Nielsen Lab
   

Publications

 
 
Recent publications
 

Research papers in international journals with peer review


2018

S. Lee; C. Zhang; A. Muhammad; L. Zhengtao; R. Benfeitas; G. Bidkhor; S. Deshmukh; M.A. Shobky; A. Lovric; J. Boren; J. Nielsen; M. Uhlen; A Mardinoglu (2018) TCSBN: a database of tissue and cancer specific biological networks. Nucl. Acid. Res. 46:D595-D600

E. Brunk; S. Sahoo; D.C. Zielinski; A. Altunkaya; A. Dräger; N. Mih; F. Gatto; A. Nilsson; G.A.P. Gonzalez; M.K. Aurich; A. Prlic; A. Sastry; A.D. Danielsdottir; A. Heinken; A. Noronha; P.W. Rose; S.K. Burley; R.M.T. Fleming; J. Nielsen; I. Thiele; B.O. Palsson (2018) Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnol. 36:272-281

R. Ferreira; C. Skrekas; J. Nielsen; F. David (2018) Multiplexed CRISPR/Cas9 genome editing and gene regulation using Csy9 in Saccharomyces cerevisiae. ACS Syn. Biol. 7:10-15

Y. Hu; Z. Zhu; J. Nielsen; V. Siewers (2018) Transporter engineering for improved fatty alcohol secretion in yeast. Meg. Eng. 45:51-58

D. Bergenholm; M. Gossing; Y. Wei; V. Siewers; J. Nielsen (2018) Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids. Biotechnol. Bioeng. 115:932-942

A. Mardinoglu; H. Wu; E. Bjornson; C. Zhang; A. Hakkarainen; S.M. Räsänen; S. Lee; R.M. Mancina; M. Bergentall; K.H. Pietiläinen; S. Söderlund; N. Matikainen; M. Ståhlman; P.-O. Bergh; M. Adiels; B.D. Piening; M. Graner; N. Lundbom; K.J. Williams; S. Romeo; J. Nielsen; M. Snyder; M. Uhlen; G. Bergström; R. Perkins; H.-U. Marschall; F. Bäckhed; M.-R. Taskinen; J. Boren (2018) An integrated understanding of the rapid metabolic benefits of a carbohydrate restricted diet on hepatic steatosis in humans. Cell Metab. 27:559-571

Y. Zhou; Y. Hu; Z. Zhu; V. Siewers; J. Nielsen (2018) Engineering of 1-alkene biosynthesis and secretion by dynamic regulation in yeast. ACS Syn. Biol., in press

R. Ferreira; P.G. Teixeira; V. Siewers; J. Nielsen (2018) Redirection of lipid flux towards phospholipids in yeast increases fatty acid turnover and secretion. Proc. Nat. Acad. Sci. USA, in press

P. Jenjaroenpun; T. Wongsurawat; R. Pereira; P. Patumcharoenpol; D.W. Ussery; J. Nielsen; I. Nookaew (2018) Complete genomic and transcriptional landscape analysis using third generation sequencing: A case study of Saccharomyces cerevisiae CEN.PK113-7D. Nuc. Acid Res., in press

A. Azimi; S. Caramuta; R. Jafari; B.S. Ludlow; J. Boström; J. Robinson; F. Edfors; R. Tuominen; J. Nielsen; J. Hansson; S.E. Brage; M. Altun; J. Lehtiö; M. Uhlen; G. Maddalo (2018) Targeting CDK2 overcomes melanoma reistance against BRAF and Hsp90 inhibitors. Mol. Systems Biol., in press

Y. Wei; D. Bergenholm; M. Gossing; V. Siewers; J. Nielsen (2018) Expression of cocoa genes in Saccharomyces cerevisiae improves cocoa butter production. Microb. Cell Fac., in press

R. Ferreira; P.G. Teixeira; M. Gossing; F. David; V. Siewers; J. Nielsen (2018) Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols. Met. Eng. Com. 6:22-27

D. Carmona-Gutierrez; M.A. Bauer; A. Zimmermann; A. Aguilera; N. Austriaco; K. Ayscough; R. Balzan; S. Bar-Nun; A. Barrientos; P. Belenky; M. Blondel; R.J. Braun; M. Breitenbach; W.C. Burhans; S. Büttner; D. Cavalieri; M. Chang; K.F. Cooper; M. Côrte-Real; V. Costa; C. Cullin; I. Dawes; J. Dengjel; M.B. Dickman; T. Eisenberg; B. Fahrenkrog; N. Fasel; K.-U. Fröhlich; A. Gargouri; S. Giannattasio; P. Goffrini; C.W. Gourlay; C.M. Grant; M.T. Greenwood; N. Guaragnella; T. Heger; J. Heinisch; E. Herker; J.M. Herrmann; S. Hofer; A. Jiménez-Ruiz; H. Jungwirth; K. Kainz; D.P. Kontoyiannis; P. Ludovico; S. Manon; E. Martegani; C. Mazzoni; L.A. Megeney; C. Meisinger; J. Nielsen; T. Nyström; H.D. Osiewacz; T.F. Outeiro; H.-O. Park; T. Pendl; D. Petranovic; S. Picot; P. Polčic; T. Powers; M. Ramsdale; M. Rinnerthaler; P. Rockenfeller; C. Ruckenstuh; R. Schaffrath; M. Segovia; F.F. Severin; A. Sharon; S.J. Sigrist; C. Sommer-Ruck; M.J. Sousa; J.M. Thevelein; K. Thevissen; V. Titorenko; M.B. Toledano; M. Tuite; F.-N. Vögtle; B. Westermann; J. Winderickx; S. Wissing; S. Wölfl; Z.J. Zhang; R.Y. Zhao; B. Zhou; L. Galluzzi; G. Kroemer; F. Madeo (2018) Guidelines and recommendations on yeast cell death nomenclature. Microb. Cell 5:4-31

J. Bao; M. Huang; D. Petranovic; J. Nielsen (2018) Balanced trafficking between the ER and the Golgi apparatus increases protein secretion in yeast. AMB Express 8:37

P. Das; B. Ji; P. Kovatcheva-Datchary; F. Bäckhed; J. Nielsen (2018) In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis. PLOS One, in press

F. Gatto; K.A. Blum; S.S. Hosseini; M. Ghanaat; M. Kashan; F. Maccari; F. Galeotti; J. Hsieh; N. Volpi; A.A. Hakimi; J. Nielsen (2018) Plasma glycosaminoglycans as diagnostic and prognostic biomarkers in surgically treated renal cell carcinoma. Eur. Urol. Onc., in press

J. Maury; S. Kannan; N.B. Jensen; F.K. Öberg; K.R. Kildegaard; J. Förster; J. Nielsen; C.T. Workman; I. Borodina (2018) Glucose-dependent promoters for dynamic regulation of metabolic pathways. Fron. Bioeng. Biotechnol., in press

2017

Z. Zhu; Y.J. Zhou; A. Krivoruchko; M. Grininger; Z.K. Zhao; J. Nielsen (2017) Expanding the product portfolio of fungal type I fatty acid synthases. Nature Chem. Biol. 13:360-362

L. Wenning; T. Yu; F. David; J. Nielsen; V. Siewers (2016) Establishing very long-chain fatty alcohol and wax ester biosynthesis. Biotechnol. Bioeng. 114:1025-1035

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. 101:13577-3585

A. Nilsson; A. Mardinoglu; J. Nielsen (2017) Predicting growth of the healthy infant using a genome-scale metabolic model. npj Systems Biol. Appl. 3:3
A. Mardinoglu; E. Bjornson; C. Zhang; M. Klevstig; S. Söderlund; M. Ståhlman; M. Adiels; A. Hakkarainen; N. Lundbom; M. Kilicarslan; B.M. Hallström; J. Lundbom; B. Verges; P.H.R. Barret; G.F. Watts; M. Serlie; J. Nielsen; M. Uhlen; U. Smith; H.-U. Marschall; M.-R. Taskine; J. Boren (2017) Personalized genome-scale modeling identifies NAD+ and glutathione metabolism as a target for treatment of NAFLD. Mol. Sys. Biol. 13:916

