Nielsen Lab
   

Publications

 
 
Recent publications
 

Research papers in international journals with peer review


2017

Z. Zhu; Y.J. Zhou; A. Krivoruchko; M. Grininger; Z.K. Zhao; J. Nielsen (2016) Expanding the product portfolio of fungal type I fatty acid synthases. Nature Chem. Biol., in press

L. Wenning; T. Yu; F. David; J. Nielsen; V. Siewers (2016) Establishing very long-chain fatty alcohol and wax ester biosynthesis. Biotechnol. Bioeng., in press

Y. Wei; V. Siewers; J. Nielsen (2017) Cocoa butter-like lipid production ability of non-oleaginous and oleaginous yeasts under nitrogen limited culture conditions. Appl. Microbiol. Biotechnol., in press

A. Nilsson; A. Mardinoglu; J. Nielsen (2017) Predicting growth of the healthy infant using a genome-scale metabolic model. Systems Biol. Appl., in press

2016

Z.A. Irani; E. Kerkhoven; S.A. Shojaosadati; J. Nielsen (2015) Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins. Biotechnol. Bioeng. 113:961-969

E. Kerkhoven; K. Pmoraning; S. Baker; J. Nielsen (2015) Regulation of amino acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. Systems Biol. Appl. 2:16005

S. Shi; J. Haichuan; V. Siewers; J. Nielsen (2015) Improved production of fatty acids by Saccharomyces cerevisiae through screening a cDNA library from the oleaginous yeast Yarrowia lipolytica. FEMS Yeast Res. 16:fv108

B. de Jong; V. Siewers; J. Nielsen (2016) Physiological and transcriptional characterization of Saccharomyces cerevisiae engineered for production of fatty acid ethyl esters. FEMS Yeast Res. Fov105:1-9

S. Tippmann; G. Scalcinati; V. Siewers; J. Nielsen (2015) Production of farnesene and santalane by Saccharomyces cerevisiae using fed-batch cultivations with RQ-controlled feed. Biotechnol. Bioeng. 113:72-81

S. Tippmann; J. Nielsen; S. Khoomrung (2016) Improved quantification of farnesene during microbial production from Saccharomyces cerevisiae in two-liquid-phase fermentations. Talanta 146:100-106

F. David; J. Nielsen; V. Siewers (2016) Flux control at the malonyl-CoA node through hierarchical dynamic pathway regulation in Saccharomyces cerevisiae. ACS Syn. Biol. 5:224-233

L. Pedersen; M. Idorn; G.H. Olofsson; B. Lauenborg; I. Nookaew; R.H. Hansen; H.H. Johannesen; J.C. Becker; K.S. Pedersen; C. Dethlefsen; J. Nielsen; J. Gehl; B.K. Pedersen; P.T. Straten; P. Hojman (2016) Voluntary running suppresses tumor growth through epinephrine- and IL-6-dependent NK cell mobilization and redistribution. Cell Met. 23:1-9

J, Maury; S.M. Germann; S.A.B. Jacobsen; N.B. Jensen; K.R. Kildegaard; M.J. Heergård; K. Schneider; A. Koza; J. Förster; J. Nielsen; I. Borodina (2016) EasyCloneMulti: A set of vectors for simultaneous and multiple genomic integrations in Saccharomyces cerevisiae. PLOS One 0150394:1-22

F. Gatto; J. Nielsen (2016) Systematic analysis of overall survival and interactions between tumor metabolism and drug treatment. J. Hematology Oncology 9:15

A. Nilsson; J. Nielsen (2016) Metabolic trade-offs in yeast are caused by F1F0-ATP synthase. Sci. Rep. 6:22264
K. Kildegaard; N.B. Jensen; K. Schneider; E. Czarnotta; E. Özdemir; T. Klein; J. Maury; B.E. Ebert; H.B. Christensen; Y. Chen; I.-K. Kim; M.J. Herrgård; L.M. Blank; J. Forster; J. Nielsen; I. Borodina (2016) Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway. Microb. Cell Fac. 15:53

Y. Zhou; N. A. Buijs; Z. Zhu; J. Qin; V. Siewers; J. Nielsen (2016) Production of fatty acid derived oleochemicals and biofuels by synthetic yeast cell factories. Nature Com. 7:11709

I. E. Elsemman; A. Mardinoglu; S. Shoaie; T.H. Soliman; J. Nielsen (2016) Systems biology analysis of metabolism reveals the role of copy number increase in parts of chromosome 1q in hepatitis C virus associated hepatocellular carcinoma. Mol. Biosystems 12:1496-1506

G. Liu; D. Bergenholm; J. Nielsen (2016) Genome-wide mapping of binding sites reveals multiple biological functions of the transcription factor Cst6p in Saccharomyces cerevisiae. mBio 7:e00559-16

F. Gatto; N. Volpi; H. Nilsson; I. Nookaew; M. Maruzzo; A. Roma; M. E. Johansson; U. Steiner; S. Lundstam; U. Basso; J. Nielsen (2016) Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma. Cell Rep. 15:1-15

S.L. Svahn; L. Väremo; B. Gabrielsson; E. Peris; I. Nookaew; L. Grahnemo; A.-S. Sandberg; I.W. Asterholm; J.-O. Jansson; J. Nielsen; M.E. Johansson (2016) Dietary fat composition regulates the transcriptome, especially of immune genes, in the spleen. PLOS One 11:e0155099

R. Pereira; J. Nielsen; I. Rocha (2016) Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae, Met. Eng. Com. 3:153-163

S. Lee; M. Kilicarslan; C. Zhang; E. Björnson; B.M. Hallström; A.K. Groen; E. Ferrannini; M. Laakso; M. Blüher; M. Uhlen; J. Nielsen; U. Smith; J. Boren; M. Serlie; A. Mardinoglu (2016) Integrated network analysis reveals an association between increased plasma mannose levels and insulin resistance and secretion. Cell Met. 24:172-184

L. Caspeta; Y. Chen; J. Nielsen (2016) Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30C. Sci. Rep. 6:27003

S. Lee; A. Marginoglu; C. Zhang; D. Lee; J. Nielsen (2016) Dysregulated signaling hubs of liver metabolism reveal hepatocellular carcinoma pathogenesis. Nuc. Acid Res. 44:5529-5539

S. Busti; V. Mapelli; F. Tripodi; R. Sanvito; F. Magni; M.C. Jewett; J. Nielsen; L. Alberghina; M. Vanoni (2016) Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast. Sci. Rep. 6:27942

F. Gatto; A. Schultze; J. Nielsen (2016) Systematic analysis reveals that cancer mutations converge on deregulated metabolism of arachinodate and xenobiotics. Cell Rep. 16:878-895

P.-J. Lahtvee; R. Kumar; B.M. Hallström; J. Nielsen (2016) Adaption to different types of stress converge on mitochondrial metabolism. Mol. Biol. Cell 27:2505-2514

A.S. Rajkumar; G. Liu; D. Bergenholm; D. Arsovska; M. Kristensen; J. Nielsen; M.K. Jensen; J.D. Keasling (2016) Engineering of synthetic, stress sensitive yeast promoters. Nuc. Acid Res. 44:e136

J.L. Martinez; E. Meza; D. Petranovic; J. Nielsen (2016) The impact of respiration and oxidative stress response on recombinant a-amylase production by Saccharomyces cerevisiae. Metab. Eng. Com. 3:205-210

S. Grijseels; J.C. Nielsen; M. Randelovic; J. Nielsen; K.F. Nielsen; M. Workman; J.C. Frisvad (2015) Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites. Sci. Rep. 6:35112

J. Casey; A. Mardinoglu; J. Nielsen; D. Kari (2016) Adaptive evolution of phosphorous metabolism in Prochlorococcus. mSystems 1:e00065-16

Y. Zhou; N.A.. Buijs; Z. Zhu; D.O. Gomez; A. Boonsombuti; V. Siewers; J. Nielsen (2016) Harnessing peroxisomes for production of fatty acid-derived biofuels and chemicals in yeast. J. Am. Chem. Soc. 138:15368-15377

