Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists

Cancer reproducibility project releases first results

(2017) Monya Baker et al.   NATURE

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

(2017) Babak Momeni et al.   eLife

Modeling Biofilms: From Genes to Communities

(2017) Tianyu Zhang   Processes

Combination Effects of Antimicrobial Peptides

(2016) Guozhi Yu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Potential economic losses to the US corn industry from aflatoxin contamination

(2016) Nicole J. Mitchell et al.   Food Additives and Contaminants Part A-Chemistry Analysis Control Exposure & Risk Assessment

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model

(2016) Ali Ebrahimi et al.   GLOBAL CHANGE BIOLOGY

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates

(2016) Elin E Lilja et al.   ISME Journal

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction

(2016) Christopher S. Henry et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Advancing microbial sciences by individual-based modelling

(2016) Ferdi L. Hellweger et al.   NATURE REVIEWS MICROBIOLOGY

Biodegradation of Mycotoxins: Tales from Known and Unexplored Worlds

(2016) Ilse Vanhoutte et al.   Frontiers in Microbiology

A growth-rate composition formula for the growth of E. coli on co-utilized carbon substrates

(2015) R. Hermsen et al.   Molecular Systems Biology

Microbiology: Create a global microbiome effort

(2015) Nicole Dubilier et al.   NATURE

A prudent path forward for genomic engineering and germline gene modification

(2015) D. Baltimore et al.   SCIENCE

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Theory, models and biology

(2015) Wenying Shou et al.   eLife

Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

(2015) Mark Hanemaaijer et al.   Frontiers in Microbiology

1970s Nostalgia for the Modern Day

(2015) Quincey Justman   Cell Systems

Antagonism between Bacteriostatic and Bactericidal Antibiotics Is Prevalent

(2014) Paolo S. Ocampo et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Models in biology: ‘accurate descriptions of our pathetic thinking’

(2014) Jeremy Gunawardena   BMC BIOLOGY

On the structural stability of mutualistic systems

(2014) R. P. Rohr et al.   SCIENCE

Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks

(2014) Ali N. Ebrahimi et al.   WATER RESOURCES RESEARCH

Modeling biofilm dynamics and hydraulic properties in variably saturated soils using a channel network model

(2014) Ravid Rosenzweig et al.   WATER RESOURCES RESEARCH

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

(2014) Hyun-Seob Song et al.   Processes

Consortia-mediated bioprocessing of cellulose to ethanol with a symbiotic Clostridium phytofermentans/yeast co-culture

(2013) Trevor R Zuroff et al.   Biotechnology for Biofuels

Range expansion promotes cooperation in an experimental microbial metapopulation

(2013) M. S. Datta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

(2013) Jeremy J. Minty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

(2013) Alvaro Sanchez et al.   PLOS BIOLOGY

Spatial self-organization favors heterotypic cooperation over cheating

(2013) Babak Momeni et al.   eLife

Strong inter-population cooperation leads to partner intermixing in microbial communities

(2013) Babak Momeni et al.   eLife

Rethinking Community Assembly through the Lens of Coexistence Theory

(2012) J. HilleRisLambers et al.   Annual Review of Ecology Evolution and Systematics

Engineering microbial systems to explore ecological and evolutionary dynamics

(2012) Yu Tanouchi et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metabolic specialization and the assembly of microbial communities

(2012) David R Johnson et al.   ISME Journal

Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction

(2012) Peter Larsen et al.   JOURNAL OF BIOTECHNOLOGY

Engineering ecosystems and synthetic ecologies

(2012) Michael T. Mee et al.   Molecular BioSystems

Stability criteria for complex ecosystems

(2012) Stefano Allesina et al.   NATURE

Selective sweeps in growing microbial colonies

(2012) Kirill S Korolev et al.   PHYSICAL BIOLOGY

Diversity of Interaction Types and Ecological Community Stability

(2012) A. Mougi et al.   SCIENCE

Designing biological compartmentalization

(2012) Anna H. Chen et al.   TRENDS IN CELL BIOLOGY

Using artificial systems to explore the ecology and evolution of symbioses

(2011) Babak Momeni et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Evaluation of models to predict the stoichiometry of volatile fatty acid profiles in rumen fluid of lactating Holstein cows

(2011) Y. Morvay et al.   JOURNAL OF DAIRY SCIENCE

Social evolution in multispecies biofilms

(2011) S. Mitri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural functions of mycotoxins and control of their biosynthesis in fungi

(2010) Massimo Reverberi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Dynamics in the mixed microbial concourse

(2010) E. H. Wintermute et al.   GENES & DEVELOPMENT

Stability of Ecological Communities and the Architecture of Mutualistic and Trophic Networks

(2010) E. Thebault et al.   SCIENCE

Mathematical Description of Microbial Biofilms

(2010) Isaac Klapper et al.   SIAM REVIEW

Three-dimensional simulations of biofilm growth in porous media

(2009) D. A. Graf von der Schulenburg et al.   AICHE JOURNAL

Social Evolution of Spatial Patterns in Bacterial Biofilms: When Conflict Drives Disorder

(2009) João B. Xavier et al.   AMERICAN NATURALIST

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

The architecture of mutualistic networks minimizes competition and increases biodiversity

(2009) Ugo Bastolla et al.   NATURE

Network structural properties mediate the stability of mutualistic communities

(2008) Toshinori Okuyama et al.   ECOLOGY LETTERS

Aspects of rumen microbiology central to mechanistic modelling of methane production in cattle

(2008) J. L. ELLIS et al.   JOURNAL OF AGRICULTURAL SCIENCE

Individual-based Modelling: An Essential Tool for Microbiology

(2008) Jordi Ferrer et al.   JOURNAL OF BIOLOGICAL PHYSICS

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY

Ustilago maydis, a new fungal model system for cell biology

(2008) Gero Steinberg et al.   TRENDS IN CELL BIOLOGY