Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

(2017) Anush Chiappino-Pepe et al.   PLoS Computational Biology

High-Throughput Assay and Discovery of Small Molecules that Interrupt Malaria Transmission

(2016) David M. Plouffe et al.   Cell Host & Microbe

Malaria Parasite Metabolic Pathways (MPMP) Upgraded with Targeted Chemical Compounds

(2016) Hagai Ginsburg et al.   TRENDS IN PARASITOLOGY

Integrated analysis of the Plasmodium species transcriptome

(2016) Regina Hoo et al.   EBioMedicine

Genetic Characterization of Plasmodium Putative Pantothenate Kinase Genes Reveals Their Essential Role in Malaria Parasite Transmission to the Mosquito

(2016) Robert J. Hart et al.   Scientific Reports

Nowhere to hide: interrogating different metabolic parameters of Plasmodium falciparum gametocytes in a transmission blocking drug discovery pipeline towards malaria elimination

(2015) Janette Reader et al.   MALARIA JOURNAL

Sexual development in Plasmodium parasites: knowing when it's time to commit

(2015) Gabrielle A. Josling et al.   NATURE REVIEWS MICROBIOLOGY

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

(2015) Stepan Tymoshenko et al.   PLoS Computational Biology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

(2014) Wai Ong et al.   BMC Systems Biology

Mitochondrial metabolism of sexual and asexual blood stages of the malaria parasite Plasmodium falciparum

(2013) James I MacRae et al.   BMC BIOLOGY

Type II Fatty Acid Biosynthesis Is Essential for Plasmodium falciparum Sporozoite Development in the Midgut of Anopheles Mosquitoes

(2013) Ben C. L. van Schaijk et al.   EUKARYOTIC CELL

Plasmodium falciparum: Generation of pure gametocyte culture by heparin treatment

(2013) Jun Miao et al.   EXPERIMENTAL PARASITOLOGY

Kinetic Flux Profiling Elucidates Two Independent Acetyl-CoA Biosynthetic Pathways inPlasmodium falciparum

(2013) Simon A. Cobbold et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Targeting Plasmodium PI(4)K to eliminate malaria

(2013) Case W. McNamara et al.   NATURE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence

(2012) Shannan J. Ho Sui et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

(2011) María J López-Barragán et al.   BMC GENOMICS

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

(2011) H. U. Kim et al.   Molecular Systems Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

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

(2010) Carola Huthmacher et al.   BMC Systems Biology

Uptake of purines in Plasmodium falciparum-infected human erythrocytes is mostly mediated by the human Equilibrative Nucleoside Transporter and the human Facilitative Nucleobase Transporter

(2010) Neils B Quashie et al.   MALARIA JOURNAL

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

(2010) Germán Plata et al.   Molecular Systems Biology

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Blueprint for antimicrobial hit discovery targeting metabolic networks

(2010) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Rodent and nonrodent malaria parasites differ in their phospholipid metabolic pathways

(2009) Sandrine Déchamps et al.   JOURNAL OF LIPID RESEARCH

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

(2009) Patrick F. Suthers et al.   PLoS Computational Biology

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

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

Plasmodium falciparumPurine Nucleoside Phosphorylase Is Critical for Viability of Malaria Parasites

(2008) Dennis C. Madrid et al.   JOURNAL OF BIOLOGICAL CHEMISTRY