M. Li; K.R. Kildegaard; Y. Chen; A. Rodriguez; I. Borodina; J. Nielsen (2016) Engineering yeast for high-level production of stilbenoid antioxidants. Sci. Rep. 6:36827

E. Fletcher; A. Feizi; B. Hallström, M. Bisschops; S. Koomrung; V. Siewers; J. Nielsen (2016) Evolutionary engineering revewals divergent paths when yeast is adapted to different acidic environments. Met. Eng. 113:1164-1170

F. Gatto; M. Maruzzo; C. Magro; U. Basso; J. Nielsen (2016) Prognostic value of plasma and urine glycosaminoglycan scores in clear cell renal cell carcinoma. Front. Oncol. 6:253

Bergman; V. Siewers; J. Nielsen; Y. Chen (2016) Functional expression and evaluation of heterologous phosphoketolases in Saccharomyces cerevisiae. AMB Express 6:115

2015

M. Uhlén, L. Fagerberg, B.M. Hallström, C. Lindskog, P. Oksvold, A. Mardinoglu, Å. Sivertsson, C. Kampf, E. Sjöstedt, A. Asplund, I. Olsson, K. Edlund, E. Lundberg, S. Navani, C.A.-K. Szigyarto, J. Odeberg, D. Djureinovic, J.O. Takanen,  S. Hober, T. Alm, H. Berling, H. Tegel, J. Mulder, J. Rockberg, P. Nilsson, J.M. Schwenk, M. Hamsten, K. von Feilitzen, M. Forsberg, L. Persson, F. Johansson, M. Zwahlen, G. von Heijne, J. Nielsen; F. Ponten (2015) Tissue based map of the humane proteome. Science 347:1260419,1-9

N.A. Buijs; Y.J. Zhou; V. Siewers; J. Nielsen (2015) Long-chain alkane production by the yeast Saccharomyces cerevisiae. Biotechnol. Bioeng. 112:1275-1279

P. Ghaffari; A. Mardinoglu; A. Asplund; S. Shoaie; C. Kampf; M. Uhlen; J. Nielsen (2015) Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling. Sci. Rep. 5:8183

I. Borodina; K. Kildegaard; N.B. Jensen; T.H. Blicher; J. Maury; S. Sherstyk; K. Schneider; P. Lamosa; M.J. Herrgård; I. Rosenstand; F. Öberg; J. Förster; J. Nielsen (2015) Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via beta-alanine. Met. Eng. 27:57-64

C. Zhang; B. Ji; A. Mardinoglu; J. Nielsen; Q. Hua (2015) Logical transformation of genome scale metabolic models for genetic applications and analysis. Bioinfor. 31:2324-2331

B. de Jong; S. Shi; J.O. Valle-Rodriguez; V. Siewers; J. Nielsen (2015) Metabolic pathway engineering for fatty acid ethyl ester production in Saccharomyces cerevisiae using stable chromosomal integration. J. Ind. Microbiol. Biotechnol. 42:477-486

Y. Chen; Y. Zhang; V. Siewers; J. Nielsen (2015) Ach1 is involved in shutting mitochondrial acetyl units for cytosolic C2 provision in Saccharomyces cerevisiae lacking pyruvate carboxylase. FEMS Yeast Res. 15:fov015

R. Nicastro; F. Tripodi; C. Guzzi; V. Reghellin; S. Khoomrung; C. Airoldi; J. Nielsen; L. Alberghina; P. Cocetti (2015) Enhanced amino acid utilization sustains growth of cells lacking Snf1/AMPK. BBA Mol. Cell Res. 1853:1615-1625

K.V.Y. Gossens; F.S. Ielasi; I. Nookaew; I. Stals; L. Alonso-Sarduy; L. Daenen; S.E. Van Mulders; R.G.E. van Eijsden; C. Stassen; V. Siewers; F.R. Delvaux; S. Kasas; J. Nielsen; B. Devreese; R.G. Willaert (2015) Molecular mechanisms of flocculation self-recognition in yeast and its role in mating and survival. MBio 6:e00427-15

