| | Education A Primer on Python for Life Science Researchers Sebastian Bassi PMCID: PMC2098836 Editorial Ten Simple Rules for Graduate Students Jenny Gu and Philip E Bourne PMCID: PMC2098857 Perspectives Computational Biology in Cuba: An Opportunity to Promote Science in a Developing Country Tirso Pons, Luis A Montero, and Juan P Febles PMCID: PMC2098855 Research Articles Phenotypic Mutation Rates and the Abundance of Abnormal Proteins in Yeast Martin Willensdorfer, Reinhard Bürger, and Martin A Nowak PMCID: PMC2082502 From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses Sven Zenker, Jonathan Rubin, and Gilles Clermont PMCID: PMC2065888 Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes Kevin P Keegan, Suraj Pradhan, Ji-Ping Wang, and Ravi Allada PMCID: PMC2098839 Are There Rearrangement Hotspots in the Human Genome? Max A Alekseyev and Pavel A Pevzner PMCID: PMC2065889 Self-Assembly and DNA Binding of the Blocking Factor in X Chromosome Inactivation Mario Nicodemi and Antonella Prisco PMCID: PMC2065890 Detecting Coevolution in and among Protein Domains Chen-Hsiang Yeang and David Haussler PMCID: PMC2098842 Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites Kaoru Sugimura, Kohei Shimono, Tadashi Uemura, and Atsushi Mochizuki PMCID: PMC2077899 Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps Hailiang Huang, Bruno M Jedynak, and Joel S Bader PMCID: PMC2082503 A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast Leelavati Narlikar, Raluca Gordân, and Alexander J Hartemink PMCID: PMC2065891 MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules Saurabh Sinha and Xin He PMCID: PMC2065892 In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators Lei Xie, Jian Wang, and Philip E Bourne PMCID: PMC2098847 Stochastic Noise and Synchronisation during Dictyostelium Aggregation Make cAMP Oscillations Robust Jongrae Kim, Pat Heslop-Harrison, Ian Postlethwaite, and Declan G Bates PMCID: PMC2065893 From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism Toni Gabaldón and Martijn A Huynen PMCID: PMC2062474 Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics Peter M Kasson and Vijay S Pande PMCID: PMC2077900 STDP in a Bistable Synapse Model Based on CaMKII and Associated Signaling Pathways Michael Graupner and Nicolas Brunel PMCID: PMC2098851 Computational Analysis of Mouse piRNA Sequence and Biogenesis Doron Betel, Robert Sheridan, Debora S Marks, and Chris Sander PMCID: PMC2065894 Genetic Progression and the Waiting Time to Cancer Niko Beerenwinkel, Tibor Antal, David Dingli, Arne Traulsen, Kenneth W Kinzler, Victor E Velculescu, Bert Vogelstein, and Martin A Nowak PMCID: PMC2065895 Molecular Basis for Evolving Modularity in the Yeast Protein Interaction Network Ariel Fernández PMCID: PMC2065896 A Dynamical Systems Hypothesis of Schizophrenia Marco Loh, Edmund T Rolls, and Gustavo Deco PMCID: PMC2065887 Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael Stumpf, Sylvia Richardson, and Carsten Wiuf PMCID: PMC2098858 An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope Art F. Y Poon, Fraser I Lewis, Sergei L. Kosakovsky Pond, and Simon D. W Frost PMCID: PMC2082504 CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures Oliver C Redfern, Andrew Harrison, Tim Dallman, Frances M. G Pearl, and Christine A Orengo PMCID: PMC2098860 Small Regulatory RNAs May Sharpen Spatial Expression Patterns Erel Levine, Peter McHale, and Herbert Levine PMCID: PMC2098861 A Universal Mechanism Ties Genotype to Phenotype in Trinucleotide Diseases Shai Kaplan, Shalev Itzkovitz, and Ehud Shapiro PMCID: PMC2082501 Gamma Oscillations of Spiking Neural Populations Enhance Signal Discrimination Naoki Masuda and Brent Doiron PMCID: PMC2098863 Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes Juan A. G Ranea, Corin Yeats, Alastair Grant, and Christine A Orengo PMCID: PMC2098864 Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants Morten Lindow, Anders Jacobsen, Sanne Nygaard, Yuan Mang, and Anders Krogh PMCID: PMC2098865 Predicting Gene Expression from Sequence: A Reexamination Yuan Yuan, Lei Guo, Lei Shen, and Jun S Liu PMCID: PMC2098866 Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection Xiaohong Li, Steven G Self, Patricia C Galipeau, Thomas G Paulson, and Brian J Reid PMCID: PMC2098867 Retinal Wave Behavior through Activity- Dependent Refractory Periods Keith B Godfrey and Nicholas V Swindale PMCID: PMC2098868 |
