422
2010 Otero JM, Nielsen J. Industrial systems biology. Biotechnology and Bioengineering. 105: 439-60. PMID 19891008 DOI: 10.1002/bit.22592  0.332
2009 Usaite R, Jewett MC, Oliveira AP, Yates JR, Olsson L, Nielsen J. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Molecular Systems Biology. 5: 319. PMID 19888214 DOI: 10.1038/Msb.2009.67  0.37
2009 Salazar M, Vongsangnak W, Panagiotou G, Andersen MR, Nielsen J. Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Molecular Genetics and Genomics : Mgg. 282: 571-86. PMID 19784673 DOI: 10.1007/S00438-009-0486-Y  0.643
2009 Rossouw D, Olivares-Hernandes R, Nielsen J, Bauer FF. Comparative Transcriptomic Approach To Investigate Differences in Wine Yeast Physiology and Metabolism during Fermentation Applied and Environmental Microbiology. 75: 6600-6612. PMID 19700545 DOI: 10.1128/Aem.01251-09  0.365
2009 Vongsangnak W, Salazar M, Hansen K, Nielsen J. Genome-wide analysis of maltose utilization and regulation in aspergilli. Microbiology (Reading, England). 155: 3893-3902. PMID 19696104 DOI: 10.1099/mic.0.031104-0  0.365
2009 Siewers V, Chen X, Huang L, Zhang J, Nielsen J. Heterologous production of non-ribosomal peptide LLD-ACV in Saccharomyces cerevisiae Metabolic Engineering. 11: 391-397. PMID 19686863 DOI: 10.1016/J.Ymben.2009.08.002  0.352
2009 Flagfeldt DB, Siewers V, Huang L, Nielsen J. Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae. Yeast. 26: 545-551. PMID 19681174 DOI: 10.1002/Yea.1705  0.309
2009 Asadollahi M, Maury J, Patil KR, schalk M, Clark A, Nielsen J. Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metabolic Engineering. 11: 328-334. PMID 19619667 DOI: 10.1016/J.Ymben.2009.07.001  0.425
2009 Coutinho PM, Andersen MR, Kolenova K, vanKuyk PA, Benoit I, Gruben BS, Trejo-Aguilar B, Visser H, van Solingen P, Pakula T, Seiboth B, Battaglia E, Aguilar-Osorio G, de Jong JF, Ohm RA, ... ... Nielsen J, et al. Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genetics and Biology : Fg & B. 46: S161-S169. PMID 19618505 DOI: 10.1016/J.Fgb.2008.07.020  0.324
2009 Panagiotou G, Nielsen J. Nutritional systems biology: definitions and approaches. Annual Review of Nutrition. 29: 329-39. PMID 19575602 DOI: 10.1146/Annurev-Nutr-080508-141138  0.624
2009 Meijer S, Nielsen ML, Olsson L, Nielsen J. Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger. Journal of Industrial Microbiology & Biotechnology. 36: 1275-80. PMID 19554356 DOI: 10.1007/S10295-009-0607-Y  0.414
2009 Meijer SL, Jongh WAD, Olsson L, Nielsen J. Physiological characterisation of acuB deletion in Aspergillus niger Applied Microbiology and Biotechnology. 84: 157-167. PMID 19444441 DOI: 10.1007/S00253-009-2027-3  0.415
2009 Andersen MR, Lehmann LO, Nielsen J. Systemic analysis of the response of Aspergillus niger to ambient pH Genome Biology. 10: 1-14. PMID 19409083 DOI: 10.1186/Gb-2009-10-5-R47  0.327
2009 Diano A, Peeters J, Dynesen J, Nielsen J. Physiology of Aspergillus niger in oxygen-limited continuous cultures: Influence of aeration, carbon source concentration and dilution rate. Biotechnology and Bioengineering. 103: 956-65. PMID 19382249 DOI: 10.1002/Bit.22329  0.345
2009 Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proceedings of the National Academy of Sciences of the United States of America. 106: 6477-82. PMID 19346491 DOI: 10.1073/Pnas.0811091106  0.418
2009 Cimini D, Patil KR, Schiraldi C, Nielsen J. Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3 Bmc Systems Biology. 3: 17-17. PMID 19200357 DOI: 10.1186/1752-0509-3-17  0.306
2009 Panagiotou G, Andersen MR, Grotkjaer T, Regueira TB, Nielsen J, Olsson L. Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools. Applied and Environmental Microbiology. 75: 2212-20. PMID 19168657 DOI: 10.1128/Aem.01461-08  0.668
2009 Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, Andersen MR, Archer D, Bencina M, Braus G, Coutinho P, von Döhren H, Doonan J, Driessen AJ, Durek P, Espeso E, ... ... Nielsen J, et al. The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genetics and Biology : Fg & B. 46: S2-13. PMID 19146970 DOI: 10.1016/J.Fgb.2008.12.003  0.319
2009 Christensen TS, Oliveira APSd, Nielsen J. Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae Bmc Systems Biology. 3: 7-7. PMID 19144179 DOI: 10.1186/1752-0509-3-7  0.324
2009 Kjeldsen KR, Nielsen J. In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network. Biotechnology and Bioengineering. 102: 583-597. PMID 18985611 DOI: 10.1002/Bit.22067  0.422
2009 Hofmann G, Diano A, Nielsen J. Recombinant bacterial hemoglobin alters metabolism of Aspergillus niger Metabolic Engineering. 11: 8-12. PMID 18694843 DOI: 10.1016/J.Ymben.2008.07.002  0.382
2009 Pedersen L, Hansen K, Nielsen KF, Nielsen J, Lantz AE, Thykaer J. In-depth analysis of Aspergillus niger metabolism during industrial fed-batch fermentations New Biotechnology. 25: 210-211. DOI: 10.1016/J.Nbt.2009.06.158  0.364
2008 Panagiotou G, Andersen MR, Grotkjaer T, Regueira TB, Hofmann G, Nielsen J, Olsson L. Systems analysis unfolds the relationship between the phosphoketolase pathway and growth in Aspergillus nidulans. Plos One. 3: e3847. PMID 19052639 DOI: 10.1371/Journal.Pone.0003847  0.645
2008 Rocha M, Maia P, Mendes R, Pinto JP, Ferreira EC, Nielsen J, Patil KR, Rocha I. Natural computation meta-heuristics for the in silico optimization of microbial strains. Bmc Bioinformatics. 9: 499. PMID 19038030 DOI: 10.1186/1471-2105-9-499  0.39
2008 Maury J, Asadollahi MA, Møller K, Schalk M, Clark A, Formenti LR, Nielsen J. Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae Febs Letters. 582: 4032-4038. PMID 18996117 DOI: 10.1016/J.Febslet.2008.10.045  0.364
2008 HerrgÃ¥rd MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, ... ... Nielsen J, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology. 26: 1155-60. PMID 18846089 DOI: 10.1038/Nbt1492  0.378
2008 Pizarro FJ, Jewett MC, Nielsen J, Agosin E. Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae. Applied and Environmental Microbiology. 74: 6358-68. PMID 18723660 DOI: 10.1128/Aem.00602-08  0.361
2008 Nookaew I, Jewett MC, Meechai A, Thammarongtham C, Laoteng K, Cheevadhanarak S, Nielsen J, Bhumiratana S. The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. Bmc Systems Biology. 2: 71. PMID 18687109 DOI: 10.1186/1752-0509-2-71  0.388
