메뉴 건너뛰기




Volumn 14, Issue 11, 2013, Pages

Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PROTOZOAL RNA; TRANSCRIPTOME;

EID: 84887911820     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2013-14-11-r128     Document Type: Article
Times cited : (118)

References (79)
  • 1
    • 84874499711 scopus 로고    scopus 로고
    • WHO
    • WHO World Malaria Report 2012, http://www.who.int/malaria/publications/world_malaria_report_2012/en/, WHO.
    • (2012) World Malaria Report
  • 2
    • 4243071596 scopus 로고    scopus 로고
    • The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    • 176545, 12929205
    • Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1:E5. 176545, 12929205.
    • (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
  • 5
    • 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
    • 10.1093/nar/gki709, 1178005, 16040597
    • Balaji S, Babu MM, Iyer LM, Aravind L. 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 2005, 33:3994-4006. 10.1093/nar/gki709, 1178005, 16040597.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3994-4006
    • Balaji, S.1    Babu, M.M.2    Iyer, L.M.3    Aravind, L.4
  • 6
    • 4444339460 scopus 로고    scopus 로고
    • Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum
    • 10.1101/gr.2218604, 509263, 15256513
    • Coulson RM, Hall N, Ouzounis CA. Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res 2004, 14:1548-1554. 10.1101/gr.2218604, 509263, 15256513.
    • (2004) Genome Res , vol.14 , pp. 1548-1554
    • Coulson, R.M.1    Hall, N.2    Ouzounis, C.A.3
  • 7
    • 79956326042 scopus 로고    scopus 로고
    • Nucleosome occupancy at transcription start sites in the human malaria parasite: a hard-wired evolution of virulence?
    • 10.1016/j.meegid.2010.08.002, 3466077, 20708104
    • Ponts N, Harris EY, Lonardi S, Le Roch KG. Nucleosome occupancy at transcription start sites in the human malaria parasite: a hard-wired evolution of virulence?. Infect Genet Evol 2011, 11:716-724. 10.1016/j.meegid.2010.08.002, 3466077, 20708104.
    • (2011) Infect Genet Evol , vol.11 , pp. 716-724
    • Ponts, N.1    Harris, E.Y.2    Lonardi, S.3    Le Roch, K.G.4
  • 9
    • 58349118483 scopus 로고    scopus 로고
    • Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites
    • 10.1186/gb-2008-9-12-r177, 2646281, 19091060
    • Foth BJ, Zhang N, Mok S, Preiser PR, Bozdech Z. Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites. Genome Biol 2008, 9:R177. 10.1186/gb-2008-9-12-r177, 2646281, 19091060.
    • (2008) Genome Biol , vol.9
    • Foth, B.J.1    Zhang, N.2    Mok, S.3    Preiser, P.R.4    Bozdech, Z.5
  • 15
    • 0347985825 scopus 로고    scopus 로고
    • Plasmodium biology: genomic gleanings
    • 10.1016/S0092-8674(03)01023-7, 14697197
    • Aravind L, Iyer LM, Wellems TE, Miller LH. Plasmodium biology: genomic gleanings. Cell 2003, 115:771-785. 10.1016/S0092-8674(03)01023-7, 14697197.
    • (2003) Cell , vol.115 , pp. 771-785
    • Aravind, L.1    Iyer, L.M.2    Wellems, T.E.3    Miller, L.H.4
  • 16
    • 79959727271 scopus 로고    scopus 로고
    • Polysome profiling of the malaria parasite Plasmodium falciparum
    • 10.1016/j.molbiopara.2011.05.003, 3135974, 21605599
    • Lacsina JR, LaMonte G, Nicchitta CV, Chi JT. Polysome profiling of the malaria parasite Plasmodium falciparum. Mol Biochem Parasitol 2011, 179:42-46. 10.1016/j.molbiopara.2011.05.003, 3135974, 21605599.
    • (2011) Mol Biochem Parasitol , vol.179 , pp. 42-46
    • Lacsina, J.R.1    LaMonte, G.2    Nicchitta, C.V.3    Chi, J.T.4
  • 18
    • 79956001876 scopus 로고    scopus 로고
    • RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts
    • 10.1093/nar/gkq1223, 3089446, 21245033
    • Sorber K, Dimon MT, DeRisi JL. RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. Nucleic Acids Res 2011, 39:3820-3835. 10.1093/nar/gkq1223, 3089446, 21245033.
    • (2011) Nucleic Acids Res , vol.39 , pp. 3820-3835
    • Sorber, K.1    Dimon, M.T.2    DeRisi, J.L.3
  • 19
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • 10.1038/nrg2484, 2949280, 19015660
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63. 10.1038/nrg2484, 2949280, 19015660.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 20
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • 10.1016/j.cell.2011.10.002, 3225288, 22056041
    • Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 2011, 147:789-802. 10.1016/j.cell.2011.10.002, 3225288, 22056041.
    • (2011) Cell , vol.147 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 22
    • 66149118241 scopus 로고    scopus 로고
    • Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
    • 10.1073/pnas.0810916106, 2669787, 19372376
    • Calvo SE, Pagliarini DJ, Mootha VK. Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci U S A 2009, 106:7507-7512. 10.1073/pnas.0810916106, 2669787, 19372376.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 7507-7512
    • Calvo, S.E.1    Pagliarini, D.J.2    Mootha, V.K.3
  • 23
    • 0025792297 scopus 로고
    • Structural features in eukaryotic mRNAs that modulate the initiation of translation
    • Kozak M. Structural features in eukaryotic mRNAs that modulate the initiation of translation. J Biol Chem 1991, 266:19867-19870.
    • (1991) J Biol Chem , vol.266 , pp. 19867-19870
    • Kozak, M.1
  • 24
    • 0344687352 scopus 로고    scopus 로고
    • Reinitiation and recycling are distinct processes occurring downstream of translation termination in yeast
    • 10.1016/j.jmb.2003.10.049, 14659741
    • Rajkowitsch L, Vilela C, Berthelot K, Ramirez CV, McCarthy JE. Reinitiation and recycling are distinct processes occurring downstream of translation termination in yeast. J Mol Biol 2004, 335:71-85. 10.1016/j.jmb.2003.10.049, 14659741.
    • (2004) J Mol Biol , vol.335 , pp. 71-85
    • Rajkowitsch, L.1    Vilela, C.2    Berthelot, K.3    Ramirez, C.V.4    McCarthy, J.E.5
  • 25
    • 27644520989 scopus 로고    scopus 로고
    • Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay
    • 10.1016/j.molcel.2005.09.019, 16285926
    • Gaba A, Jacobson A, Sachs MS. Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay. Mol Cell 2005, 20:449-460. 10.1016/j.molcel.2005.09.019, 16285926.
    • (2005) Mol Cell , vol.20 , pp. 449-460
    • Gaba, A.1    Jacobson, A.2    Sachs, M.S.3
  • 26
    • 70350216071 scopus 로고    scopus 로고
    • Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner
    • 10.1007/s11103-009-9528-4, 19653106
    • Nyiko T, Sonkoly B, Merai Z, Benkovics AH, Silhavy D. Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner. Plant Mol Biol 2009, 71:367-378. 10.1007/s11103-009-9528-4, 19653106.
    • (2009) Plant Mol Biol , vol.71 , pp. 367-378
    • Nyiko, T.1    Sonkoly, B.2    Merai, Z.3    Benkovics, A.H.4    Silhavy, D.5
  • 27
    • 84878730100 scopus 로고    scopus 로고
    • Roles for transcript leaders in translation and mRNA decay revealed by Transcript Leader Sequencing
    • 10.1101/gr.150342.112, 3668365, 23580730
    • Arribere JA, Gilbert WV. Roles for transcript leaders in translation and mRNA decay revealed by Transcript Leader Sequencing. Genome Res 2013, 23:977-987. 10.1101/gr.150342.112, 3668365, 23580730.
