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Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update.

Cruz-Morales P, Orellana CA, Moutafis G, Moonen G, Rincon G, Nielsen LK, Marcellin E.

Genome Biol Evol. 2019 May 10. pii: evz096. doi: 10.1093/gbe/evz096. [Epub ahead of print]


Quantitative analysis of tetrahydrofolate metabolites from clostridium autoethanogenum.

de Souza Pinto Lemgruber R, Valgepea K, Hodson MP, Tappel R, Simpson SD, Köpke M, Nielsen LK, Marcellin E.

Metabolomics. 2018 Feb 16;14(3):35. doi: 10.1007/s11306-018-1331-2.


Methodological aspects of health-related quality of life measurement and analysis in patients with multiple myeloma.

Nielsen LK, Abildgaard N, Jarden M, Klausen TW.

Br J Haematol. 2019 Apr;185(1):11-24. doi: 10.1111/bjh.15759. Epub 2019 Jan 17. Review.


Systems-level engineering and characterisation of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB).

de Souza Pinto Lemgruber R, Valgepea K, Tappel R, Behrendorff JB, Palfreyman RW, Plan M, Hodson MP, Simpson SD, Nielsen LK, Köpke M, Marcellin E.

Metab Eng. 2019 May;53:14-23. doi: 10.1016/j.ymben.2019.01.003. Epub 2019 Jan 11.


Relationship between Fusarium Head Blight, Kernel Damage, Concentration of Fusarium Biomass, and Fusarium Toxins in Grain of Winter Wheat Inoculated with Fusarium culmorum.

Góral T, Wiśniewska H, Ochodzki P, Nielsen LK, Walentyn-Góral D, Stępień Ł.

Toxins (Basel). 2018 Dec 21;11(1). pii: E2. doi: 10.3390/toxins11010002.


Clarithromycin added to bortezomib-cyclophosphamide-dexamethasone impairs health-related quality of life in multiple myeloma patients.

Nielsen LK, Klausen TW, Jarden M, Frederiksen H, Vangsted AJ, Do T, Kristensen IB, Frølund UC, Andersen CL, Abildgaard N, Gregersen H.

Eur J Haematol. 2019 Jan;102(1):70-78. doi: 10.1111/ejh.13175. Epub 2018 Oct 29.


A randomized placebo-controlled phase II study of clarithromycin or placebo combined with VCD induction therapy prior to high-dose melphalan with stem cell support in patients with newly diagnosed multiple myeloma.

Gregersen H, Do T, Kristensen IB, Frølund UC, Andersen NF, Nielsen LK, Andersen CL, Klausen TW, Vangsted AJ, Abildgaard N.

Exp Hematol Oncol. 2018 Aug 13;7:18. doi: 10.1186/s40164-018-0110-0. eCollection 2018.


Linking genotype and phenotype in an economically viable propionic acid biosynthesis process.

Luna-Flores CH, Stowers CC, Cox BM, Nielsen LK, Marcellin E.

Biotechnol Biofuels. 2018 Aug 13;11:224. doi: 10.1186/s13068-018-1222-9. eCollection 2018.


Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis.

Hardwick SA, Chen WY, Wong T, Kanakamedala BS, Deveson IW, Ongley SE, Santini NS, Marcellin E, Smith MA, Nielsen LK, Lovelock CE, Neilan BA, Mercer TR.

Nat Commun. 2018 Aug 6;9(1):3096. doi: 10.1038/s41467-018-05555-0.


Minimizing Clonal Variation during Mammalian Cell Line Engineering for Improved Systems Biology Data Generation.

Grav LM, Sergeeva D, Lee JS, Marin de Mas I, Lewis NE, Andersen MR, Nielsen LK, Lee GM, Kildegaard HF.

ACS Synth Biol. 2018 Sep 21;7(9):2148-2159. doi: 10.1021/acssynbio.8b00140. Epub 2018 Aug 16.


From reconstruction to C4 metabolic engineering: A case study for overproduction of polyhydroxybutyrate in bioenergy grasses.

Gomes de Oliveira Dal'Molin C, Quek LE, Saa PA, Palfreyman R, Nielsen LK.

Plant Sci. 2018 Aug;273:50-60. doi: 10.1016/j.plantsci.2018.03.027. Epub 2018 Apr 5.


Improving culture performance and antibody production in CHO cell culture processes by reducing the Warburg effect.

Buchsteiner M, Quek LE, Gray P, Nielsen LK.

Biotechnol Bioeng. 2018 Sep;115(9):2315-2327. doi: 10.1002/bit.26724. Epub 2018 May 22.


H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum.

Valgepea K, de Souza Pinto Lemgruber R, Abdalla T, Binos S, Takemori N, Takemori A, Tanaka Y, Tappel R, Köpke M, Simpson SD, Nielsen LK, Marcellin E.

Biotechnol Biofuels. 2018 Mar 1;11:55. doi: 10.1186/s13068-018-1052-9. eCollection 2018.


The association of IgA deficiency on infection rate, self-perceived health, and levels of C-reactive protein in healthy blood donors.

Hauge SC, Jensen CK, Nielsen LK, Pedersen OB, Sørensen E, Thørner LW, Hjalgrim H, Erikstrup C, Nielsen KR, Kaspersen KA, Didriksen M, Dziegiel M, Ullum H.

APMIS. 2018 Mar;126(3):248-256. doi: 10.1111/apm.12807.


Engineered protein degradation of farnesyl pyrophosphate synthase is an effective regulatory mechanism to increase monoterpene production in Saccharomyces cerevisiae.

Peng B, Nielsen LK, Kampranis SC, Vickers CE.

Metab Eng. 2018 May;47:83-93. doi: 10.1016/j.ymben.2018.02.005. Epub 2018 Feb 19.


Advances in analytical tools for high throughput strain engineering.

Marcellin E, Nielsen LK.

Curr Opin Biotechnol. 2018 Dec;54:33-40. doi: 10.1016/j.copbio.2018.01.027. Epub 2018 Feb 12. Review.


Universal Alternative Splicing of Noncoding Exons.

Deveson IW, Brunck ME, Blackburn J, Tseng E, Hon T, Clark TA, Clark MB, Crawford J, Dinger ME, Nielsen LK, Mattick JS, Mercer TR.

Cell Syst. 2018 Feb 28;6(2):245-255.e5. doi: 10.1016/j.cels.2017.12.005. Epub 2018 Jan 24.


RNA-Seq Highlights High Clonal Variation in Monoclonal Antibody Producing CHO Cells.

Orellana CA, Marcellin E, Palfreyman RW, Munro TP, Gray PP, Nielsen LK.

Biotechnol J. 2018 Mar;13(3):e1700231. doi: 10.1002/biot.201700231. Epub 2018 Feb 1.


An Expanded Heterologous GAL Promoter Collection for Diauxie-Inducible Expression in Saccharomyces cerevisiae.

Peng B, Wood RJ, Nielsen LK, Vickers CE.

ACS Synth Biol. 2018 Feb 16;7(2):748-751. doi: 10.1021/acssynbio.7b00355. Epub 2018 Jan 23.


Toward industrial production of isoprenoids in Escherichia coli: Lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway.

Alonso-Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS.

Biotechnol Bioeng. 2018 Apr;115(4):1000-1013. doi: 10.1002/bit.26530. Epub 2018 Feb 7.


Genome-scale model guided design of Propionibacterium for enhanced propionic acid production.

Navone L, McCubbin T, Gonzalez-Garcia RA, Nielsen LK, Marcellin E.

Metab Eng Commun. 2017 Nov 24;6:1-12. doi: 10.1016/j.meteno.2017.11.001. eCollection 2018 Jun.


Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks.

Averesch NJH, Martínez VS, Nielsen LK, Krömer JO.

ACS Synth Biol. 2018 Feb 16;7(2):490-509. doi: 10.1021/acssynbio.7b00304. Epub 2017 Dec 26.


Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest.

Mills RJ, Titmarsh DM, Koenig X, Parker BL, Ryall JG, Quaife-Ryan GA, Voges HK, Hodson MP, Ferguson C, Drowley L, Plowright AT, Needham EJ, Wang QD, Gregorevic P, Xin M, Thomas WG, Parton RG, Nielsen LK, Launikonis BS, James DE, Elliott DA, Porrello ER, Hudson JE.

Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):E8372-E8381. doi: 10.1073/pnas.1707316114. Epub 2017 Sep 15.


Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks.

Saa PA, Nielsen LK.

Biotechnol Adv. 2017 Dec;35(8):981-1003. doi: 10.1016/j.biotechadv.2017.09.005. Epub 2017 Sep 13. Review.


Plant genome-scale reconstruction: from single cell to multi-tissue modelling and omics analyses.

Gomes de Oliveira Dal'Molin C, Nielsen LK.