2008 Mapelli V, Olsson L, Nielsen J. Metabolic footprinting in microbiology: methods and applications in functional genomics and biotechnology. Trends in Biotechnology. 26: 490-7. PMID 18675480 DOI: 10.1016/j.tibtech.2008.05.008  0.34
2008 Fazio A, Jewett MC, Daran-Lapujade P, Mustacchi R, Usaite R, Pronk JT, Workman CT, Nielsen J. Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design. Bmc Genomics. 9: 341. PMID 18638364 DOI: 10.1186/1471-2164-9-341  0.343
2008 Borodina I, Siebring J, Zhang J, Smith CP, van Keulen G, Dijkhuizen L, Nielsen J. Antibiotic overproduction in Streptomyces coelicolor A3 2 mediated by phosphofructokinase deletion. The Journal of Biological Chemistry. 283: 25186-99. PMID 18606812 DOI: 10.1074/Jbc.M803105200  0.447
2008 Wattanachaisaereekul S, Lantz AE, Nielsen ML, Nielsen J. Production of the polyketide 6-MSA in yeast engineered for increased malonyl-CoA supply. Metabolic Engineering. 10: 246-54. PMID 18555717 DOI: 10.1016/J.Ymben.2008.04.005  0.374
2008 Vongsangnak W, Olsen P, Hansen K, Krogsgaard S, Nielsen J. Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. Bmc Genomics. 9: 245. PMID 18500999 DOI: 10.1186/1471-2164-9-245  0.304
2008 David H, Özçelik İŞ, Hofmann G, Nielsen J. Analysis of Aspergillus nidulans metabolism at the genome-scale Bmc Genomics. 9: 163-163. PMID 18405346 DOI: 10.1186/1471-2164-9-163  0.347
2008 Rocha I, Förster J, Nielsen J. Design and application of genome-scale reconstructed metabolic models. Methods in Molecular Biology (Clifton, N.J.). 416: 409-31. PMID 18392985 DOI: 10.1007/978-1-59745-321-9_29  0.704
2008 Thykaer J, Rueksomtawin K, Noorman H, Nielsen J. NADPH-dependent glutamate dehydrogenase in Penicillium chrysogenum is involved in regulation of β-lactam production Microbiology. 154: 1242-1250. PMID 18375816 DOI: 10.1099/Mic.0.2007/010017-0  0.314
2008 Andersen MR, Nielsen ML, Nielsen J. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Molecular Systems Biology. 4: 178. PMID 18364712 DOI: 10.1038/Msb.2008.12  0.408
2008 Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J. A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proceedings of the National Academy of Sciences of the United States of America. 105: 4387-92. PMID 18332432 DOI: 10.1073/Pnas.0709964105  0.615
2008 Jongh WAd, Nielsen J. Enhanced citrate production through gene insertion in Aspergillus niger. Metabolic Engineering. 10: 87-96. PMID 18162426 DOI: 10.1016/J.Ymben.2007.11.002  0.355
2008 Nielsen J, Jewett MC. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. Fems Yeast Research. 8: 122-31. PMID 17727659 DOI: 10.1111/J.1567-1364.2007.00302.X  0.392
2008 Asadollahi MA, Maury J, Møller K, Nielsen KF, Schalk M, Clark A, Nielsen J. Production of plant sesquiterpenes in Saccharomyces cerevisiae: Effect of ERG9 repression on sesquiterpene biosynthesis Biotechnology and Bioengineering. 99: 666-677. PMID 17705244 DOI: 10.1002/Bit.21581  0.364
2008 Prathumpai W, Gabelgaard JB, Wanchanthuek P, Vondervoort PJIvd, Groot MJLd, Mcintyre M, Nielsen J. Metabolic Control Analysis of Xylose Catabolism in Aspergillus Biotechnology Progress. 19: 1136-1141. PMID 12892473 DOI: 10.1021/Bp034020R  0.371
2008 Penttilä M, Nielsen J, Boekhout T. Yeast systems biology. Fems Yeast Research. 8: 121-121. DOI: 10.1111/J.1567-1364.2007.00346.X  0.306
2007 van der Werf MJ, Takors R, Smedsgaard J, Nielsen J, Ferenci T, Portais JC, Wittmann C, Hooks M, Tomassini A, Oldiges M, Fostel J, Sauer U. Standard reporting requirements for biological samples in metabolomics experiments: microbial and in vitro biology experiments. Metabolomics : Official Journal of the Metabolomic Society. 3: 189-194. PMID 25653575 DOI: 10.1007/S11306-007-0080-4  0.31
2007 Rokem JS, Lantz AE, Nielsen J. Systems biology of antibiotic production by microorganisms. Natural Product Reports. 24: 1262-87. PMID 18033579 DOI: 10.1039/B617765B  0.364
2007 Nielsen ML, de Jongh WA, Meijer SL, Nielsen J, Mortensen UH. Transient marker system for iterative gene targeting of a prototrophic fungus. Applied and Environmental Microbiology. 73: 7240-5. PMID 17921280 DOI: 10.1128/Aem.01839-07  0.315
2007 Nielsen J. Principles of optimal metabolic network operation Molecular Systems Biology. 3. PMID 17625514 DOI: 10.1038/Msb4100169  0.369
2007 Çakır T, Kırdar B, Önsan Zİ, Ülgen KÖ, Nielsen J. Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae. Bmc Systems Biology. 1: 18-18. PMID 17408508 DOI: 10.1186/1752-0509-1-18  0.368
2007 Meijer SL, Panagiotou G, Olsson L, Nielsen J. Physiological characterization of xylose metabolism in Aspergillus niger under oxygen‐limited conditions Biotechnology and Bioengineering. 98: 462-475. PMID 17335061 DOI: 10.1002/Bit.21397  0.647
2007 Vemuri GN, Eiteman MA, McEwen JE, Olsson L, Nielsen J. Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae Proceedings of the National Academy of Sciences of the United States of America. 104: 2402-2407. PMID 17287356 DOI: 10.1073/Pnas.0607469104  0.389
2007 Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, ... ... Nielsen J, et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology. 25: 221-31. PMID 17259976 DOI: 10.1038/Nbt1282  0.407
2007 Arga KY, Onsan ZI, Kirdar B, Ulgen KO, Nielsen J. Understanding signaling in yeast: Insights from network analysis. Biotechnology and Bioengineering. 97: 1246-1258. PMID 17252576 DOI: 10.1002/Bit.21317  0.314
2007 Nookaew I, Meechai A, Thammarongtham C, Laoteng K, Ruanglek V, Cheevadhanarak S, Nielsen J, Bhumiratana S. Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks. Biotechnology and Bioengineering. 97: 1535-49. PMID 17238207 DOI: 10.1002/Bit.21339  0.351
2007 Højer-Pedersen J, Smedsgaard J, Nielsen J. Elucidating the mode-of-action of compounds from metabolite profiling studies Progress in Drug Research. 64: 103-129. PMID 17195473 DOI: 10.1007/978-3-7643-7567-6_5  0.334
2007 Wattanachaisaereekul S, Lantz AE, Nielsen ML, Andrésson OS, Nielsen J. Optimization of heterologous production of the polyketide 6-MSA in Saccharomyces cerevisiae. Biotechnology and Bioengineering. 97: 893-900. PMID 17171715 DOI: 10.1002/Bit.21286  0.386