Y. Wei; M. Gossing; D. Bergenholm; V. Siewers; J. Nielsen (2017) Increasing cocoa butter-like lipid production of Saccharomyces cerevisiae by expression of selected cocoa genes. AMB Express 7:34

S. Tippmann; R. Ferreira; V. Siewers; J. Nielsen; Y. Chen (2017) Effects of acetoacetyl-CoA synthase expression on production of farnesene in Saccharomyces cerevisiae. J. Ind. Biotechnol. Microbiol. 44:911-922

S. Tippmann; J. Anfelt; F. David; J.M. Rand; V. Siewers; M. Uhlen; J. Nielsen; E.P. Hudson (2017) Affibody scaffold improve sesquiterpene production in Saccharomyces cerevisiae. ACS Syn. Biol. 6:19-28

E.L. Bredeweg; K.R. Pomraning; Z. Dai; J. Nielsen; E. Kerkhoven; S.E. Baker (2017) A molecular genetic toolbox for Yarrowia lipolytica. Biotechnol. Biofuels 10:2

Y. Chen; Y. Wang; J. Nielsen (2017) Systematic inference of functional phosphorylation events in yeast metabolism. Bioinformatics 33:1995-2001
P.-J. Lahtvee; B.J. Sanchez; A. Smialowska; S. Kasvandik; I. Elsemman; F. Gatto; J. Nielsen (2017) Absolute quantification of protein and mRNA abundances demonstrate variability in gene-specific translation efficiency in yeast. Cell Systems 4:495-504

Y. Hu; J. Zhou; J. Bao; L. Huang; J. Nielsen; A. Krivoruchko (2017) Metabolic engineering of Saccharomyces cerevisiae for production of germacreme A, a precursor of beta-elemene. J. Ind. Microbiol. Biotechnol. 44:1065-1072

T. Yu; Y.J. Zhou; L. Wenning; Q. Liu; A. Krivoruchko; V. Siewers; J. Nielsen; F. David (2017) Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals. Nature Com. 8:15587

P.G. Teixeira; R. Ferreira; Y.J. Zhou; V. Siewers; J. Nielsen (2017) Dynamic regulation of fatty acid pools for improved production of fatty alcohols in Saccharomyces cerevisiae. Microb. Cell Fac. 16:45

E.D. Jensen; R. Ferreira; T. Jakociunas; D. Arsovska; L. Ding; J.D. Smith; F. David; J. Nielsen; M.K. Jensen; J.D. Keasling (2017) Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies. Microb. Cell Fac. 16:46

R. Babazadeh; P.-J. Lahtvee; C. Beck; M. Goksör; J. Nielsen; S. Hohmann (2017) The yeast osmostress response is carbon source dependent. Sci. Rep. 7:990

M.-K. Kang; Y. Zhou; N.A. Buijs; J. Nielsen (2017) Functional screening of aldehyde decarboxylases for long-chain alkane production by Saccharomyces cerevisiae. Microb. Cell Fac. 16:74

L. Väremo; T.I. Henriksen; C. Scheele; C. Broholm; M. Pedersen; M. Uhlen; B.K. Pedersen; J. Nielsen (2017) Type 2 diabetes and obesity are independently associated with similar inherent transcriptional reprogramming in human myocytes. Genome Med. 9:47

J.C. Nielsen; S. Grijseels; S. Prigent; B. Ji; J. Dainat; K.F. Nielsen; J.C. Frisvad; M. Workman; J. Nielsen (2017) Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species. Nature Microbiol. 2:17044

J. Bao; M. Huang; D. Petranovic; J. Nielsen (2017) Moderate expression of SEC16 increases protein secretion by Saccharomyces cerevisiae. Appl. Environ. Microbiol. 83:e03400-16

E.J. Kerkhoven; Y.-M. Kim; S. Wei; C.D. Nicora; T.L. Filllmore; S.O. Purvine; B.-J. Webb-Robertson; R.D. Smith; S.E. Baker; T.O. Metz; J. Nielsen (2017) Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica. mBio 6:e00857-17

P. Sen; A. Mardinoglu; J. Nielsen (2017) Selection of complementary foods based on optimal nutrition values. Sci. Rep. 7:5413

A. Rodriguez; T. Strucko; S.G. Stahlhut; M. Kristensen; D.K. Svenssen; J. Forster; J. Nielsen; I. Borodina (2017) Metabolic engineering of yeast for fermentative production of flavonoids. Biores. Technol. 245:1645-1654

A. Feizi; F. Gatto; M. Uhlen; J. Nielsen (2017) Human protein secretory pathway genes are expressed in a tissue-specific pattern to match secretion demand. Systems Biol. Appl. 3:22

B.J. Sanchez; C. Zhang; A- Nilsson; P.-J. Lahtvee; E. Kerkhoven; J. Nielsen (2017) Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints. Mol. Systems Biol. 13:935

K. Thorell; J. Bengtsson-Palme; O. Liu; R.V. Gonzales; I. Nookaew; L. Rabeneck; L. Paszat; D. Graham; J. Nielsen; S, Lundin; Å. Sjöling (2017) In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastic infection and early stages of carcinogenesis. Infect. Immun. 85:e00031-17

S. Lee; C. Zhang; Z. Liu; M. Klevstig; B. Mukhopadhyay; M. Bergentall; R. Cinar; M. Ståhlman; N. Sikanic; J.K. Park; S. Deshmukh; A.M. Pour; T. Kuijpers; M. Grøtli; S.J. Elsässer; B.D. Piening; M. Snyder; J. Nielsen; F. Bäckhed; G. Kunos; M. Uhlen; J. Boren; A. Mardinoglu (2017) Network analysis identify liver-specific targets for treating liver diseases. Mol. Sys. Biol. 13:938

M. Huang; J. Bao; B.M. Hallström; D. Petranovic; J. Nielsen (2017) Efficient protein production by yeast requires global tuning of metabolism. Nature Com. 8:1131

G. Liu; Y. Chen; N. Færgeman; J. Nielsen (2017) Elimination of the last reactions in ergosterol biosynthesis alters the reistance of Saccharomyces cerevisiae to multiple stress. FEMS Yeast Res. 17:fox063

R. Ferreira; F. Gatto; J. Nielsen (2017) Exploiting off-targeting in guide-RNAs for CRISPR systems for editing of multiple genes. FEBS Let. 591:3288-3295

Z. Zhu; Y.J. Zhou; M.-K. Kang; A. Krivoruchko; N.A. Buijs; J. Nielsen (2017) Enabling the synthesis of medium chain alkanes and 1-alkenes in yeast. Met. Eng. 44:81-88

S. Grijseels; J.C. Nielsen; J. Nielsen; T.O. Larsen; J.C. Frisvad; K.F. Nielsen; R. Frandsen; M. Workman (2017) Physiological characterization of secondary metabolite producing Penicillium cell factories. Fungal Biol. Biotechnol. 4:8

A. Rodriguez; Y. Chen; S. Khoomrung; E. Özdemir; I. Borodina; J. Nielsen (2017) Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains. Met. Eng. 44:265-272

Reviews in international journals with peer review

2018

A. Mardinoglu; J. Boren; U. Smith; M. Uhlen; J. Nielsen (2018) The employment of systems biology in gastroenterology and hepatology. Nature Rev. Gastro. Hep., in press

R. Ferreira; F. David; J. Nielsen (2018) Advancing biotechnology with CRISPR/Cas9: Recent applications and patent landscape. J. Ind. Microbiol. Biotechnol., in press

F.R. Pinu; N. Granucci; J. Daniell; T.-L. Han; S. Carneiro; I. Rocha; J. Nielsen; S.G. Villas-Boas (2018) Metabolite secretion in microorganisms: The theory of metabolic overflow put to the test. Metabolomics 14:43

