A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

I Dukovski, D Bajić, JM Chacón, M Quintin, JCC Vila… - Nature protocols, 2021 - nature.com
Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …

Tumor evolution: Linear, branching, neutral or punctuated?

A Davis, R Gao, N Navin - Biochimica et Biophysica Acta (BBA)-Reviews …, 2017 - Elsevier
Intratumor heterogeneity has been widely reported in human cancers, but our knowledge of
how this genetic diversity emerges over time remains limited. A central challenge in studying …

A Big Bang model of human colorectal tumor growth

A Sottoriva, H Kang, Z Ma, TA Graham, MP Salomon… - Nature …, 2015 - nature.com
What happens in early, still undetectable human malignancies is unknown because direct
observations are impractical. Here we present and validate a'Big Bang'model, whereby …

Morphological instability and roughening of growing 3D bacterial colonies

A Martínez-Calvo, T Bhattacharjee, RK Bay… - Proceedings of the …, 2022 - pnas.org
How do growing bacterial colonies get their shapes? While colony morphogenesis is well
studied in two dimensions, many bacteria grow as large colonies in three-dimensional (3D) …

[HTML][HTML] Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells

HJ Snippert, LG Van Der Flier, T Sato, JH Van Es… - Cell, 2010 - cell.com
Intestinal stem cells, characterized by high Lgr5 expression, reside between Paneth cells at
the small intestinal crypt base and divide every day. We have carried out fate map** of …

Solutions to the public goods dilemma in bacterial biofilms

K Drescher, CD Nadell, HA Stone, NS Wingreen… - Current Biology, 2014 - cell.com
Bacteria frequently live in densely populated surface-bound communities, termed biofilms [1–
4]. Biofilm-dwelling cells rely on secretion of extracellular substances to construct their …

Impact of deleterious passenger mutations on cancer progression

CD McFarland, KS Korolev, GV Kryukov… - Proceedings of the …, 2013 - pnas.org
Cancer progression is driven by the accumulation of a small number of genetic alterations.
However, these few driver alterations reside in a cancer genome alongside tens of …

Universal patterns of stem cell fate in cycling adult tissues

AM Klein, BD Simons - Development, 2011 - journals.biologists.com
In cycling tissues that exhibit high turnover, tissue maintenance and repair are coordinated
by stem cells. But, how frequently stem cells are replaced following differentiation, aging or …

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 …

Fluid mixing from viscous fingering

B Jha, L Cueto-Felgueroso, R Juanes - Physical review letters, 2011 - APS
Mixing efficiency at low Reynolds numbers can be enhanced by exploiting hydrodynamic
instabilities that induce heterogeneity and disorder in the flow. The unstable displacement of …