The simulation of small-scale processes allows the analysis of ecosystem responses to environmental change. Colonies of two massive (polygons) and two branching (stars) coral species compete for space with each other and algae (macroalgae as green spots; turf algae as grid). Higher level properties, such as population dynamics and community composition, emerge from local interactions of neighboring organisms, which are additionally influenced by environmental conditions. See Kubicek et al.
Image Credit: Andreas Kubicek, Leibniz Center for Tropical Marine Ecology.
Editorials
The PLOS Computational Biology Software Section
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002799
Ten Simple Rules to Protect Your Intellectual Property
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002766
Perspective
Bioinformatics for the Human Microbiome Project
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002779
Research Articles
Internal Representations of Temporal Statistics and Feedback Calibrate Motor-Sensory Interval Timing
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002771
Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002777
Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002778
Temporal Expression-based Analysis of Metabolism
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002781
Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002782
The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002784
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Universal Pacemaker of Genome Evolution
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002785
How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002786
Weakly Circadian Cells Improve Resynchrony
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002787
Reconstructing Mammalian Sleep Dynamics with Data Assimilation
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002788
Simulations of Long-Term Community Dynamics in Coral Reefs - How Perturbations Shape Trajectories
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002791
Experimental Studies and Dynamics Modeling Analysis of the Swimming and Diving of Whirligig Beetles (Coleoptera: Gyrinidae)
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002792
Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e
PLOS Computational Biology: published November 29, 2012 | https://doi.org/10.1371/journal.pcbi.1002794
Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles
PLOS Computational Biology: published November 15, 2012 | https://doi.org/10.1371/journal.pcbi.1002660
This Déjà Vu Feeling—Analysis of Multidomain Protein Evolution in Eukaryotic Genomes
PLOS Computational Biology: published November 15, 2012 | https://doi.org/10.1371/journal.pcbi.1002701
Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens
PLOS Computational Biology: published November 15, 2012 | https://doi.org/10.1371/journal.pcbi.1002763
A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data
PLOS Computational Biology: published November 15, 2012 | https://doi.org/10.1371/journal.pcbi.1002768
Elastic Energy Storage and Radial Forces in the Myofilament Lattice Depend on Sarcomere Length
PLOS Computational Biology: published November 15, 2012 | https://doi.org/10.1371/journal.pcbi.1002770
Sensorimotor Learning Biases Choice Behavior: A Learning Neural Field Model for Decision Making
PLOS Computational Biology: published November 15, 2012 | https://doi.org/10.1371/journal.pcbi.1002774
Functional Connectivity and Tuning Curves in Populations of Simultaneously Recorded Neurons
PLOS Computational Biology: published November 15, 2012 | https://doi.org/10.1371/journal.pcbi.1002775
The Dominant Folding Route Minimizes Backbone Distortion in SH3
PLOS Computational Biology: published November 15, 2012 | https://doi.org/10.1371/journal.pcbi.1002776
The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors
PLOS Computational Biology: published November 15, 2012 | https://doi.org/10.1371/journal.pcbi.1002783
Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002466
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A Graphical Modelling Approach to the Dissection of Highly Correlated Transcription Factor Binding Site Profiles
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002725
Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002751
Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002756
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Efficient “Communication through Coherence” Requires Oscillations Structured to Minimize Interference between Signals
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002760
The Role of Exposure History on HIV Acquisition: Insights from Repeated Low-dose Challenge Studies
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002767
Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002769
Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002772
Distinct Neurogenomic States in Basal Ganglia Subregions Relate Differently to Singing Behavior in Songbirds
PLOS Computational Biology: published November 8, 2012 | https://doi.org/10.1371/journal.pcbi.1002773
Disease Prevention versus Data Privacy: Using Landcover Maps to Inform Spatial Epidemic Models
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002723
Evolution of Associative Learning in Chemical Networks
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002739
Theory on the Coupled Stochastic Dynamics of Transcription and Splice-Site Recognition
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002747
A Characterization of Scale Invariant Responses in Enzymatic Networks
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002748
The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002749
Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002752
Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002753
Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002754
Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002755
A Mathematical Model of CR3/TLR2 Crosstalk in the Context of Francisella tularensis Infection
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002757
Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002758
Music in Our Ears: The Biological Bases of Musical Timbre Perception
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002759
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pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002761
Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002762
Mesoscopic Model of Actin-Based Propulsion
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002764
Structural Insights into the Inhibition of Actin-Capping Protein by Interactions with Phosphatidic Acid and Phosphatidylinositol (4,5)-Bisphosphate
PLOS Computational Biology: published November 1, 2012 | https://doi.org/10.1371/journal.pcbi.1002765