Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

PubWeight™: 0.81‹?›

🔗 View Article (PMC 1665468)

Published in Malar J on November 17, 2006

Authors

Lyn-Marie Birkholtz1, Olivier Bastien, Gordon Wells, Delphine Grando, Fourie Joubert, Vinod Kasam, Marc Zimmermann, Philippe Ortet, Nicolas Jacq, Nadia Saïdani, Sylvaine Roy, Martin Hofmann-Apitius, Vincent Breton, Abraham I Louw, Eric Maréchal

Author Affiliations

1: Department of Biochemistry and African Centre for Gene Technologies, Faculty of Natural and Agricultural Sciences, University of Pretoria, 0002, Pretoria, South Africa. lynmarie.birkholtz@up.ac.za <lynmarie.birkholtz@up.ac.za>

Articles cited by this

(truncated to the top 100)

Identification of common molecular subsequences. J Mol Biol (1981) 130.53

The sequence of the human genome. Science (2001) 101.55

DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79

Rapid and sensitive protein similarity searches. Science (1985) 76.83

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (2000) 70.33

The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98

From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35

Finishing the euchromatic sequence of the human genome. Nature (2004) 41.40

Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96

Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89

OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res (2003) 33.03

GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics (2004) 30.14

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics (2004) 26.64

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A (1990) 24.42

The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66

GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63

MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol (2003) 20.83

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics (2002) 19.27

The Pathway Tools software. Bioinformatics (2002) 14.89

The Gene Ontology (GO) project in 2006. Nucleic Acids Res (2006) 13.79

The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol (2003) 11.86

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res (2006) 11.43

A proteomic view of the Plasmodium falciparum life cycle. Nature (2002) 10.65

Discovery of gene function by expression profiling of the malaria parasite life cycle. Science (2003) 10.57

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92

Resistance of Plasmodium falciparum field isolates to in-vitro artemether and point mutations of the SERCA-type PfATPase6. Lancet (2005) 8.30

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol (2005) 7.94

Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. Science (1999) 7.54

Reliability and reproducibility issues in DNA microarray measurements. Trends Genet (2005) 6.79

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res (2003) 6.19

A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science (2005) 5.99

MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2006) 5.79

A plastid of probable green algal origin in Apicomplexan parasites. Science (1997) 5.73

Global mapping of pharmacological space. Nat Biotechnol (2006) 4.99

Effectiveness of antimalarial drugs. N Engl J Med (2005) 4.83

GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76

Medical need, scientific opportunity and the drive for antimalarial drugs. Nature (2002) 4.73

The druggable genome: an update. Drug Discov Today (2005) 4.48

The Plasmodium genome database. Nature (2002) 4.36

Chris Lipinski discusses life and chemistry after the Rule of Five. Drug Discov Today (2003) 3.99

ProtoMap: automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res (2000) 3.97

A protein interaction network of the malaria parasite Plasmodium falciparum. Nature (2005) 3.81

Kingdom protozoa and its 18 phyla. Microbiol Rev (1993) 3.74

Hemoglobin metabolism in the malaria parasite Plasmodium falciparum. Annu Rev Microbiol (1997) 3.66

Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res (2004) 3.63

GeneLynx: a gene-centric portal to the human genome. Genome Res (2001) 3.42

Phylogenetic analysis using PHYLIP. Methods Mol Biol (2000) 3.27

Plastid in human parasites. Nature (1996) 3.25

Insights into antifolate resistance from malarial DHFR-TS structures. Nat Struct Biol (2003) 3.20

The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol Biochem Parasitol (2005) 3.02

The predictive power of the CluSTr database. Bioinformatics (2005) 2.85

MIAME, we have a problem. Trends Genet (2005) 2.84

Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res (2006) 2.78

The genome of the malaria parasite. Curr Opin Genet Dev (1999) 2.72

Interpolated Markov models for eukaryotic gene finding. Genomics (1999) 2.71

CryptoDB: a Cryptosporidium bioinformatics resource update. Nucleic Acids Res (2006) 2.68

Guilt-by-association goes global. Nature (2000) 2.62

Heterologous expression of proteins from Plasmodium falciparum: results from 1000 genes. Mol Biochem Parasitol (2006) 2.45

From XML to RDF: how semantic web technologies will change the design of 'omic' standards. Nat Biotechnol (2005) 2.41

Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A (2003) 2.38

Inferential literacy for experimental high-throughput biology. Trends Genet (2005) 2.30

The apicoplast as a potential therapeutic target in and other apicomplexan parasites. Parasitol Today (1999) 2.29

