Predictive interactome modeling for precision microbiome engineering

The plant growth promoting bacteria Gluconacetobacter diazotrophicus and Azospirillum brasilense contribute to the iron nutrition of strawberry plants through siderophores production

(2020) Paola Delaporte-Quintana et al.   PLANT GROWTH REGULATION

Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data

(2020) Joon-Yong Lee et al.   Frontiers in Microbiology

Emerging Priorities for Microbiome Research

(2020) Chad M. Cullen et al.   Frontiers in Microbiology

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

(2020) Christian Diener et al.   mSystems

Synergies Between Division of Labor and Gut Microbiomes of Social Insects

(2020) Veronica M. Sinotte et al.   Frontiers in Ecology and Evolution

The National Microbiome Data Collaborative: enabling microbiome science

(2020) Elisha M. Wood-Charlson et al.   NATURE REVIEWS MICROBIOLOGY

Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses

(2020) Mohammad Moniruzzaman et al.   Nature Communications

Deep Learning Predicts Microbial Interactions from Self-organized Spatiotemporal Patterns

(2020) Joon-Yong Lee et al.   Computational and Structural Biotechnology Journal

Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments

(2020) Elena Perrin et al.   Nature Communications

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations

(2020) Ryan S. McClure et al.   Scientific Reports

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

(2019) Laurence Yang et al.   BMC Systems Biology

Host-microbiota interactions: from holobiont theory to analysis

(2019) Jean-Christophe Simon et al.   Microbiome

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

(2019) Sabine Koch et al.   PLoS Computational Biology

NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

(2019) Jingying Zhang et al.   NATURE BIOTECHNOLOGY

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

(2019) Vikash Pandey et al.   PLoS Computational Biology

Reconciling Ecological and Engineering Design Principles for Building Microbiomes

(2019) Hans C. Bernstein   mSystems

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling

(2019) Brian W. Ji et al.   NATURE METHODS

Machine and deep learning meet genome-scale metabolic modeling

(2019) Guido Zampieri et al.   PLoS Computational Biology

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

(2019) Hyun-Seob Song et al.   Frontiers in Microbiology

Common principles and best practices for engineering microbiomes

(2019) Christopher E. Lawson et al.   NATURE REVIEWS MICROBIOLOGY

An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data

(2019) Chenhao Li et al.   Microbiome

Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions

(2019) Mohammad Mazharul Islam et al.   Frontiers in Microbiology

Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities

(2019) Duo Jiang et al.   Frontiers in Genetics

Biocontrol of the Major Plant Pathogen Ralstonia solanacearum in Irrigation Water and Host Plants by Novel Waterborne Lytic Bacteriophages

(2019) Belén Álvarez et al.   Frontiers in Microbiology

Designing a bioremediator: mechanistic models guide cellular and molecular specialization

(2019) Marco Zaccaria et al.   CURRENT OPINION IN BIOTECHNOLOGY

OUP accepted manuscript

(2018)   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Infant Gut Microbiome Associated With Cognitive Development

(2018) Alexander L. Carlson et al.   BIOLOGICAL PSYCHIATRY

Hydrogen bioproduction with anaerobic bacteria consortium from brewery wastewater

(2018) Renan Pachiega et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

An exclusive metabolic niche enables strain engraftment in the gut microbiota

(2018) Elizabeth Stanley Shepherd et al.   NATURE

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

(2018) Jun Lou et al.   PeerJ

Earth Microbiome Project and Global Systems Biology

(2018) Jack A. Gilbert et al.   mSystems

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

(2018) Jotham Suez et al.   CELL

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

(2018) Shin Haruta et al.   CURRENT GENOMICS

Niche partitioning of a pathogenic microbiome driven by chemical gradients

(2018) Robert A. Quinn et al.   Science Advances

Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities

(2018) Ashley R. Coenen et al.   mSystems

Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut

(2018) Yoshihisa Wakita et al.   BMC MICROBIOLOGY

Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks

(2018) Demetrius DiMucci et al.   mSystems

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Model-based quantification of metabolic interactions from dynamic microbial-community data

(2017) Mark Hanemaaijer et al.   PLoS One

Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

(2017) Edik M. Blais et al.   Nature Communications

SteadyCom: Predicting microbial abundances while ensuring community stability

(2017) Siu Hung Joshua Chan et al.   PLoS Computational Biology

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

(2017) Eugen Bauer et al.   PLoS Computational Biology

The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions

(2017) Richard Jacoby et al.   Frontiers in Plant Science

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

(2017) Sergei Maslov et al.   Scientific Reports

An algorithm for designing minimal microbial communities with desired metabolic capacities

(2016) Alexander Eng et al.   BIOINFORMATICS

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

Learning Microbial Interaction Networks from Metagenomic Count Data

(2016) Surojit Biswas et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Predicting microbial interactions through computational approaches

(2016) Chenhao Li et al.   METHODS

The microbiota in adaptive immune homeostasis and disease

(2016) Kenya Honda et al.   NATURE

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

(2016) Octavio Perez-Garcia et al.   Frontiers in Microbiology

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

Oral Probiotic VSL#3 Prevents Autoimmune Diabetes by Modulating Microbiota and Promoting Indoleamine 2,3-Dioxygenase-Enriched Tolerogenic Intestinal Environment

(2016) Jayashree Dolpady et al.   Journal of Diabetes Research

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

(2016) Maike K. Aurich et al.   Frontiers in Physiology

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

(2015) Steven N. Steinway et al.   PLoS Computational Biology

A Method to Constrain Genome-Scale Models with 13C Labeling Data

(2015) Héctor García Martín et al.   PLoS Computational Biology

Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities

(2015) Hyun-Seob Song et al.   Frontiers in Microbiology

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle

(2014) Hyun-Seob Song et al.   PLoS One

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

(2014) Hyun-Seob Song et al.   Processes

Dynamic models of metabolism: Review of the cybernetic approach

(2012) Doraiswami Ramkrishna et al.   AICHE JOURNAL

Prediction of dynamic behavior of mutant strains from limited wild-type data

(2012) Hyun-Seob Song et al.   METABOLIC ENGINEERING

Stability criteria for complex ecosystems

(2012) Stefano Allesina et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

On enhancing productivity of bioethanol with multiple species

(2011) Jun Geng et al.   BIOTECHNOLOGY AND BIOENGINEERING

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY