2019

Meibalan, E. et al. (2019) Plasmodium falciparum gametocyte density and infectivity in peripheral blood and skin tissue of naturally infected parasite carriers in Burkina Faso. Journal of Infectious Diseases, (doi: 10.1093/infdis/jiz680) (PMID:31875909) (Early Online Publication)

Ngotho, P. , Blancke Soares, A. , Hentzschel, F. , Achcar, F. , Bertuccini, L. and Marti, M. (2019) Revisiting gametocyte biology in malaria parasites. FEMS Microbiology Reviews, 43(4), pp. 401-414. (doi: 10.1093/femsre/fuz010) (PMID:31220244) (PMCID:PMC6606849)

Johnston, K. , Kim, D.-H. , Kerkhoven, E. J. , Burchmore, R. , Barrett, M. P. and Achcar, F. (2019) Mapping the metabolism of five amino acids in bloodstream form Trypanosoma brucei using U-13C-labelled substrates and LC-MS. Bioscience Reports, 39(5), BSR2018160. (doi: 10.1042/BSR20181601) (PMID:31028136) (PMCID:PMC6522824)

2018

Steketee, P. C. et al. (2018) Benzoxaborole treatment perturbs S-adenosyl-L-methionine metabolism in Trypanosoma brucei. PLoS Neglected Tropical Diseases, 12(5), e0006450. (doi: 10.1371/journal.pntd.0006450) (PMID:29758036) (PMCID:PMC5976210)

Kovarova, J. , Pountain, A. W. , Wildridge, D. , Weidt, S. , Bringaud, F. , Burchmore, R. J.S. , Achcar, F. and Barrett, M. P. (2018) Deletion of transketolase triggers a stringent metabolic response in promastigotes and loss of virulence in amastigotes of Leishmania mexicana. PLoS Pathogens, 14(3), e1006953. (doi: 10.1371/journal.ppat.1006953) (PMID:29554142) (PMCID:PMC5882173)

Rattigan, K. M. , Pountain, A. W. , Regnault, C. , Achcar, F. , Vincent, I. M. , Goodyear, C. S. and Barrett, M. P. (2018) Metabolomic profiling of macrophages determines the discrete metabolomic signature and metabolomic interactome triggered by polarising immune stimuli. PLoS ONE, 13(3), e0194126. (doi: 10.1371/journal.pone.0194126) (PMID:29538444) (PMCID:PMC5851634)

2015

Kim, D.-H. , Achcar, F. , Breitling, R. , Burgess, K. E. and Barrett, M. P. (2015) LC–MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes. Metabolomics, 11(6), pp. 1721-1732. (doi: 10.1007/s11306-015-0827-2) (PMID:26491423) (PMCID:PMC4605981)

Creek, D. J. et al. (2015) Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose. PLoS Pathogens, 11(3), e1004689. (doi: 10.1371/journal.ppat.1004689) (PMID:25775470) (PMCID:PMC4361558)

Shameer, S. et al. (2015) TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 43(D1), D637-D644. (doi: 10.1093/nar/gku944) (PMID:25300491) (PMCID:PMC4384016)

2014

Achcar, F. , Kerkhoven, E. J. and Barrett, M. P. (2014) Trypanosoma brucei: meet the system. Current Opinion in Microbiology, 20, pp. 162-169. (doi: 10.1016/j.mib.2014.06.007)

Achcar, F. et al. (2014) The silicon trypanosome: a test case of iterative model extension in systems biology. Advances in Microbial Physiology, 64, pp. 115-143. (doi: 10.1016/B978-0-12-800143-1.00003-8) (PMID:24797926) (PMCID:PMC4773886)

2013

Achcar, F. , Barrett, M.P. and Breitling, R. (2013) Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis. FEBS Journal, 280(18), pp. 4640-4651. (doi: 10.1111/febs.12436) (PMID:23865459) (PMCID:PMC4768353)

Breitling, R. , Achcar, F. and Takano, E. (2013) Modeling challenges in the synthetic biology of secondary metabolism. ACS Synthetic Biology, 2(7), pp. 373-378. (doi: 10.1021/sb4000228)

Chokkathukalam, A. , Jankevics, A. , Creek, D.J. , Achcar, F. , Barrett, M.P. and Breitling, R. (2013) mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. Bioinformatics, 29(2), pp. 281-283. (doi: 10.1093/bioinformatics/bts674) (PMID:23162054) (PMCID:PMC3546800)

Kerkhoven, E. J. et al. (2013) Handling uncertainty in dynamic models: the pentose phosphate pathway in trypanosoma brucei. PLoS ONE, 9(12), e1003371. (doi: 10.1371/journal.pcbi.1003371) (PMID:24339766) (PMCID:24339766)

2012

Achcar, F. , Kerkhoven, E.J. , SilicoTryp Consortium, , Bakker, B.M. , Barrett, M.P. and Breitling, R. (2012) Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism. PLoS Computational Biology, 8(1), e1002352. (doi: 10.1371/journal.pcbi.1002352) (PMID:22379410) (PMCID:PMC3269904)

2011

Achcar, F. , Camadro, J.-M. and Mestivier, D. (2011) A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress. BMC Systems Biology, 5, 51. (doi: 10.1186/1752-0509-5-51) (PMID:26050742) (PMCID:PMC4464606)

2009

Achcar, F. , Camadro, J.-M. and Mestivier, D. (2009) AutoClass@IJM: a powerful tool for Bayesian classification of heterogeneous data in biology. Nucleic Acids Research, 37(Sup 2), W63-W67. (doi: 10.1093/nar/gkp430) (PMID:19474346) (PMCID:PMC2703914)

