Carlton J: The Plasmodium vivax genome sequencing project. Trends Parasitol. 2003, 19 (5): 227-231. 10.1016/S1471-4922(03)00066-7.
Article
CAS
PubMed
Google Scholar
Carlton J, Silva J, Hall N: The genome of model malaria parasites, and comparative genomics. Curr Issues Mol Biol. 2005, 7 (1): 23-37.
CAS
PubMed
Google Scholar
Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL: Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 2002, 419 (6906): 512-519. 10.1038/nature01099.
Article
CAS
PubMed
Google Scholar
Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002, 419 (6906): 498-511. 10.1038/nature01097.
Article
CAS
PubMed
Google Scholar
Pain A, Bohme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA: The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature. 2008, 455 (7214): 799-803. 10.1038/nature07306.
Article
PubMed Central
CAS
PubMed
Google Scholar
Peterson DS, Miller LH, Wellems TE: Isolation of multiple sequences from the Plasmodium falciparum genome that encode conserved domains homologous to those in erythrocyte-binding proteins. Proc Natl Acad Sci USA. 1995, 92 (15): 7100-7104. 10.1073/pnas.92.15.7100.
Article
PubMed Central
CAS
PubMed
Google Scholar
Su XZ, Heatwole VM, Wertheimer SP, Guinet F, Herrfeldt JA, Peterson DS, Ravetch JA, Wellems TE: The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes. Cell. 1995, 82 (1): 89-100. 10.1016/0092-8674(95)90055-1.
Article
CAS
PubMed
Google Scholar
Jomaa H, Wiesner J, Sanderbrand S, Altincicek B, Weidemeyer C, Hintz M, Turbachova I, Eberl M, Zeidler J, Lichtenthaler HK: Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. Science. 1999, 285 (5433): 1573-1576. 10.1126/science.285.5433.1573.
Article
CAS
PubMed
Google Scholar
Kuang R, Gu J, Cai H, Wang Y: Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel. Genetica. 2009, 136 (1): 189-209. 10.1007/s10709-008-9336-9.
Article
PubMed Central
PubMed
Google Scholar
Wang Y, Wu Y: Computer assisted searches for drug targets with emphasis on malarial proteases and their inhibitors. Curr Drug Targets Infect Disord. 2004, 4 (1): 25-40. 10.2174/1568005043480952.
Article
PubMed
Google Scholar
Wu Y, Wang X, Liu X, Wang Y: Data-mining approaches reveal hidden families of proteases in the genome of malaria parasite. Genome Res. 2003, 13 (4): 601-616. 10.1101/gr.913403.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mu JB, Ferdig MT, Feng XR, Joy DA, Duan JH, Furuya T, Subramanian G, Aravind L, Cooper RA, Wootton JC: Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol Microbiol. 2003, 49 (4): 977-989. 10.1046/j.1365-2958.2003.03627.x.
Article
CAS
PubMed
Google Scholar
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 (1): E5-10.1371/journal.pbio.0000005.
Article
PubMed Central
PubMed
Google Scholar
Bozdech Z, Mok S, Hu G, Imwong M, Jaidee A, Russell B, Ginsburg H, Nosten F, Day NP, White NJ: The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites. Proc Natl Acad Sci USA. 2008, 105 (42): 16290-16295. 10.1073/pnas.0807404105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Florens L, Liu X, Wang YF, Yang SG, Schwartz O, Peglar M, Carucci DJ, Yates JR, Wu YM: Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes. Mol Biochem Parasitol. 2004, 135 (1): 1-11. 10.1016/j.molbiopara.2003.12.007.
Article
CAS
PubMed
Google Scholar
Florens L, Washburn MP, Raine JD, Anthony RM, Grainger M, Haynes JD, Moch JK, Muster N, Sacci JB, Tabb DL: A proteomic view of the Plasmodium falciparum life cycle. Nature. 2002, 419 (6906): 520-526. 10.1038/nature01107.
Article
CAS
PubMed
Google Scholar
Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK: A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science. 2005, 307 (5706): 82-86. 10.1126/science.1103717.
Article
CAS
PubMed
Google Scholar
Lasonder E, Ishihama Y, Andersen JS, Vermunt AMW, Pain A, Sauerwein RW, Eling WMC, Hall N, Waters AP, Stunnenberg HG: Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature. 2002, 419 (6906): 537-542. 10.1038/nature01111.