C. Malina; C. Larsson; J. Nielsen (2018) Yeast mitochondria: An overview of mitochondrial biology and the potential of mitochondrial systems biology. FEMS Yeast Res., in press

B. Turanli; M. Grøtli; J. Boren; J. Nielsen; M. Uhlen; K.Y. Arga; A. Mardinoglu (2018) Drug repositioning for effective prostate cancer treatment. Fron. Physiol., in press

2017

A. Nilsson; J. Nielsen (2017) Genome-scale metabolic modeling of cancer. Met. Eng. 43:103-112

L.J. Sweetlove; J. Nielsen; A.R. Fernie (2017) Engineering central metabolism – a grand challenge for plant biologists. Plant J. 90:749-763

J. Geng; J. Nielsen (2017) In silico analysis of human metabolism: Reconstruction, contextualization and application. Curr. Op. Systems Biol. 2:28-37

J. Nielsen (2017) Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine. Cell Met. 25:572-579

J.C. Nielsen; J. Nielsen (2017) Development of fungal cell factories for the production of secondary metabolites: linking genomics and metabolism. Synth. Systems Biotechnol. 2:5-12

G. Wang; M. Huang; J. Nielsen (2017) Exploring the potential of Saccharomyces cerevisiae for biopharmaceutical protein production. Curr. Opion. Biotechnol. 48:77-84

J. Nielsen (2017) Systems Biology of Metabolism. Ann. Rev. Biochem. 86:245-275

J.L. Robinson; J. Nielsen (2017) Anticancer drug discovery through genome-scale metabolic modeling. Curr. Opion. Syst. Biol. 4:1-8

J. Nielsen; J. Archer; V. Bajic; T. Gojobori; I. Mijakovic (2017) Building a biobased industry in the Middle East through harnessing the potential of the Red See biodiversity. Appl. Microbiol. Biotechnol., in press

D. Cook; J. Nielsen (2017) Genome-scale metabolic models applied to human health and disease. WIRE Systems Biol. Med. 9:e1393

X. Chen; C. Gao; L. Guo; G. Hu; Q. Luo; J. Liu; J. Nielsen; J. Chen; L. Liu (2017) DCEO Biotechnology: Tools to Design, Construct, Evaluate and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem. Rev., in press

A. Mardinoglu; J. Boren; U. Smith; M. Uhlen; J. Nielsen (2017) The employment of systems biology in gastroenterology and hepatology. Nature Rev. Gastro. Hep., in press

R. Benfeitas; M. Uhlen; J. Nielsen; A. Mardinoglu (2017) New challenges to study heterogeneity in cancer redox metabolism. Fron. Cell Develop. Biol. 5:65

J. Bosley; C. Boren; S. Lee; M. Grøtli; J. Nielsen; M. Uhlen; J. Boren; A. Mardinoglu (2017) Improving economics of NASH/NAFLD treatment through the use of systems biology. Drug Discov. Today 22:1532-1538

Z. Gong; J. Nielsen; Y. Zhou (2017) Engineering robustness of microbial cell factories. Biotechnol. J. 12:1700014

K. Campbell; J. Xia; J. Nielsen (2017) The impact of systems biology on bioprocessing. Trends Biotechnol. 35:1156-1168

Y. Zhang; J. Nielsen; Z. Liu (2017) Engineering yeast metabolism for production of terpenoids for use a perfume ingredients, pharmaceuticals, and biofuels. FEMS Yeast Res., in press

 

Commentaries and Short Papers

2018

A. Nilsson; J.R. Haanstra; B. Teusink; J. Nielsen (2018) Metabolite depletion affects flux profiling of cell lines. Trends Biochem. Sci., in press


2017

J. Nielsen (2017) Built on stable catalysts. Nature Microbiol. 2:17085

A. Nilsson; J. Nielsen; B. Palsson (2017) Metabolic models of protein allocation call for the Kinetome. Cell Systems 5:538-541

   
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