A growing population of digital organisms, started from one individual, colonizes an initially empty space (black). As it does so, the population evolves by random mutation and selection, based on each organism's resulting phenotype. Every colored square represents one digital organism, with different colors reflecting different fitness levels. The speed, control, and ease of data collection in the Avida digital evolution platform permits experiments that would be difficult or even impossible with natural organisms, such as the present study (Clune et al., doi:10.1371/journal.pcbi.1000187) on the evolution of mutation rates.
Image Credit: Kaben Nanlohy, Michigan State University
Education Articles
Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000151
Advanced Genomic Data Mining
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000121
Review
Structural Biology by NMR: Structure, Dynamics, and Interactions
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000168
Research Articles
Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex
PLOS Computational Biology: published September 5, 2008 | https://doi.org/10.1371/journal.pcbi.1000169
Insights into Protein–DNA Interactions through Structure Network Analysis
PLOS Computational Biology: published September 5, 2008 | https://doi.org/10.1371/journal.pcbi.1000170
Sizing Up Allometric Scaling Theory
PLOS Computational Biology: published September 12, 2008 | https://doi.org/10.1371/journal.pcbi.1000171
Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis
PLOS Computational Biology: published September 12, 2008 | https://doi.org/10.1371/journal.pcbi.1000174
Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae
PLOS Computational Biology: published September 12, 2008 | https://doi.org/10.1371/journal.pcbi.1000175
Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks
PLOS Computational Biology: published September 12, 2008 | https://doi.org/10.1371/journal.pcbi.1000177
Identifying the Important HIV-1 Recombination Breakpoints
PLOS Computational Biology: published September 12, 2008 | https://doi.org/10.1371/journal.pcbi.1000178
Probabilistic Phylogenetic Inference with Insertions and Deletions
PLOS Computational Biology: published September 19, 2008 | https://doi.org/10.1371/journal.pcbi.1000172
Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth
PLOS Computational Biology: published September 19, 2008 | https://doi.org/10.1371/journal.pcbi.1000163
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Modeling Recursive RNA Interference
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A Genomewide Functional Network for the Laboratory Mouse
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Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000181
Adaptation and Selective Information Transmission in the Cricket Auditory Neuron AN2
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000182
Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000184
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A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000185
Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000186
Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000187
Cavities and Atomic Packing in Protein Structures and Interfaces
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000188
Organization of Excitable Dynamics in Hierarchical Biological Networks
PLOS Computational Biology: published September 26, 2008 | https://doi.org/10.1371/journal.pcbi.1000190