    • (2013) Genome Res , vol.23 , pp. 977-987
    • Arribere, J.A.1    Gilbert, W.V.2
  • 28
    • 38349145774 scopus 로고    scopus 로고
    • Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle
    • 10.1186/gb-2007-8-7-r134, 2323219, 17612404
    • Shock JL, Fischer KF, DeRisi JL. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle. Genome Biol 2007, 8:R134. 10.1186/gb-2007-8-7-r134, 2323219, 17612404.
    • (2007) Genome Biol , vol.8
    • Shock, J.L.1    Fischer, K.F.2    DeRisi, J.L.3
  • 29
    • 0029153552 scopus 로고
    • The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae
    • 10.1006/jmbi.1995.0438, 7650736
    • Bonetti B, Fu L, Moon J, Bedwell DM. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J Mol Biol 1995, 251:334-345. 10.1006/jmbi.1995.0438, 7650736.
    • (1995) J Mol Biol , vol.251 , pp. 334-345
    • Bonetti, B.1    Fu, L.2    Moon, J.3    Bedwell, D.M.4
  • 30
    • 0001828219 scopus 로고    scopus 로고
    • UAG readthrough in mammalian cells: effect of upstream and downstream stop codon contexts reveal different signals
    • 10.1186/1471-2199-2-3, 29092, 11242562
    • Cassan M, Rousset JP. UAG readthrough in mammalian cells: effect of upstream and downstream stop codon contexts reveal different signals. BMC Mol Biol 2001, 2:3. 10.1186/1471-2199-2-3, 29092, 11242562.
    • (2001) BMC Mol Biol , vol.2 , pp. 3
    • Cassan, M.1    Rousset, J.P.2
  • 31
    • 80055074497 scopus 로고    scopus 로고
    • Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element
    • 10.1093/nar/gkr224, 3159437, 21525127
    • Firth AE, Wills NM, Gesteland RF, Atkins JF. Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element. Nucleic Acids Res 2011, 39:6679-6691. 10.1093/nar/gkr224, 3159437, 21525127.
    • (2011) Nucleic Acids Res , vol.39 , pp. 6679-6691
    • Firth, A.E.1    Wills, N.M.2    Gesteland, R.F.3    Atkins, J.F.4
  • 32
    • 80055001959 scopus 로고    scopus 로고
    • Evidence of abundant stop codon readthrough in Drosophila and other metazoa
    • 10.1101/gr.119974.110, 3227100, 21994247
    • Jungreis I, Lin MF, Spokony R, Chan CS, Negre N, Victorsen A, White KP, Kellis M. Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res 2011, 21:2096-2113. 10.1101/gr.119974.110, 3227100, 21994247.
    • (2011) Genome Res , vol.21 , pp. 2096-2113
    • Jungreis, I.1    Lin, M.F.2    Spokony, R.3    Chan, C.S.4    Negre, N.5    Victorsen, A.6    White, K.P.7    Kellis, M.8
  • 33
    • 13544262685 scopus 로고    scopus 로고
    • Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae
    • 10.1093/nar/gkh1004, 545446, 15602002
    • Williams I, Richardson J, Starkey A, Stansfield I. Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2004, 32:6605-6616. 10.1093/nar/gkh1004, 545446, 15602002.
    • (2004) Nucleic Acids Res , vol.32 , pp. 6605-6616
    • Williams, I.1    Richardson, J.2    Starkey, A.3    Stansfield, I.4
  • 34
    • 0025979337 scopus 로고
    • Type I iodothyronine deiodinase is a selenocysteine-containing enzyme
    • 10.1038/349438a0, 1825132
    • Berry MJ, Banu L, Larsen PR. Type I iodothyronine deiodinase is a selenocysteine-containing enzyme. Nature 1991, 349:438-440. 10.1038/349438a0, 1825132.
