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Items: 25

1.

Investigating the Influence of Glycerol on the Utilization of Glucose in Yarrowia lipolytica Using RNA-Seq-Based Transcriptomics.

Lubuta P, Workman M, Kerkhoven EJ, Workman CT.

G3 (Bethesda). 2019 Dec 3;9(12):4059-4071. doi: 10.1534/g3.119.400469.

2.

Genome-scale model of Rhodotorula toruloides metabolism.

Tiukova IA, Prigent S, Nielsen J, Sandgren M, Kerkhoven EJ.

Biotechnol Bioeng. 2019 Dec;116(12):3396-3408. doi: 10.1002/bit.27162. Epub 2019 Sep 22.

PMID:
31502665
3.

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism.

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.

Nat Commun. 2019 Aug 8;10(1):3586. doi: 10.1038/s41467-019-11581-3.

4.

Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production.

Tiukova IA, Brandenburg J, Blomqvist J, Sampels S, Mikkelsen N, Skaugen M, Arntzen MØ, Nielsen J, Sandgren M, Kerkhoven EJ.

Biotechnol Biofuels. 2019 Jun 4;12:137. doi: 10.1186/s13068-019-1478-8. eCollection 2019.

5.

Mapping the metabolism of five amino acids in bloodstream form Trypanosoma brucei using U-13C-labelled substrates and LC-MS.

Johnston K, Kim DH, Kerkhoven EJ, Burchmore R, Barrett MP, Achcar F.

Biosci Rep. 2019 May 17;39(5). pii: BSR20181601. doi: 10.1042/BSR20181601. Print 2019 May 31.

6.

SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework.

Sánchez BJ, Li F, Kerkhoven EJ, Nielsen J.

BMC Syst Biol. 2019 Jan 11;13(1):4. doi: 10.1186/s12918-018-0673-8.

7.

Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica.

Pomraning KR, Bredeweg EL, Kerkhoven EJ, Barry K, Haridas S, Hundley H, LaButti K, Lipzen A, Yan M, Magnuson JK, Simmons BA, Grigoriev IV, Nielsen J, Baker SE.

mSphere. 2018 Dec 5;3(6). pii: e00541-18. doi: 10.1128/mSphere.00541-18.

8.

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ.

PLoS Comput Biol. 2018 Oct 18;14(10):e1006541. doi: 10.1371/journal.pcbi.1006541. eCollection 2018 Oct.

9.

Advancing metabolic engineering of Yarrowia lipolytica using the CRISPR/Cas system.

Shi TQ, Huang H, Kerkhoven EJ, Ji XJ.

Appl Microbiol Biotechnol. 2018 Nov;102(22):9541-9548. doi: 10.1007/s00253-018-9366-x. Epub 2018 Sep 21. Review.

10.

Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.

Sánchez BJ, Zhang C, Nilsson A, Lahtvee PJ, Kerkhoven EJ, Nielsen J.

Mol Syst Biol. 2017 Aug 3;13(8):935. doi: 10.15252/msb.20167411.

11.

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.

Kerkhoven EJ, Kim YM, Wei S, Nicora CD, Fillmore TL, Purvine SO, Webb-Robertson BJ, Smith RD, Baker SE, Metz TO, Nielsen J.

MBio. 2017 Jun 20;8(3). pii: e00857-17. doi: 10.1128/mBio.00857-17.

12.

Erratum to: A molecular genetic toolbox for Yarrowia lipolytica.

Bredeweg EL, Pomraning KR, Dai Z, Nielsen J, Kerkhoven EJ, Baker SE.

Biotechnol Biofuels. 2017 Feb 22;10:45. doi: 10.1186/s13068-017-0731-2. eCollection 2017.

13.

A molecular genetic toolbox for Yarrowia lipolytica.

Bredeweg EL, Pomraning KR, Dai Z, Nielsen J, Kerkhoven EJ, Baker SE.

Biotechnol Biofuels. 2017 Jan 3;10:2. doi: 10.1186/s13068-016-0687-7. eCollection 2017. Erratum in: Biotechnol Biofuels. 2017 Feb 22;10 :45.

