[HTML][HTML] Computational modeling, formal analysis, and tools for systems biology

E Bartocci, P Lió - PLoS computational biology, 2016 - journals.plos.org
As the amount of biological data in the public domain grows, so does the range of modeling
and analysis techniques employed in systems biology. In recent years, a number of …

Dissipative structures in biological systems: bistability, oscillations, spatial patterns and waves

A Goldbeter - … Transactions of the Royal Society A …, 2018 - royalsocietypublishing.org
The goal of this review article is to assess how relevant is the concept of dissipative structure
for understanding the dynamical bases of non-equilibrium self-organization in biological …

[图书][B] The mathematics and mechanics of biological growth

A Goriely - 2017 - books.google.com
This monograph presents a general mathematical theory for biological growth. It provides
both a conceptual and a technical foundation for the understanding and analysis of …

Multi-scale modeling of tissues using CompuCell3D

MH Swat, GL Thomas, JM Belmonte, A Shirinifard… - Methods in cell …, 2012 - Elsevier
The study of how cells interact to produce tissue development, homeostasis, or diseases
was, until recently, almost purely experimental. Now, multi-cell computer simulation …

[HTML][HTML] Comparing individual-based approaches to modelling the self-organization of multicellular tissues

JM Osborne, AG Fletcher, JM Pitt-Francis… - PLoS computational …, 2017 - journals.plos.org
The coordinated behaviour of populations of cells plays a central role in tissue growth and
renewal. Cells react to their microenvironment by modulating processes such as movement …

Plant synthetic biology

W Liu, CN Stewart - Trends in Plant Science, 2015 - cell.com
Plant synthetic biology is an emerging field that combines engineering principles with plant
biology toward the design and production of new devices. This emerging field should play …

[HTML][HTML] Cellular potts modeling of tumor growth, tumor invasion, and tumor evolution

A Szabó, RMH Merks - Frontiers in oncology, 2013 - frontiersin.org
Despite a growing wealth of available molecular data, the growth of tumors, invasion of
tumors into healthy tissue, and response of tumors to therapies are still poorly understood …

[HTML][HTML] Agent-based modeling of morphogenetic systems: Advantages and challenges

CM Glen, ML Kemp, EO Voit - PLoS computational biology, 2019 - journals.plos.org
The complexity of morphogenesis poses a fundamental challenge to understanding the
mechanisms governing the formation of biological patterns and structures. Over the past …

Consensus report on the future of animal-free systemic toxicity testing

M Leist, N Hasiwa, C Rovida, M Daneshian… - 2014 - kops.uni-konstanz.de
Since March 2013, animal use for cosmetics testing for the European market has been
banned. This requires a renewed view on risk assessment in this field. However, in other …

libRoadRunner: a high performance SBML simulation and analysis library

ET Somogyi, JM Bouteiller, JA Glazier, M König… - …, 2015 - academic.oup.com
Motivation: This article presents libRoadRunner, an extensible, high-performance, cross-
platform, open-source software library for the simulation and analysis of models expressed …