The Community Simulator: A Python package for microbial ecology

A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns

(2020) Robert Marsland et al.   Scientific Reports

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

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

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

(2019) Robert Marsland et al.   PLoS Computational Biology

A high-bias, low-variance introduction to Machine Learning for physicists

(2019) Pankaj Mehta et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Statistical physics of community ecology: a cavity solution to MacArthur’s consumer resource model

(2018) Madhu Advani et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Generic assembly patterns in complex ecological communities

(2018) Matthieu Barbier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Stochastic assembly produces heterogeneous communities in the Caenorhabditis elegans intestine

(2017) Nicole M. Vega et al.   PLOS BIOLOGY

Generalized model of island biodiversity

(2015) David A. Kessler et al.   PHYSICAL REVIEW E

Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The transition between the niche and neutral regimes in ecology

(2014) C. K. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes

(2012) P. Jeraldo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION