Cytokine-mediated communication: a quantitative appraisal of immune complexity

G Altan-Bonnet, R Mukherjee - Nature Reviews Immunology, 2019 - nature.com
Intercellular communication mediated by cytokines is the main mechanism by which cells of
the immune system talk to each other. Many aspects of cytokine signalling in the immune …

Metabolic interaction models recapitulate leaf microbiota ecology

M Schäfer, AR Pacheco, R Künzler, M Bortfeld-Miller… - Science, 2023 - science.org
Resource allocation affects the structure of microbiomes, including those associated with
living hosts. Understanding the degree to which this dependency determines interspecies …

Designing More Informative Multiple-Driver Experiments

MK Thomas, R Ranjan - Annual Review of Marine Science, 2024 - annualreviews.org
For decades, multiple-driver/stressor research has examined interactions among drivers that
will undergo large changes in the future: temperature, pH, nutrients, oxygen, pathogens, and …

From competition to facilitation and mutualism: a general theory of the niche

T Koffel, T Daufresne, CA Klausmeier - Ecological Monographs, 2021 - Wiley Online Library
Niche Theory is a central framework in ecology based on the recognition that most
interactions between organisms are indirect, mediated by the biotic and abiotic dynamical …

Diversity begets stability: Sublinear growth and competitive coexistence across ecosystems

IA Hatton, O Mazzarisi, A Altieri, M Smerlak - Science, 2024 - science.org
The worldwide loss of species diversity brings urgency to understanding how diverse
ecosystems maintain stability. Whereas early ecological ideas and classic observations …

Engineering complex communities by directed evolution

CY Chang, JCC Vila, M Bender, R Li… - Nature ecology & …, 2021 - nature.com
Directed evolution has been used for decades to engineer biological systems at or below
the organismal level. Above the organismal level, a small number of studies have attempted …

Stabilization of extensive fine-scale diversity by ecologically driven spatiotemporal chaos

MT Pearce, A Agarwala… - Proceedings of the …, 2020 - National Acad Sciences
It has recently become apparent that the diversity of microbial life extends far below the
species level to the finest scales of genetic differences. Remarkably, extensive fine-scale …

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

R Marsland III, W Cui, J Goldford… - PLoS computational …, 2019 - journals.plos.org
A fundamental goal of microbial ecology is to understand what determines the diversity,
stability, and structure of microbial ecosystems. The microbial context poses special …

Non-additive microbial community responses to environmental complexity

AR Pacheco, ML Osborne, D Segrè - Nature communications, 2021 - nature.com
Environmental composition is a major, though poorly understood, determinant of
microbiome dynamics. Here we ask whether general principles govern how microbial …

Memorizing without overfitting: Bias, variance, and interpolation in overparameterized models

JW Rocks, P Mehta - Physical review research, 2022 - APS
The bias-variance trade-off is a central concept in supervised learning. In classical statistics,
increasing the complexity of a model (eg, number of parameters) reduces bias but also …