메뉴 건너뛰기




Volumn , Issue , 2016, Pages 457-486

Mathematical Modeling and Omic Data Integration to Understand Dynamic Adaptation of Apicomplexan Parasites and Identify Pharmaceutical Targets

Author keywords

Apicomplexan parasite diseases; Data mining; Epigenomics; Fluxomics; Mathematical modeling; Metabolomics; Omics based approaches; Parasite adaptation dynamics; Proteomics; Transcriptomics

Indexed keywords


EID: 85017468189     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527694082.ch20     Document Type: Chapter
Times cited : (6)

References (124)
  • 1
    • 84892678585 scopus 로고    scopus 로고
    • Cell division in apicomplexan parasites
    • Francia, M.E. and Striepen, B. (2014) Cell division in apicomplexan parasites. Nat. Rev. Microbiol., 12, 125-136.
    • (2014) Nat. Rev. Microbiol , vol.12 , pp. 125-136
    • Francia, M.E.1    Striepen, B.2
  • 3
    • 84884307143 scopus 로고    scopus 로고
    • Lipid synthesis in protozoan parasites: A comparison between kinetoplastids and apicomplexans
    • Ramakrishnan, S., Serricchio, M., Striepen, B., and Butikofer, P. (2013) Lipid synthesis in protozoan parasites: a comparison between kinetoplastids and apicomplexans. Prog. Lipid Res., 52, 488-512.
    • (2013) Prog. Lipid Res , vol.52 , pp. 488-512
    • Ramakrishnan, S.1    Serricchio, M.2    Striepen, B.3    Butikofer, P.4
  • 4
    • 84857645152 scopus 로고    scopus 로고
    • Reality check for malaria proteomics
    • Sinden, R.E. (2009) Reality check for malaria proteomics. Genome Biol., 10, 211.
    • (2009) Genome Biol , vol.10 , pp. 211
    • Sinden, R.E.1
  • 5
    • 84896390775 scopus 로고    scopus 로고
    • Toxoplasma development-turn the switch on or off?
    • White, M.W., Radke, J.R., and Radke, J.B. (2014) Toxoplasma development-turn the switch on or off? Cell. Microbiol., 16, 466-472.
    • (2014) Cell. Microbiol , vol.16 , pp. 466-472
    • White, M.W.1    Radke, J.R.2    Radke, J.B.3
  • 6
    • 84921535019 scopus 로고    scopus 로고
    • Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum
    • Ay, F., Bunnik, E.M., Varoquaux, N., Vert, J.-P., Noble, W.S., and Le Roch, K.G. (2015) Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum. BioEssays, 37, 182-194.
    • (2015) BioEssays , vol.37 , pp. 182-194
    • Ay, F.1    Bunnik, E.M.2    Varoquaux, N.3    Vert, J.-P.4    Noble, W.S.5    Le Roch, K.G.6
  • 7
    • 33644854445 scopus 로고    scopus 로고
    • Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains
    • Llinas, M., Bozdech, Z., Wong, E.D., Adai, A.T., and DeRisi, J.L. (2006) Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res., 34, 1166-1173.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1166-1173
    • Llinas, M.1    Bozdech, Z.2    Wong, E.D.3    Adai, A.T.4    DeRisi, J.L.5
  • 9
    • 78951483348 scopus 로고    scopus 로고
    • The Apicomplexan AP2 family: Integral factors regulating Plasmodium development
    • Painter, H.J., Campbell, T.L., and Llinas, M. (2011) The Apicomplexan AP2 family: integral factors regulating Plasmodium development. Mol. Biochem. Parasitol., 176, 1-7.
    • (2011) Mol. Biochem. Parasitol , vol.176 , pp. 1-7
    • Painter, H.J.1    Campbell, T.L.2    Llinas, M.3
  • 10
    • 0035370701 scopus 로고    scopus 로고
    • Phosphatidylserine delivery to endoplasmic reticulum-derived vesicles of plant cells depends on two biosynthetic pathways
    • Vincent, P., Maneta-Peyret, L., Cassagne, C., and Moreau, P. (2001) Phosphatidylserine delivery to endoplasmic reticulum-derived vesicles of plant cells depends on two biosynthetic pathways. FEBS Lett., 498, 32-36.
    • (2001) FEBS Lett , vol.498 , pp. 32-36
    • Vincent, P.1    Maneta-Peyret, L.2    Cassagne, C.3    Moreau, P.4
  • 16
    • 84887911820 scopus 로고    scopus 로고
    • Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum
    • Bunnik, E.M., Chung, D.-W., Hamilton, M., Ponts, N., Saraf, A., Prudhomme, J., Florens, L., and Le Roch, K.G. (2013) Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum. Genome Biol., 14, R128.
    • (2013) Genome Biol , vol.14 , pp. R128
    • Bunnik, E.M.1    Chung, D.-W.2    Hamilton, M.3    Ponts, N.4    Saraf, A.5    Prudhomme, J.6    Florens, L.7    Le Roch, K.G.8
  • 19
    • 80051654221 scopus 로고    scopus 로고
    • Quantitative time-course profiling of parasite and host cell proteins in the human malaria parasite Plasmodium falciparum
    • M110.006411.
    • Foth, B.J., Zhang, N., Chaal, B.K., Sze, S.K., Preiser, P.R., and Bozdech, Z. (2011) Quantitative time-course profiling of parasite and host cell proteins in the human malaria parasite Plasmodium falciparum. Mol. Cell. Proteomics, 10, M110.006411.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Foth, B.J.1    Zhang, N.2    Chaal, B.K.3    Sze, S.K.4    Preiser, P.R.5    Bozdech, Z.6
  • 21
    • 84863993448 scopus 로고    scopus 로고
    • A quantitative liquid chromatography tandem mass spectrometry method for metabolomic analysis of Plasmodium falciparum lipid related metabolites
    • Duy, S.V., Berry, L., Perigaud, C., Bressolle, F., Vial, H., Lefebvre-Tournier, I. et al. (2012) A quantitative liquid chromatography tandem mass spectrometry method for metabolomic analysis of Plasmodium falciparum lipid related metabolites. Anal. Chim. Acta, 739, 47-55.
    • (2012) Anal. Chim. Acta , vol.739 , pp. 47-55
    • Duy, S.V.1    Berry, L.2    Perigaud, C.3    Bressolle, F.4    Vial, H.5    Lefebvre-Tournier, I.6
  • 26
    • 84925031191 scopus 로고    scopus 로고
    • Methods of integrating data to uncover genotype-phenotype interactions
    • Ritchie, M.D., Holzinger, E.R., Li, R., Pendergrass, S.A., and Kim, D. (2015) Methods of integrating data to uncover genotype-phenotype interactions. Nat. Rev. Genet., 16, 85-97.
    • (2015) Nat. Rev. Genet , vol.16 , pp. 85-97
    • Ritchie, M.D.1    Holzinger, E.R.2    Li, R.3    Pendergrass, S.A.4    Kim, D.5
  • 27
    • 84868107919 scopus 로고    scopus 로고
    • Plasmodium falciparum gametocyte development 1 (Pfgdv1) and gametocytogenesis early gene identification and commitment to sexual development
    • Eksi, S., Morahan, B.J., Haile, Y., Furuya, T., Jiang, H., Ali, O., Xu, H., Kiattibutr, K., Suri, A., and Czesny, B. (2012) Plasmodium falciparum gametocyte development 1 (Pfgdv1) and gametocytogenesis early gene identification and commitment to sexual development. PLoS Pathog., 8 (10), e1002964.
    • (2012) PLoS Pathog , vol.8 , Issue.10
    • Eksi, S.1    Morahan, B.J.2    Haile, Y.3    Furuya, T.4    Jiang, H.5    Ali, O.6    Xu, H.7    Kiattibutr, K.8    Suri, A.9    Czesny, B.10
  • 28
    • 84924478172 scopus 로고    scopus 로고
    • Changes in metabolic phenotypes of Plasmodium falciparum in vitro cultures during gametocyte development
    • Lamour, S.D., Straschil, U., Saric, J., and Delves, M.J. (2014) Changes in metabolic phenotypes of Plasmodium falciparum in vitro cultures during gametocyte development. Malar. J., 13, 468.
    • (2014) Malar. J , vol.13 , pp. 468
    • Lamour, S.D.1    Straschil, U.2    Saric, J.3    Delves, M.J.4
  • 30
    • 10344250457 scopus 로고    scopus 로고
    • Targeting malaria virulence and remodeling proteins to the host erythrocyte
    • Marti, M., Good, R.T., Rug, M., Knuepfer, E., and Cowman, A.F. (2004) Targeting malaria virulence and remodeling proteins to the host erythrocyte. Science, 306, 1930-1933.
    • (2004) Science , vol.306 , pp. 1930-1933
    • Marti, M.1    Good, R.T.2    Rug, M.3    Knuepfer, E.4    Cowman, A.F.5
  • 33
    • 23144448511 scopus 로고    scopus 로고
    • Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains
    • Balaji, S., Babu, M.M., Iyer, L.M., and Aravind, L. (2005) Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res., 33, 3994-4006.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3994-4006
    • Balaji, S.1    Babu, M.M.2    Iyer, L.M.3    Aravind, L.4
  • 38
    • 78249253329 scopus 로고    scopus 로고
    • HMMSplicer: A tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data
    • Dimon, M.T., Sorber, K., and DeRisi, J.L. (2010) HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PLoS One, 5, e13875.
