Novel Approaches for Systems Biology of Metabolism-Oriented Pathogen-Human Interactions: A Mini-Review

Dual gene expression analysis identifies factors associated with Staphylococcus aureus virulence in diabetic mice

(2019) Rudy Jacquet et al.   INFECTION AND IMMUNITY

Modeling Host-Pathogen Interaction to Elucidate the Metabolic Drug Response of Intracellular Mycobacterium tuberculosis

(2019) Rienk A. Rienksma et al.   Frontiers in Cellular and Infection Microbiology

Determination of an Interaction Network between an Extracellular Bacterial Pathogen and the Human Host

(2019) Brad Griesenauer et al.   mBio

Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans

(2019) José F. Muñoz et al.   Nature Communications

Glucose Homeostasis Is Important for Immune Cell Viability during Candida Challenge and Host Survival of Systemic Fungal Infection

(2018) Timothy M. Tucey et al.   Cell Metabolism

Biomedical applications of genome-scale metabolic network reconstructions of human pathogens

(2018) Laura J Dunphy et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Pathway based therapeutic targets identification and development of an interactive database CampyNIBase of Campylobacter jejuni RM1221 through non-redundant protein dataset

(2018) Mohammad Uzzal Hossain et al.   PLoS One

Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction

(2018) Monise Petrucelli et al.   Genes

Towards predicting the environmental metabolome from metagenomics with a mechanistic model

(2018) Daniel R. Garza et al.   Nature Microbiology

A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection

(2018) Amanda Jacobson et al.   Cell Host & Microbe

Staphylococcus aureus Biofilm Growth on Cystic Fibrosis Airway Epithelial Cells Is Enhanced during Respiratory Syncytial Virus Coinfection

(2018) Megan R. Kiedrowski et al.   mSphere

Identification of Histone Deacetylase (HDAC) as a drug target against MRSA via interolog method of protein-protein interaction prediction

(2017) Reaz Uddin et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host–pathogen transcriptomes

(2017) Aaron M. Nuss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving host–pathogen interactions by dual RNA-seq

(2017) Alexander J. Westermann et al.   PLoS Pathogens

Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection

(2017) Michael Zimmermann et al.   mSystems

Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes

(2017) Matthew L. Jenior et al.   mSystems

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Dual Transcriptome Profiling of Leishmania -Infected Human Macrophages Reveals Distinct Reprogramming Signatures

(2016) Maria Cecilia Fernandes et al.   mBio

Dual-seq transcriptomics reveals the battle for iron during Pseudomonas aeruginosa acute murine pneumonia

(2016) F. Heath Damron et al.   Scientific Reports

Structure-Based Design of Inhibitors of the Crucial Cysteine Biosynthetic Pathway Enzyme O-Acetyl Serine Sulfhydrylase

(2015) Mohit Mazumder et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk

(2015) B. Baddal et al.   mBio

Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods

(2015) Neema Jamshidi et al.   Frontiers in Microbiology

A review on computational systems biology of pathogen–host interactions

(2015) Saliha DurmuÅŸ et al.   Frontiers in Microbiology

Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection

(2014) Kelly J Pittman et al.   BMC GENOMICS

Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics

(2014) Muriel Vayssier-Taussat et al.   Frontiers in Cellular and Infection Microbiology

Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells

(2013) Michael S. Humphrys et al.   PLoS One

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

The chemical interactome space between the human host and the genetically defined gut metabotypes

(2012) Ulrik Plesner Jacobsen et al.   ISME Journal

Metabolic network modeling and simulation for drug targeting and discovery

(2011) Hyun Uk Kim et al.   Biotechnology Journal

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

(2010) Carola Huthmacher et al.   BMC Systems Biology

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

(2010) Aarash Bordbar et al.   Molecular Systems Biology

System-level analysis of Salmonella metabolism during infection

(2009) Dirk Bumann   CURRENT OPINION IN MICROBIOLOGY