Article
CAS
PubMed
Google Scholar
Le Roch KG, Zhou Y, Blair PL, Grainger M, Moch JK, Haynes JD, De La Vega P, Holder AA, Batalov S, Carucci DJ: Discovery of gene function by expression profiling of the malaria parasite life cycle. Science. 2003, 301 (5639): 1503-1508. 10.1126/science.1087025.
Article
CAS
PubMed
Google Scholar
Date SV, Stoeckert CJ: Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Res. 2006, 16 (4): 542-549. 10.1101/gr.4573206.
Article
PubMed Central
CAS
PubMed
Google Scholar
LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, Hesselberth JR, Schoenfeld LW, Ota I, Sahasrabudhe S, Kurschner C: A protein interaction network of the malaria parasite Plasmodium falciparum. Nature. 2005, 438 (7064): 103-107. 10.1038/nature04104.
Article
CAS
PubMed
Google Scholar
Llinas M, Bozdech Z, Wong ED, Adai AT, DeRisi JL: Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res. 2006, 34 (4): 1166-1173. 10.1093/nar/gkj517.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cox-Singh J, Davis TM, Lee KS, Shamsul SS, Matusop A, Ratnam S, Rahman HA, Conway DJ, Singh B: Plasmodium knowlesi malaria in humans is widely distributed and potentially life threatening. Clin Infect Dis. 2008, 46 (2): 165-171. 10.1086/524888.
Article
PubMed Central
CAS
PubMed
Google Scholar
Callebaut I, Prat K, Meurice E, Mornon JP, Tomavo S: Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes. BMC Genomics. 2005, 6: 100-10.1186/1471-2164-6-100.
Article
PubMed Central
PubMed
Google Scholar
Wu J, Sieglaff DH, Gervin J, Xie XS: Discovering regulatory motifs in the Plasmodium genome using comparative genomics. Bioinformatics. 2008, 24 (17): 1843-1849. 10.1093/bioinformatics/btn348.
Article
PubMed Central
CAS
PubMed
Google Scholar
Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA: In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics. 2008, 9: 70-10.1186/1471-2164-9-70.
Article
PubMed Central
PubMed
Google Scholar
Doerig C, Meijer L, Mottram JC: Protein kinases as drug targets in parasitic protozoa. Trends Parasitol. 2002, 18 (8): 366-371. 10.1016/S1471-4922(02)02321-8.
Article
CAS
PubMed
Google Scholar
Rangarajan R, Bei A, Henry N, Madamet M, Parzy D, Nivez MP, Doerig C, Sultan A: Pbcrk-1, the Plasmodium berghei orthologue of P. falciparum cdc-2 related kinase-1 (Pfcrk-1), is essential for completion of the intraerythrocytic asexual cycle. Exp Parasitol. 2006, 112 (3): 202-207. 10.1016/j.exppara.2005.11.002.
Article
CAS
PubMed
Google Scholar
Reininger L, Billker O, Tewari R, Mukhopadhyay A, Fennell C, Dorin-Semblat D, Doerig C, Goldring D, Harmse L, Ranford-Cartwright L: A NIMA-related protein kinase is essential for completion of the sexual cycle of malaria parasites. J Biol Chem. 2005, 280 (36): 31957-31964. 10.1074/jbc.M504523200.
Article
CAS
PubMed
Google Scholar
Tienda-Luna IM, Yin Y, Carrion MC, Huang Y, Cai H, Sanchez M, Wang Y: Inferring the skeleton cell cycle regulatory network of malaria parasite using comparative genomic and variational Bayesian approaches. Genetica. 2008, 132 (2): 131-142. 10.1007/s10709-007-9155-4.
Article
PubMed
Google Scholar
Harrison T, Samuel BU, Akompong T, Hamm H, Mohandas N, Lomasney JW, Haldar K: Erythrocyte G protein-coupled receptor signaling in malarial infection. Science. 2003, 301 (5640): 1734-1736. 10.1126/science.1089324.
Article
CAS
PubMed
Google Scholar
Pachebat JA, Kadekoppala M, Grainger M, Dluzewski AR, Gunaratne RS, Scott-Finnigan TJ, Ogun SA, Ling IT, Bannister LH, Taylor HM: Extensive proteolytic processing of the malaria parasite merozoite surface protein 7 during biosynthesis and parasite release from erythrocytes. Mol Biochem Parasitol. 2007, 151 (1): 59-69. 10.1016/j.molbiopara.2006.10.006.