14.

Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica.

Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J.

NPJ Syst Biol Appl. 2016 Mar 3;2:16005. doi: 10.1038/npjsba.2016.5. eCollection 2016.

15.

Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins.

Irani ZA, Kerkhoven EJ, Shojaosadati SA, Nielsen J.

Biotechnol Bioeng. 2016 May;113(5):961-9. doi: 10.1002/bit.25863. Epub 2015 Nov 2.

PMID:
26480251
16.

Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose.

Creek DJ, Mazet M, Achcar F, Anderson J, Kim DH, Kamour R, Morand P, Millerioux Y, Biran M, Kerkhoven EJ, Chokkathukalam A, Weidt SK, Burgess KE, Breitling R, Watson DG, Bringaud F, Barrett MP.

PLoS Pathog. 2015 Mar 16;11(3):e1004689. doi: 10.1371/journal.ppat.1004689. eCollection 2015 Mar.

17.

Crystal structure of an arginase-like protein from Trypanosoma brucei that evolved without a binuclear manganese cluster.

Hai Y, Kerkhoven EJ, Barrett MP, Christianson DW.

Biochemistry. 2015 Jan 20;54(2):458-71. doi: 10.1021/bi501366a. Epub 2014 Dec 23.

18.

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.

Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F.

Nucleic Acids Res. 2015 Jan;43(Database issue):D637-44. doi: 10.1093/nar/gku944. Epub 2014 Oct 9.

19.

Applications of computational modeling in metabolic engineering of yeast.

Kerkhoven EJ, Lahtvee PJ, Nielsen J.

FEMS Yeast Res. 2015 Feb;15(1):1-13. Epub 2015 Jan 14. Review.

PMID:
25156867
20.

Trypanosoma brucei: meet the system.

Achcar F, Kerkhoven EJ, Barrett MP.

Curr Opin Microbiol. 2014 Aug;20:162-9. doi: 10.1016/j.mib.2014.06.007. Epub 2014 Jul 16. Review.

PMID:
25037028
21.

The silicon trypanosome: a test case of iterative model extension in systems biology.

Achcar F, Fadda A, Haanstra JR, Kerkhoven EJ, Kim DH, Leroux AE, Papamarkou T, Rojas F, Bakker BM, Barrett MP, Clayton C, Girolami M, Krauth-Siegel RL, Matthews KR, Breitling R.

Adv Microb Physiol. 2014;64:115-43. doi: 10.1016/B978-0-12-800143-1.00003-8. Review.

22.

Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii.

Ledesma-Amaro R, Kerkhoven EJ, Revuelta JL, Nielsen J.

Biotechnol Bioeng. 2014 Jun;111(6):1191-9. doi: 10.1002/bit.25167. Epub 2013 Dec 27.

PMID:
24374726
23.

Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei.

Kerkhoven EJ, Achcar F, Alibu VP, Burchmore RJ, Gilbert IH, Trybiło M, Driessen NN, Gilbert D, Breitling R, Bakker BM, Barrett MP.

PLoS Comput Biol. 2013;9(12):e1003371. doi: 10.1371/journal.pcbi.1003371. Epub 2013 Dec 5.

24.

Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism.

Achcar F, Kerkhoven EJ; SilicoTryp Consortium, Bakker BM, Barrett MP, Breitling R.

PLoS Comput Biol. 2012 Jan;8(1):e1002352. doi: 10.1371/journal.pcbi.1002352. Epub 2012 Jan 19.

25.

A domino effect in drug action: from metabolic assault towards parasite differentiation.

Haanstra JR, Kerkhoven EJ, van Tuijl A, Blits M, Wurst M, van Nuland R, Albert MA, Michels PA, Bouwman J, Clayton C, Westerhoff HV, Bakker BM.

Mol Microbiol. 2011 Jan;79(1):94-108. doi: 10.1111/j.1365-2958.2010.07435.x. Epub 2010 Nov 5.

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