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Comparative analysis of extremely thermophilic Caldicellulosiruptor species reveals common and differentiating cellular strategies for plant biomass utilization.

Zurawski JV, Conway JM, Lee LL, Simpson H, Izquierdo JA, Blumer-Schuette S, Nookaew I, Adams MW, Kelly RM.

Appl Environ Microbiol. 2015 Aug 7. pii: AEM.01622-15. [Epub ahead of print]


Human metabolic atlas: an online resource for human metabolism.

Pornputtapong N, Nookaew I, Nielsen J.

Database (Oxford). 2015 Jul 24;2015:bav068. doi: 10.1093/database/bav068. Print 2015.


Eicosapentaenoic and docosahexaenoic acid-enriched high fat diet delays the development of fatty liver in mice.

Soni NK, Nookaew I, Sandberg AS, Gabrielsson BG.

Lipids Health Dis. 2015 Jul 22;14:74. doi: 10.1186/s12944-015-0072-8.


Ebolavirus comparative genomics.

Jun SR, Leuze MR, Nookaew I, Uberbacher EC, Land M, Zhang Q, Wanchai V, Chai J, Nielsen M, Trolle T, Lund O, Buzard GS, Pedersen TD, Wassenaar TM, Ussery DW.

FEMS Microbiol Rev. 2015 Jul 14. pii: fuv031. [Epub ahead of print] Review.


Proteome- and transcriptome-driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes.

Väremo L, Scheele C, Broholm C, Mardinoglu A, Kampf C, Asplund A, Nookaew I, Uhlén M, Pedersen BK, Nielsen J.

Cell Rep. 2015 May 12;11(6):921-33. doi: 10.1016/j.celrep.2015.04.010. Epub 2015 Apr 30.


Site-specific programming of the host epithelial transcriptome by the gut microbiota.

Sommer F, Nookaew I, Sommer N, Fogelstrand P, Bäckhed F.

Genome Biol. 2015 Mar 28;16:62. doi: 10.1186/s13059-015-0614-4.


Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival.

Goossens KV, Ielasi FS, Nookaew I, Stals I, Alonso-Sarduy L, Daenen L, Van Mulders SE, Stassen C, van Eijsden RG, Siewers V, Delvaux FR, Kasas S, Nielsen J, Devreese B, Willaert RG.

MBio. 2015 Apr 14;6(2). pii: e00427-15. doi: 10.1128/mBio.00427-15.


Insights from 20 years of bacterial genome sequencing.

Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW.

Funct Integr Genomics. 2015 Mar;15(2):141-61. doi: 10.1007/s10142-015-0433-4. Epub 2015 Feb 27.


Dietary polyunsaturated fatty acids increase survival and decrease bacterial load during septic Staphylococcus aureus infection and improve neutrophil function in mice.

Svahn SL, Grahnemo L, Pálsdóttir V, Nookaew I, Wendt K, Gabrielsson B, Schéle E, Benrick A, Andersson N, Nilsson S, Johansson ME, Jansson JO.

Infect Immun. 2015 Feb;83(2):514-21. doi: 10.1128/IAI.02349-14. Epub 2014 Nov 17.


A dedicated database system for handling multi-level data in systems biology.

Pornputtapong N, Wanichthanarak K, Nilsson A, Nookaew I, Nielsen J.

Source Code Biol Med. 2014 Jul 10;9:17. doi: 10.1186/1751-0473-9-17. eCollection 2014.


yStreX: yeast stress expression database.

Wanichthanarak K, Nookaew I, Petranovic D.

Database (Oxford). 2014 Jul 14;2014. pii: bau068. doi: 10.1093/database/bau068. Print 2014.


Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue.

Karlsson FH, Nookaew I, Nielsen J.

PLoS Comput Biol. 2014 Jul 10;10(7):e1003706. doi: 10.1371/journal.pcbi.1003706. eCollection 2014 Jul.


Veillonella, Firmicutes: Microbes disguised as Gram negatives.

Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW.

Stand Genomic Sci. 2013 Dec 15;9(2):431-48. doi: 10.4056/sigs.2981345. eCollection 2013 Dec 20.


BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.

Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, Väremo L, Nookaew I, Nielsen J.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W175-81. doi: 10.1093/nar/gku371. Epub 2014 May 3.


Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.

El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH, Nielsen J.

BMC Syst Biol. 2014 Apr 3;8:41. doi: 10.1186/1752-0509-8-41.


Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma.

Gatto F, Nookaew I, Nielsen J.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):E866-75. doi: 10.1073/pnas.1319196111. Epub 2014 Feb 18.


Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast.

Chumnanpuen P, Nookaew I, Nielsen J.

BMC Syst Biol. 2013 Oct 16;7 Suppl 3:S7. doi: 10.1186/1752-0509-7-S3-S7.


Physiological characterization of the high malic acid-producing Aspergillus oryzae strain 2103a-68.

Knuf C, Nookaew I, Remmers I, Khoomrung S, Brown S, Berry A, Nielsen J.

Appl Microbiol Biotechnol. 2014 Apr;98(8):3517-27. doi: 10.1007/s00253-013-5465-x. Epub 2014 Jan 11.


Maternal beef and postweaning herring diets increase bone mineral density and strength in mouse offspring.

Hussain A, Olausson H, Nilsson S, Nookaew I, Khoomrung S, Andersson L, Koskela A, Tuukkanen J, Ohlsson C, Holmäng A.

Exp Biol Med (Maywood). 2013 Dec;238(12):1362-9. doi: 10.1177/1535370213506436. Epub 2013 Oct 24.


Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker.

Nookaew I, Thorell K, Worah K, Wang S, Hibberd ML, Sjövall H, Pettersson S, Nielsen J, Lundin SB.

BMC Med Genomics. 2013 Oct 11;6:41. doi: 10.1186/1755-8794-6-41.

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