2007 Baxter CJ, Redestig H, Schauer N, Repsilber D, Patil KR, Nielsen J, Selbig J, Liu J, Fernie AR, Sweetlove LJ. The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiology. 143: 312-25. PMID 17122072 DOI: 10.1104/Pp.106.090431  0.372
2007 Mas S, Villas-Bôas SG, Hansen ME, Åkesson M, Nielsen J. A comparison of direct infusion MS and GC-MS for metabolic footprinting of yeast mutants. Biotechnology and Bioengineering. 96: 1014-1022. PMID 17022091 DOI: 10.1002/Bit.21194  0.324
2007 Westergaard SL, Oliveira APSd, Bro C, Olsson L, Nielsen J. A systems biology approach to study glucose repression in the yeast Saccharomyces cerevisiae Biotechnology and Bioengineering. 96: 134-145. PMID 16878332 DOI: 10.1002/Bit.21135  0.448
2007 Thykaer J, Nielsen J. Evidence, through C13-labelling analysis, of phosphoketolase activity in fungi Process Biochemistry. 42: 1050-1055. DOI: 10.1016/J.Procbio.2007.04.004  0.31
2007 Lantz AE, Wattanachaisaereekul S, Nielsen ML, Nielsen J. Towards a yeast cell factory platform for polyketide production Journal of Biotechnology. 131. DOI: 10.1016/J.Jbiotec.2007.07.355  0.313
2006 David HSM, Hofmann G, Oliveira APSd, Jarmer HØ, Nielsen J. Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans Genome Biology. 7: 1-16. PMID 17107606 DOI: 10.1186/Gb-2006-7-11-R108  0.424
2006 Regenberg B, Grotkjaer T, Winther O, Fausbøll A, Akesson M, Bro C, Hansen LK, Brunak S, Nielsen J. Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biology. 7: R107. PMID 17105650 DOI: 10.1186/Gb-2006-7-11-R107  0.329
2006 Çakir T, Patil KR, Önsan ZI, Ülgen KÖ, Kirdar B, Nielsen J. Integration of metabolome data with metabolic networks reveals reporter reactions Molecular Systems Biology. 2: 50-50. PMID 17016516 DOI: 10.1038/Msb4100085  0.37
2006 Usaite R, Patil KR, Grotkjær T, Nielsen J, Regenberg B. Global Transcriptional and Physiological Responses of Saccharomyces cerevisiae to Ammonium, l-Alanine, or l-Glutamine Limitation Applied and Environmental Microbiology. 72: 6194-6203. PMID 16957246 DOI: 10.1128/Aem.00548-06  0.34
2006 Diano A, Bekker-Jensen S, Dynesen JØ, Nielsen J. Polyol synthesis in Aspergillus niger: influence of oxygen availability, carbon and nitrogen sources on the metabolism. Biotechnology and Bioengineering. 94: 899-908. PMID 16718677 DOI: 10.1002/Bit.20915  0.355
2006 Mogensen J, Nielsen HB, Hofmann G, Nielsen J. Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol. Fungal Genetics and Biology. 43: 593-603. PMID 16698295 DOI: 10.1016/J.Fgb.2006.03.003  0.337
2006 Raghevendran V, Patil KR, Olsson L, Nielsen J. Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae. Journal of Biological Chemistry. 281: 12308-12314. PMID 16522629 DOI: 10.1074/Jbc.M512972200  0.418
2006 Mustacchi R, Hohmann S, Nielsen J. Yeast systems biology to unravel the network of life Yeast. 23: 227-238. PMID 16498699 DOI: 10.1002/Yea.1357  0.313
2006 Jewett MC, Hofmann G, Nielsen J. Fungal metabolite analysis in genomics and phenomics. Current Opinion in Biotechnology. 17: 191-7. PMID 16488600 DOI: 10.1016/J.Copbio.2006.02.001  0.409
2006 Eckert-Boulet N, Larsson K, Wu B, Poulsen P, Regenberg B, Nielsen J, Kielland-Brandt MC. Deletion of RTS1, encoding a regulatory subunit of protein phosphatase 2A, results in constitutive amino acid signaling via increased Stp1p processing. Eukaryotic Cell. 5: 174-9. PMID 16400180 DOI: 10.1128/Ec.5.1.174-179.2006  0.311
2006 Bro C, Regenberg B, Förster J, Nielsen J. In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metabolic Engineering. 8: 102-11. PMID 16289778 DOI: 10.1016/J.Ymben.2005.09.007  0.722
2005 Raghevendran V, Nielsen J, Olsson L. Teaching microbial physiology using glucose repression phenomenon in baker's yeast as an example. Biochemistry and Molecular Biology Education. 33: 404-410. PMID 21638610 DOI: 10.1002/Bmb.2005.49403306404  0.328
2005 Patil KR, Rocha I, Förster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. Bmc Bioinformatics. 6: 308. PMID 16375763 DOI: 10.1186/1471-2105-6-308  0.721
2005 Maury J, Asadollahi MA, Møller K, Clark A, Nielsen J. Microbial isoprenoid production: an example of green chemistry through metabolic engineering. Advances in Biochemical Engineering \/ Biotechnology. 100: 19-51. PMID 16270655 DOI: 10.1007/B136410  0.412
2005 Bro C, Knudsen S, Regenberg B, Olsson L, Nielsen J. Improvement of Galactose Uptake in Saccharomyces cerevisiae through Overexpression of Phosphoglucomutase: Example of Transcript Analysis as a Tool in Inverse Metabolic Engineering Applied and Environmental Microbiology. 71: 6465-6472. PMID 16269670 DOI: 10.1128/Aem.71.11.6465-6472.2005  0.394
2005 Nielsen J, Oliver S. The next wave in metabolome analysis Trends in Biotechnology. 23: 544-546. PMID 16154652 DOI: 10.1016/J.Tibtech.2005.08.005  0.345
2005 Grotkjær T, Christakopoulos P, Nielsen J, Olsson L. Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains Metabolic Engineering. 7: 437-444. PMID 16140032 DOI: 10.1016/J.Ymben.2005.07.003  0.422
2005 David H, Krogh AM, Roca C, Akesson M, Nielsen J. CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose. Microbiology (Reading, England). 151: 2209-21. PMID 16000711 DOI: 10.1099/Mic.0.27787-0  0.424
2005 Oliveira AP, Nielsen J, Förster J. Modeling Lactococcus lactis using a genome-scale flux model. Bmc Microbiology. 5: 39. PMID 15982422 DOI: 10.1186/1471-2180-5-39  0.721
2005 Borodina I, Nielsen J. From genomes to in silico cells via metabolic networks. Current Opinion in Biotechnology. 16: 350-355. PMID 15961036 DOI: 10.1016/J.Copbio.2005.04.008  0.415
2005 Borodina I, Krabben P, Nielsen J. Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism Genome Research. 15: 820-829. PMID 15930493 DOI: 10.1101/Gr.3364705  0.41
2005 Borodina I, Schöller C, Eliasson A, Nielsen J. Metabolic network analysis of Streptomyces tenebrarius, a streptomyces species with an active entner-doudoroff pathway Applied and Environmental Microbiology. 71: 2294-2302. PMID 15870314 DOI: 10.1128/Aem.71.5.2294-2302.2005  0.409
2005 Villas-Bôas SG, Åkesson M, Nielsen J. Biosynthesis of glyoxylate from glycine in Saccharomyces cerevisiae. Fems Yeast Research. 5: 703-709. PMID 15851099 DOI: 10.1016/J.Femsyr.2005.03.001  0.408
2005 Patil KR, Nielsen J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proceedings of the National Academy of Sciences of the United States of America. 102: 2685-2689. PMID 15710883 DOI: 10.1073/Pnas.0406811102  0.39
2005 Villas-Bôas SG, Moxley JF, Akesson M, Stephanopoulos G, Nielsen J. High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts. The Biochemical Journal. 388: 669-77. PMID 15667247 DOI: 10.1042/Bj20041162  0.415
2005 Panagiotou G, Villas-Bôas SG, Christakopoulos P, Nielsen J, Olsson L. Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. Journal of Biotechnology. 115: 425-434. PMID 15639104 DOI: 10.1016/J.Jbiotec.2004.09.011  0.622
2005 Smedsgaard J, Nielsen J. Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics. Journal of Experimental Botany. 56: 273-286. PMID 15618299 DOI: 10.1093/Jxb/Eri068  0.433
2005 Eckert-Boulet N, Regenberg B, Nielsen J. Grr1p is required for transcriptional induction of amino acid permease genes and proper transcriptional regulation of genes in carbon metabolism of Saccharomyces cerevisiae Current Genetics. 47: 139-149. PMID 15611869 DOI: 10.1007/S00294-004-0553-1  0.387
2005 Seker T, Møller K, Nielsen J. Analysis of acyl CoA ester intermediates of the mevalonate pathway in Saccharomyces cerevisiae Applied Microbiology and Biotechnology. 67: 119-124. PMID 15448940 DOI: 10.1007/S00253-004-1697-0  0.366
2005 Villas-Bôas SG, Mas S, Åkesson MF, Smedsgaard J, Nielsen J. Mass spectrometry in metabolome analysis Mass Spectrometry Reviews. 24: 613-646. PMID 15389842 DOI: 10.1002/Mas.20032  0.32
2005 Jewett MC, Oliveira AP, Patil KR, Nielsen J. The role of high-throughput transcriptome analysis in metabolic engineering Biotechnology and Bioprocess Engineering. 10: 385-399. DOI: 10.1007/Bf02989821  0.412
2004 Gunnarsson N, Eliasson A, Nielsen J. Control of fluxes towards antibiotics and the role of primary metabolism in production of antibiotics Advances in Biochemical Engineering/Biotechnology. 88: 137-178. PMID 15719555 DOI: 10.1007/B99260  0.44
2004 Westergaard SL, Bro C, Olsson L, Nielsen J. Elucidation of the role of Grr1p in glucose sensing by Saccharomyces cerevisiae through genome-wide transcription analysis. Fems Yeast Research. 5: 193-204. PMID 15556081 DOI: 10.1016/J.Femsyr.2004.06.013  0.404
2004 Santos MMd, Raghevendran V, Kötter P, Olsson L, Nielsen J. Manipulation of malic enzyme in Saccharomyces cerevisiae for increasing NADPH production capacity aerobically in different cellular compartments Metabolic Engineering. 6: 352-363. PMID 15491864 DOI: 10.1016/J.Ymben.2004.06.002  0.376
2004 Cannizzaro C, Christensen B, Nielsen J, von Stockar U. Metabolic network analysis on Phaffia rhodozyma yeast using 13C-labeled glucose and gas chromatography-mass spectrometry. Metabolic Engineering. 6: 340-51. PMID 15491863 DOI: 10.1016/J.Ymben.2004.06.001  0.425
2004 Akesson M, Förster J, Nielsen J. Integration of gene expression data into genome-scale metabolic models. Metabolic Engineering. 6: 285-93. PMID 15491858 DOI: 10.1016/J.Ymben.2003.12.002  0.731
2004 Gunnarsson N, Bruheim P, Nielsen J. Glucose metabolism in the antibiotic producing actinomycete Nonomuraea sp. ATCC 39727. Biotechnology and Bioengineering. 88: 652-663. PMID 15472928 DOI: 10.1002/Bit.20279  0.41
2004 Prathumpai W, Flitter SJ, McIntyre M, Nielsen J. Lipase production by recombinant strains of Aspergillus niger expressing a lipase-encoding gene from Thermomyces lanuginosus Applied Microbiology and Biotechnology. 65: 714-719. PMID 15316684 DOI: 10.1007/S00253-004-1699-Y  0.363
2004 Raghevendran V, Gombert AK, Christensen B, Kötter P, Nielsen J. Phenotypic characterization of glucose repression mutants of Saccharomyces cerevisiae using experiments with 13C-labelled glucose. Yeast. 21: 769-779. PMID 15282800 DOI: 10.1002/Yea.1136  0.427
2004 Bro C, Nielsen J. Impact of 'ome' analyses on inverse metabolic engineering. Metabolic Engineering. 6: 204-211. PMID 15256210 DOI: 10.1016/J.Ymben.2003.11.005  0.397
2004 Eckert-Boulet N, Nielsen PS, Friis C, Santos MMd, Nielsen J, Kielland-Brandt MC, Regenberg B. Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp1p and Stp2p. Yeast. 21: 635-648. PMID 15197729 DOI: 10.1002/Yea.1120  0.335
2004 Patil KR, Åkesson M, Nielsen J. Use of genome-scale microbial models for metabolic engineering Current Opinion in Biotechnology. 15: 64-69. PMID 15102469 DOI: 10.1016/J.Copbio.2003.11.003  0.386
2004 Gunnarsson N, Mortensen UH, Sosio M, Nielsen J. Identification of the Entner-Doudoroff pathway in an antibiotic-producing actinomycete species Molecular Microbiology. 52: 895-902. PMID 15101992 DOI: 10.1111/J.1365-2958.2004.04028.X  0.44
2004 Bro C, Regenberg B, Nielsen J. Genome‐wide transcriptional response of a Saccharomyces cerevisiae strain with an altered redox metabolism Biotechnology and Bioengineering. 85: 269-276. PMID 14748081 DOI: 10.1002/Bit.10899  0.388
2004 Larsen GG, Appel KF, Wolff A, Nielsen J, Arnau J. Characterisation of the Mucor circinelloides regulated promoter gpd1P. Current Genetics. 45: 225-234. PMID 14735314 DOI: 10.1007/S00294-003-0484-2  0.341
2004 Lübbehüsen T, Polo VG, Rossi S, Nielsen J, Moreno S, McIntyre M, Arnau J. Protein kinase A is involved in the control of morphology and branching during aerobic growth of Mucor circinelloides. Microbiology. 150: 143-150. PMID 14702407 DOI: 10.1099/Mic.0.26708-0  0.33
2004 Møller K, Langkjær RB, Nielsen J, Piskur J, Olsson L. Pyruvate decarboxylases from the petite-negative yeast Saccharomyces kluyveri. Molecular Genetics and Genomics. 270: 558-568. PMID 14648197 DOI: 10.1007/S00438-003-0950-Z  0.337
2004 Prathumpai W, Mcintyre M, Nielsen J. The effect of CreA in glucose and xylose catabolism in Aspergillus nidulans. Applied Microbiology and Biotechnology. 63: 748-753. PMID 12920487 DOI: 10.1007/S00253-003-1409-1  0.346
2004 Nielsen J. The First International Workshop on Systems Biology of Yeast, St. Louis, USA, 9 November, 2003 Fems Yeast Research. 4: 757-758. DOI: 10.1016/J.Femsyr.2004.02.001  0.344
2003 Villas-Bôas SG, Delicado DG, Åkesson M, Nielsen J. Simultaneous analysis of amino and nonamino organic acids as methyl chloroformate derivatives using gas chromatography-mass spectrometry Analytical Biochemistry. 322: 134-138. PMID 14705791 DOI: 10.1016/J.Ab.2003.07.018  0.316
