Much like the "Ford-T assembly line," Escherichia coli can be thought of as a factory producing RNA polymerase, ribosomes, and other molecular machinery, all inside the crowded cytoplasm of the cell. In this simplified picture, genes and proteins of similar function are lumped together, resulting in an effective, coarse-grained representation of the cell (see Tadmor, Tlusty, doi:10.1371/journal.pcbi.1000038).
Image Credit: Genia Brodsky, Weizmann Institute of Science
Editorial
Ten Simple Rules for Aspiring Scientists in a Low-Income Country
PLOS Computational Biology: published May 30, 2008 | https://doi.org/10.1371/journal.pcbi.1000024
Education
An Introduction to Bioinformatics for Glycomics Research
PLOS Computational Biology: published May 30, 2008 | https://doi.org/10.1371/journal.pcbi.1000075
Review
Why Are Computational Neuroscience and Systems Biology So Separate?
PLOS Computational Biology: published May 30, 2008 | https://doi.org/10.1371/journal.pcbi.1000078
Research Articles
A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number
PLOS Computational Biology: published May 2, 2008 | https://doi.org/10.1371/journal.pcbi.1000038
Estimating Cell Depth from Somatic Mutations
PLOS Computational Biology: published May 9, 2008 | https://doi.org/10.1371/journal.pcbi.1000058
Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins
PLOS Computational Biology: published May 16, 2008 | https://doi.org/10.1371/journal.pcbi.1000063
Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation
PLOS Computational Biology: published May 9, 2008 | https://doi.org/10.1371/journal.pcbi.1000064
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation
PLOS Computational Biology: published May 30, 2008 | https://doi.org/10.1371/journal.pcbi.1000069
The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures
PLOS Computational Biology: published May 16, 2008 | https://doi.org/10.1371/journal.pcbi.1000070
Discovering Sequence Motifs with Arbitrary Insertions and Deletions
PLOS Computational Biology: published May 9, 2008 | https://doi.org/10.1371/journal.pcbi.1000071
Transient Cognitive Dynamics, Metastability, and Decision Making
PLOS Computational Biology: published May 2, 2008 | https://doi.org/10.1371/journal.pcbi.1000072
Short-Term Memory Trace in Rapidly Adapting Synapses of Inferior Temporal Cortex
PLOS Computational Biology: published May 16, 2008 | https://doi.org/10.1371/journal.pcbi.1000073
Viral Population Estimation Using Pyrosequencing
PLOS Computational Biology: published May 9, 2008 | https://doi.org/10.1371/journal.pcbi.1000074
An Allosteric Mechanism for Switching between Parallel Tracks in Mammalian Sulfur Metabolism
PLOS Computational Biology: published May 2, 2008 | https://doi.org/10.1371/journal.pcbi.1000076
Measuring Global Credibility with Application to Local Sequence Alignment
PLOS Computational Biology: published May 16, 2008 | https://doi.org/10.1371/journal.pcbi.1000077
Computational Lipidology: Predicting Lipoprotein Density Profiles in Human Blood Plasma
PLOS Computational Biology: published May 23, 2008 | https://doi.org/10.1371/journal.pcbi.1000079
Context-Specific Metabolic Networks Are Consistent with Experiments
PLOS Computational Biology: published May 16, 2008 | https://doi.org/10.1371/journal.pcbi.1000082
Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments
PLOS Computational Biology: published May 23, 2008 | https://doi.org/10.1371/journal.pcbi.1000083
Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics
PLOS Computational Biology: published May 23, 2008 | https://doi.org/10.1371/journal.pcbi.1000084
Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing
PLOS Computational Biology: published May 23, 2008 | https://doi.org/10.1371/journal.pcbi.1000085
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Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks
PLOS Computational Biology: published May 23, 2008 | https://doi.org/10.1371/journal.pcbi.1000086
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Uncovering Interactions in the Frequency Domain
PLOS Computational Biology: published May 30, 2008 | https://doi.org/10.1371/journal.pcbi.1000087
Astrocytes Optimize the Synaptic Transmission of Information
PLOS Computational Biology: published May 30, 2008 | https://doi.org/10.1371/journal.pcbi.1000088