Articles

Meibalan, E. et al. (2019) Plasmodium falciparum gametocyte density and infectivity in peripheral blood and skin tissue of naturally infected parasite carriers in Burkina Faso. Journal of Infectious Diseases, (doi: 10.1093/infdis/jiz680) (PMID:31875909) (Early Online Publication)

Ngotho, P. , Blancke Soares, A. , Hentzschel, F. , Achcar, F. , Bertuccini, L. and Marti, M. (2019) Revisiting gametocyte biology in malaria parasites. FEMS Microbiology Reviews, 43(4), pp. 401-414. (doi: 10.1093/femsre/fuz010) (PMID:31220244) (PMCID:PMC6606849)

Johnston, K. , Kim, D.-H. , Kerkhoven, E. J. , Burchmore, R. , Barrett, M. P. and Achcar, F. (2019) Mapping the metabolism of five amino acids in bloodstream form Trypanosoma brucei using U-13C-labelled substrates and LC-MS. Bioscience Reports, 39(5), BSR2018160. (doi: 10.1042/BSR20181601) (PMID:31028136) (PMCID:PMC6522824)

Steketee, P. C. et al. (2018) Benzoxaborole treatment perturbs S-adenosyl-L-methionine metabolism in Trypanosoma brucei. PLoS Neglected Tropical Diseases, 12(5), e0006450. (doi: 10.1371/journal.pntd.0006450) (PMID:29758036) (PMCID:PMC5976210)

Kovarova, J. , Pountain, A. W. , Wildridge, D. , Weidt, S. , Bringaud, F. , Burchmore, R. J.S. , Achcar, F. and Barrett, M. P. (2018) Deletion of transketolase triggers a stringent metabolic response in promastigotes and loss of virulence in amastigotes of Leishmania mexicana. PLoS Pathogens, 14(3), e1006953. (doi: 10.1371/journal.ppat.1006953) (PMID:29554142) (PMCID:PMC5882173)

Rattigan, K. M. , Pountain, A. W. , Regnault, C. , Achcar, F. , Vincent, I. M. , Goodyear, C. S. and Barrett, M. P. (2018) Metabolomic profiling of macrophages determines the discrete metabolomic signature and metabolomic interactome triggered by polarising immune stimuli. PLoS ONE, 13(3), e0194126. (doi: 10.1371/journal.pone.0194126) (PMID:29538444) (PMCID:PMC5851634)

Kim, D.-H. , Achcar, F. , Breitling, R. , Burgess, K. E. and Barrett, M. P. (2015) LC–MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes. Metabolomics, 11(6), pp. 1721-1732. (doi: 10.1007/s11306-015-0827-2) (PMID:26491423) (PMCID:PMC4605981)

Creek, D. J. et al. (2015) Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose. PLoS Pathogens, 11(3), e1004689. (doi: 10.1371/journal.ppat.1004689) (PMID:25775470) (PMCID:PMC4361558)

Shameer, S. et al. (2015) TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 43(D1), D637-D644. (doi: 10.1093/nar/gku944) (PMID:25300491) (PMCID:PMC4384016)

Achcar, F. , Kerkhoven, E. J. and Barrett, M. P. (2014) Trypanosoma brucei: meet the system. Current Opinion in Microbiology, 20, pp. 162-169. (doi: 10.1016/j.mib.2014.06.007)

Achcar, F. et al. (2014) The silicon trypanosome: a test case of iterative model extension in systems biology. Advances in Microbial Physiology, 64, pp. 115-143. (doi: 10.1016/B978-0-12-800143-1.00003-8) (PMID:24797926) (PMCID:PMC4773886)

Achcar, F. , Barrett, M.P. and Breitling, R. (2013) Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis. FEBS Journal, 280(18), pp. 4640-4651. (doi: 10.1111/febs.12436) (PMID:23865459) (PMCID:PMC4768353)

Breitling, R. , Achcar, F. and Takano, E. (2013) Modeling challenges in the synthetic biology of secondary metabolism. ACS Synthetic Biology, 2(7), pp. 373-378. (doi: 10.1021/sb4000228)

Chokkathukalam, A. , Jankevics, A. , Creek, D.J. , Achcar, F. , Barrett, M.P. and Breitling, R. (2013) mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. Bioinformatics, 29(2), pp. 281-283. (doi: 10.1093/bioinformatics/bts674) (PMID:23162054) (PMCID:PMC3546800)

Kerkhoven, E. J. et al. (2013) Handling uncertainty in dynamic models: the pentose phosphate pathway in trypanosoma brucei. PLoS ONE, 9(12), e1003371. (doi: 10.1371/journal.pcbi.1003371) (PMID:24339766) (PMCID:24339766)

Achcar, F. , Kerkhoven, E.J. , SilicoTryp Consortium, , Bakker, B.M. , Barrett, M.P. and Breitling, R. (2012) Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism. PLoS Computational Biology, 8(1), e1002352. (doi: 10.1371/journal.pcbi.1002352) (PMID:22379410) (PMCID:PMC3269904)

Achcar, F. , Camadro, J.-M. and Mestivier, D. (2011) A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress. BMC Systems Biology, 5, 51. (doi: 10.1186/1752-0509-5-51) (PMID:26050742) (PMCID:PMC4464606)

Achcar, F. , Camadro, J.-M. and Mestivier, D. (2009) AutoClass@IJM: a powerful tool for Bayesian classification of heterogeneous data in biology. Nucleic Acids Research, 37(Sup 2), W63-W67. (doi: 10.1093/nar/gkp430) (PMID:19474346) (PMCID:PMC2703914)