    • (1991) Nature , vol.349 , pp. 438-440
    • Berry, M.J.1    Banu, L.2    Larsen, P.R.3
  • 38
    • 34848872590 scopus 로고    scopus 로고
    • Mechanisms underlying mutually exclusive expression of virulence genes by malaria parasites
    • 10.1038/sj.embor.7401063, 2002552, 17762879
    • Dzikowski R, Li F, Amulic B, Eisberg A, Frank M, Patel S, Wellems TE, Deitsch KW. Mechanisms underlying mutually exclusive expression of virulence genes by malaria parasites. EMBO Rep 2007, 8:959-965. 10.1038/sj.embor.7401063, 2002552, 17762879.
    • (2007) EMBO Rep , vol.8 , pp. 959-965
    • Dzikowski, R.1    Li, F.2    Amulic, B.3    Eisberg, A.4    Frank, M.5    Patel, S.6    Wellems, T.E.7    Deitsch, K.W.8
  • 39
    • 60649095351 scopus 로고    scopus 로고
    • Genome-wide analysis of heterochromatin associates clonally variant gene regulation with perinuclear repressive centers in malaria parasites
    • 10.1016/j.chom.2008.12.012, 19218088
    • Lopez-Rubio JJ, Mancio-Silva L, Scherf A. Genome-wide analysis of heterochromatin associates clonally variant gene regulation with perinuclear repressive centers in malaria parasites. Cell Host Microbe 2009, 5:179-190. 10.1016/j.chom.2008.12.012, 19218088.
    • (2009) Cell Host Microbe , vol.5 , pp. 179-190
    • Lopez-Rubio, J.J.1    Mancio-Silva, L.2    Scherf, A.3
  • 41
    • 36549069632 scopus 로고    scopus 로고
    • 5′ flanking region of var genes nucleate histone modification patterns linked to phenotypic inheritance of virulence traits in malaria parasites
    • 2228885, 18028313
    • Lopez-Rubio JJ, Gontijo AM, Nunes MC, Issar N, Hernandez Rivas R, Scherf A. 5′ flanking region of var genes nucleate histone modification patterns linked to phenotypic inheritance of virulence traits in malaria parasites. Mol Microbiol 2007, 66:1296-1305. 2228885, 18028313.
    • (2007) Mol Microbiol , vol.66 , pp. 1296-1305
    • Lopez-Rubio, J.J.1    Gontijo, A.M.2    Nunes, M.C.3    Issar, N.4    Hernandez Rivas, R.5    Scherf, A.6
  • 42
    • 58149089272 scopus 로고    scopus 로고
    • Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum
    • 2612763, 19037012
    • Epp C, Li F, Howitt CA, Chookajorn T, Deitsch KW. Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum. RNA 2009, 15:116-127. 2612763, 19037012.
    • (2009) RNA , vol.15 , pp. 116-127
    • Epp, C.1    Li, F.2    Howitt, C.A.3    Chookajorn, T.4    Deitsch, K.W.5
  • 43
    • 84876961381 scopus 로고    scopus 로고
    • Plasmodium falciparum DOZI, an RNA helicase interacts with eIF4E
    • 10.1016/j.gene.2013.03.063, 23562722
    • Tarique M, Ahmad M, Ansari A, Tuteja R. Plasmodium falciparum DOZI, an RNA helicase interacts with eIF4E. Gene 2013, 522:46-59. 10.1016/j.gene.2013.03.063, 23562722.
    • (2013) Gene , vol.522 , pp. 46-59
    • Tarique, M.1    Ahmad, M.2    Ansari, A.3    Tuteja, R.4
  • 44
    • 84876288562 scopus 로고    scopus 로고
    • Analysis of the spatial and temporal arrangement of transcripts over intergenic regions in the human malarial parasite Plasmodium falciparum
    • 10.1186/1471-2164-14-267, 3681616, 23601558
    • Russell K, Hasenkamp S, Emes R, Horrocks P. Analysis of the spatial and temporal arrangement of transcripts over intergenic regions in the human malarial parasite Plasmodium falciparum. BMC Genomics 2013, 14:267. 10.1186/1471-2164-14-267, 3681616, 23601558.