T. Österlund; S. Bordel; J. Nielsen (2015) Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors. Integr. Biol. 7:560-568

S. Tymoshenko; R.D. Oppenheim; R. Agren; J. Nielsen; D. Soldati-Favre; V. Hatzimanikatis (2015) Metabolic needs and capabilities of Toxoplasma gondii through combined computational and experimental analysis. PLOS Comp. Biol. 11:e1004261

L. Väremo; C. Scheele; C. Broholm; A. Mardinoglu; C. Kampf; A. Asplund; I. Nookaew; M. Uhlen; B.K. Pedersen; J. Nielsen (2015) Transcriptome and proteome driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes. Cell Rep. 11:1-13

M. Engqvist; J. Nielsen (2015) ANT: Software for generating and evaluationg degenerate codons for natural and expandic genetic codes. ACS Synthetic Biol. 4:935-938

A. Feizi; A. Banaei-Esfahani; J. Nielsen (2015) HCSD: the human cancer secretome database. Database bav051:1-8

J. Lopez; K. Essus; I.-K. Kim; R. Pereira; J. Herzog; V. Siewers; J. Nielsen; E. Agosin (2015) Production of b-ionone by combined expression of carotenogenic and plant CCD1 genes in Saccharomyces cerevisiae. Mic. Cell Fac. 14:84

Y. Zhang; Z. Dai; A. Krivoruchko; Y. Chen; V. Siewers; J. Nielsen (2015) Functional pyruvate formate lyase pathway expressed in different electron donors in Saccharomyces cerevisiae at aerobic growth. FEMS Yeast Res. 15:fov024

F. Gatto; H. Miess; A. Schulze; J. Nielsen (2015) Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism. Sci. Rep. 5:10738

C. Lindskog; J. Linne; L. Fagerberg; B.M. Hallström; C.-J. Sundberg; M. Lindholm; M. Huus; C. Kampf; H. Choi; A. Liem; P. Ping; L. Väremo; A. Mardinoglu; J. Nielsen; E. Larsson; F. Ponten; M. Uhlen (2015) The human cardiac and skeletal muscle proteome defined by transcriptomics and antibody-based profiling. BMC Genom. 16:475

S. Shoaie; P. Ghaffari; P. Kovatcheva-Datchary; A. Mardinoglu; P. Sen; E. Pujos-Guillot; T. de Wouters; C. Juste; S. Rizkalla; J. Chilloux; L. Hoyles; J.K. Nicholson; ANR MicroObese Consortium; J. Dore; M.E. Dumas; K. Clement; F. Bäckhed; J. Nielsen (2015) Quantifying diet-induced metabolic changes of the human gut microbiome. Cell Metabolism 22:320-331

L. Caspeta; J. Nielsen (2015) Thermotolerant yeast strains adapted by laboratory evolution show trade-off at ancestral temperatures to other stresses. MBio 6:e00431-15

V. Tremaroli; F. Karlsson; M. Weling; M. Ståhlman; P. Kovatcheva-Datchary; T. Olbers; L. Fändriks; C. W. le Roux; J. Nielsen; F. Bäckhed (2015) Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation. Cell Metabolism 22:228-238

N. Pornputtaporn; I. Nookaew; J. Nielsen (2015) Human metabolic atlas: An online resource for human metabolism. Database bav068:1-9

M. Garcia-Albornoz; J. Nielsen (2015) Finding directionality and gene-disease predictions in disease associations. BMC Systems Biol. 9:35