    • (2010) PLoS One , vol.5
    • Dimon, M.T.1    Sorber, K.2    DeRisi, J.L.3
  • 39
    • 41949113248 scopus 로고    scopus 로고
    • Nuclear non-coding RNAs are transcribed from the centromeres of Plasmodium falciparum and are associated with centromeric chromatin
    • Li, F., Sonbuchner, L., Kyes, S.A., Epp, C., and Deitsch, K.W. (2008) Nuclear non-coding RNAs are transcribed from the centromeres of Plasmodium falciparum and are associated with centromeric chromatin. J. Biol. Chem., 283, 5692-5698.
    • (2008) J. Biol. Chem , vol.283 , pp. 5692-5698
    • Li, F.1    Sonbuchner, L.2    Kyes, S.A.3    Epp, C.4    Deitsch, K.W.5
  • 43
    • 78650242370 scopus 로고    scopus 로고
    • Cell cycle-dependent, intercellular transmission of Toxoplasma gondii is accompanied by marked changes in parasite gene expression
    • Gaji, R.Y., Behnke, M.S., Lehmann, M.M., White, M.W., and Carruthers, V.B. (2011) Cell cycle-dependent, intercellular transmission of Toxoplasma gondii is accompanied by marked changes in parasite gene expression. Mol. Microbiol., 79, 192-204.
    • (2011) Mol. Microbiol , vol.79 , pp. 192-204
    • Gaji, R.Y.1    Behnke, M.S.2    Lehmann, M.M.3    White, M.W.4    Carruthers, V.B.5
  • 47
    • 70349338787 scopus 로고    scopus 로고
    • Malaria sporozoite proteome leaves a trail
    • Vignali, M., Speake, C., and Duffy, P.E. (2009) Malaria sporozoite proteome leaves a trail. Genome Biol., 10, 216.
    • (2009) Genome Biol , vol.10 , pp. 216
    • Vignali, M.1    Speake, C.2    Duffy, P.E.3
  • 48
    • 0036139224 scopus 로고    scopus 로고
    • Characterization of TgROP9 (p36), a novel rhoptry protein of Toxoplasma gondii tachyzoites identified by T cell clone
    • Reichmann, G., Długońska, H., and Fischer, H.-G. (2002) Characterization of TgROP9 (p36), a novel rhoptry protein of Toxoplasma gondii tachyzoites identified by T cell clone. Mol. Biochem. Parasitol., 119, 43-54.
    • (2002) Mol. Biochem. Parasitol , vol.119 , pp. 43-54
    • Reichmann, G.1    Długońska, H.2    Fischer, H.-G.3
  • 51
    • 63149174170 scopus 로고    scopus 로고
    • Glycerol: An unexpected major metabolite of energy metabolism by the human malaria parasite
    • Lian, L.-Y., Al-Helal, M., Roslaini, A.M., Fisher, N., Bray, P.G., Ward, S.A., Biagini, G.A. et al. (2009) Glycerol: an unexpected major metabolite of energy metabolism by the human malaria parasite. Malar. J., 8, 1-4.
    • (2009) Malar. J , vol.8 , pp. 1-4
    • Lian, L.-Y.1    Al-Helal, M.2    Roslaini, A.M.3    Fisher, N.4    Bray, P.G.5    Ward, S.A.6    Biagini, G.A.7
  • 52
    • 33749483184 scopus 로고    scopus 로고
    • Glycolysis in Plasmodium falciparum results in modulation of host enzyme activities
    • Mehta, M., Sonawat, H.M., and Sharma, S. (2006) Glycolysis in Plasmodium falciparum results in modulation of host enzyme activities. J. Vector Borne Dis., 43, 95.
    • (2006) J. Vector Borne Dis , vol.43 , pp. 95
    • Mehta, M.1    Sonawat, H.M.2    Sharma, S.3
  • 53
    • 84869167609 scopus 로고    scopus 로고
    • Mitochondrial metabolism of glucose and glutamine is required for intracellular growth of Toxoplasma gondii
    • MacRae, J.I., Sheiner, L., Nahid, A., Tonkin, C., Striepen, B., and McConville, M.J. (2012) Mitochondrial metabolism of glucose and glutamine is required for intracellular growth of Toxoplasma gondii. Cell Host Microbe, 12, 682-692.
    • (2012) Cell Host Microbe , vol.12 , pp. 682-692
    • McRae, J.I.1    Sheiner, L.2    Nahid, A.3    Tonkin, C.4    Striepen, B.5    McConville, M.J.6
  • 56
    • 64949105863 scopus 로고    scopus 로고
    • Metabolite profiling of the intraerythrocytic malaria parasite Plasmodium falciparum by 1H NMR spectroscopy
    • Teng, R., Junankar, P.R., Bubb, W.A., Rae, C., Mercier, P., and Kirk, K. (2009) Metabolite profiling of the intraerythrocytic malaria parasite Plasmodium falciparum by 1H NMR spectroscopy. NMR Biomed., 22, 292-302.
    • (2009) NMR Biomed , vol.22 , pp. 292-302
    • Teng, R.1    Junankar, P.R.2    Bubb, W.A.3    Rae, C.4    Mercier, P.5    Kirk, K.6
  • 57
    • 0021068228 scopus 로고
    • Mathematical analysis of isotope labeling in the citric acid cycle with applications to 13C NMR studies in perfused rat hearts
    • Chance, E.M., Seeholzer, S.H., Kobayashi, K., and Williamson, J.R. (1983) Mathematical analysis of isotope labeling in the citric acid cycle with applications to 13C NMR studies in perfused rat hearts. J. Biol. Chem., 258, 13785-13794.
    • (1983) J. Biol. Chem , vol.258 , pp. 13785-13794
    • Chance, E.M.1    Seeholzer, S.H.2    Kobayashi, K.3    Williamson, J.R.4
  • 59
    • 0030908445 scopus 로고    scopus 로고
    • Phospholipid metabolism of serine in Plasmodium-infected erythrocytes involves phosphatidylserine and direct serine decarboxylation
    • Elabbadi, N., Ancelin, M., and Vial, H. (1997) Phospholipid metabolism of serine in Plasmodium-infected erythrocytes involves phosphatidylserine and direct serine decarboxylation. Biochem. J., 324, 435-445.
    • (1997) Biochem. J , vol.324 , pp. 435-445
    • Elabbadi, N.1    Ancelin, M.2    Vial, H.3
  • 60
    • 33847413750 scopus 로고    scopus 로고
    • Transport of the essential nutrient isoleucine in human erythrocytes infected with the malaria parasite Plasmodium falciparum
    • Martin, R.E. and Kirk, K. (2007) Transport of the essential nutrient isoleucine in human erythrocytes infected with the malaria parasite Plasmodium falciparum. Blood, 109, 2217-2224.
    • (2007) Blood , vol.109 , pp. 2217-2224
    • Martin, R.E.1    Kirk, K.2
  • 62
    • 84896829991 scopus 로고    scopus 로고
    • Stable isotopelabeling studies in metabolomics: New insights into structure and dynamics of metabolic networks
    • Chokkathukalam, A., Kim, D.-H., Barrett, M.P., Breitling, R., and Creek, D.J. (2014) Stable isotopelabeling studies in metabolomics: new insights into structure and dynamics of metabolic networks. Bioanalysis, 6, 511-524.
    • (2014) Bioanalysis , vol.6 , pp. 511-524
    • Chokkathukalam, A.1    Kim, D.-H.2    Barrett, M.P.3    Breitling, R.4    Creek, D.J.5
  • 64
    • 0036749434 scopus 로고    scopus 로고
    • Monitoring the chromosome 2 intraerythrocytic transcriptome of Plasmodium falciparum using oligonucleotide arrays
    • Le Roch, K.G., Zhou, Y., Batalov, S., and Winzeler, E.A. (2002) Monitoring the chromosome 2 intraerythrocytic transcriptome of Plasmodium falciparum using oligonucleotide arrays. Am. J. Trop. Med. Hyg., 67, 233-243.
    • (2002) Am. J. Trop. Med. Hyg , vol.67 , pp. 233-243
    • Le Roch, K.G.1    Zhou, Y.2    Batalov, S.3    Winzeler, E.A.4
  • 66
    • 4243071596 scopus 로고    scopus 로고
    • The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    • Bozdech, Z., Llinas, M., Pulliam, B.L., Wong, E.D., Zhu, J., and DeRisi, J.L. (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol., 1, e5.
    • (2003) PLoS Biol , vol.1
    • Bozdech, Z.1    Llinas, M.2    Pulliam, B.L.3    Wong, E.D.4    Zhu, J.5    DeRisi, J.L.6
  • 67
    • 1342303735 scopus 로고    scopus 로고
    • Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a longoligonucleotide microarray
    • Bozdech, Z., Zhu, J., Joachimiak, M.P., Cohen, F.E., Pulliam, B., and DeRisi, J.L. (2003) Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a longoligonucleotide microarray. Genome Biol., 4, R9.
    • (2003) Genome Biol , vol.4 , pp. R9
    • Bozdech, Z.1    Zhu, J.2    Joachimiak, M.P.3    Cohen, F.E.4    Pulliam, B.5    DeRisi, J.L.6
  • 69
    • 84907920040 scopus 로고    scopus 로고
    • A nested real-time PCR assay for the quantification of Plasmodium falciparum DNA extracted from dried blood spots
    • Tran, T.M., Aghili, A., Li, S., Ongoiba, A., Kayentao, K., Doumbo, S., Traore, B., and Crompton, P.D. (2014) A nested real-time PCR assay for the quantification of Plasmodium falciparum DNA extracted from dried blood spots. Malar. J., 13, 393.
