Revealing the world of RNA interference, Nature, vol.567, issue.7006, pp.338-342, 2004. ,
DOI : 10.1038/415810a
Fitting a mixture model by expectation maximization to discover motifs in biopolymers, ISMB. International Conference on Intelligent Systems for Molecular Biology, p.28, 1994. ,
Computational identification of Cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae, Journal of Molecular Biology, vol.296, issue.5, pp.1205-1214, 2000. ,
DOI : 10.1006/jmbi.2000.3519
An algorithm for finding signals of unknown length in DNA sequences, Bioinformatics, vol.17, issue.Suppl 1, p.207, 2001. ,
DOI : 10.1093/bioinformatics/17.suppl_1.S207
Improved benchmarks for computational motif discovery, BMC Bioinformatics, vol.8, issue.1, p.193, 2007. ,
DOI : 10.1186/1471-2105-8-193
A universal framework for regulatory element discovery across all genomes and data types. Molecular cell, pp.337-350, 2007. ,
In silico discovery of transcription regulatory elements in Plasmodium falciparum, BMC Genomics, vol.9, issue.1, p.70, 2008. ,
DOI : 10.1186/1471-2164-9-70
Genome sequence of the human malaria parasite Plasmodium falciparum, Nature, vol.241, issue.6906, pp.498-511, 2002. ,
DOI : 10.1038/nature01099
Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes, Bioinformatics, vol.15, issue.10, p.776, 1999. ,
DOI : 10.1093/bioinformatics/15.10.776
Gene Regulation by Transcription Factors and MicroRNAs, Science, vol.319, issue.5871, p.1785, 2008. ,
DOI : 10.1126/science.1151651
The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum, PLoS Biology, vol.280, issue.1, p.5, 2003. ,
DOI : 10.1371/journal.pbio.0000005.st007
RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors, Bioinformatics, vol.23, issue.13, p.72, 2007. ,
DOI : 10.1093/bioinformatics/btm224
Discovering Motifs in Ranked Lists of DNA Sequences, PLoS Computational Biology, vol.13, issue.3, p.39, 2007. ,
DOI : 10.1371/journal.pcbi.0030039.st005
Regulatory element detection using correlation with expression, Nature Genetics, vol.27, issue.2, pp.167-174, 2001. ,
DOI : 10.1038/84792
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast, Proceedings of the National Academy of Sciences, vol.102, issue.49, p.17675, 2005. ,
DOI : 10.1073/pnas.0503803102
Finding regulatory elements using joint likelihoods for sequence and expression profile data, Proc. Int, pp.202-210, 2000. ,
Specific DNA-binding by Apicomplexan AP2 transcription factors, Proceedings of the National Academy of Sciences, p.8393, 2008. ,
DOI : 10.1073/pnas.0801993105
Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite, PLoS Pathogens, vol.33, issue.10, pp.5-526, 2010. ,
DOI : 10.1371/journal.ppat.1001165.s025
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome, Nucleic Acids Research, vol.39, issue.4, 2010. ,
DOI : 10.1093/nar/gkq920
Hubs in space: Popular nearest neighbors in high-dimensional data, The Journal of Machine Learning Research, vol.11, pp.2487-2531, 2010. ,
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes, Molecular Biology of the Cell, vol.11, issue.12, p.4241, 2000. ,
DOI : 10.1091/mbc.11.12.4241
Deciphering principles of transcription regulation in eukaryotic genomes. Molecular systems biology, 2006. ,
Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization, Molecular Biology of the Cell, vol.9, issue.12, p.3273, 1998. ,
DOI : 10.1091/mbc.9.12.3273
R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2011. ,
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles, Nucleic Acids Research, vol.38, issue.Database, p.105, 2010. ,
DOI : 10.1093/nar/gkp950
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species, Nucleic Acids Research, vol.40, issue.D1, pp.162-168, 2012. ,
DOI : 10.1093/nar/gkr1180
Quantifying similarity between motifs, Genome Biology, vol.8, issue.2, p.24, 2007. ,
DOI : 10.1186/gb-2007-8-2-r24
Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society. Series B (Methodological), pp.289-300, 1995. ,
Discovering regulatory motifs in the Plasmodium genome using comparative genomics, Bioinformatics, vol.24, issue.17, p.1843, 2008. ,
DOI : 10.1093/bioinformatics/btn348
Galvestine-1, a novel chemical probe for the study of the glycerolipid homeostasis system in plant cells, Molecular BioSystems, vol.116, issue.8, 2012. ,
DOI : 10.1039/c2mb25067e
Genome sequence of the human malaria parasite Plasmodium falciparum, Nature, vol.241, issue.6906, pp.498-511, 2002. ,
DOI : 10.1038/nature01099
Control of gene expression in Plasmodium falciparum ??? Ten years on, Molecular and Biochemical Parasitology, vol.164, issue.1, pp.9-25, 2009. ,
DOI : 10.1016/j.molbiopara.2008.11.010
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains, Nucleic Acids Research, vol.33, issue.13, p.3994, 2005. ,
DOI : 10.1093/nar/gki709
Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle, Genome Biology, vol.8, issue.7, p.134, 2007. ,
DOI : 10.1186/gb-2007-8-7-r134
A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses, Science, vol.307, issue.5706, pp.82-86, 2005. ,
DOI : 10.1126/science.1103717
Statistical methods in bioinformatics: an introduction, 2005. ,
PlasmoDB: a functional genomic database for malaria parasites, Nucleic Acids Research, vol.37, issue.Database, pp.37-539, 2009. ,
DOI : 10.1093/nar/gkn814
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, p.2178, 2003. ,
DOI : 10.1101/gr.1224503