Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002, 419 (6906): 498-511. 10.1038/nature01097.
Article
PubMed
CAS
Google Scholar
Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ: Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 2002, 419 (6906): 512-519. 10.1038/nature01099.
Article
PubMed
CAS
Google Scholar
Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK, James K, Rutherford K, Harris B, Harris D, Churcher C, Quail MA, Ormond D, Doggett J, Trueman HE, Mendoza J, Bidwell SL, Rajandream MA, Carucci DJ, Yates JR, Kafatos FC, Janse CJ, Barrell B, Turner CM, Waters AP, Sinden RE: 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
PubMed
CAS
Google Scholar
Horrocks P, Kilbey BJ: Physical and functional mapping of the transcriptional start sites of Plasmodium falciparum proliferating cell nuclear antigen. Mol Biochem Parasitol. 1996, 82 (2): 207-215. 10.1016/0166-6851(96)02737-5.
Article
PubMed
CAS
Google Scholar
Crabb BS, Cowman AF: Characterization of promoters and stable transfection by homologous and nonhomologous recombination in Plasmodium falciparum. Proc Natl Acad Sci U S A. 1996, 93 (14): 7289-7294. 10.1073/pnas.93.14.7289.
Article
PubMed
CAS
PubMed Central
Google Scholar
Su XZ, Wellems TE: Sequence, transcript characterization and polymorphisms of a Plasmodium falciparum gene belonging to the heat-shock protein (HSP) 90 family. Gene. 1994, 151 (1-2): 225-230. 10.1016/0378-1119(94)90661-0.
Article
PubMed
CAS
Google Scholar
Horrocks P, Lanzer M: Mutational analysis identifies a five base pair cis-acting sequence essential for GBP130 promoter activity in Plasmodium falciparum. Mol Biochem Parasitol. 1999, 99 (1): 77-87. 10.1016/S0166-6851(98)00182-0.
Article
PubMed
CAS
Google Scholar
Voss TS, Kaestli M, Vogel D, Bopp S, Beck HP: Identification of nuclear proteins that interact differentially with Plasmodium falciparum var gene promoters. Mol Microbiol. 2003, 48 (6): 1593-1607. 10.1046/j.1365-2958.2003.03528.x.
Article
PubMed
CAS
Google Scholar
Militello KT, Dodge M, Bethke L, Wirth DF: Identification of regulatory elements in the Plasmodium falciparum genome. Mol Biochem Parasitol. 2004, 134 (1): 75-88. 10.1016/j.molbiopara.2003.11.004.
Article
PubMed
CAS
Google Scholar
Osta M, Gannoun-Zaki L, Bonnefoy S, Roy C, Vial HJ: A 24 bp cis-acting element essential for the transcriptional activity of Plasmodium falciparum CDP-diacylglycerol synthase gene promoter. Mol Biochem Parasitol. 2002, 121 (1): 87-98. 10.1016/S0166-6851(02)00029-4.
Article
PubMed
CAS
Google Scholar
Pace T, Olivieri A, Sanchez M, Albanesi V, Picci L, Kiamos IS, Janse CJ, Waters AP, Pizzi E, Ponzi M: Set regulation in asexual and sexual Plasmodium parasites reveals a novel mechanism of stage-specific expression. Mol Microbiol. 2006, 60 (4): 870-882. 10.1111/j.1365-2958.2006.05141.x.
Article
PubMed
CAS
Google Scholar
Tham WH, Payne PD, Brown GV, Rogerson SJ: Identification of basic transcriptional elements required for rif gene transcription. Int J Parasitol. 2007, 37 (6): 605-615. 10.1016/j.ijpara.2006.11.006.
Article
PubMed
CAS
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
PubMed Central
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, Winzeler EA: Discovery of gene function by expression profiling of the malaria parasite life cycle. Science. 2003, 301 (5639): 1503-1508. 10.1126/science.1087025.
Article
PubMed
CAS
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
PubMed Central
Google Scholar
Patankar S, Munasinghe A, Shoaibi A, Cummings LM, Wirth DF: Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malarial parasite. Mol Biol Cell. 2001, 12 (10): 3114-3125.
Article
PubMed
CAS
PubMed Central
Google Scholar
Munasinghe A, Patankar S, Cook BP, Madden SL, Martin RK, Kyle DE, Shoaibi A, Cummings LM, Wirth DF: Serial analysis of gene expression (SAGE) in Plasmodium falciparum: application of the technique to A-T rich genomes. Mol Biochem Parasitol. 2001, 113 (1): 23-34. 10.1016/S0166-6851(00)00378-9.
Article
PubMed
CAS
Google Scholar
Militello KT, Patel V, Chessler AD, Fisher JK, Kasper JM, Gunasekera A, Wirth DF: RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum. Rna. 2005, 11 (4): 365-370. 10.1261/rna.7940705.
Article
PubMed
CAS
PubMed Central
Google Scholar
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 (1): 35-42. 10.1016/j.molbiopara.2004.02.007.
Article
PubMed
CAS
Google Scholar
Mair GR, Braks JA, Garver LS, Wiegant JC, Hall N, Dirks RW, Khan SM, Dimopoulos G, Janse CJ, Waters AP: Regulation of sexual development of Plasmodium by translational repression. Science. 2006, 313 (5787): 667-669. 10.1126/science.1125129.
Article
PubMed
CAS
PubMed Central
Google Scholar
Florens L, Washburn MP, Raine JD, Anthony RM, Grainger M, Haynes JD, Moch JK, Muster N, Sacci JB, Tabb DL, Witney AA, Wolters D, Wu Y, Gardner MJ, Holder AA, Sinden RE, Yates JR, Carucci DJ: A proteomic view of the Plasmodium falciparum life cycle. Nature. 2002, 419 (6906): 520-526. 10.1038/nature01107.
Article
PubMed
CAS
Google Scholar
Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, Grainger M, Yan SF, Williamson KC, Holder AA, Carucci DJ, Yates JR, Winzeler EA: Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 2004, 14 (11): 2308-2318. 10.1101/gr.2523904.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chookajorn T, Dzikowski R, Frank M, Li F, Jiwani AZ, Hartl DL, Deitsch KW: Epigenetic memory at malaria virulence genes. Proc Natl Acad Sci U S A. 2007, 104 (3): 899-902. 10.1073/pnas.0609084103.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bailey TLE: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994, 2: 28-36.
Google Scholar
Hughes JD, Estep PW, Tavazoie S, Church GM: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol. 2000, 296 (5): 1205-1214. 10.1006/jmbi.2000.3519.
Article
PubMed
CAS
Google Scholar
Liu XS, Brutlag DL, Liu JS: An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol. 2002, 20 (8): 835-839.
Article
PubMed
CAS
Google Scholar
Pavesi G, Mauri G, Pesole G: An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics. 2001, 17 Suppl 1: S207-14.
Article
PubMed
CAS
Google Scholar
D'Haeseleer P: How does DNA sequence motif discovery work?. Nat Biotechnol. 2006, 24 (8): 959-961. 10.1038/nbt0806-959.
Article
PubMed
Google Scholar
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA: Transcriptional regulatory code of a eukaryotic genome. Nature. 2004, 431 (7004): 99-104. 10.1038/nature02800.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhou Y, Young JA, Santrosyan A, Chen K, Yan SF, Winzeler EA: In silico gene function prediction using ontology-based pattern identification. Bioinformatics. 2005, 21 (7): 1237-1245. 10.1093/bioinformatics/bti111.
Article
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556.
Article
PubMed
CAS
PubMed Central
Google Scholar
Young JA, Fivelman QL, Blair PL, de la Vega P, Le Roch KG, Zhou Y, Carucci DJ, Baker DA, Winzeler EA: The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol Biochem Parasitol. 2005, 143 (1): 67-79. 10.1016/j.molbiopara.2005.05.007.
Article
PubMed
CAS
Google Scholar
GEMS: P. falciparum Analysis Homepage . [http://carrier.gnf.org/publications/motif/]
GEMS: P. falciparum Intron Analysis Results. [http://carrier.gnf.org/publications/motif/Intron]
Chow CS, Wirth DF: Linker scanning mutagenesis of the Plasmodium gallinaceum sexual stage specific gene pgs28 reveals a novel downstream cis-control element. Mol Biochem Parasitol. 2003, 129 (2): 199-208. 10.1016/S0166-6851(03)00101-4.