    • (2013) BMC Genomics , vol.14 , pp. 267
    • Russell, K.1    Hasenkamp, S.2    Emes, R.3    Horrocks, P.4
  • 45
    • 84877123218 scopus 로고    scopus 로고
    • Functional analysis of the 5′ untranslated region of the phosphoglutamase 2 transcript in Plasmodium falciparum
    • 10.1016/j.actatropica.2013.03.007, 23567550
    • Hasenkamp S, Russell K, Ullah I, Horrocks P. Functional analysis of the 5′ untranslated region of the phosphoglutamase 2 transcript in Plasmodium falciparum. Acta tropica 2013, 127:69-74. 10.1016/j.actatropica.2013.03.007, 23567550.
    • (2013) Acta tropica , vol.127 , pp. 69-74
    • Hasenkamp, S.1    Russell, K.2    Ullah, I.3    Horrocks, P.4
  • 46
    • 84887105353 scopus 로고    scopus 로고
    • A molecular switch in the efficiency of translation reinitiation controls expression of var2csa, a gene implicated in pregnancy associated malaria
    • Bancells C, Deitsch KW. A molecular switch in the efficiency of translation reinitiation controls expression of var2csa, a gene implicated in pregnancy associated malaria. Mol Microbiol 2013, 90:472-488.
    • (2013) Mol Microbiol , vol.90 , pp. 472-488
    • Bancells, C.1    Deitsch, K.W.2
  • 47
    • 0028949735 scopus 로고
    • The relationship between eukaryotic translation and mRNA stability, A short upstream open reading frame strongly inhibits translational initiation and greatly accelerates mRNA degradation in the yeast Saccharomyces cerevisiae
    • 10.1074/jbc.270.15.8936, 7721802
    • Oliveira CC, McCarthy JE. The relationship between eukaryotic translation and mRNA stability, A short upstream open reading frame strongly inhibits translational initiation and greatly accelerates mRNA degradation in the yeast Saccharomyces cerevisiae. J Biol Chem 1995, 270:8936-8943. 10.1074/jbc.270.15.8936, 7721802.
    • (1995) J Biol Chem , vol.270 , pp. 8936-8943
    • Oliveira, C.C.1    McCarthy, J.E.2
  • 48
    • 0028854680 scopus 로고
    • Translational inhibition by a human cytomegalovirus upstream open reading frame despite inefficient utilization of its AUG codon
    • 188673, 7815480
    • Cao J, Geballe AP. Translational inhibition by a human cytomegalovirus upstream open reading frame despite inefficient utilization of its AUG codon. J Virol 1995, 69:1030-1036. 188673, 7815480.
    • (1995) J Virol , vol.69 , pp. 1030-1036
    • Cao, J.1    Geballe, A.P.2
  • 49
    • 0032484213 scopus 로고    scopus 로고
    • The inhibitory upstream open reading frame from mammalian S-adenosylmethionine decarboxylase mRNA has a strict sequence specificity in critical positions
    • 10.1074/jbc.273.49.32500, 9829983
    • Mize GJ, Ruan H, Low JJ, Morris DR. The inhibitory upstream open reading frame from mammalian S-adenosylmethionine decarboxylase mRNA has a strict sequence specificity in critical positions. J Biol Chem 1998, 273:32500-32505. 10.1074/jbc.273.49.32500, 9829983.
    • (1998) J Biol Chem , vol.273 , pp. 32500-32505
    • Mize, G.J.1    Ruan, H.2    Low, J.J.3    Morris, D.R.4
  • 50
    • 84875465945 scopus 로고    scopus 로고
    • Positively charged residues are the major determinants of ribosomal velocity
    • 10.1371/journal.pbio.1001508, 3595205, 23554576
    • Charneski CA, Hurst LD. Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol 2013, 11:e1001508. 10.1371/journal.pbio.1001508, 3595205, 23554576.