Article
CAS
PubMed
Google Scholar
Fanning SL, Czesny B, Sedegah M, Carucci DJ, van Gemert GJ, Eling W, Williamson KC: A glycosylphosphatidylinositol anchor signal sequence enhances the immunogenicity of a DNA vaccine encoding Plasmodium falciparum sexual-stage antigen, Pfs230. Vaccine. 2003, 21 (23): 3228-3235. 10.1016/S0264-410X(03)00265-2.
Article
CAS
PubMed
Google Scholar
Kooij TW, Carlton JM, Bidwell SL, Hall N, Ramesar J, Janse CJ, Waters AP: Plasmodium whole-genome synteny map: indels and synteny breakpoints as foci for species-specific genes. PLoS Pathog. 2005, 1 (4): e44-10.1371/journal.ppat.0010044.
Article
PubMed Central
PubMed
Google Scholar
Sargeant TJ, Marti M, Caler E, Carlton JM, Simpson K, Speed TP, Cowman AF: Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol. 2006, 7 (2): R12-10.1186/gb-2006-7-2-r12.
Article
PubMed Central
PubMed
Google Scholar
Cheng Q, Cloonan N, Fischer K, Thompson J, Waine G, Lanzer M, Saul A: stevor and rif are Plasmodium falciparum multicopy gene families which potentially encode variant antigens. Mol Biochem Parasitol. 1998, 97 (1-2): 161-176. 10.1016/S0166-6851(98)00144-3.
Article
CAS
PubMed
Google Scholar
Joannin N, Abhiman S, Sonnhammer EL, Wahlgren M: Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family. BMC Genomics. 2008, 9: 19-10.1186/1471-2164-9-19.
Article
PubMed Central
PubMed
Google Scholar
Hernandez-Rivas R, Hinterberg K, Scherf A: Compartmentalization of genes coding for immunodominant antigens to fragile chromosome ends leads to dispersed subtelomeric gene families and rapid gene evolution in Plasmodium falciparum. Mol Biochem Parasitol. 1996, 78 (1-2): 137-148. 10.1016/S0166-6851(96)02618-7.
Article
CAS
PubMed
Google Scholar
Robinson BA, Welch TL, Smith JD: Widespread functional specialization of Plasmodium falciparum erythrocyte membrane protein 1 family members to bind CD36 analysed across a parasite genome. Mol Microbiol. 2003, 47 (5): 1265-1278. 10.1046/j.1365-2958.2003.03378.x.
Article
CAS
PubMed
Google Scholar
del Portillo HA, Fernandez-Becerra C, Bowman S, Oliver K, Preuss M, Sanchez CP, Schneider NK, Villalobos JM, Rajandream MA, Harris D: A superfamily of variant genes encoded in the subtelomeric region of Plasmodium vivax. Nature. 2001, 410 (6830): 839-842. 10.1038/35071118.
Article
CAS
PubMed
Google Scholar
del Portillo HA, Lanzer M, Rodriguez-Malaga S, Zavala F, Fernandez-Becerra C: Variant genes and the spleen in Plasmodium vivax malaria. Int J Parasitol. 2004, 34 (13-14): 1547-1554. 10.1016/j.ijpara.2004.10.012.
Article
CAS
PubMed
Google Scholar
Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS: PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 2009, 37 (Databaseissue): D539-543. 10.1093/nar/gkn814.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH: Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol. 2002, 19 (3): 256-262.
Article
CAS
PubMed
Google Scholar
Li L, Stoeckert CJ, Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003, 13 (9): 2178-2189. 10.1101/gr.1224503.
Article
PubMed Central
CAS
PubMed
Google Scholar
Thompson JD, Gibson TJ, Higgins DG: Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics. 2002, Chapter2:Unit23
Google Scholar
Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302 (1): 205-217. 10.1006/jmbi.2000.4042.
Kumar S, Nei M, Dudley J, Tamura K: MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008, 9 (4): 299-306. 10.1093/bib/bbn017.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556.
Article
PubMed Central
CAS
PubMed
Google Scholar
Saier MH, Tran CV, Barabote RD: TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res. 2006, 34 (Databaseissue): D181-186. 10.1093/nar/gkj001.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cheek S, Ginalski K, Zhang H, Grishin NV: A comprehensive update of the sequence and structure classification of kinases. BMC Struct Biol. 2005, 5: 6-10.1186/1472-6807-5-6.
Article
PubMed Central
PubMed
Google Scholar
Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ: MEROPS: the peptidase database. Nucleic Acids Res. 2008, 36 (Databaseissue): D320-325.
PubMed Central
CAS
PubMed
Google Scholar