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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. Achcar F, et al. Among authors: breitling r. Adv Microb Physiol. 2014;64:115-43. doi: 10.1016/B978-0-12-800143-1.00003-8. Adv Microb Physiol. 2014. PMID: 24797926 Free PMC article. Review.
Metabolomic systems biology of trypanosomes.
Barrett MP, Bakker BM, Breitling R. Barrett MP, et al. Among authors: breitling r. Parasitology. 2010 Aug;137(9):1285-90. doi: 10.1017/S003118201000017X. Epub 2010 Feb 17. Parasitology. 2010. PMID: 20158937 Free article. Review.
mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data.
Chokkathukalam A, Jankevics A, Creek DJ, Achcar F, Barrett MP, Breitling R. Chokkathukalam A, et al. Among authors: breitling r. Bioinformatics. 2013 Jan 15;29(2):281-3. doi: 10.1093/bioinformatics/bts674. Epub 2012 Nov 17. Bioinformatics. 2013. PMID: 23162054 Free PMC article.
We demonstrate the power and versatility of mzMatch-ISO by analysing a (13)C-labelled metabolome dataset from trypanosomal parasites. AVAILABILITY: mzMatch.R and mzMatch-ISO are available free of charge from http://mzmatch.sourceforge.net and can be used on Linux and Windo …
We demonstrate the power and versatility of mzMatch-ISO by analysing a (13)C-labelled metabolome dataset from trypanosomal parasites. AVAILA …
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. Creek DJ, et al. Among authors: breitling r. PLoS Pathog. 2015 Mar 16;11(3):e1004689. doi: 10.1371/journal.ppat.1004689. eCollection 2015 Mar. PLoS Pathog. 2015. PMID: 25775470 Free PMC article.
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. Shameer S, et al. Among authors: breitling r. Nucleic Acids Res. 2015 Jan;43(Database issue):D637-44. doi: 10.1093/nar/gku944. Epub 2014 Oct 9. Nucleic Acids Res. 2015. PMID: 25300491 Free PMC article.
216 results