    • (2013) PLoS Biol , vol.11
    • Charneski, C.A.1    Hurst, L.D.2
  • 51
    • 67650123654 scopus 로고    scopus 로고
    • Sucrose control of translation mediated by an upstream open reading frame-encoded peptide
    • 10.1104/pp.109.136036, 2705056, 19403731
    • Rahmani F, Hummel M, Schuurmans J, Wiese-Klinkenberg A, Smeekens S, Hanson J. Sucrose control of translation mediated by an upstream open reading frame-encoded peptide. Plant Physiol 2009, 150:1356-1367. 10.1104/pp.109.136036, 2705056, 19403731.
    • (2009) Plant Physiol , vol.150 , pp. 1356-1367
    • Rahmani, F.1    Hummel, M.2    Schuurmans, J.3    Wiese-Klinkenberg, A.4    Smeekens, S.5    Hanson, J.6
  • 52
    • 84877111454 scopus 로고    scopus 로고
    • Widespread and extensive lengthening of 3′ UTRs in the mammalian brain
    • 10.1101/gr.139469.112, 3530671, 23172872
    • Miura P, Shenker S, Andreu-Agullo C, Westholm JO, Lai EC. Widespread and extensive lengthening of 3′ UTRs in the mammalian brain. Genome Res 2013, 23:12-25. 10.1101/gr.139469.112, 3530671, 23172872.
    • (2013) Genome Res , vol.23 , pp. 12-25
    • Miura, P.1    Shenker, S.2    Andreu-Agullo, C.3    Westholm, J.O.4    Lai, E.C.5
  • 54
    • 2342452423 scopus 로고    scopus 로고
    • Widespread distribution of antisense transcripts in the Plasmodium falciparum genome
    • 10.1016/j.molbiopara.2004.02.007, 15138065
    • Gunasekera AM, Patankar S, Schug J, Eisen G, Kissinger J, Roos D, Wirth DF. Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. Mol Biochem Parasitol 2004, 136:35-42. 10.1016/j.molbiopara.2004.02.007, 15138065.
    • (2004) Mol Biochem Parasitol , vol.136 , pp. 35-42
    • Gunasekera, A.M.1    Patankar, S.2    Schug, J.3    Eisen, G.4    Kissinger, J.5    Roos, D.6    Wirth, D.F.7
  • 56
    • 35548994539 scopus 로고    scopus 로고
    • Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis
    • 10.1261/rna.751807, 2040097, 17901154
    • Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP, Ares M. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA 2007, 13:1923-1939. 10.1261/rna.751807, 2040097, 17901154.
    • (2007) RNA , vol.13 , pp. 1923-1939
    • Chakrabarti, K.1    Pearson, M.2    Grate, L.3    Sterne-Weiler, T.4    Deans, J.5    Donohue, J.P.6    Ares, M.7
  • 59
    • 0017311840 scopus 로고
    • Human malaria parasites in continuous culture
    • 10.1126/science.781840, 781840
    • Trager W, Jensen JB. Human malaria parasites in continuous culture. Science 1976, 193:673-675. 10.1126/science.781840, 781840.
    • (1976) Science , vol.193 , pp. 673-675
    • Trager, W.1    Jensen, J.B.2
  • 60
    • 0018704491 scopus 로고
    • Synchronization of Plasmodium falciparum erythrocytic stages in culture
    • 10.2307/3280287, 383936
    • Lambros C, Vanderberg JP. Synchronization of Plasmodium falciparum erythrocytic stages in culture. J Parasitol 1979, 65:418-420. 10.2307/3280287, 383936.
    • (1979) J Parasitol , vol.65 , pp. 418-420
    • Lambros, C.1    Vanderberg, J.P.2
  • 61
    • 0036684101 scopus 로고    scopus 로고
    • Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: single-dimension LCMS/MS, 2-phase MudPIT, and 3-phase MudPIT
    • McDonald WH, Ohi R, Miyamoto DT, Mitchison TJ, Yates JR. Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: single-dimension LCMS/MS, 2-phase MudPIT, and 3-phase MudPIT. Int J Mass Spectrom 2002, 251:245-251.