M.H. Medema; R. Kottmann; P. Yilmaz; M. Cummings; J.B. Biggins; K. Blin: I. de Bruijn; Y.H. Chooi; J. Claesen; R.C. Coates; P. Cruz-Morales; S. Duddela; S. Düsterhus; D.J. Edwards; D.P. Fewer; N. Garg; C. Geiger; J.P. Gomez-Escribano; A. Greule; M. Hadjithomas; A.S. Haines; E.J.N. Helfrich; M.L. Hillwig; K. Ishida; A.C. Jones; C.S. Jones; K. Jungmann; C. Kegler; H.U. Kim; P. Kötter; D. Krug; J. Masschelein; A.V. Melnik; S.M. Mantovani; E.A. Monroe; M. Moore; N. Moss; H.-W. Nützmann; G. Pan; A. Pati; D. Petras; J. Reen; F. Rosconi; Z. Rui; Z. Tian; N.J. Tobias; Y. Tsunematsu; P. Wiemann; E. Wyckoff; X. Yan; G. Yim; F. Yu; Y. Xie; B. Aigle; A.K. Apel; C.J. Balibar; E.P. Balskus; F. Barona-Gómez; A. Bechthold; H.B. Bode; R. Borriss; S.F. Brady; A.A. Brakhage; P. Caffrey; Y.-Q. Cheng; J. Clardy; R.J. Cox; R. De Mot; S. Donadio; M.S. Donia; W.A. van der Donk; P.C. Dorrestein; S. Doyle; A.J.M. Driessen; M. Ehling-Schulz; K.-D. Entian; M.A. Fischbach; L. Gerwick; W.H. Gerwick; H. Gross; B. Gust; C. Hertweck; M. Höfte; S.E. Jensen; J. Ju; L. Katz; L. Kaysser; J.L. Klassen; N.P. Keller; J. Kormanec; O.P. Kuipers; T. Kuzuyama; N.C. Kyrpides; H.-J. Kwon; S. Lautru; R. Lavigne; C. Lee; B. Linquan; X. Liu; W. Liu; A. Luzhetskyy; T. Mahmud; Y. Mast; C. Méndez; M. Metsä-Ketelä; J. Micklefield; D.A. Mitchell; B.S. Moore; L.M. Moreira; R. Müller; B.A. Neilan; M. Nett; J. Nielsen; F. O’Gara; H. Oikawa; A. Osbourn; M.S. Osburne; B. Ostash; S.M. Payne; J.-L. Pernodet; M. Petricek; J. Piel; O. Ploux; J.M. Raaijmakers; J.A. Salas; E.K. Schmitt; B. Scott; R.F. Seipke; B. Shen; D.H. Sherman; K. Sivonen; M.J. Smanski; M. Sosio; R.D. Süssmuth; K. Tahlan; C.M. Thomas; Y. Tang; A.W. Truman; M. Viaud; J.D. Walton; C.T. Walsh; T. Weber; G.P. van Wezel; B. Wilkinson; J.M. Willey; W. Wohlleben; G.D. Wright; N. Ziemert; C. Zhang; S.B. Zotchev; R. Breitling; E. Takano; F.O. Glöckner (2015) The Minimum Information about a Biosynthetic Gene cluster (MIBiG) specification. Nature Chem. Biol. 11:625-631

L. Liu; Y. Zhang; Z. Liu; D. Petranovic; J. Nielsen (2015) Improving heterologous protein secretion at aerobic conditions by activating hypoxia induced genes in Saccharomyces cerevisiae. FEMS Yeast Research 15:fov070

Y. Zhang; G. Liu; M.K.M. Engqvist; A. Krivoruchko; B.M. Hallström; Y. Chen; V. Siewers; J. Nielsen (2015) Adaptive mutations in sugar metabolism restores growth on glucose in a pyruvate decarboxylase negative yeast strain. Microb. Cell Fac. 14:116

J.C. Qin; Y.J. Zhou; A. Krivoruchko; M. Huang; L. Liu; S. Khoomrung; V. Siewers; B. Jiang; J. Nielsen (2015) Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornitine. Nature Com. 6:8224

A. Rodriguez; K.R. Kildegaard; M. Li; I. Borodina; J. Nielsen (2015) Establishment of a yeast platform strain for production of p-coumaric acid through metabolic engineering of aromatic amino acid biosynthesis. Met. Eng. 31:181-188

M. Huang; Y. Bai; S.L. Sjostrom; B.M. Hallström; Z. Liu; D. Petranovic; M. Uhlen; H.N. Joensson; H. Andersson-Svahn; J. Nielsen (2015) Microfluidic screening and whole genome sequencing identifies mutations associated with improved protein secretion by yeast. Proc. Nat. Acad. Sci. USA 112:E4689-96

