An important goal of computational approaches in aging is to develop integrated systems models, predicting progression of aging phenotypes grounded on molecular mechanisms. The authors assemble a rule-based, fuzzy-logic cell systems model that considers the interplay of damage, metabolism, and stress signaling by positive and negative feedback-loop motifs. This artistic montage, which shows part of the network model on the left and a simulation outcome on the right, reflects the ability to investigate, rapidly and repeatedly, complex and interlocked molecular mechanisms progressing over an entire lifespan (see Kriete et al., doi:10.1371/journal.pcbi.1000820).
Image Credit: Andres Kriete
Message from ISCB
2010 ISCB Overton Prize Awarded to Steven E. Brenner
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000831
Education
Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000807
Perspective
The Roots of Bioinformatics
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000809
Research Articles
Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000822
Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000823
Computational Prediction and Experimental Assessment of Secreted/Surface Proteins from Mycobacterium tuberculosis H37Rv
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000824
Slope-Based Stochastic Resonance: How Noise Enables Phasic Neurons to Encode Slow Signals
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000825
Mammalian Sleep Dynamics: How Diverse Features Arise from a Common Physiological Framework
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000826
Multiscale Coarse-Graining of the Protein Energy Landscape
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000827
Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000828
Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000829
The 20S Proteasome Splicing Activity Discovered by SpliceMet
PLOS Computational Biology: published June 24, 2010 | https://doi.org/10.1371/journal.pcbi.1000830
Nonlinearity of Mechanochemical Motions in Motor Proteins
PLOS Computational Biology: published June 17, 2010 | https://doi.org/10.1371/journal.pcbi.1000814
NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail
PLOS Computational Biology: published June 17, 2010 | https://doi.org/10.1371/journal.pcbi.1000815
Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology
PLOS Computational Biology: published June 17, 2010 | https://doi.org/10.1371/journal.pcbi.1000816
Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks
PLOS Computational Biology: published June 17, 2010 | https://doi.org/10.1371/journal.pcbi.1000817
Fast- or Slow-inactivated State Preference of Na+ Channel Inhibitors: A Simulation and Experimental Study
PLOS Computational Biology: published June 17, 2010 | https://doi.org/10.1371/journal.pcbi.1000818
A Cell-Based Model for Quorum Sensing in Heterogeneous Bacterial Colonies
PLOS Computational Biology: published June 17, 2010 | https://doi.org/10.1371/journal.pcbi.1000819
Rule-Based Cell Systems Model of Aging using Feedback Loop Motifs Mediated by Stress Responses
PLOS Computational Biology: published June 17, 2010 | https://doi.org/10.1371/journal.pcbi.1000820
Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way
PLOS Computational Biology: published June 17, 2010 | https://doi.org/10.1371/journal.pcbi.1000821
Enhancement of Transport Selectivity through Nano-Channels by Non-Specific Competition
PLOS Computational Biology: published June 10, 2010 | https://doi.org/10.1371/journal.pcbi.1000804
Rapid Transition towards the Division of Labor via Evolution of Developmental Plasticity
PLOS Computational Biology: published June 10, 2010 | https://doi.org/10.1371/journal.pcbi.1000805
Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations
PLOS Computational Biology: published June 10, 2010 | https://doi.org/10.1371/journal.pcbi.1000806
The Organization of Local and Distant Functional Connectivity in the Human Brain
PLOS Computational Biology: published June 10, 2010 | https://doi.org/10.1371/journal.pcbi.1000808
Polarizable Water Model for the Coarse-Grained MARTINI Force Field
PLOS Computational Biology: published June 10, 2010 | https://doi.org/10.1371/journal.pcbi.1000810
Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations?
PLOS Computational Biology: published June 10, 2010 | https://doi.org/10.1371/journal.pcbi.1000811
The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes
PLOS Computational Biology: published June 10, 2010 | https://doi.org/10.1371/journal.pcbi.1000812
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