    • (2002) Int J Mass Spectrom , vol.251 , pp. 245-251
    • McDonald, W.H.1    Ohi, R.2    Miyamoto, D.T.3    Mitchison, T.J.4    Yates, J.R.5
  • 62
    • 33746500659 scopus 로고    scopus 로고
    • Proteomic analysis by multidimensional protein identification technology
    • Florens L, Washburn MP. Proteomic analysis by multidimensional protein identification technology. Methods Mol Biol 2006, 328:159-175.
    • (2006) Methods Mol Biol , vol.328 , pp. 159-175
    • Florens, L.1    Washburn, M.P.2
  • 63
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • 10.1016/1044-0305(94)80016-2, 24226387
    • Eng JK, McCormack AL, Yates JR. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994, 5:976-989. 10.1016/1044-0305(94)80016-2, 24226387.
    • (1994) J Am Soc Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 64
    • 0036393898 scopus 로고    scopus 로고
    • DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics
    • 10.1021/pr015504q, 2811961, 12643522
    • Tabb DL, McDonald WH, Yates JR. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 2002, 1:21-26. 10.1021/pr015504q, 2811961, 12643522.
    • (2002) J Proteome Res , vol.1 , pp. 21-26
    • Tabb, D.L.1    McDonald, W.H.2    Yates, J.R.3
  • 65
    • 77949795829 scopus 로고    scopus 로고
    • Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins
    • 10.1021/ac9023999, 20166708
    • Zhang Y, Wen Z, Washburn MP, Florens L. Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Anal Chem 2010, 82:2272-2281. 10.1021/ac9023999, 20166708.
    • (2010) Anal Chem , vol.82 , pp. 2272-2281
    • Zhang, Y.1    Wen, Z.2    Washburn, M.P.3    Florens, L.4
  • 66
    • 84887176520 scopus 로고    scopus 로고
    • ProteomeXchange
    • ProteomeXchange. http://proteomecentral.proteomexchange.org.
  • 68
    • 84890439298 scopus 로고    scopus 로고
    • Stowers Institute Original Data Repository
    • Stowers Institute Original Data Repository. http://srdr.stowers.org/.
  • 69
    • 77955975125 scopus 로고    scopus 로고
    • Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
    • 10.1186/gb-2010-11-8-r87, 2945789, 20796282
    • Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol 2010, 11:R87. 10.1186/gb-2010-11-8-r87, 2945789, 20796282.
    • (2010) Genome Biol , vol.11
    • Yassour, M.1    Pfiffner, J.2    Levin, J.Z.3    Adiconis, X.4    Gnirke, A.5    Nusbaum, C.6    Thompson, D.A.7    Friedman, N.8    Regev, A.9
  • 70
    • 84874604550 scopus 로고    scopus 로고
    • FASTX-Toolkit
    • FASTX-Toolkit. http://hannonlab.cshl.edu/fastx_toolkit/index.html.
  • 71
    • 84890425342 scopus 로고    scopus 로고
    • Scythe
    • Scythe. https://github.com/ucdavis-bioinformatics/scythe.
  • 72
    • 84890436026 scopus 로고    scopus 로고
    • Sickle
    • Sickle. https://github.com/ucdavis-bioinformatics/sickle.
  • 73
    • 84886766867 scopus 로고    scopus 로고
    • PlasmoDB
    • PlasmoDB. http://plasmodb.org/plasmo/.
  • 74
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • 10.1093/bioinformatics/btp120, 2672628, 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 76
    • 84890441694 scopus 로고    scopus 로고
    • Picard
    • Picard. http://picard.sourceforge.net/.
  • 77
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • 10.1093/bioinformatics/btq033, 2832824, 20110278
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 79
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for RNA-seq: accounting for selection bias
    • 10.1186/gb-2010-11-2-r14, 2872874, 20132535
    • Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 2010, 11:R14. 10.1186/gb-2010-11-2-r14, 2872874, 20132535.
    • (2010) Genome Biol , vol.11
    • Young, M.D.1    Wakefield, M.J.2    Smyth, G.K.3    Oshlack, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.