    • (2014) Malar. J , vol.13 , pp. 393
    • Tran, T.M.1    Aghili, A.2    Li, S.3    Ongoiba, A.4    Kayentao, K.5    Doumbo, S.6    Traore, B.7    Crompton, P.D.8
  • 70
    • 70349284642 scopus 로고    scopus 로고
    • Proteome analysis of Plasmodium falciparum extracellular secretory antigens at asexual blood stages reveals a cohort of proteins with possible roles in immune modulation and signaling
    • Singh, M., Mukherjee, P., Narayanasamy, K., Arora, R., Sen, S.D., Gupta, S., Natarajan, K., and Malhotra, P. (2009) Proteome analysis of Plasmodium falciparum extracellular secretory antigens at asexual blood stages reveals a cohort of proteins with possible roles in immune modulation and signaling. Mol. Cell. Proteomics, 8, 2102-2118.
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 2102-2118
    • Singh, M.1    Mukherjee, P.2    Narayanasamy, K.3    Arora, R.4    Sen, S.D.5    Gupta, S.6    Natarajan, K.7    Malhotra, P.8
  • 73
    • 84891591598 scopus 로고    scopus 로고
    • Protein microarray analysis of antibody responses to Plasmodium falciparum in western Kenyan highland sites with differing transmission levels
    • Baum, E., Badu, K., Molina, D.M., Liang, X., Felgner, P.L., and Yan, G. (2013) Protein microarray analysis of antibody responses to Plasmodium falciparum in western Kenyan highland sites with differing transmission levels. PLoS One, 8 (12), e82246.
    • (2013) PLoS One , vol.8 , Issue.12
    • Baum, E.1    Badu, K.2    Molina, D.M.3    Liang, X.4    Felgner, P.L.5    Yan, G.6
  • 75
    • 80053458415 scopus 로고    scopus 로고
    • Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex
    • Nebl, T., Prieto, J.H., Kapp, E., Smith, B.J., Williams, M.J., Yates, J.R. III, Cowman, A.F., and Tonkin, C.J. (2011) Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex. PLoS Pathog., 7, e1002222.
    • (2011) PLoS Pathog , vol.7
    • Nebl, T.1    Prieto, J.H.2    Kapp, E.3    Smith, B.J.4    Williams, M.J.5    Yates, J.R.6    Cowman, A.F.7    Tonkin, C.J.8
  • 76
  • 77
    • 64849093931 scopus 로고    scopus 로고
    • Discriminating the intraerythrocytic lifecycle stages of the malaria parasite using synchrotron FT-IR microspectroscopy and an artificial neural network
    • Webster, G.T., De Villiers, K.A., Egan, T.J., Deed, S., Tilley, L., Tobin, M.J., Bambery, K.R., McNaughton, D., and Wood, B.R. (2009) Discriminating the intraerythrocytic lifecycle stages of the malaria parasite using synchrotron FT-IR microspectroscopy and an artificial neural network. Anal. Chem., 81, 2516-2524.
    • (2009) Anal. Chem , vol.81 , pp. 2516-2524
    • Webster, G.T.1    De Villiers, K.A.2    Egan, T.J.3    Deed, S.4    Tilley, L.5    Tobin, M.J.6    Bambery, K.R.7    McNaughton, D.8    Wood, B.R.9
  • 78
    • 0020419660 scopus 로고
    • 1H-NMR spectroscopic study of aerobic glucose metabolism in Toxoplasma gondii harvested from the peritoneal exudate of experimentally infected mice
    • Ohsaka, A., Yoshikawa, K., and Hagiwara, T. (1981) 1H-NMR spectroscopic study of aerobic glucose metabolism in Toxoplasma gondii harvested from the peritoneal exudate of experimentally infected mice. Physiol. Chem. Phys., 14, 381-384.
    • (1981) Physiol. Chem. Phys , vol.14 , pp. 381-384
    • Ohsaka, A.1    Yoshikawa, K.2    Hagiwara, T.3
  • 81
    • 57449114130 scopus 로고    scopus 로고
    • A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum
    • Le Roch, K.G., Johnson, J.R., Ahiboh, H., Chung, D.W.D., Prudhomme, J., Plouffe, D., Henson, K., Zhou, Y., Witola, W., Yates, J.R. et al (2008) A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum. BMC Genomics, 9, 513.
    • (2008) BMC Genomics , vol.9 , pp. 513
    • Le Roch, K.G.1    Johnson, J.R.2    Ahiboh, H.3    Chung, D.W.D.4    Prudhomme, J.5    Plouffe, D.6    Henson, K.7    Zhou, Y.8    Witola, W.9    Yates, J.R.10
  • 83
    • 0346095291 scopus 로고    scopus 로고
    • Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae
    • Ihmels, J., Levy, R., and Barkai, N. (2003) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat. Biotechnol., 22, 86-92.
    • (2003) Nat. Biotechnol , vol.22 , pp. 86-92
    • Ihmels, J.1    Levy, R.2    Barkai, N.3
  • 84
    • 38349173848 scopus 로고    scopus 로고
    • Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis
    • Takigawa, I. and Mamitsuka, H. (2008) Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis. Bioinformatics, 24, 250-257.
    • (2008) Bioinformatics , vol.24 , pp. 250-257
    • Takigawa, I.1    Mamitsuka, H.2
  • 85
    • 77950684712 scopus 로고    scopus 로고
    • Plasmodium falciparum spermidine synthase inhibition results in unique perturbation-specific effects observed on transcript, protein and metabolite levels
    • Becker, J.V., Mtwisha, L., Crampton, B.G., Stoychev, S., van Brummelen, A.C., Reeksting, S., Louw, A.I., Birkholtz, L.-M., and Mancama, D.T. (2010) Plasmodium falciparum spermidine synthase inhibition results in unique perturbation-specific effects observed on transcript, protein and metabolite levels. BMC Genomics, 11, 235.
    • (2010) BMC Genomics , vol.11 , pp. 235
    • Becker, J.V.1    Mtwisha, L.2    Crampton, B.G.3    Stoychev, S.4    van Brummelen, A.C.5    Reeksting, S.6    Louw, A.I.7    Birkholtz, L.-M.8    Mancama, D.T.9
  • 86
    • 63249088844 scopus 로고    scopus 로고
    • Coinhibition of Plasmodium falciparum S-adenosylmethionine decarboxylase/ ornithine decarboxylase reveals perturbation-specific compensatory mechanisms by transcriptome, proteome, and metabolome analyses
    • van Brummelen, A.C., Olszewski, K.L., Wilinski, D., Llinas, M., Louw, A.I., and Birkholtz, L.-M. (2009) Coinhibition of Plasmodium falciparum S-adenosylmethionine decarboxylase/ ornithine decarboxylase reveals perturbation-specific compensatory mechanisms by transcriptome, proteome, and metabolome analyses. J. Biol. Chem., 284, 4635-4646.
    • (2009) J. Biol. Chem , vol.284 , pp. 4635-4646
    • van Brummelen, A.C.1    Olszewski, K.L.2    Wilinski, D.3    Llinas, M.4    Louw, A.I.5    Birkholtz, L.-M.6
  • 89
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: Integrating 'omics' data sets
    • Joyce, A.R. and Palsson, B.O. (2006) The model organism as a system: integrating 'omics' data sets. Nat. Rev. Mol. Cell Biol., 7, 198-210.
    • (2006) Nat. Rev. Mol. Cell Biol , vol.7 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.O.2
  • 91
    • 84878979335 scopus 로고    scopus 로고
    • Biology: The big challenges of big data
    • Marx, V. (2013) Biology: the big challenges of big data. Nature, 498, 255-260.
    • (2013) Nature , vol.498 , pp. 255-260
    • Marx, V.1
  • 93
    • 33645510456 scopus 로고    scopus 로고
    • Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genomewide scale
    • Date, S.V. and Stoeckert, C.J. (2006) Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genomewide scale. Genome Res., 16, 542-549.
    • (2006) Genome Res , vol.16 , pp. 542-549
    • Date, S.V.1    Stoeckert, C.J.2
  • 94
    • 78449231932 scopus 로고    scopus 로고
    • Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite
    • Campbell, T.L., De Silva, E.K., Olszewski, K.L., Elemento, O., and Llinas, M. (2010) Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathog., 6, e1001165.
    • (2010) PLoS Pathog , vol.6
    • Campbell, T.L.1    De Silva, E.K.2    Olszewski, K.L.3    Elemento, O.4    Llinas, M.5
  • 97
    • 84900465317 scopus 로고    scopus 로고
    • Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
    • Ay, F., Bunnik, E.M., Varoquaux, N., Bol, S.M., Prudhomme, J., Vert, J.-P., Noble, W.S., and Le Roch, K.G. (2014) Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Res., 24, 974-988.
    • (2014) Genome Res , vol.24 , pp. 974-988
    • Ay, F.1    Bunnik, E.M.2    Varoquaux, N.3    Bol, S.M.4    Prudhomme, J.5    Vert, J.-P.6    Noble, W.S.7    Le Roch, K.G.8
  • 98
    • 64549142857 scopus 로고    scopus 로고
    • Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico
    • Fatumo, S., Plaimas, K., Mallm, J.-P., Schramm, G., Adebiyi, E., Oswald, M., Eils, R., and Konig, R. (2009) Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico. Infect. Genet. Evol., 9, 351-358.