Protein families and TRIBES in genome sequence space. Nucleic Acids Res (2003) 2.27

The PDB is a covering set of small protein structures. J Mol Biol (2003) 2.26

Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biol (2006) 2.25

Malaria: a reemerging disease in Africa. Emerg Infect Dis (1998) 2.21

Data-mining approaches reveal hidden families of proteases in the genome of malaria parasite. Genome Res (2003) 2.18

Malaria parasites can develop stable resistance to artemisinin but lack mutations in candidate genes atp6 (encoding the sarcoplasmic and endoplasmic reticulum Ca2+ ATPase), tctp, mdr1, and cg10. Antimicrob Agents Chemother (2006) 2.16

Domains, motifs and clusters in the protein universe. Curr Opin Chem Biol (2003) 2.02

Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res (2004) 1.92

Aspartic proteases of Plasmodium falciparum and other parasitic protozoa as drug targets. Trends Parasitol (2001) 1.90

ProtoNet: hierarchical classification of the protein space. Nucleic Acids Res (2003) 1.88

Comparative genomic and phylogenetic analyses of calcium ATPases and calcium-regulated proteins in the apicomplexa. Mol Biol Evol (2006) 1.83

PCR-based gene synthesis as an efficient approach for expression of the A+T-rich malaria genome. Protein Eng (1999) 1.82

The Plasmodium protein network diverges from those of other eukaryotes. Nature (2005) 1.76

A re-annotation of the Saccharomyces cerevisiae genome. Comp Funct Genomics (2001) 1.75

Intracellular targets of cyclin-dependent kinase inhibitors: identification by affinity chromatography using immobilised inhibitors. Chem Biol (2000) 1.75

Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome Res (2006) 1.68

Genome-wide identification of genes upregulated at the onset of gametocytogenesis in Plasmodium falciparum. Mol Biochem Parasitol (2005) 1.66

Predicting protein druggability. Drug Discov Today (2005) 1.66

The apicoplast as a potential therapeutic target in Toxoplasma and other apicomplexan parasites: some additional thoughts. Parasitol Today (1999) 1.65

SIMAP--the similarity matrix of proteins. Bioinformatics (2005) 1.62

Discovery of novel targets of quinoline drugs in the human purine binding proteome. Mol Pharmacol (2002) 1.59

The apicoplast: a review of the derived plastid of apicomplexan parasites. Curr Issues Mol Biol (2005) 1.54

Progress in in silico functional genomics: the malaria Metabolic Pathways database. Trends Parasitol (2006) 1.54

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) 1.53

CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules. FEBS Lett (2005) 1.51

Recycled plastids: a 'green movement' in eukaryotic evolution. Trends Genet (2002) 1.49

sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. J Chem Inf Model (2006) 1.47

In vivo transcriptome of Plasmodium falciparum reveals overexpression of transcripts that encode surface proteins. J Infect Dis (2005) 1.46

Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discov Today (2005) 1.46

In silico gene function prediction using ontology-based pattern identification. Bioinformatics (2004) 1.44

Extracting gene networks for low-dose radiation using graph theoretical algorithms. PLoS Comput Biol (2006) 1.41

Malaria breakthrough raises spectre of drug resistance. Nature (2006) 1.40

Quantitative proteomics of the human malaria parasite Plasmodium falciparum and its application to studies of development and inhibition. Mol Microbiol (2004) 1.36

Integrated programme is key to malaria control. Nature (2002) 1.31

Large scale hierarchical clustering of protein sequences. BMC Bioinformatics (2005) 1.28

Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparum. Proc Natl Acad Sci U S A (1996) 1.26

Transcriptome analysis of antigenic variation in Plasmodium falciparum--var silencing is not dependent on antisense RNA. Genome Biol (2005) 1.25

Effect of codon optimization on expression levels of a functionally folded malaria vaccine candidate in prokaryotic and eukaryotic expression systems. Infect Immun (2003) 1.24

Articles by these authors

A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proc Natl Acad Sci U S A (2005) 4.49

Autonomic tone variations before the onset of paroxysmal atrial fibrillation. Circulation (2002) 3.22

Research capacity. Enabling the genomic revolution in Africa. Science (2014) 3.05

ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Res (2007) 2.93

Respiratory variations in pulse oximetry plethysmographic waveform amplitude to predict fluid responsiveness in the operating room. Anesthesiology (2007) 2.63