2003 Nielsen J. It Is All about Metabolic Fluxes Journal of Bacteriology. 185: 7031-7035. PMID 14645261 DOI: 10.1128/Jb.185.24.7031-7035.2003  0.351
2003 David H, Åkesson M, Nielsen J. Reconstruction of the central carbon metabolism of Aspergillus niger Febs Journal. 270: 4243-4253. PMID 14622289 DOI: 10.1046/J.1432-1033.2003.03798.X  0.459
2003 Famili I, Forster J, Nielsen J, Palsson BO. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proceedings of the National Academy of Sciences of the United States of America. 100: 13134-9. PMID 14578455 DOI: 10.1073/Pnas.2235812100  0.756
2003 Santos MMd, Thygesen G, Kötter P, Olsson L, Nielsen J. Aerobic physiology of redox-engineered Saccharomyces cerevisiae strains modified in the ammonium assimilation for increased NADPH availability. Fems Yeast Research. 4: 59-68. PMID 14554197 DOI: 10.1016/S1567-1356(03)00155-7  0.37
2003 Förster J, Famili I, Palsson BO, Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. Omics : a Journal of Integrative Biology. 7: 193-202. PMID 14506848 DOI: 10.1089/153623103322246584  0.735
2003 Roca C, Nielsen J, Olsson L. Metabolic Engineering of Ammonium Assimilation in Xylose-Fermenting Saccharomyces cerevisiae Improves Ethanol Production Applied and Environmental Microbiology. 69: 4732-4736. PMID 12902265 DOI: 10.1128/Aem.69.8.4732-4736.2003  0.335
2003 Santos MMd, Gombert AK, Christensen B, Olsson L, Nielsen J. Identification of In Vivo Enzyme Activities in the Cometabolism of Glucose and Acetate by Saccharomyces cerevisiae by Using 13C-Labeled Substrates Eukaryotic Cell. 2: 599-608. PMID 12796305 DOI: 10.1128/Ec.2.3.599-608.2003  0.365
2003 Bro C, Regenberg B, Lagniel G, Labarre J, Montero-Lomelí M, Nielsen J. Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells. Journal of Biological Chemistry. 278: 32141-32149. PMID 12791685 DOI: 10.1074/Jbc.M304478200  0.391
2003 Robin JJC, Lettier G, Mcintyre M, Noorman H, Nielsen J. Continuous cultivations of a Penicillium chrysogenum strain expressing the expandase gene from Streptomyces clavuligerus: Growth yields and morphological characterization. Biotechnology and Bioengineering. 83: 361-368. PMID 12783492 DOI: 10.1002/Bit.10677  0.358
2003 Robin J, Bruheim P, Nielsen ML, Noorman H, Nielsen J. Continuous cultivations of a Penicillium chrysogenum strain expressing the expandase gene from Streptomyces clavuligerus: Kinetics of adipoyl-7-aminodeacetoxycephalosporanic acid and byproduct formations. Biotechnology and Bioengineering. 83: 353-360. PMID 12783491 DOI: 10.1002/Bit.10678  0.363
2003 Christiansen T, Michaelsen S, Wümpelmann M, Nielsen J. Production of Savinase and population viability of Bacillus clausii during high-cell-density fed-batch cultivations Biotechnology and Bioengineering. 83: 344-352. PMID 12783490 DOI: 10.1002/Bit.10675  0.319
2003 Thykaer J, Nielsen J. Metabolic engineering of β-lactam production Metabolic Engineering. 5: 56-69. PMID 12749845 DOI: 10.1016/S1096-7176(03)00003-X  0.388
2003 Robin J, Bonneau S, Schipper D, Noorman H, Nielsen J. Influence of the adipate and dissolved oxygen concentrations on the beta-lactam production during continuous cultivations of a Penicillium chrysogenum strain expressing the expandase gene from Streptomyces clavuligerus. Metabolic Engineering. 5: 42-8. PMID 12749843 DOI: 10.1016/S1096-7176(03)00006-5  0.302
2003 Hofmann G, McIntyre M, Nielsen J. Fungal genomics beyond Saccharomyces cerevisiae Current Opinion in Biotechnology. 14: 226-231. PMID 12732326 DOI: 10.1016/S0958-1669(03)00020-X  0.304
2003 Förster J, Famili I, Fu P, Palsson BØ, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Research. 13: 244-53. PMID 12566402 DOI: 10.1101/Gr.234503  0.741
2002 Møller K, Bro C, Piškur J, Nielsen J, Olsson L. Steady‐state and transient‐state analyses of aerobic fermentation in Saccharomyces kluyveri Fems Yeast Research. 2: 233-244. PMID 12702311 DOI: 10.1111/J.1567-1364.2002.Tb00088.X  0.365
2002 Nielsen J, Olsson L. An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology Fems Yeast Research. 2: 175-181. PMID 12702306 DOI: 10.1111/J.1567-1364.2002.Tb00083.X  0.393
2002 Müller C, Hjort CM, Hansen K, Nielsen J. Altering the expression of two chitin synthase genes differentially affects the growth and morphology of Aspergillus oryzae. Microbiology. 148: 4025-4033. PMID 12480906 DOI: 10.1099/00221287-148-12-4025  0.302
2002 Förster J, Gombert AK, Nielsen J. A functional genomics approach using metabolomics and in silico pathway analysis. Biotechnology and Bioengineering. 79: 703-12. PMID 12209793 DOI: 10.1002/Bit.10378  0.705
2002 Zaldivar J, Borges A, Johansson B, Smits HP, Villas-Boas SG, Nielsen J, Olsson L. Fermentation performance and intracellular metabolite patterns in laboratory and industrial xylose-fermenting Saccharomyces cerevisiae. Applied Microbiology and Biotechnology. 59: 436-442. PMID 12172606 DOI: 10.1007/S00253-002-1056-Y  0.332
2002 Piper MD, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J, Pronk JT. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. The Journal of Biological Chemistry. 277: 37001-8. PMID 12121991 DOI: 10.1074/Jbc.M204490200  0.372
2002 Christiansen T, Nielsen J. Production of extracellular protease and glucose uptake in Bacillus clausii in steady-state and transient continuous cultures. Journal of Biotechnology. 97: 265-273. PMID 12084482 DOI: 10.1016/S0168-1656(02)00109-8  0.322
2002 Christensen B, Gombert AK, Nielsen J. Analysis of flux estimates based on 13C-labelling experiments Febs Journal. 269: 2795-2800. PMID 12047390 DOI: 10.1046/J.1432-1033.2002.02959.X  0.354
2002 Christiansen T, Christensen B, Nielsen J. Metabolic Network Analysis of Bacillus clausii on Minimal and Semirich Medium Using 13C-Labeled Glucose Metabolic Engineering. 4: 159-169. PMID 12009795 DOI: 10.1006/Mben.2001.0219  0.394
2002 Thykaer J, Christensen B, Nielsen J. Metabolic network analysis of an adipoyl-7-ADCA-producing strain of Penicillium chrysogenum: elucidation of adipate degradation. Metabolic Engineering. 4: 151-158. PMID 12009794 DOI: 10.1006/Mben.2001.0218  0.406