    • (2009) Infect. Genet. Evol , vol.9 , pp. 351-358
    • Fatumo, S.1    Plaimas, K.2    Mallm, J.-P.3    Schramm, G.4    Adebiyi, E.5    Oswald, M.6    Eils, R.7    Konig, R.8
  • 99
    • 77956419824 scopus 로고    scopus 로고
    • Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network
    • Plata, G., Hsiao, T.L., Olszewski, K.L., Llinas, M., and Vitkup, D. (2010) Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Mol. Syst. Biol., 6, 408.
    • (2010) Mol. Syst. Biol , vol.6 , pp. 408
    • Plata, G.1    Hsiao, T.L.2    Olszewski, K.L.3    Llinas, M.4    Vitkup, D.5
  • 100
    • 77956456621 scopus 로고    scopus 로고
    • Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis
    • Huthmacher, C., Hoppe, A., Bulik, S., and Holzhutter, H.-G. (2010) Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC Syst. Biol., 4, 120.
    • (2010) BMC Syst. Biol , vol.4 , pp. 120
    • Huthmacher, C.1    Hoppe, A.2    Bulik, S.3    Holzhutter, H.-G.4
  • 102
  • 103
    • 84927624323 scopus 로고    scopus 로고
    • Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum
    • Penkler, G., du Toit, F., Adams, W., Rautenbach, M., Palm, D.C., van Niekerk, D.D., and Snoep, J.L. (2015) Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum. FEBS J., 282, 1481-1511.
    • (2015) FEBS J , vol.282 , pp. 1481-1511
    • Penkler, G.1    du Toit, F.2    Adams, W.3    Rautenbach, M.4    Palm, D.C.5    van Niekerk, D.D.6    Snoep, J.L.7
  • 104
    • 84887038430 scopus 로고    scopus 로고
    • Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways
    • Sen, P., Vial, H.J., and Radulescu, O. (2013) Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways. BMC Syst. Biol., 7, 123.
    • (2013) BMC Syst. Biol , vol.7 , pp. 123
    • Sen, P.1    Vial, H.J.2    Radulescu, O.3
  • 105
    • 84883053661 scopus 로고    scopus 로고
    • Methylerythritol phosphate pathway to isoprenoids: Kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum
    • Singh, V.K. and Ghosh, I. (2013) Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum. FEBS Lett., 587, 2806-2817.
    • (2013) FEBS Lett , vol.587 , pp. 2806-2817
    • Singh, V.K.1    Ghosh, I.2
  • 106
    • 70149120308 scopus 로고    scopus 로고
    • Plasmodium falciparum biology: Analysis of in vitro versus in vivo growth conditions
    • LeRoux, M., Lakshmanan, V., and Daily, J.P. (2009) Plasmodium falciparum biology: analysis of in vitro versus in vivo growth conditions. Trends Parasitol., 25, 474-481.
    • (2009) Trends Parasitol , vol.25 , pp. 474-481
    • LeRoux, M.1    Lakshmanan, V.2    Daily, J.P.3
  • 107
    • 4544381198 scopus 로고    scopus 로고
    • Biochemical mechanisms of drug action: What does it take for success?
    • Swinney, D.C. (2004) Biochemical mechanisms of drug action: what does it take for success? Nat. Rev. Drug Discovery, 3, 801-808.
    • (2004) Nat. Rev. Drug Discovery , vol.3 , pp. 801-808
    • Swinney, D.C.1
  • 108
    • 84872896832 scopus 로고    scopus 로고
    • The landscape for pharmaceutical innovation: Drivers of cost-effective clinical research
    • Kaitin, K.I. (2010) The landscape for pharmaceutical innovation: drivers of cost-effective clinical research. Pharm. Outsourcing, 2010, 3605.
    • (2010) Pharm. Outsourcing , vol.2010 , pp. 3605
    • Kaitin, K.I.1
  • 109
    • 85017449841 scopus 로고    scopus 로고
    • the Causative Parasite of Malaria (Universite Montpellier II-Sciences et Techniques du Languedoc)
    • Sen, P. (2013) Integrated Modelling of Lipid Metabolism in Plasmodium, the Causative Parasite of Malaria (Universite Montpellier II-Sciences et Techniques du Languedoc).
    • (2013) Integrated Modelling of Lipid Metabolism in Plasmodium
    • Sen, P.1
  • 110
    • 79960361078 scopus 로고    scopus 로고
    • Glycerophospholipid acquisition in Plasmodium-A puzzling assembly of biosynthetic pathways
    • Dechamps, S., Shastri, S., Wengelnik, K., and Vial, H.J. (2010) Glycerophospholipid acquisition in Plasmodium-A puzzling assembly of biosynthetic pathways. Int. J. Parasitol., 40, 1347-1365.