Curr Opin Biotechnol. 2018 Feb;49:42-48. doi: 10.1016/j.copbio.2017.07.009. Epub 2017 Aug 11. Review.


Cell-free pipeline for discovery of thermotolerant xylanases and endo-1,4-β-glucanases.

Gagoski D, Shi Z, Nielsen LK, Vickers CE, Mahler S, Speight R, Johnston WA, Alexandrov K.

J Biotechnol. 2017 Oct 10;259:191-198. doi: 10.1016/j.jbiotec.2017.07.014. Epub 2017 Jul 17.


Awakening sleeping beauty: production of propionic acid in Escherichia coli through the sbm operon requires the activity of a methylmalonyl-CoA epimerase.

Gonzalez-Garcia RA, McCubbin T, Wille A, Plan M, Nielsen LK, Marcellin E.

Microb Cell Fact. 2017 Jul 17;16(1):121. doi: 10.1186/s12934-017-0735-4.


Maintenance of ATP Homeostasis Triggers Metabolic Shifts in Gas-Fermenting Acetogens.

Valgepea K, de Souza Pinto Lemgruber R, Meaghan K, Palfreyman RW, Abdalla T, Heijstra BD, Behrendorff JB, Tappel R, Köpke M, Simpson SD, Nielsen LK, Marcellin E.

Cell Syst. 2017 May 24;4(5):505-515.e5. doi: 10.1016/j.cels.2017.04.008. Epub 2017 May 17.


Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum.

Valgepea K, Loi KQ, Behrendorff JB, Lemgruber RSP, Plan M, Hodson MP, Köpke M, Nielsen LK, Marcellin E.

Metab Eng. 2017 May;41:202-211. doi: 10.1016/j.ymben.2017.04.007. Epub 2017 Apr 23.


Overexpression of the regulatory subunit of glutamate-cysteine ligase enhances monoclonal antibody production in CHO cells.

Orellana CA, Marcellin E, Gray PP, Nielsen LK.

Biotechnol Bioeng. 2017 Aug;114(8):1825-1836. doi: 10.1002/bit.26316. Epub 2017 May 8.


A systematic review of health-related quality of life in longitudinal studies of myeloma patients.

Nielsen LK, Jarden M, Andersen CL, Frederiksen H, Abildgaard N.

Eur J Haematol. 2017 Jul;99(1):3-17. doi: 10.1111/ejh.12882. Epub 2017 Apr 25. Review.


Coupling gene regulatory patterns to bioprocess conditions to optimize synthetic metabolic modules for improved sesquiterpene production in yeast.

Peng B, Plan MR, Carpenter A, Nielsen LK, Vickers CE.

Biotechnol Biofuels. 2017 Feb 21;10:43. doi: 10.1186/s13068-017-0728-x. eCollection 2017.


A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae.

Peng B, Plan MR, Chrysanthopoulos P, Hodson MP, Nielsen LK, Vickers CE.

Metab Eng. 2017 Jan;39:209-219. doi: 10.1016/j.ymben.2016.12.003. Epub 2016 Dec 8.


Hand bone loss in early rheumatoid arthritis during a methotrexate-based treat-to-target strategy with or without adalimumab-a substudy of the optimized treatment algorithm in early RA (OPERA) trial.

Ørnbjerg LM, Østergaard M, Jensen T, Hørslev-Petersen K, Stengaard-Pedersen K, Junker P, Ellingsen T, Ahlquist P, Lindegaard H, Linauskas A, Schlemmer A, Dam MY, Hansen I, Lottenburger T, Ammitzbøll CG, Jørgensen A, Krintel SB, Raun J, Hetland ML; OPERA Study Group, Slot O, Nielsen LK, Skjødt H, Majgaard O, Lorenzen T, Horn HC, Kowalski M, Johansen IL, Pedersen PM, Manilo N, Bliddal H.

Clin Rheumatol. 2017 Apr;36(4):781-789. doi: 10.1007/s10067-016-3489-1. Epub 2016 Dec 5.


A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE.

Cell Syst. 2016 Nov 23;3(5):434-443.e8. doi: 10.1016/j.cels.2016.10.020.


Improved production of propionic acid using genome shuffling.

Luna-Flores CH, Palfreyman RW, Krömer JO, Nielsen LK, Marcellin E.

Biotechnol J. 2017 Feb;12(2). doi: 10.1002/biot.201600120. Epub 2016 Oct 20.


In vitro production of baculoviruses: identifying host and virus genes associated with high productivity.

Nguyen Q, Tb Tran T, Chan LC, Nielsen LK, Reid S.