Article
PubMed
CAS
Google Scholar
Khan SM, Franke-Fayard B, Mair GR, Lasonder E, Janse CJ, Mann M, Waters AP: Proteome analysis of separated male and female gametocytes reveals novel sex-specific Plasmodium biology. Cell. 2005, 121 (5): 675-687. 10.1016/j.cell.2005.03.027.
Article
PubMed
CAS
Google Scholar
Planta RJ, Goncalves PM, Mager WH: Global regulators of ribosome biosynthesis in yeast. Biochem Cell Biol. 1995, 73 (11-12): 825-834.
Article
PubMed
CAS
Google Scholar
Cowman AF, Crabb BS: Invasion of red blood cells by malaria parasites. Cell. 2006, 124 (4): 755-766. 10.1016/j.cell.2006.02.006.
Article
PubMed
CAS
Google Scholar
Bradley PJ, Ward C, Cheng SJ, Alexander DL, Coller S, Coombs GH, Dunn JD, Ferguson DJ, Sanderson SJ, Wastling JM, Boothroyd JC: Proteomic analysis of rhoptry organelles reveals many novel constituents for host-parasite interactions in Toxoplasma gondii. J Biol Chem. 2005, 280 (40): 34245-34258. 10.1074/jbc.M504158200.
Article
PubMed
CAS
Google Scholar
Flick K, Chen Q: var genes, PfEMP1 and the human host. Mol Biochem Parasitol. 2004, 134 (1): 3-9. 10.1016/j.molbiopara.2003.09.010.
Article
PubMed
CAS
Google Scholar
Kurtz S, Shore D: RAP1 protein activates and silences transcription of mating-type genes in yeast. Genes Dev. 1991, 5 (4): 616-628. 10.1101/gad.5.4.616.
Article
PubMed
CAS
Google Scholar
Sussel L, Shore D: Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor/activator protein 1: isolation of viable mutants affecting both silencing and telomere length. Proc Natl Acad Sci U S A. 1991, 88 (17): 7749-7753. 10.1073/pnas.88.17.7749.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bro C, Regenberg B, Lagniel G, Labarre J, Montero-Lomeli M, Nielsen J: Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells. J Biol Chem. 2003, 278 (34): 32141-32149. 10.1074/jbc.M304478200.
Article
PubMed
CAS
Google Scholar
Cinato E, Peleraux A, Silve S, Galiegue S, Dhers C, Picard C, Jbilo O, Loison G, Casellas P: A DNA microarray-based approach to elucidate the effects of the immunosuppressant SR31747A on gene expression in Saccharomyces cerevisiae. Gene Expr. 2002, 10 (5-6): 213-230.
Article
PubMed
CAS
Google Scholar
Zakrzewska A, Boorsma A, Brul S, Hellingwerf KJ, Klis FM: Transcriptional response of Saccharomyces cerevisiae to the plasma membrane-perturbing compound chitosan. Eukaryot Cell. 2005, 4 (4): 703-715. 10.1128/EC.4.4.703-715.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
GEMS: P. falciparum Heat Shock Analysis Results. [http://carrier.gnf.org/publications/motif/HeatShock2k/MAP/]
Voss TS, Thompson JK, Waterkeyn J, Felger I, Weiss N, Cowman AF, Beck HP: Genomic distribution and functional characterisation of two distinct and conserved Plasmodium falciparum var gene 5' flanking sequences. Mol Biochem Parasitol. 2000, 107 (1): 103-115. 10.1016/S0166-6851(00)00176-6.
Article
PubMed
CAS
Google Scholar
Nussenzweig RS, Zavala F: A malaria vaccine based on a sporozoite antigen. N Engl J Med. 1997, 336 (2): 128-130. 10.1056/NEJM199701093360210.
Article
PubMed
CAS
Google Scholar
Ginsburg H: Malaria Parasite Metabolic Pathways. [http://sites.huji.ac.il/malaria/]
Waller RF, McFadden GI: The apicoplast: a review of the derived plastid of apicomplexan parasites. Curr Issues Mol Biol. 2005, 7 (1): 57-79.
