Modeling biology spanning different scales: an open challenge

F Castiglione, F Pappalardo, C Bianca… - BioMed research …, 2014 - Wiley Online Library
It is coming nowadays more clear that in order to obtain a unified description of the different
mechanisms governing the behavior and causality relations among the various parts of a …

Global relative parameter sensitivities of the feed-forward loops in genetic networks

P Wang, J Lü, MJ Ogorzalek - Neurocomputing, 2012 - Elsevier
It is well known that the feed-forward loops (FFLs) are typical network motifs in many real
world biological networks. The structures, functions, as well as noise characteristics of FFLs …

Metabolic control analysis indicates a change of strategy in the treatment of cancer

R Moreno-Sánchez, E Saavedra… - Mitochondrion, 2010 - Elsevier
Much of the search for the “magic cancer bullet” or “block buster” has followed the
expectation of a single gene or protein as “the rate-limiting step” for tumor persistence …

Cell growth and cell cycle in Saccharomyces cerevisiae: basic regulatory design and protein–protein interaction network

L Alberghina, G Mavelli, G Drovandi, P Palumbo… - Biotechnology …, 2012 - Elsevier
In this review we summarize the major connections between cell growth and cell cycle in the
model eukaryote Saccharomyces cerevisiae. In S. cerevisiae regulation of cell cycle …

One or two? A process view of pregnancy

AS Meincke - Philosophical Studies, 2022 - Springer
How many individuals are present where we see a pregnant individual? Within a substance
ontological framework, there are exactly two possible answers to this question. The standard …

Systems biology towards life in silico: mathematics of the control of living cells

HV Westerhoff, A Kolodkin, R Conradie… - Journal of mathematical …, 2009 - Springer
Abstract Systems Biology is the science that aims to understand how biological function
absent from macromolecules in isolation, arises when they are components of their system …

Computational strategies for a system-level understanding of metabolism

P Cazzaniga, C Damiani, D Besozzi, R Colombo… - Metabolites, 2014 - mdpi.com
Cell metabolism is the biochemical machinery that provides energy and building blocks to
sustain life. Understanding its fine regulation is of pivotal relevance in several fields, from …

Mathematical modeling of cancer metabolism

MÁ Medina - Critical reviews in oncology/hematology, 2018 - Elsevier
Systemic approaches are needed and useful for the study of the very complex issue of
cancer. Modeling has a central position in these systemic approaches. Metabolic …

[HTML][HTML] LC-MS metabolomics from study design to data-analysis–using a versatile pathogen as a test case

M Berg, M Vanaerschot, A Jankevics, B Cuypers… - Computational and …, 2013 - Elsevier
Thanks to significant improvements in LC-MS technology, metabolomics is increasingly
used as a tool to discriminate the responses of organisms to various stimuli or drugs. In this …

A framework for evolutionary systems biology

L Loewe - BMC systems biology, 2009 - Springer
Background Many difficult problems in evolutionary genomics are related to mutations that
have weak effects on fitness, as the consequences of mutations with large effects are often …