Life is physics: evolution as a collective phenomenon far from equilibrium

N Goldenfeld, C Woese - Annu. Rev. Condens. Matter Phys., 2011 - annualreviews.org
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it
is widely treated as a subset of population genetics, and thus its scope is artificially limited …

Genome-scale models of bacterial metabolism: reconstruction and applications

M Durot, PY Bourguignon… - FEMS microbiology …, 2008 - academic.oup.com
Genome-scale metabolic models bridge the gap between genome-derived biochemical
information and metabolic phenotypes in a principled manner, providing a solid …

[HTML][HTML] Mechanisms in science

C Craver, J Tabery, P Illari - 2015 - plato.stanford.edu
The concept of mechanism has been an important organizing principle in science and
philosophy since at least the early modern period (Dijksterhuis 1950 [1961]; Boas 1952) …

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

S Greenblum, PJ Turnbaugh, E Borenstein - Proceedings of the National …, 2012 - pnas.org
The human microbiome plays a key role in a wide range of host-related processes and has
a profound effect on human health. Comparative analyses of the human microbiome have …

Performance of modularity maximization in practical contexts

BH Good, YA De Montjoye, A Clauset - Physical Review E—Statistical …, 2010 - APS
Although widely used in practice, the behavior and accuracy of the popular module
identification technique called modularity maximization is not well understood in practical …

[LIBRO][B] The origins of evolutionary innovations: a theory of transformative change in living systems

A Wagner - 2011 - books.google.com
The history of life is a nearly four billion year old story of transformative change. This change
ranges from dramatic macroscopic innovations such as the evolution of wings or eyes, to a …

Streptomyces

P Kämpfer - Bergey's manual of systematics of archaea and …, 2015 - Wiley Online Library
Strep. to. my'ces. Gr. adj. streptos pliant, bent; Gr. masc. n. mukês fungus; NL masc. n.
Streptomyces pliant or bent fungus. Actinobacteria/Actinobacteria/Streptomycetales …

The microbial exometabolome: ecological resource and architect of microbial communities

AE Douglas - … Transactions of the Royal Society B, 2020 - royalsocietypublishing.org
All microorganisms release many metabolites, collectively known as the exometabolome.
The resultant multi-way cross-feeding of metabolites among microorganisms distributes …

Toward a population genetic framework of developmental evolution: the costs, limits, and consequences of phenotypic plasticity

EC Snell‐Rood, JD Van Dyken, T Cruickshank… - …, 2010 - Wiley Online Library
Adaptive phenotypic plasticity allows organisms to cope with environmental variability, and
yet, despite its adaptive significance, phenotypic plasticity is neither ubiquitous nor infinite. In …

Infectious disease and group size: more than just a numbers game

CL Nunn, F Jordán, CM McCabe… - … of the Royal …, 2015 - royalsocietypublishing.org
Increased risk of infectious disease is assumed to be a major cost of group living, yet
empirical evidence for this effect is mixed. We studied whether larger social groups are more …