M. Li; K.R. Kildegaard; Y. Chen; A. Rodriguez; I. Borodina; J. Nielsen (2015) De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae. Met. Eng. 32:1-11

E. Fletcher; A. Feizi; S. Kim; V. Siewers; J. Nielsen (2015) RNAseq analysis of Pichia anomaia reveals important mechansisms required for survival at low pH. Mic. Cell Fac. 14:143

A. Mardinoglu; J. Helker; D. Gärtner; E. Bjornson; M.R. Schön; G. Flehmig; N. Klöting; M. Fasshauer; M. Stumvoll; J. Nielsen; M. Blüher (2015) Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue. Sci. Rep. 5:14841

A. Mardinoglu; S. Shoaie; M. Bergentall; P. Ghaffari; C. Zhang; E. Larsson; F. Bäckhed; J. Nielsen (2015) The gut microbiome modulates host amino acid and glutathione metabolism in mice. Mol. Systems Biol. 11:834

E. Björnson; B. Mukhopadhyay; A. Asplund; N. Pristovsek; R. Cinar; S. Romeo; M. Uhlen; G. Kunos; J. Nielsen; A. Mardinoglu (2015) Stratification of Hepatocellular Carcinoma Patients based on Acetate Utilization. Cell Rep. 13:2014-2026

S. Khoomrung; J.L. Martinez; S. Tippmann; S. Jansa-Ard; M. Buffing; R. Nicastro; J. Nielsen (2015) Expanded metabolite coverage of Saccharomyces cerevisiae extract through improved chemical derivatization. Anal. Chem. Res. 6:9-16

K.R. Kildegaard; Y. Chen; Z. Wang; J. Nielsen; I. Borodina (2015) Production of 3-hydroxypropionic acid from glucose and xylose by metabolically engineered Saccharomyces cerevisiae. Met. Eng. Com. 2:132-136

J. Anfelt; D. Kaczmarzyk; K. Shabestary; B. Renberg; J. Rockberg; J. Nielsen; M. Uhlen; E.P. Hudson (2015) Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol production. Mic. Cell Fac. 14:167

 

Reviews in international journals with peer review

2017

L.J. Sweetlove; J. Nielsen; A.R. Fernie (2017) Engineering central metabolism – a grand challenge for plant biologists. Plant J., in press

J. Geng; J. Nielsen (2017) In silico analysis of human metabolism: Reconstruction, contextualization and application. Curr. Op. Systems Biol., in press

2016

E. Fletcher; A. Krivoruchko; J. Nielsen (2016) Industrial systems biology and its impact on synthetic biology of yeast cell factories. Biotechnol. Bioeng. 113:1164-1170

J.L. Martinez; D. Petranovic; J. Nielsen (2016) Heme metabolism in stress regulation and protein production: From cinderalla to key player. BioEngineered, in press

F. Gatto; J. Nielsen (2016) In search for symmetries in the metabolism of cancer. WIREs Systems Biol. Med. 8:23-35

J. Nielsen; J. Keasling (2016) Engineering Cellular Metabolism. Cell 164:1185-1197

M. Uhlen; B.M. Hallström; C. Lindskog; A. Mardinoglu; F. Ponten; J. Nielsen (2016) The human-tissue-based proteome defined by transcriptomics and metabolic modeling. Mol. Sys. Biol. 12:862

M. Kumar; P. Babaei; B. Ji; J. Nielsen (2016) Human gut microbiota and healthy ageing: Recent developments and future perspective. Nutr. Healthy Ageing, in press

M.-K. Kang; J. Nielsen (2016) Biobased production of alkanes and alkenes through metabolic engineering of microorganisms. J. Ind. Microbiol. Biotechnol., in press

J. Robinson; J. Nielsen (2016) Integrative analysis of human omics data using biomolecular networks. Mol. BioSystems 12:2953-2964