2002 McIntyre M, Breum J, Arnau J, Nielsen J. Growth physiology and dimorphism of Mucor circinelloides (syn. racemosus) during submerged batch cultivation. Applied Microbiology and Biotechnology. 58: 495-502. PMID 11954797 DOI: 10.1007/S00253-001-0916-1  0.303
2002 Müller C, McIntyre M, Hansen K, Nielsen J. Metabolic engineering of the morphology of Aspergillus oryzae by altering chitin synthesis. Applied and Environmental Microbiology. 68: 1827-1836. PMID 11916702 DOI: 10.1128/Aem.68.4.1827-1836.2002  0.321
2002 Jonsbu E, McIntyre M, Nielsen J. The influence of carbon sources and morphology on nystatin production by Streptomyces noursei. Journal of Biotechnology. 95: 133-144. PMID 11911923 DOI: 10.1016/S0168-1656(02)00003-2  0.336
2002 Vara AG, Hochkoepple A, Nielsen J, Villadsen J. Production of teicoplanin by Actinoplanes teichomyceticus in continuous fermentation Biotechnology and Bioengineering. 77: 589-598. PMID 11788956 DOI: 10.1002/Bit.10137  0.333
2002 Møller K, Christensen B, Förster J, Piskur J, Nielsen J, Olsson L. Aerobic glucose metabolism of Saccharomyces kluyveri: growth, metabolite production, and quantification of metabolic fluxes. Biotechnology and Bioengineering. 77: 186-93. PMID 11753925 DOI: 10.1002/Bit.10122  0.7
2002 Agger T, Petersen JB, O'Connor SM, Murphy RL, Kelly JM, Nielsen J. Physiological characterisation of recombinant Aspergillus nidulans strains with different creA genotypes expressing A. oryzae alpha-amylase. Journal of Biotechnology. 92: 279-85. PMID 11689252 DOI: 10.1016/S0168-1656(01)00366-2  0.311
2002 Zangirolami T, Carlsen M, Nielsen J, Jørgensen SB. GROWTH AND ENZYME PRODUCTION DURING CONTINUOUS CULTURES OF A HIGH AMYLASE-PRODUCING VARIANT OF Aspergillus Oryzae Brazilian Journal of Chemical Engineering. 19: 55-68. DOI: 10.1590/S0104-66322002000100005  0.36
2002 Christiansen T, Nielsen J. Growth energetics of an alkaline serine protease-producing strain of Bacillus clausii during continuous cultivation Bioprocess and Biosystems Engineering. 24: 329-339. DOI: 10.1007/S00449-001-0276-3  0.335
2001 Ostergaard S, Walløe KO, Gomes CSG, Olsson L, Nielsen J. The impact of GAL6, GAL80, and MIG1 on glucose control of the GAL system in Saccharomyces cerevisiae Fems Yeast Research. 1: 47-55. PMID 12702462 DOI: 10.1111/J.1567-1364.2001.Tb00012.X  0.335
2001 McIntyre M, Müller C, Dynesen J, Nielsen J. Metabolic engineering of the morphology of Aspergillus. Advances in Biochemical Engineering \/ Biotechnology. 73: 103-128. PMID 11816809 DOI: 10.1007/3-540-45300-8_6  0.337
2001 Robin JJC, Jakobsen M, Beyer M, Noorman H, Nielsen J. Physiological characterisation of Penicillium chrysogenum strains expressing the expandase gene from Streptomyces clavuligerus during batch cultivations. Growth and adipoyl-7-aminodeacetoxycephalosporanic acid production. Applied Microbiology and Biotechnology. 57: 357-362. PMID 11759685 DOI: 10.1007/S002530100787  0.358
2001 Carlsen M, Nielsen J. Influence of carbon source on alpha-amylase production by Aspergillus oryzae. Applied Microbiology and Biotechnology. 57: 346-349. PMID 11759683 DOI: 10.1007/S002530100772  0.325
2001 Møller K, Tidemand LD, Winther JR, Olsson L, Piskur J, Nielsen J. Production of a heterologous proteinase A by Saccharomyces kluyveri. Applied Microbiology and Biotechnology. 57: 216-219. PMID 11693924 DOI: 10.1007/S002530100680  0.327
2001 Jonsbu E, Christensen B, Nielsen J. Changes of in vivo fluxes through central metabolic pathways during the production of nystatin by Streptomyces noursei in batch culture Applied Microbiology and Biotechnology. 56: 93-100. PMID 11499953 DOI: 10.1007/S002530100613  0.406
2001 Zaldivar J, Nielsen J, Olsson L. Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration. Applied Microbiology and Biotechnology. 56: 17-34. PMID 11499926 DOI: 10.1007/S002530100624  0.328
2001 Christensen B, Christiansen T, Gombert AK, Thykaer J, Nielsen J. Simple and robust method for estimation of the split between the oxidative pentose phosphate pathway and the Embden-Meyerhof-Parnas pathway in microorganisms. Biotechnology and Bioengineering. 74: 517-523. PMID 11494219 DOI: 10.1002/Bit.1143  0.351
2001 Ostergaard S, Olsson L, Nielsen J. In vivo dynamics of galactose metabolism in Saccharomyces cerevisiae: metabolic fluxes and metabolite levels. Biotechnology and Bioengineering. 73: 412-425. PMID 11320512 DOI: 10.1002/Bit.1075  0.38
2001 Agger T, Spohr AB, Nielsen J. alpha-Amylase production in high cell density submerged cultivation of Aspergillus oryzae and A. nidulans. Applied Microbiology and Biotechnology. 55: 81-84. PMID 11234963 DOI: 10.1007/S002530000456  0.316
2001 Theilgaard HA, Berg MAvd, Mulder CA, Bovenberg RAL, Nielsen J. Quantitative analysis of Penicillium chrysogenum Wis54-1255 transformants overexpressing the penicillin biosynthetic genes. Biotechnology and Bioengineering. 72: 379-388. PMID 11180058 DOI: 10.1002/1097-0290(20000220)72:4<379::Aid-Bit1000>3.0.Co;2-5  0.335
2001 McIntyre M, Dynesen J, Nielsen J. Morphological characterization of Aspergillus nidulans: growth, septation and fragmentation. Microbiology. 147: 239-246. PMID 11160817 DOI: 10.1099/00221287-147-1-239  0.304
2001 Gombert AK, Santos MMd, Christensen B, Nielsen J. Network Identification and Flux Quantification in the Central Metabolism of Saccharomyces cerevisiae under Different Conditions of Glucose Repression Journal of Bacteriology. 183: 1441-1451. PMID 11157958 DOI: 10.1128/Jb.183.4.1441-1451.2001  0.419
2001 Nissen TL, Anderlund M, Nielsen J, Villadsen J, Kielland-Brandt MC. 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. PMID 11124698 DOI: 10.1002/1097-0061(200101)18:1<19::Aid-Yea650>3.0.Co;2-5  0.388
2000 Jonsbu E, Ellingsen TE, Nielsen J. Effects of nitrogen sources on cell growth and production of nystatin by Streptomyces noursei. The Journal of Antibiotics. 53: 1354-1362. PMID 11217800 DOI: 10.7164/Antibiotics.53.1354  0.316
2000 Ostergaard S, Olsson L, Johnston M, Nielsen J. Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network. Nature Biotechnology. 18: 1283-1286. PMID 11101808 DOI: 10.1038/82400  0.463
2000 Bautista LF, Aleksenko A, Hentzer M, Santerre-Henriksen A, Nielsen J. Antisense silencing of the creA gene in Aspergillus nidulans. Applied and Environmental Microbiology. 66: 4579-4581. PMID 11010922 DOI: 10.1128/Aem.66.10.4579-4581.2000  0.332