Appl Microbiol Biotechnol. 2016 Nov;100(21):9239-9253. Epub 2016 Sep 9.


Metabolic Reconstruction of Setaria italica: A Systems Biology Approach for Integrating Tissue-Specific Omics and Pathway Analysis of Bioenergy Grasses.

de Oliveira Dal'Molin CG, Orellana C, Gebbie L, Steen J, Hodson MP, Chrysanthopoulos P, Plan MR, McQualter R, Palfreyman RW, Nielsen LK.

Front Plant Sci. 2016 Aug 10;7:1138. doi: 10.3389/fpls.2016.01138. eCollection 2016.


Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models.

Saa PA, Nielsen LK.

Bioinformatics. 2016 Dec 15;32(24):3807-3814. Epub 2016 Aug 24.


Spliced synthetic genes as internal controls in RNA sequencing experiments.

Hardwick SA, Chen WY, Wong T, Deveson IW, Blackburn J, Andersen SB, Nielsen LK, Mattick JS, Mercer TR.

Nat Methods. 2016 Sep;13(9):792-8. doi: 10.1038/nmeth.3958. Epub 2016 Aug 8.


Representing genetic variation with synthetic DNA standards.

Deveson IW, Chen WY, Wong T, Hardwick SA, Andersen SB, Nielsen LK, Mattick JS, Mercer TR.

Nat Methods. 2016 Sep;13(9):784-91. doi: 10.1038/nmeth.3957. Epub 2016 Aug 8.


Tetanus toxin production is triggered by the transition from amino acid consumption to peptides.

Licona-Cassani C, Steen JA, Zaragoza NE, Moonen G, Moutafis G, Hodson MP, Power J, Nielsen LK, Marcellin E.

Anaerobe. 2016 Oct;41:113-124. doi: 10.1016/j.anaerobe.2016.07.006. Epub 2016 Aug 1.


Retrospective evaluation of the incidence and prognostic significance of spontaneous echocardiographic contrast in relation to cardiac disease and congestive heart failure in cats: 725 cases (2006-2011).

Peck CM, Nielsen LK, Quinn RL, Laste NJ, Price LL.

J Vet Emerg Crit Care (San Antonio). 2016 Sep;26(5):704-12. doi: 10.1111/vec.12509. Epub 2016 Aug 1.


Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach.

Saa PA, Nielsen LK.

Sci Rep. 2016 Jul 15;6:29635. doi: 10.1038/srep29635.


Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals.

Ormerod KL, Wood DL, Lachner N, Gellatly SL, Daly JN, Parsons JD, Dal'Molin CG, Palfreyman RW, Nielsen LK, Cooper MA, Morrison M, Hansbro PM, Hugenholtz P.

Microbiome. 2016 Jul 7;4(1):36. doi: 10.1186/s40168-016-0181-2.


Recon 2.2: from reconstruction to model of human metabolism.

Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M, Zielinski DC, Ang KS, Gardiner NJ, Gutierrez JM, Kyriakopoulos S, Lakshmanan M, Li S, Liu JK, Martínez VS, Orellana CA, Quek LE, Thomas A, Zanghellini J, Borth N, Lee DY, Nielsen LK, Kell DB, Lewis NE, Mendes P.

Metabolomics. 2016;12:109. Epub 2016 Jun 7.


Genome Sequence of Propionibacterium acidipropionici ATCC 55737.

Luna-Flores CH, Nielsen LK, Marcellin E.

Genome Announc. 2016 May 19;4(3). pii: e00248-16. doi: 10.1128/genomeA.00248-16.


The Saccharomyces cerevisiae pheromone-response is a metabolically active stationary phase for bio-production.

Williams TC, Peng B, Vickers CE, Nielsen LK.

Metab Eng Commun. 2016 May 11;3:142-152. doi: 10.1016/j.meteno.2016.05.001. eCollection 2016 Dec.


ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks.

Saa PA, Nielsen LK.

Bioinformatics. 2016 Aug 1;32(15):2330-7. doi: 10.1093/bioinformatics/btw132. Epub 2016 Mar 11.


Genetic and biochemical characterization of genes involved in hyaluronic acid synthesis in Streptococcus zooepidemicus.

Zhang Y, Luo K, Zhao Q, Qi Z, Nielsen LK, Liu H.

Appl Microbiol Biotechnol. 2016 Apr;100(8):3611-20. doi: 10.1007/s00253-016-7286-1. Epub 2016 Jan 13.


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