(Q37577586)

21 August 2017

Individual-based modelling: an essential tool for microbiology (English)

1 reference

21 August 2017

Clara Prats

2

0 references

author name string

Jordi Ferrer

series ordinal

1

1 reference

PMCID

2577750

21 August 2017

Daniel López

series ordinal

3

1 reference

21 August 2017

1 April 2008

1 reference

Journal of Biological Physics

21 August 2017

1 reference

21 August 2017

34

1 reference

21 August 2017

1-2

1 reference

21 August 2017

19-37

1 reference

https://scigraph.springernature.com/pub.10.1007/s10867-008-9082-3

21 August 2017

0 references

cites work

Molecular simulations of protein dynamics: new windows on mechanisms in biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Visualization, modelling and prediction in soil microbiology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Mesoscale simulation of blood flow in small vessels

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Microbial metabolomics: past, present and future methodologies

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Simulation as experiment: a philosophical reassessment for biological modeling.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Molecular dynamics: survey of methods for simulating the activity of proteins

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Individual-based modelling of bacterial cultures to study the microscopic causes of the lag phase

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Pattern-oriented modeling of agent-based complex systems: lessons from ecology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Cell division theory and individual-based modeling of microbial lag: part I. The theory of cell division.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Toward large-scale modeling of the microbial cell for computer simulation.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Predictive modelling of the microbial lag phase: a review

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

An ecological perspective on bacterial biodiversity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

The microbiology of biological phosphorus removal in activated sludge systems

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

An evolutionary scenario for the transition to undifferentiated multicellularity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Antibiotic production by bacterial biocontrol agents.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Agent-based modeling: a revolution?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Predictive microbiology: towards the interface and beyond

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Gene ontology: tool for the unification of biology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

THINKING ABOUT BACTERIAL POPULATIONS AS MULTICELLULAR ORGANISMS

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Prokaryotes: the unseen majority

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

The stationary phase of the bacterial life cycle

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Analysis of microcalorimetric curves for bacterial identification

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Human malaria parasites in continuous culture

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Introduction. Bioinformatics: from molecules to systems.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

The era of microbiology: a golden phoenix.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Analysis of cell size and DNA content in exponentially growing and stationary-phase batch cultures of Escherichia coli

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Relationship between temperature and growth rate of bacterial cultures.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Model for bacterial culture growth rate throughout the entire biokinetic temperature range.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

E-CELL: software environment for whole-cell simulation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

A Monte Carlo simulation of the Escherichia coli cell cycle

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Complex patterns formed by motile cells of Escherichia coli.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Individual-based modelling of biofilms.

25 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10867-008-9082-3

Rule-based computing system for microbial interactions and communications: evolution in virtual bacterial populations.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Controlling chaos in ecology: from deterministic to individual-based models.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Individual-based model and simulation of Plasmodium falciparum infected erythrocyte in vitro cultures.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Three-dimensional biofilm model with individual cells and continuum EPS matrix.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

A single-cell-based model of tumor growth in vitro: monolayers and spheroids

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Cell division theory and individual-based modeling of microbial lag: part II. Modeling lag phenomena induced by temperature shifts.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Three-dimensional dual-morphotype species modeling of activated sludge flocs

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Evolvable social agents for bacterial systems modeling.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

From local interactions to population dynamics in site-based models of ecology.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Top-down or bottom-up regulation of intra-host blood-stage malaria: do malaria parasites most resemble the dynamics of prey or predator?

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

A new combined differential-discrete cellular automaton approach for biofilm modeling: application for growth in gel beads.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

From individuals to aggregations: the interplay between behavior and physics.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

BacSim, a simulator for individual-based modelling of bacterial colony growth.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Generic modelling of cooperative growth patterns in bacterial colonies.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

On the analysis of microbiological processes by Monte Carlo simulation techniques.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2577750

Synchronous division of microorganisms

1 September 2018

1 reference

12 December 2020

The Paton individual-based model legacy

1 reference

12 December 2020

Hydrodynamic description of protein folding

1 reference

12 December 2020

INDISIM, An Individual-based Discrete Simulation Model to Study Bacterial Cultures

1 reference

12 December 2020

On-line monitoring of growth of Escherichia coli in batch cultures by bioluminescence

1 reference

12 December 2020

Parallelising a model of bacterial interaction and evolution

1 reference

12 December 2020

Equations of substrate-limited growth: the case for blackman kinetics

1 reference

12 December 2020

Simulation modelling of bacterial growth in yoghurt

1 reference

12 December 2020

1 reference

12 December 2020

Control of wall band splitting in Streptococcus faecalis

1 reference

12 December 2020

Flocculation in brewing yeasts: A computer simulation study

1 reference

12 December 2020

10.1007/S10867-008-9082-3

Identifiers

DOI

1 reference

21 August 2017

1 reference

21 August 2017

1 reference

PMCID

2577750