Kinetic, metabolic, and statistical analytics: addressing metabolic transport limitations among organelles and microbial communities

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

(2021) Sonja Blasche et al.   Nature Microbiology

The sum is greater than the parts: exploiting microbial communities to achieve complex functions

(2021) Livia S Zaramela et al.   CURRENT OPINION IN BIOTECHNOLOGY

Subcellular Chemical Imaging: New Avenues in Cell Biology

(2020) Johan Decelle et al.   TRENDS IN CELL BIOLOGY

An assessment of genome annotation coverage across the bacterial tree of life

(2020) Briallen Lobb et al.   Microbial Genomics

Life cycle of a cyanobacterial carboxysome

(2020) Nicholas C. Hill et al.   Science Advances

A guide to deciphering microbial interactions and metabolic fluxes in microbiome communities

(2020) Maciek R Antoniewicz   CURRENT OPINION IN BIOTECHNOLOGY

Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

(2020) Cristal Zuñiga et al.   Nature Communications

Machine learning: A powerful tool for gene function prediction in plants

(2020) Elizabeth H. Mahood et al.   Applications in Plant Sciences

Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes

(2020) Juan D. Tibocha-Bonilla et al.   npj Systems Biology and Applications

Reconstructing organisms in silico: genome-scale models and their emerging applications

(2020) Xin Fang et al.   NATURE REVIEWS MICROBIOLOGY

Nutrient-Dependent Trade-Offs between Ribosomes and Division Protein Synthesis Control Bacterial Cell Size and Growth

(2020) Diana Serbanescu et al.   Cell Reports

Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms

(2020) Patrick F. Suthers et al.   METABOLIC ENGINEERING

The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

(2020) Daniel Craig Zielinski et al.   Microorganisms

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

(2019) Alan R. Pacheco et al.   Nature Communications

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen

(2019) Joanne K. Liu et al.   PLoS Computational Biology

The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

(2019) Sankha Ghatak et al.   NUCLEIC ACIDS RESEARCH

Spatial metagenomic characterization of microbial biogeography in the gut

(2019) Ravi U. Sheth et al.   NATURE BIOTECHNOLOGY

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

(2019) Laurence Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Learning representations of microbe–metabolite interactions

(2019) James T. Morton et al.   NATURE METHODS

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities

(2019) Cristal Zuñiga et al.   Nature Microbiology

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

(2019) Bin Du et al.   PLoS Computational Biology

Creating a synthetic lichen: Mutualistic co-culture of fungi and extracellular polysaccharide-secreting cyanobacterium Nostoc PCC 7413

(2019) Tingting Li et al.   Algal Research-Biomass Biofuels and Bioproducts

Sensing the unreachable: challenges and opportunities in biofilm detection

(2019) Yikang Xu et al.   CURRENT OPINION IN BIOTECHNOLOGY

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

The in silico human surfaceome

(2018) Damaris Bausch-Fluck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating Metabolic Equilibrium Constants: Progress and Future Challenges

(2018) Bin Du et al.   TRENDS IN BIOCHEMICAL SCIENCES

Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

(2018) David Heckmann et al.   Nature Communications

Predicting Dynamic Metabolic Demands in the Photosynthetic EukaryoteChlorella vulgaris

(2017) Cristal Zuñiga et al.   PLANT PHYSIOLOGY

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis

(2017) Teruaki Nakatsuji et al.   Science Translational Medicine

Quantifying the benefit of a proteome reserve in fluctuating environments

(2017) Matteo Mori et al.   Nature Communications

Elucidation of complexity and prediction of interactions in microbial communities

(2017) Cristal Zuñiga et al.   Microbial Biotechnology

Unraveling interactions in microbial communities - from co-cultures to microbiomes

(2015) Justin Tan et al.   JOURNAL OF MICROBIOLOGY

Mechanistic links between cellular trade-offs, gene expression, and growth

(2015) Andrea Y. Weiße et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

(2014) Joanne K Liu et al.   BMC Systems Biology

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

(2014) Amit Ghosh et al.   PLoS Computational Biology

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

The Transporter Classification Database

(2013) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

(2013) Harish Nagarajan et al.   Nature Communications

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

(2012) Ines Thiele et al.   PLoS One

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology