| | Education Analyzing ChIP-chip Data Using Bioconductor Joern Toedling and Wolfgang Huber PMCID: PMC2582686 Review Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities Marcel E. Dinger, Ken C. Pang, Tim R. Mercer, and John S. Mattick PMCID: PMC2518207 Research Articles Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments Merav Parter, Nadav Kashtan, and Uri Alon PMCID: PMC2563028 A Hierarchy of Time-Scales and the Brain Stefan J. Kiebel, Jean Daunizeau, and Karl J. Friston PMCID: PMC2568860 Hierarchical Models in the Brain Karl Friston PMCID: PMC2570625 A Model of Brain Circulation and Metabolism: NIRS Signal Changes
during Physiological Challenges Murad Banaji, Alfred Mallet, Clare E. Elwell, Peter Nicholls, and Chris E. Cooper PMCID: PMC2573000 Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks Sheila M. Reynolds, Lukas Käll, Michael E. Riffle, Jeff A. Bilmes, and William Stafford Noble PMCID: PMC2570248 Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes Osnat Penn, Adi Stern, Nimrod D. Rubinstein, Julien Dutheil, Eran Bacharach, Nicolas Galtier, and Tal Pupko PMCID: PMC2566816 Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals Yair Field, Noam Kaplan, Yvonne Fondufe-Mittendorf, Irene K. Moore, Eilon Sharon, Yaniv Lubling, Jonathan Widom, and Eran Segal PMCID: PMC2570626 Inferring Pathway Activity toward Precise Disease Classification Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, and Doheon Lee PMCID: PMC2563693 Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins Mark Yandell, Barry Moore, Fidel Salas, Chris Mungall, Andrew MacBride, Charles White, and Martin G. Reese PMCID: PMC2565504 A Low Dimensional Description of Globally Coupled Heterogeneous Neural Networks of Excitatory and Inhibitory Neurons Roxana A. Stefanescu and Viktor K. Jirsa PMCID: PMC2574034 Emergence of Functional Hierarchy in a Multiple Timescale Neural
Network Model: A Humanoid Robot Experiment Yuichi Yamashita and Jun Tani PMCID: PMC2570613 Polar or Apolar—The Role of Polarity for Urea-Induced Protein Denaturation Martin C. Stumpe and Helmut Grubmüller PMCID: PMC2570617 A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates Stefan Auer, Filip Meersman, Christopher M. Dobson, and Michele Vendruscolo PMCID: PMC2572140 Quantification of Local Morphodynamics and Local GTPase Activity by Edge Evolution Tracking Yuki Tsukada, Kazuhiro Aoki, Takeshi Nakamura, Yuichi Sakumura, Michiyuki Matsuda, and Shin Ishii PMCID: PMC2573959 A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, and Christina Leslie PMCID: PMC2573020 Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag Jonathan M. Carlson, Zabrina L. Brumme, Christine M. Rousseau, Chanson J. Brumme, Philippa Matthews, Carl Kadie, James I. Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J. R. Goulder, and David Heckerman PMCID: PMC2579584 Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition Andreea Munteanu and Ricard V. Solé PMCID: PMC2577890 Order-Based Representation in Random Networks of Cortical Neurons Goded Shahaf, Danny Eytan, Asaf Gal, Einat Kermany, Vladimir Lyakhov, Christoph Zrenner, and Shimon Marom PMCID: PMC2580731 Behavioral Sequence Analysis Reveals a Novel Role for
ß2* Nicotinic Receptors in Exploration Nicolas Maubourguet, Annick Lesne, Jean-Pierre Changeux, Uwe Maskos, and Philippe Faure PMCID: PMC2581917 Optimal Learning Rules for Discrete Synapses Adam B. Barrett and M. C. W. van Rossum PMCID: PMC2580035 Structural and Thermodynamic Approach to Peptide Immunogenicity Carlos J. Camacho, Yasuhiro Katsumata, and Dana P. Ascherman PMCID: PMC2577884 Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence Wan Kyu Kim and Edward M. Marcotte PMCID: PMC2583957 PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution Jonathan M. Guberman, Allison Fay, Jonathan Dworkin, Ned S. Wingreen, and Zemer Gitai PMCID: PMC2581597 A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes Cedric Chauve and Eric Tannier PMCID: PMC2580819 Multistable Decision Switches for Flexible Control of Epigenetic Differentiation Raúl Guantes and Juan F. Poyatos PMCID: PMC2580821 Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data Shubhada R. Hegde, Palanisamy Manimaran, and Shekhar C. Mande PMCID: PMC2580820 Corrections Correction: Similarity Queries for Temporal Toxicogenomic Expression Profiles Adam A. Smith, Aaron Vollrath, Christopher A. Bradfield, and Mark Craven PMCID: PMC2597899 Corrects: Adam A. Smith, et al. Similarity Queries for Temporal Toxicogenomic Expression Profiles. PLoS Comput Biol. 2008 July; 4(7): e1000116. Correction: The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function Marco Punta and Yanay Ofran PMCID: PMC2583278 Corrects: Marco Punta, et al. The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function. PLoS Comput Biol. 2008 October; 4(10): e1000160. |
