Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Churakov et al.
Image Credit: Churakov et al.
Message from ISCB
ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing
PLOS Computational Biology: published March 24, 2016 | https://doi.org/10.1371/journal.pcbi.1004816
Perspectives
Understanding Genotype-Phenotype Effects in Cancer via Network Approaches
PLOS Computational Biology: published March 10, 2016 | https://doi.org/10.1371/journal.pcbi.1004747
Systems Approaches to the Eukaryotic Stress Response
PLOS Computational Biology: published March 10, 2016 | https://doi.org/10.1371/journal.pcbi.1004757
Review
NMR Methods to Study Dynamic Allostery
PLOS Computational Biology: published March 10, 2016 | https://doi.org/10.1371/journal.pcbi.1004620
Research Articles
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications
PLOS Computational Biology: published March 30, 2016 | https://doi.org/10.1371/journal.pcbi.1004805
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes
PLOS Computational Biology: published March 30, 2016 | https://doi.org/10.1371/journal.pcbi.1004847
Deep Learning for Population Genetic Inference
PLOS Computational Biology: published March 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004845
Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes
PLOS Computational Biology: published March 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004834
Modeling the Excess Cell Surface Stored in a Complex Morphology of Bleb-Like Protrusions
PLOS Computational Biology: published March 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004841
Revealing the True Incidence of Pandemic A(H1N1)pdm09 Influenza in Finland during the First Two Seasons — An Analysis Based on a Dynamic Transmission Model
PLOS Computational Biology: published March 24, 2016 | https://doi.org/10.1371/journal.pcbi.1004803
Impaired Air Conditioning within the Nasal Cavity in Flat-Faced Homo
PLOS Computational Biology: published March 24, 2016 | https://doi.org/10.1371/journal.pcbi.1004807
Cellular Growth Arrest and Persistence from Enzyme Saturation
PLOS Computational Biology: published March 24, 2016 | https://doi.org/10.1371/journal.pcbi.1004825
Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases
PLOS Computational Biology: published March 24, 2016 | https://doi.org/10.1371/journal.pcbi.1004826
Evolutionary Conserved Positions Define Protein Conformational Diversity
PLOS Computational Biology: published March 23, 2016 | https://doi.org/10.1371/journal.pcbi.1004775
Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis
PLOS Computational Biology: published March 22, 2016 | https://doi.org/10.1371/journal.pcbi.1004754
Inhibition as a Binary Switch for Excitatory Plasticity in Pyramidal Neurons
PLOS Computational Biology: published March 22, 2016 | https://doi.org/10.1371/journal.pcbi.1004768
Noise Expands the Response Range of the Bacillus subtilis Competence Circuit
PLOS Computational Biology: published March 22, 2016 | https://doi.org/10.1371/journal.pcbi.1004793
Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses
PLOS Computational Biology: published March 21, 2016 | https://doi.org/10.1371/journal.pcbi.1004801
Quantitative Analysis of Axonal Branch Dynamics in the Developing Nervous System
PLOS Computational Biology: published March 21, 2016 | https://doi.org/10.1371/journal.pcbi.1004813
A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry
PLOS Computational Biology: published March 21, 2016 | https://doi.org/10.1371/journal.pcbi.1004823
Feedback, Lineages and Self-Organizing Morphogenesis
PLOS Computational Biology: published March 18, 2016 | https://doi.org/10.1371/journal.pcbi.1004814
Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search
PLOS Computational Biology: published March 18, 2016 | https://doi.org/10.1371/journal.pcbi.1004818
A Sensorimotor Model for Computing Intended Reach Trajectories
PLOS Computational Biology: published March 17, 2016 | https://doi.org/10.1371/journal.pcbi.1004734
Systems Pharmacology and Rational Polypharmacy: Nitric Oxide−Cyclic GMP Signaling Pathway as an Illustrative Example and Derivation of the General Case
PLOS Computational Biology: published March 17, 2016 | https://doi.org/10.1371/journal.pcbi.1004822
Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome
PLOS Computational Biology: published March 16, 2016 | https://doi.org/10.1371/journal.pcbi.1004762
The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB
PLOS Computational Biology: published March 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004749
Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces
PLOS Computational Biology: published March 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004752
Causal Inference for Spatial Constancy across Saccades
PLOS Computational Biology: published March 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004766
Distinguishing Antimicrobial Models with Different Resistance Mechanisms via Population Pharmacodynamic Modeling
PLOS Computational Biology: published March 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004782
Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection
PLOS Computational Biology: published March 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004784
Motor Demands Constrain Cognitive Rule Structures
PLOS Computational Biology: published March 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004785
H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation
PLOS Computational Biology: published March 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004788
Dynamic Modelling Reveals ‘Hotspots’ on the Pathway to Enzyme-Substrate Complex Formation
PLOS Computational Biology: published March 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004811
Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data
PLOS Computational Biology: published March 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004812
Integrating Transgenic Vector Manipulation with Clinical Interventions to Manage Vector-Borne Diseases
PLOS Computational Biology: published March 10, 2016 | https://doi.org/10.1371/journal.pcbi.1004695
SMOG 2: A Versatile Software Package for Generating Structure-Based Models
PLOS Computational Biology: published March 10, 2016 | https://doi.org/10.1371/journal.pcbi.1004794
Stability of Ensemble Models Predicts Productivity of Enzymatic Systems
PLOS Computational Biology: published March 10, 2016 | https://doi.org/10.1371/journal.pcbi.1004800
Pathway-Based Genomics Prediction using Generalized Elastic Net
PLOS Computational Biology: published March 9, 2016 | https://doi.org/10.1371/journal.pcbi.1004790
Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies
PLOS Computational Biology: published March 9, 2016 | https://doi.org/10.1371/journal.pcbi.1004802
BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data
PLOS Computational Biology: published March 8, 2016 | https://doi.org/10.1371/journal.pcbi.1004796
Annealed Importance Sampling for Neural Mass Models
PLOS Computational Biology: published March 4, 2016 | https://doi.org/10.1371/journal.pcbi.1004797
Reconstruction of Tissue-Specific Metabolic Networks Using CORDA
PLOS Computational Biology: published March 4, 2016 | https://doi.org/10.1371/journal.pcbi.1004808
Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication
PLOS Computational Biology: published March 3, 2016 | https://doi.org/10.1371/journal.pcbi.1004678
Stability and Competition in Multi-spike Models of Spike-Timing Dependent Plasticity
PLOS Computational Biology: published March 3, 2016 | https://doi.org/10.1371/journal.pcbi.1004750
Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability
PLOS Computational Biology: published March 3, 2016 | https://doi.org/10.1371/journal.pcbi.1004773
Power-Law Dynamics of Membrane Conductances Increase Spiking Diversity in a Hodgkin-Huxley Model
PLOS Computational Biology: published March 3, 2016 | https://doi.org/10.1371/journal.pcbi.1004776
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
PLOS Computational Biology: published March 3, 2016 | https://doi.org/10.1371/journal.pcbi.1004780
Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference
PLOS Computational Biology: published March 3, 2016 | https://doi.org/10.1371/journal.pcbi.1004789
Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb
PLOS Computational Biology: published March 3, 2016 | https://doi.org/10.1371/journal.pcbi.1004798