2000 Christensen B, Thykær J, Nielsen J. Metabolic characterization of high- and low-yielding strains of Penicillium chrysogenum Applied Microbiology and Biotechnology. 54: 212-217. PMID 10968635 DOI: 10.1007/S002530000371  0.378
2000 Nissen TL, Kielland-Brandt MC, Nielsen J, Villadsen J. Optimization of Ethanol Production in Saccharomyces Cerevisiae by Metabolic Engineering of the Ammonium Assimilation Metabolic Engineering. 2: 69-77. PMID 10935936 DOI: 10.1006/Mben.1999.0140  0.359
2000 Pedersen H, Christensen B, Hjort C, Nielsen J. Construction and Characterization of an Oxalic Acid Nonproducing Strain of Aspergillus niger Metabolic Engineering. 2: 34-41. PMID 10935933 DOI: 10.1006/Mben.1999.0136  0.38
2000 Olsson L, Nielsen J. The role of metabolic engineering in the improvement of Saccharomyces cerevisiae: utilization of industrial media. Enzyme and Microbial Technology. 26: 785-792. PMID 10862886 DOI: 10.1016/S0141-0229(00)00172-1  0.396
2000 Christensen B, Nielsen J. Metabolic network analysis of penicillium chrysogenum using 13c‐labeled glucose Biotechnology and Bioengineering. 68: 652-659. PMID 10799990 DOI: 10.1002/(Sici)1097-0290(20000620)68:6<652::Aid-Bit8>3.0.Co;2-J  0.357
2000 Pedersen H, Beyer M, Nielsen J. Glucoamylase production in batch, chemostat and fed-batch cultivations by an industrial strain of Aspergillus niger. Applied Microbiology and Biotechnology. 53: 272-277. PMID 10772465 DOI: 10.1007/S002530050020  0.348
2000 Gombert AK, Nielsen J. Mathematical modelling of metabolism. Current Opinion in Biotechnology. 11: 180-186. PMID 10753761 DOI: 10.1016/S0958-1669(00)00079-3  0.425
2000 Østergaard S, Roca CFA, Ronnow B, Nielsen J, Olsson L. Physiological studies in aerobic batch cultivations of Saccharomyces cerevisiae strains harboring the MEL1 gene Biotechnology and Bioengineering. 68: 252-259. PMID 10745193 DOI: 10.1002/(Sici)1097-0290(20000505)68:3<252::Aid-Bit3>3.0.Co;2-K  0.324
2000 Nissen TL, Hamann CW, Kielland-Brandt MC, Nielsen J, Villadsen J. Anaerobic and aerobic batch cultivations of Saccharomyces cerevisiae mutants impaired in glycerol synthesis Yeast. 16: 463-474. PMID 10705374 DOI: 10.1002/(Sici)1097-0061(20000330)16:5<463::Aid-Yea535>3.0.Co;2-3  0.364
2000 Ostergaard S, Olsson L, Nielsen J. Metabolic Engineering of Saccharomyces cerevisiae Microbiology and Molecular Biology Reviews. 64: 34-50. PMID 10704473 DOI: 10.1128/Mmbr.64.1.34-50.2000  0.406
2000 Heydorn A, Petersen BO, Duus JO, Bergmann S, Suhr-Jessen T, Nielsen J. Biosynthetic studies of the glycopeptide teicoplanin by (1)H and (13)C NMR. The Journal of Biological Chemistry. 275: 6201-6. PMID 10692413 DOI: 10.1074/Jbc.275.9.6201  0.305
2000 Zangirolami TC, Carlsen M, Nielsen J, Jørgensen SB. Selection and characterization of a high α-amylase-producing variant in glucose-limited continuous cultures of Aspergillus oryzae Fungal Biology. 104: 1241-1249. DOI: 10.1017/S0953756200002665  0.307
1999 Rønnow B, Olsson L, Nielsen J, Mikkelsen JD. Derepression of galactose metabolism in melibiase producing bakers' and distillers' yeast. Journal of Biotechnology. 72: 213-228. PMID 12680392 DOI: 10.1016/S0168-1656(99)00108-X  0.349
1999 Agger T, Nielsen J. Genetically structured modeling of protein production in filamentous fungi Biotechnology and Bioengineering. 66: 164-170. PMID 10577470 DOI: 10.1002/(Sici)1097-0290(1999)66:3<164::Aid-Bit4>3.0.Co;2-O  0.339
1999 Schmidt K, Nielsen J, Villadsen J. Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. Journal of Biotechnology. 71: 175-189. PMID 10483105 DOI: 10.1016/S0168-1656(99)00021-8  0.397
1999 Aleksenko A, Liu W, Gojkovic Z, Nielsen J, Piskur J. Structural and transcriptional analysis of the pyrABCN, pyrD and pyrF genes in Aspergillus nidulans and the evolutionary origin of fungal dihydroorotases. Molecular Microbiology. 33: 599-611. PMID 10417650 DOI: 10.1046/J.1365-2958.1999.01507.X  0.321
1999 Anderlund M, Nissen TL, Nielsen J, Villadsen J, Rydström J, Hahn-Hägerdal B, Kielland-Brandt MC. Expression of the Escherichia coli pntA and pntB Genes, Encoding Nicotinamide Nucleotide Transhydrogenase, in Saccharomyces cerevisiae and Its Effect on Product Formation during Anaerobic Glucose Fermentation Applied and Environmental Microbiology. 65: 2333-2340. PMID 10347010 DOI: 10.1128/Aem.65.6.2333-2340.1999  0.334
1999 Santerre Henriksen AL, Even S, Müller C, Punt PJ, van den Hondel CA, Nielsen J. Study of the glucoamylase promoter in Aspergillus niger using green fluorescent protein. Microbiology (Reading, England). 145: 729-34. PMID 10217507 DOI: 10.1099/13500872-145-3-729  0.321
1999 Klein CL, Rasmussen J, Rønnow B, Olsson L, Nielsen J. Investigation of the impact of MIG1 and MIG2 on the physiology of Saccharomyces cerevisiae. Journal of Biotechnology. 68: 197-212. PMID 10194857 DOI: 10.1016/S0168-1656(98)00205-3  0.382
1998 Henriksen CM, Nielsen J, Villadsen J. High exogenous concentrations of phenoxyacetic acid are crucial for a high penicillin V productivity in Penicillium chrysogenum Microbiology. 144: 2001-2006. PMID 33757233 DOI: 10.1099/00221287-144-7-2001  0.329
1998 Schmidt K, Marx A, Graaf AAd, Wiechert W, Sahm H, Nielsen J, Villadsen J. 13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches Biotechnology and Bioengineering. 58: 254-257. PMID 10191397 DOI: 10.1002/(Sici)1097-0290(19980420)58:2/3<254::Aid-Bit19>3.0.Co;2-C  0.385
1998 Nielsen J. Metabolic engineering: techniques for analysis of targets for genetic manipulations. Biotechnology and Bioengineering. 58: 125-132. PMID 10191381 DOI: 10.1002/(Sici)1097-0290(19980420)58:2/3<125::Aid-Bit3>3.0.Co;2-N  0.412
1998 Dynesen J, Smits HP, Olsson L, Nielsen J. Carbon catabolite repression of invertase during batch cultivations of Saccharomyces cerevisiae : the role of glucose, fructose, and mannose Applied Microbiology and Biotechnology. 50: 579-582. PMID 9866176 DOI: 10.1007/S002530051338  0.321
1998 Spohr A, Carlsen M, Nielsen J, Villadsen J. α-Amylase production in recombinant Aspergillus oryzae during fed-batch and continuous cultivations Journal of Fermentation and Bioengineering. 86: 49-56. DOI: 10.1016/S0922-338X(98)80033-0  0.316
1997 Zangirolami TC, Johansen CL, Nielsen J, Jørgensen SB. Simulation of penicillin production in fed-batch cultivations using a morphologically structured model. Biotechnology and Bioengineering. 56: 593-604. PMID 18642330 DOI: 10.1002/(Sici)1097-0290(19971220)56:6<593::Aid-Bit1>3.0.Co;2-I  0.32
1997 Olsson L, Larsen ME, Rønnow B, Mikkelsen JD, Nielsen J. Silencing MIG1 in Saccharomyces cerevisiae: Effects of Antisense MIG1 Expression and MIG1 Gene Disruption Applied and Environmental Microbiology. 63: 2366-2371. PMID 9172357 DOI: 10.1128/Aem.63.6.2366-2371.1997  0.31
1997 Nielsen J. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates Biochemical Journal. 321: 133-138. PMID 9003411 DOI: 10.1042/Bj3210133  0.337
1997 Pissarra PDN, Nielsen J. Thermodynamics of Metabolic Pathways for Penicillin Production: Analysis of Thermodynamic Feasibility and Free Energy Changes During Fed‐Batch Cultivation Biotechnology Progress. 13: 156-165. DOI: 10.1021/Bp970010C  0.352
1996 Pissara PdN, Nielsen J, Bazin MJ. Pathway kinetics and metabolic control analysis of a high-yielding strain of Penicillium chrysogenum during fed batch cultivations. Biotechnology and Bioengineering. 51: 168-176. PMID 18624326 DOI: 10.1002/(Sici)1097-0290(19960720)51:2<168::Aid-Bit6>3.0.Co;2-H  0.372
1996 Klein CJ, Olsson L, Rønnow B, Mikkelsen JD, Nielsen J. Alleviation of glucose repression of maltose metabolism by MIG1 disruption in Saccharomyces cerevisiae. Applied and Environmental Microbiology. 62: 4441-4449. PMID 8953715 DOI: 10.1128/Aem.62.12.4441-4449.1996  0.365
1996 Carlsen M, Nielsen J, Villadsen J. Growth and α-amylase production by Aspergillus oryzae during continuous cultivations Journal of Biotechnology. 45: 81-93. DOI: 10.1016/0168-1656(95)00147-6  0.343
1995 Jørgensen H, Nielsen J, Villadsen J, Møllgaard H. Metabolic flux distributions in Penicillium chrysogenum during fed‐batch cultivations Biotechnology and Bioengineering. 46: 117-131. PMID 18623271 DOI: 10.1002/Bit.260460205  0.363
1995 Jørgensen H, Nielsen J, Villadsen J, Møllgaard H. Analysis of penicillin V biosynthesis during fed-batch cultivations with a high-yielding strain of Penicillium chrysogenum. Applied Microbiology and Biotechnology. 43: 123-130. PMID 7766125 DOI: 10.1007/Bf00170633  0.324
1995 Nielsen J, Jørgensen HS. Metabolic Control Analysis of the Penicillin Biosynthetic Pathway in a High‐Yielding Strain of Penicillium chrysogenum Biotechnology Progress. 11: 299-305. PMID 7619400 DOI: 10.1021/Bp00033A010  0.365
1995 Mørkeberg R, Carlsen M, Nielsen J. Induction and repression of α-amylase production in batch and continuous cultures of Aspergillus oryzae Microbiology. 141: 2449-2454. PMID 7582005 DOI: 10.1099/13500872-141-10-2449  0.307
1995 Christensen LH, Henriksen CM, Nielsen J, Villadsen J, Egel-Mitani M. Continuous cultivation of Penicillium chrysogenum. Growth on glucose and penicillin production. Journal of Biotechnology. 42: 95-107. PMID 7576537 DOI: 10.1016/0168-1656(95)00056-V  0.361
1995 Nielsen J, Jørgensen HS. A Kinetic Model for the Penicillin Biosynthetic Pathway in Penicillium Chrysogenum Ifac Proceedings Volumes. 28: 136-141. DOI: 10.1016/S1474-6670(17)45615-1  0.318
1995 Min RW, Nielsen J, Villadsen J. Simultaneous monitoring of glucose, lactic acid and penicillin by sequential injection analysis Analytica Chimica Acta. 312: 149-156. DOI: 10.1016/0003-2670(95)00239-V  0.305
1994 Benthin S, Nielsen J, Villadsen J. Galactose Expulsion during Lactose Metabolism in Lactococcus lactis subsp. cremoris FD1 Due to Dephosphorylation of Intracellular Galactose 6-Phosphate Applied and Environmental Microbiology. 60: 1254-1259. PMID 16349233 DOI: 10.1128/Aem.60.4.1254-1259.1994  0.345
1994 Nielsen J, Johansen CL, Villadsen J. Culture fluorescence measurements during batch and fed-batch cultivations with Penicillium chrysogenum Journal of Biotechnology. 38: 51-62. DOI: 10.1016/0168-1656(94)90147-3  0.31
1993 Benthin S, Nielsen J, Villadsen J. Two uptake systems for fructose in Lactococcus lactis subsp. cremoris FD1 produce glycolytic and gluconeogenic fructose phosphates and induce oscillations in growth and lactic acid formation Applied and Environmental Microbiology. 59: 3206-3211. PMID 16349061 DOI: 10.1128/Aem.59.10.3206-3211.1993  0.324
1992 Nielsen J. Modelling the growth of filamentous fungi Advances in Biochemical Engineering/Biotechnology. 46: 187-223. PMID 1636480 DOI: 10.1007/Bfb0000711  0.308
1992 Nielsen J, Villadsen J. Modelling of microbial kinetics Chemical Engineering Science. 47: 4225-4270. DOI: 10.1016/0009-2509(92)85104-J  0.31
1992 Benthin S, Nielsen J, Villadsen J. Flow-injection analysis of micromolar concentrations of glucose and lactate in fermentation media Analytica Chimica Acta. 261: 145-153. DOI: 10.1016/0003-2670(92)80185-A  0.307
1992 Strudsholm K, Nielsen J, Emborg C. Product formation during batch fermentation with recombinant Escherichia coli containing a runaway plasmid Bioprocess Engineering. 8: 173-181. DOI: 10.1007/Bf01254234  0.316
1991 Nikolajsen K, Nielsen J, Villadsen J. Structured modeling of a microbial system: III. Growth on mixed substrates Biotechnology and Bioengineering. 38: 24-29. PMID 18600694 DOI: 10.1002/Bit.260380104  0.328
1991 Nielsen J, Nikolajsen K, Villadsen J. Structured modeling of a microbial system: II. Experimental verification of a structured lactic acid fermentation model Biotechnology and Bioengineering. 38: 11-23. PMID 18600693 DOI: 10.1002/Bit.260380103  0.331
1991 Nielsen J, Nikolajsen K, Villadsen J. Structured modeling of a microbial system: I. A theoretical study of lactic acid fermentation. Biotechnology and Bioengineering. 38: 1-10. PMID 18600692 DOI: 10.1002/Bit.260380102  0.308
1991 Benthin S, Nielsen J, Villadsen J. Characterization and application of precise and robust flow-injection analysers for on-line measurement during fermentations Analytica Chimica Acta. 247: 45-50. DOI: 10.1016/S0003-2670(00)83050-0  0.305
1989 Nielsen J, Nikolajsen K, Villadsen J. FIA for on-line monitoring of important lactic acid fermentation variables. Biotechnology and Bioengineering. 33: 1127-1134. PMID 18588030 DOI: 10.1002/Bit.260330908  0.302
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