Extracorporeal membrane oxygenation for pandemic influenza A(H1N1)-induced acute respiratory distress syndrome: a cohort study and propensity-matched analysis. Am J Respir Crit Care Med (2012) 2.45

euHCVdb: the European hepatitis C virus database. Nucleic Acids Res (2006) 2.41

Detection of IUPAC and IUPAC-like chemical names. Bioinformatics (2008) 2.26

The EMBRACE web service collection. Nucleic Acids Res (2010) 2.26

PDB_REDO: automated re-refinement of X-ray structure models in the PDB. J Appl Crystallogr (2009) 2.19

The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number. Proc Natl Acad Sci U S A (2005) 1.72

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics (2010) 1.68

A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet (2007) 1.59

Low prevalence of atrial fibrillation in asymptomatic adults in Geneva, Switzerland. Europace (2009) 1.58

Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports. J Biomed Inform (2012) 1.52

Value of P-wave signal averaging to predict atrial fibrillation recurrences after pulmonary vein isolation. Europace (2012) 1.52

Experts' recommendations for the management of adult patients with cardiogenic shock. Ann Intensive Care (2015) 1.51

Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet (2009) 1.50

Genome sequence of Pantoea ananatis LMG20103, the causative agent of Eucalyptus blight and dieback. J Bacteriol (2010) 1.40

Comparative analysis of the human gimap gene cluster encoding a novel GTPase family. Gene (2004) 1.38

Does the Pleth variability index indicate the respiratory-induced variation in the plethysmogram and arterial pressure waveforms? Anesth Analg (2008) 1.38

EST-analysis of the thermo-acidophilic red microalga Galdieria sulphuraria reveals potential for lipid A biosynthesis and unveils the pathway of carbon export from rhodoplasts. Plant Mol Biol (2004) 1.37

Phosphate deprivation induces transfer of DGDG galactolipid from chloroplast to mitochondria. J Cell Biol (2004) 1.36

Identification of new drug classification terms in textual resources. Bioinformatics (2007) 1.31

Host cell subversion by Toxoplasma GRA16, an exported dense granule protein that targets the host cell nucleus and alters gene expression. Cell Host Microbe (2013) 1.29

Reconstruction of chemical molecules from images. Conf Proc IEEE Eng Med Biol Soc (2007) 1.28

The response of Nannochloropsis gaditana to nitrogen starvation includes de novo biosynthesis of triacylglycerols, a decrease of chloroplast galactolipids, and reorganization of the photosynthetic apparatus. Eukaryot Cell (2013) 1.28

Structure, function, and evolution of the Thiomonas spp. genome. PLoS Genet (2010) 1.27

A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii. PLoS Pathog (2010) 1.27

Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters. Mol Syst Biol (2009) 1.26

Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol Cell Proteomics (2009) 1.24

Heterologous expression of plasmodial proteins for structural studies and functional annotation. Malar J (2008) 1.22

ATM-mediated transcriptional and developmental responses to gamma-rays in Arabidopsis. PLoS One (2007) 1.20

Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor. Plant Cell (2011) 1.20

The early responses of Arabidopsis thaliana cells to cadmium exposure explored by protein and metabolite profiling analyses. Proteomics (2006) 1.19

Evolution of hematophagy in ticks: common origins for blood coagulation and platelet aggregation inhibitors from soft ticks of the genus Ornithodoros. Mol Biol Evol (2002) 1.18

SET8-mediated methylations of histone H4 lysine 20 mark silent heterochromatic domains in apicomplexan genomes. Mol Cell Biol (2007) 1.17

Transient increase of phosphatidylcholine in plant cells in response to phosphate deprivation. FEBS Lett (2003) 1.14

Effect of chronic amiodarone therapy on excitable gap during typical human atrial flutter. J Cardiovasc Electrophysiol (2004) 1.14

Atrial fibrillation management by practice cardiologists: a prospective survey on the adherence to guidelines in the real world. Europace (2008) 1.13

Hepatitis C databases, principles and utility to researchers. Hepatology (2006) 1.13

Novel technologies for virtual screening. Drug Discov Today (2004) 1.13

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature. BMC Bioinformatics (2008) 1.13

P2CS: a database of prokaryotic two-component systems. Nucleic Acids Res (2010) 1.12

P2CS: a two-component system resource for prokaryotic signal transduction research. BMC Genomics (2009) 1.12

Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions. C R Biol (2005) 1.11

Glycerolipid transfer for the building of membranes in plant cells. Prog Lipid Res (2006) 1.10

Drug inhibition of HDAC3 and epigenetic control of differentiation in Apicomplexa parasites. J Exp Med (2009) 1.08

Catheter ablation of arrhythmias in ebstein's anomaly: a multicenter study. J Cardiovasc Electrophysiol (2011) 1.07

Co-inhibition of Plasmodium falciparum S-adenosylmethionine decarboxylase/ornithine decarboxylase reveals perturbation-specific compensatory mechanisms by transcriptome, proteome, and metabolome analyses. J Biol Chem (2008) 1.05

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities. BMC Bioinformatics (2005) 1.04

Atrial fibrillation in Africa: clinical characteristics, prognosis, and adherence to guidelines in Cameroon. Europace (2010) 1.04

The plant S-adenosyl-L-methionine:Mg-protoporphyrin IX methyltransferase is located in both envelope and thylakoid chloroplast membranes. Eur J Biochem (2002) 1.04

Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference. Gene (2004) 1.03

Toxoplasma gondii acyl-lipid metabolism: de novo synthesis from apicoplast-generated fatty acids versus scavenging of host cell precursors. Biochem J (2006) 1.02

Genetic heterogeneity in the foot-and-mouth disease virus Leader and 3C proteinases. Gene (2002) 1.02

Activation of the chloroplast monogalactosyldiacylglycerol synthase MGD1 by phosphatidic acid and phosphatidylglycerol. J Biol Chem (2009) 1.01

Savignygrin, a platelet aggregation inhibitor from the soft tick Ornithodoros savignyi, presents the RGD integrin recognition motif on the Kunitz-BPTI fold. J Biol Chem (2002) 1.01

Docking, synthesis, and in vitro evaluation of antimitotic estrone analogs. Chem Biol Drug Des (2011) 1.00

Atypical lipid composition in the purified relict plastid (apicoplast) of malaria parasites. Proc Natl Acad Sci U S A (2013) 1.00

Chemical inhibitors of monogalactosyldiacylglycerol synthases in Arabidopsis thaliana. Nat Chem Biol (2011) 1.00

Candida albicans and non-Candida albicans fungemia in an institutional hospital during a decade. Med Mycol (2012) 1.00

Lipidomic analysis of Toxoplasma gondii reveals unusual polar lipids. Biochemistry (2007) 1.00

Polyamine homoeostasis as a drug target in pathogenic protozoa: peculiarities and possibilities. Biochem J (2011) 0.99

Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics. Bioinformatics (2004) 0.99

Grid-enabled high-throughput in silico screening against influenza A neuraminidase. IEEE Trans Nanobioscience (2006) 0.98

From integrative disease modeling to predictive, preventive, personalized and participatory (P4) medicine. EPMA J (2013) 0.98

Successful cardiac resynchronization therapy after cardiac surgery. Anesth Analg (2007) 0.97

A role of histone H3 lysine 4 methyltransferase components in endosomal trafficking. J Cell Biol (2009) 0.97

Cyclosporine protects the heart during aortic valve surgery. Anesthesiology (2014) 0.97

Mutational analysis of the hexose transporter of Plasmodium falciparum and development of a three-dimensional model. J Biol Chem (2002) 0.96

Atrial tachycardia with recipient-to-donor atrioatrial conduction and isthmus-dependent donor atrial flutter in a patient after orthotopic heart transplantation. Successful treatment by radiofrequency catheter ablation. J Heart Lung Transplant (2002) 0.96

The biosynthetic capacities of the plastids and integration between cytoplasmic and chloroplast processes. Annu Rev Genet (2012) 0.94

Mining biomarker information in biomedical literature. BMC Med Inform Decis Mak (2012) 0.94

Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers. BMC Bioinformatics (2011) 0.94

The major tick salivary gland proteins and toxins from the soft tick, Ornithodoros savignyi, are part of the tick Lipocalin family: implications for the origins of tick toxicoses. Mol Biol Evol (2003) 0.93

@neuLink: a service-oriented application for biomedical knowledge discovery. Stud Health Technol Inform (2008) 0.92

Utility of the surface electrocardiogram for confirming right ventricular septal pacing: validation using electroanatomical mapping. Europace (2010) 0.92

Plant lipid-associated fibrillin proteins condition jasmonate production under photosynthetic stress. Plant J (2009) 0.92

Plasmodium falciparum apicoplast drugs: targets or off-targets? Chem Rev (2011) 0.92

Identification of plant-like galactolipids in Chromera velia, a photosynthetic relative of malaria parasites. J Biol Chem (2011) 0.92

Pathogenic mechanisms of sand tampan toxicoses induced by the tick, Ornithodoros savignyi. Toxicon (2002) 0.91

Identifying gene-specific variations in biomedical text. J Bioinform Comput Biol (2007) 0.91