    • (2010) Int. J. Parasitol , vol.40 , pp. 1347-1365
    • Dechamps, S.1    Shastri, S.2    Wengelnik, K.3    Vial, H.J.4
  • 113
    • 73149087664 scopus 로고    scopus 로고
    • Rodent and nonrodent malaria parasites differ in their phospholipid metabolic pathways
    • Dechamps, S., Maynadier, M., Wein, S., Gannoun-Zaki, L., Marechal, E., and Vial, H.J. (2010) Rodent and nonrodent malaria parasites differ in their phospholipid metabolic pathways. J. Lipid Res., 51, 81-96.
    • (2010) J. Lipid Res , vol.51 , pp. 81-96
    • Dechamps, S.1    Maynadier, M.2    Wein, S.3    Gannoun-Zaki, L.4    Marechal, E.5    Vial, H.J.6
  • 115
    • 0023709196 scopus 로고
    • Metabolic control theory: A structural approach
    • Reder, C. (1988) Metabolic control theory: a structural approach. J. Theor. Biol., 135, 175-201.
    • (1988) J. Theor. Biol , vol.135 , pp. 175-201
    • Reder, C.1
  • 119
    • 16844367110 scopus 로고    scopus 로고
    • In vivo evidence for the specificity of Plasmodium falciparum phosphoethanolamine methyltransferase and its coupling to the Kennedy pathway
    • Pessi, G., Choi, J.Y., Reynolds, J.M., Voelker, D.R., and Mamoun, C.B. (2005) In vivo evidence for the specificity of Plasmodium falciparum phosphoethanolamine methyltransferase and its coupling to the Kennedy pathway. J. Biol. Chem., 280, 12461.
    • (2005) J. Biol. Chem , vol.280 , pp. 12461
    • Pessi, G.1    Choi, J.Y.2    Reynolds, J.M.3    Voelker, D.R.4    Mamoun, C.B.5
  • 120
    • 1942437433 scopus 로고    scopus 로고
    • A pathway for phosphatidylcholine biosynthesis in Plasmodium falciparum involving phosphoethanolamine methylation
    • Pessi, G., Kociubinski, G., and Mamoun, C.B. (2004) A pathway for phosphatidylcholine biosynthesis in Plasmodium falciparum involving phosphoethanolamine methylation. Proc. Natl. Acad. Sci. U.S.A., 101, 6206.
    • (2004) Proc. Natl. Acad. Sci. U.S. A , vol.101 , pp. 6206
    • Pessi, G.1    Kociubinski, G.2    Mamoun, C.B.3
  • 121
    • 55549143016 scopus 로고    scopus 로고
    • Disruption of the Plasmodium falciparum PfPMT gene results in a complete loss of phosphatidylcholine biosynthesis via the serinedecarboxylase-phosphoethanolaminemethyltransferase pathway and severe growth and survival defects
    • Witola, W.H., El Bissati, K., Pessi, G., Xie, C., Roepe, P.D., and Mamoun, C.B. (2008) Disruption of the Plasmodium falciparum PfPMT gene results in a complete loss of phosphatidylcholine biosynthesis via the serinedecarboxylase-phosphoethanolaminemethyltransferase pathway and severe growth and survival defects. J. Biol. Chem., 283, 27636-27643.
    • (2008) J. Biol. Chem , vol.283 , pp. 27636-27643
    • Witola, W.H.1    El Bissati, K.2    Pessi, G.3    Xie, C.4    Roepe, P.D.5    Mamoun, C.B.6
  • 122
    • 84924908539 scopus 로고    scopus 로고
    • Structure, function and inhibition of the phosphoethanolamine methyltransferases of the human malaria parasites Plasmodium vivax and Plasmodium knowlesi
    • Garg, A., Lukk, T., Kumar, V., Choi, J.Y., Augagneur, Y., Voelker, D.R., Nair, S., and Ben Mamoun, C. (2015) Structure, function and inhibition of the phosphoethanolamine methyltransferases of the human malaria parasites Plasmodium vivax and Plasmodium knowlesi. Sci. Rep., 5, 9064.
    • (2015) Sci. Rep , vol.5 , pp. 9064
    • Garg, A.1    Lukk, T.2    Kumar, V.3    Choi, J.Y.4    Augagneur, Y.5    Voelker, D.R.6    Nair, S.7    Ben Mamoun, C.8
  • 124
    • 84858790233 scopus 로고    scopus 로고
    • Innovation: Metabolomics: The apogee of the omics trilogy
    • Patti, G.J., Yanes, O., and Siuzdak, G. (2012) Innovation: metabolomics: the apogee of the omics trilogy. Nat. Rev. Mol. Cell Biol., 13, 263-269.
    • (2012) Nat. Rev. Mol. Cell Biol , vol.13 , pp. 263-269
    • Patti, G.J.1    Yanes, O.2    Siuzdak, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.