Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

A quantitative liquid chromatography tandem mass spectrometry method for metabolomic analysis of Plasmodium falciparum lipid related metabolites

(2012) S. Vo Duy et al.   ANALYTICA CHIMICA ACTA

Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism

(2012) Susanna Bazzani et al.   BMC Systems Biology

Gene selective mRNA cleavage inhibits the development of Plasmodium falciparum

(2012) Y. Augagneur et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Realising the potential of metabolomics

(2012) Andrew W Nicholls   Bioanalysis

Metabolomics: the final frontier?

(2012) Timothy D Veenstra   Genome Medicine

MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis

(2012) Leonid Chindelevitch et al.   GENOME BIOLOGY

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole–time of flight mass spectrometry (UPLC–Q–ToF-MS)

(2011) Giuseppe Paglia et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Metabolic network modeling and simulation for drug targeting and discovery

(2011) Hyun Uk Kim et al.   Biotechnology Journal

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

(2011) Ali R Zomorrodi et al.   BMC Systems Biology

Functional genetics in Apicomplexa: Potentials and limits

(2011) Julien Limenitakis et al.   FEBS LETTERS

From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

(2011) Keng Cher Soh et al.   FEMS YEAST RESEARCH

High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome

(2011) S. Alsford et al.   GENOME RESEARCH

A mass spectrometric strategy for absolute quantification of Plasmodium falciparum proteins of low abundance

(2011) Paul M Southworth et al.   MALARIA JOURNAL

SuperTarget goes quantitative: update on drug-target interactions

(2011) N. Hecker et al.   NUCLEIC ACIDS RESEARCH

Metabolomics of a Single Vacuole Reveals Metabolic Dynamism in an Alga Chara australis

(2011) A. Oikawa et al.   PLANT PHYSIOLOGY

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

(2011) Matthew A. Oberhardt et al.   PLoS Computational Biology

Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis

(2010) Ruben t’Kindt et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

DETECT—a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum

(2010) Stacy S. Hung et al.   BIOINFORMATICS

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

(2010) Carola Huthmacher et al.   BMC Systems Biology

Network thermodynamics in the post-genomic era

(2010) Keng Cher Soh et al.   CURRENT OPINION IN MICROBIOLOGY

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Comparing metabolic network models based on genomic and automatically inferred enzyme information from Plasmodium and its human host to define drug targets in silico

(2010) Segun Fatumo et al.   INFECTION GENETICS AND EVOLUTION

Metabolomics and malaria biology

(2010) Viswanathan Lakshmanan et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

New insights into the blood-stage transcriptome ofPlasmodium falciparumusing RNA-Seq

(2010) Thomas D. Otto et al.   MOLECULAR MICROBIOLOGY

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

(2010) Christoph Gille et al.   Molecular Systems Biology

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network

(2010) Germán Plata et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

BRENDA, the enzyme information system in 2011

(2010) M. Scheer et al.   NUCLEIC ACIDS RESEARCH

A Genetic Screen for Attenuated Growth Identifies Genes Crucial for Intraerythrocytic Development of Plasmodium falciparum

(2010) Bharath Balu et al.   PLoS One

Production of biofuels and biochemicals: in need of an ORACLE

(2010) Ljubisa Miskovic et al.   TRENDS IN BIOTECHNOLOGY

Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi

(2009) Seth B Roberts et al.   BMC Systems Biology

Host-Parasite Interactions Revealed by Plasmodium falciparum Metabolomics

(2009) Kellen L. Olszewski et al.   Cell Host & Microbe

Glycerol: An unexpected major metabolite of energy metabolism by the human malaria parasite

(2009) Lu-Yun Lian et al.   MALARIA JOURNAL

Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites

(2009) Jake Baum et al.   NUCLEIC ACIDS RESEARCH

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico

(2008) Segun Fatumo et al.   INFECTION GENETICS AND EVOLUTION

Proteomes and transcriptomes of the Apicomplexa – Where’s the message?

(2008) J.M. Wastling et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Advances in analysis of microbial metabolic fluxes via13C isotopic labeling

(2008) Yinjie J. Tang et al.   MASS SPECTROMETRY REVIEWS

Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

(2008) Arvind K Chavali et al.   Molecular Systems Biology

Metabolite profiling of the intraerythrocytic malaria parasitePlasmodium falciparumby1H NMR spectroscopy

(2008) Rongwei Teng et al.   NMR IN BIOMEDICINE

Large-Scale Differential Proteome Analysis in Plasmodium falciparum under Drug Treatment

(2008) Judith Helena Prieto et al.   PLoS One

A combined transcriptome and proteome survey of malaria parasite liver stages

(2008) A. S. Tarun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Central carbon metabolism ofSaccharomyces cerevisiaein anaerobic, oxygen-limited and fully aerobic steady-state conditions and following a shift to anaerobic conditions

(2007) Marilyn G. Wiebe et al.   FEMS YEAST RESEARCH