PubMed
Google Scholar
McGuire AM, Hughes JD, Church GM: Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 2000, 10 (6): 744-757. 10.1101/gr.10.6.744.
Article
PubMed
CAS
Google Scholar
Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS: Computational prediction of novel components of lung transcriptional networks. Bioinformatics. 2007, 23 (1): 21-29. 10.1093/bioinformatics/btl531.
Article
PubMed
CAS
Google Scholar
van Noort V, Huynen MA: Combinatorial gene regulation in Plasmodium falciparum. Trends Genet. 2006, 22 (2): 73-78. 10.1016/j.tig.2005.12.002.
Article
PubMed
CAS
Google Scholar
Lu F, Jiang H, Ding J, Mu J, Valenzuela JG, Ribeiro JM, Su XZ: cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genomics. 2007, 8 (1): 255-10.1186/1471-2164-8-255.
Article
PubMed
PubMed Central
Google Scholar
Sinha S, Tompa M: Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res. 2002, 30 (24): 5549-5560. 10.1093/nar/gkf669.
Article
PubMed
CAS
PubMed Central
Google Scholar
Trager W, Jensen JB: Human malaria parasites in continuous culture. Science. 1976, 193 (4254): 673-675. 10.1126/science.781840.
Article
PubMed
CAS
Google Scholar
Le Roch KG, Zhou Y, Batalov S, Winzeler EA: Monitoring the chromosome 2 intraerythrocytic transcriptome of Plasmodium falciparum using oligonucleotide arrays. Am J Trop Med Hyg. 2002, 67 (3): 233-243.
PubMed
CAS
Google Scholar
Zhou Y, Abagyan R: Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics. 2002, 3: 3-10.1186/1471-2105-3-3.
Article
PubMed
PubMed Central
Google Scholar
Barrera L, Benner C, Tao YC, Winzeler E, Zhou Y: Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays. BMC Bioinformatics. 2004, 5: 42-10.1186/1471-2105-5-42.
Article
PubMed
PubMed Central
Google Scholar
Bahl A, Brunk B, Crabtree J, Fraunholz MJ, Gajria B, Grant GR, Ginsburg H, Gupta D, Kissinger JC, Labo P, Li L, Mailman MD, Milgram AJ, Pearson DS, Roos DS, Schug J, Stoeckert CJ, Whetzel P: PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res. 2003, 31 (1): 212-215. 10.1093/nar/gkg081.
Article
PubMed
CAS
PubMed Central
Google Scholar
Beer MA, Tavazoie S: Predicting gene expression from sequence. Cell. 2004, 117 (2): 185-198. 10.1016/S0092-8674(04)00304-6.
Article
PubMed
CAS
Google Scholar
Willett P, Barnard JM, Downs GM: Chemical similarity searching. J Chem Inf Comp Sci. 1998, 38: 983-996.
Article
CAS
Google Scholar
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z: Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol. 2005, 23 (1): 137-144. 10.1038/nbt1053.
Article
PubMed
CAS
Google Scholar
MDScan. [http://motif.stanford.edu/distributions/mdscan]
RepeatMasker. [http://www.repeatmasker.org]
Militello KT, Wirth DF: A new reporter gene for transient transfection of Plasmodium falciparum. Parasitol Res. 2003, 89 (2): 154-157. 10.1007/s00436-002-0721-5.
Article
PubMed
Google Scholar
Lambros C, Vanderberg JP: Synchronization of Plasmodium falciparum erythrocytic stages in culture. J Parasitol. 1979, 65 (3): 418-420. 10.2307/3280287.
Article
PubMed
CAS
Google Scholar
Deitsch K, Driskill C, Wellems T: Transformation of malaria parasites by the spontaneous uptake and expression of DNA from human erythrocytes. Nucleic Acids Res. 2001, 29 (3): 850-853. 10.1093/nar/29.3.850.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wu Y, Sifri CD, Lei HH, Su XZ, Wellems TE: Transfection of Plasmodium falciparum within human red blood cells. Proc Natl Acad Sci U S A. 1995, 92 (4): 973-977. 10.1073/pnas.92.4.973.
Article
PubMed
CAS
PubMed Central
Google Scholar