Y. Chen; J. Nielsen (2016) Biobased organic acid production by metabolically engineered microorganisms. Curr. Op. Biotechnol. 37:165-172

Y. Chen; J. Nielsen (2016) Flux control through protein phosphorylation in yeast. FEMS Yeast Res., in press

A. Nilsson; J. Nielsen (2016) Genome-scale metabolic modeling of cancer. Met. Eng., in press

2015

B. Ji; J. Nielsen (2015) New insight into the gut microbiome through metagenomcs. Adv. Genom. Genet. 5:77-91

A. Krivoruchko; Y. Zhang; V. Siewers; J. Nielsen (2015) Microbial acetyl-CoA metabolism and metabolic engineering. Met. Eng. 28:28-42

A. Krivoruchko; J. Nielsen (2015) Production of natural products through metabolic engineering of Saccharomyces cerevisiae. Curr. Op. Biotechnol. 35:7-15

A. Mardinoglu; J. Nielsen (2015) New paradigms for metabolic modeling of human cells. Curr. Op. Biotechnol. 34:91-97

B. Pfleger; M. Gossing; J. Nielsen (2015) Metabolic engineering strategies for microbial production of oleochemicals. Met. Eng. 29:1-11

D. Jullesson; F. David; B. Pfleger; J. Nielsen (2015) Impact of Synthetic Biology and Metabolic Engineering on Industrial Production of Fine Chemicals. Biotechnol. Adv. 33:1395-1402

B. J. Sanchez; J. Nielsen (2015) Genome-scale models of yeast: Towards standardized evaluation and consistent omic integration. Integrative Biol. 7:846-858

O. Kayikci; J. Nielsen (2015) Glucose repression in Saccharomyces cerevisiae. FEMS Yeast Res. 15:fov068

Z. Dai; J. Nielsen (2015) Advancing metabolic engineering through systems biology of industrial microorganisms. Curr. Op. Biotechnol. 36:8-15

P.N. Ghaffari; A. Mardinoglu; J. Nielsen (2015) Cancer metabolism: A modeling perspective. Front. Physiol. 6:Article 382

L. Caspeta; T. Castilio; J. Nielsen (2015) Modifying yeast tolerance to inhibitory conditions of ethanol production. Fron. Bioeng. Biotechnol. 3:Article 184

B. Ji; J. Nielsen (2015) From next-generation sequencing to systematic modeling of the gut microbiome. Front. Genet. 6:219

 

Commentaries and Short Papers

2016

D. Fraenkel; J. Nielsen (2016) Trehalose-6-phosphate synthase and stabilization of yeast glycolysis. FEMS Yeast Res., in press

A. Mardinoglu; J. Nielsen (2016) The impact of systems medicine on human health and disease. Fron. Physiol., in press


2015

J. Pronk; S.Y. Lee; J. Lievense; J. Pierce; B. Palsson; M. Uhlen; J. Nielsen (2015) How to set up collaborations between academia and industrial biotech companies. Nature Biotechnol. 33:237-240

L. Väremo; J. Nielsen (2015) Networking in metabolism and human disease. Oncotarget 6:18

A. Ebrahim; E. Almaas; E. Bauer; A. Bordbar; A.P. Burgard; R.L. Chang; A. Dräger; I. Famili; A.M. Feist; R.M.T. Fleming; S.S. Fong; V. Hatzimanikatis; M.J. Herrgård; A. Holder; M. Hucka; D. Hyduke; N. Jamshidi; S.Y. Lee; N. Le Novère; J.A. Lerman; N.E. Lewis; D. Ma; R. Mahadevan; C. Maranas; H. Nagarajan; A. Navid; J. Nielsen; L.K. Nielsen; J. Nogales; A. Noronha; C. Pal; B.O. Palsson; J.A. Papin; K.R. Patil; N.D. Price; J.L. Reed; M. Saunders; R.S. Senger; N. Sonnenschein; Y. Sun; I. Thiele (2015) Do genome-scale models need exact solvers or clearer standards? Mol. Sys. Biol. In press

J. Nielsen (2015) Yeast cell factories on the horizon. Science 349:1050-1051

 

 

 

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