Cover
Five Seals.
Repeat-proteins fold cooperatively into elongated arrays of similar structural elements. The image represents the structure of the I-kappa-B-alpha protein as modeled from x-ray crystallography (bottom) and as a biological object (top). Physical folding energetics is fundamentally linked to protein evolution. Espada et al.
Image Credit: May-K (@proteinart)
Messages from ISCB
2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner
PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005561
2017 Outstanding Contributions to ISCB Award: Fran Lewitter
PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005560
2017 ISCB Overton Prize awarded to Christoph Bock
PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005559
2017 ISCB Innovator Award: Aviv Regev
PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005558
Education
Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network
PLOS Computational Biology: published June 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005419
Perspective
Good enough practices in scientific computing
PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005510
Reviews
A comprehensive overview and evaluation of circular RNA detection tools
PLOS Computational Biology: published June 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005420
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A review of active learning approaches to experimental design for uncovering biological networks
PLOS Computational Biology: published June 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005466
Research Articles
Independent regulation of gene expression level and noise by histone modifications
PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005585
Active Vertex Model for cell-resolution description of epithelial tissue mechanics
PLOS Computational Biology: published June 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005569
Landscape and variation of novel retroduplications in 26 human populations
PLOS Computational Biology: published June 29, 2017 | https://doi.org/10.1371/journal.pcbi.1005567
Detecting similar binding pockets to enable systems polypharmacology
PLOS Computational Biology: published June 29, 2017 | https://doi.org/10.1371/journal.pcbi.1005522
Optimal structure of metaplasticity for adaptive learning
PLOS Computational Biology: published June 28, 2017 | https://doi.org/10.1371/journal.pcbi.1005630
MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory
PLOS Computational Biology: published June 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005614
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis
PLOS Computational Biology: published June 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005573
Linking structure and activity in nonlinear spiking networks
PLOS Computational Biology: published June 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005583
Low-dimensional spike rate models derived from networks of adaptive integrate-and-fire neurons: Comparison and implementation
PLOS Computational Biology: published June 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005545
Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression
PLOS Computational Biology: published June 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005487
High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE
PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005628
A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images
PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005612
LASSIM—A network inference toolbox for genome-wide mechanistic modeling
PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005608
Transmembrane helical interactions in the CFTR channel pore
PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005594
Olfactory learning without the mushroom bodies: Spiking neural network models of the honeybee lateral antennal lobe tract reveal its capacities in odour memory tasks of varied complexities
PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005551
Brain network eigenmodes provide a robust and compact representation of the structural connectome in health and disease
PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005550
Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome
PLOS Computational Biology: published June 22, 2017 | https://doi.org/10.1371/journal.pcbi.1005361
An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules
PLOS Computational Biology: published June 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005597
Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle
PLOS Computational Biology: published June 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005591
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A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data
PLOS Computational Biology: published June 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005601
In silico assessment of genetic variation in KCNA5 reveals multiple mechanisms of human atrial arrhythmogenesis
PLOS Computational Biology: published June 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005587
Sensory noise predicts divisive reshaping of receptive fields
PLOS Computational Biology: published June 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005582
Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE
PLOS Computational Biology: published June 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005603
GINOM: A statistical framework for assessing interval overlap of multiple genomic features
PLOS Computational Biology: published June 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005586
Inferring repeat-protein energetics from evolutionary information
PLOS Computational Biology: published June 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005584
Robust transmission of rate coding in the inhibitory Purkinje cell to cerebellar nuclei pathway in awake mice
PLOS Computational Biology: published June 15, 2017 | https://doi.org/10.1371/journal.pcbi.1005578
Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain
PLOS Computational Biology: published June 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005602
Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria
PLOS Computational Biology: published June 13, 2017 | https://doi.org/10.1371/journal.pcbi.1005593
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Rosetta:MSF: a modular framework for multi-state computational protein design
PLOS Computational Biology: published June 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005600
Locking of correlated neural activity to ongoing oscillations
PLOS Computational Biology: published June 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005534
Ribosome reinitiation can explain length-dependent translation of messenger RNA
PLOS Computational Biology: published June 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005592
Mitochondrial respiration and ROS emission during β-oxidation in the heart: An experimental-computational study
PLOS Computational Biology: published June 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005588
Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data
PLOS Computational Biology: published June 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005577
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
PLOS Computational Biology: published June 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005595
Leveraging functional annotations in genetic risk prediction for human complex diseases
PLOS Computational Biology: published June 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005589
Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders
PLOS Computational Biology: published June 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005520
Temperature–amplitude coupling for stable biological rhythms at different temperatures
PLOS Computational Biology: published June 8, 2017 | https://doi.org/10.1371/journal.pcbi.1005501
Mechanisms underlying a thalamocortical transformation during active tactile sensation
PLOS Computational Biology: published June 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005576
An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
PLOS Computational Biology: published June 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005526
Fast and general tests of genetic interaction for genome-wide association studies
PLOS Computational Biology: published June 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005556
Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes
PLOS Computational Biology: published June 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005590
Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation
PLOS Computational Biology: published June 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005571
Mechanisms of generation of membrane potential resonance in a neuron with multiple resonant ionic currents
PLOS Computational Biology: published June 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005565
A motor unit-based model of muscle fatigue
PLOS Computational Biology: published June 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005581
MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures
PLOS Computational Biology: published June 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005575
Network-assisted target identification for haploinsufficiency and homozygous profiling screens
PLOS Computational Biology: published June 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005553
A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements
PLOS Computational Biology: published June 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005542
Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions
PLOS Computational Biology: published June 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005521
Breakdown of local information processing may underlie isoflurane anesthesia effects
PLOS Computational Biology: published June 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005511