| | Education Recent Evolutions of Multiple Sequence Alignment Algorithms Cédric Notredame PMCID: PMC1963500 A Primer on Learning in Bayesian Networks for Computational Biology Chris J Needham, James R Bradford, Andrew J Bulpitt, and David R Westhead PMCID: PMC1963499 Research Articles Distributed Representations Accelerate Evolution of Adaptive Behaviours James V Stone PMCID: PMC1937014 Automated Discovery of Functional Generality of Human Gene Expression Programs Georg K Gerber, Robin D Dowell, Tommi S Jaakkola, and David K Gifford PMCID: PMC1941755 SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework Irmtraud M Meyer and István Miklós PMCID: PMC1941756 Helicobacter pylori Evolution: Lineage- Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes Masako Ogura, J. Christian Perez, Peer R. E Mittl, Hae-Kyung Lee, Geidrius Dailide, Shumin Tan, Yoshiyuki Ito, Ousman Secka, Daiva Dailidiene, Kalyani Putty, Douglas E Berg, and Awdhesh Kalia PMCID: PMC1941758 An Information-Theoretic Characterization of the Optimal Gradient Sensing Response of Cells Burton W Andrews and Pablo A Iglesias PMCID: PMC1937015 PERIOD–TIMELESS Interval Timer May Require an Additional Feedback Loop Robert S Kuczenski, Kevin C Hong, Jordi García-Ojalvo, and Kelvin H Lee PMCID: PMC1937016 Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains Sylvain V Costes, Artem Ponomarev, James L Chen, David Nguyen, Francis A Cucinotta, and Mary Helen Barcellos-Hoff PMCID: PMC1937017 Mechanisms of Firing Patterns in Fast-Spiking Cortical Interneurons David Golomb, Karnit Donner, Liron Shacham, Dan Shlosberg, Yael Amitai, and David Hansel PMCID: PMC1941757 On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A Sergey Kryazhimskiy, Ulf Dieckmann, Simon A Levin, and Jonathan Dushoff PMCID: PMC1949840 Automated Protein Subfamily Identification and Classification Duncan P Brown, Nandini Krishnamurthy, and Kimmen Sjölander PMCID: PMC1950344 Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis Andrew E Teschendorff, Michel Journée, Pierre A Absil, Rodolphe Sepulchre, and Carlos Caldas PMCID: PMC1950343 Inferring Function Using Patterns of Native Disorder in Proteins Anna Lobley, Mark B Swindells, Christine A Orengo, and David T Jones PMCID: PMC1950950 A Logical Model Provides Insights into T Cell Receptor Signaling Julio Saez-Rodriguez, Luca Simeoni, Jonathan A Lindquist, Rebecca Hemenway, Ursula Bommhardt, Boerge Arndt, Utz-Uwe Haus, Robert Weismantel, Ernst D Gilles, Steffen Klamt, and Burkhart Schraven PMCID: PMC1950951 Design of Multi-Specificity in Protein Interfaces Elisabeth L Humphris and Tanja Kortemme PMCID: PMC1950952 Perceptual Learning via Modification of Cortical Top-Down Signals Roland Schäfer, Eleni Vasilaki, and Walter Senn PMCID: PMC1950342 Slowness and Sparseness Lead to Place, Head-Direction, and Spatial-View Cells Mathias Franzius, Henning Sprekeler, and Laurenz Wiskott PMCID: PMC1963505 Functional Representation of Enzymes by Specific Peptides Vered Kunik, Yasmine Meroz, Zach Solan, Ben Sandbank, Uri Weingart, Eytan Ruppin, and David Horn PMCID: PMC1950953 A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm Meron Gurkiewicz and Alon Korngreen PMCID: PMC1963494 Buffering Mechanisms in Aging: A Systems Approach Toward Uncovering the Genetic Component of Aging Aviv Bergman, Gil Atzmon, Kenny Ye, Thomas MacCarthy, and Nir Barzilai PMCID: PMC1963511 Pathway Switching Explains the Sharp Response Characteristic of Hypoxia Response Network Yihai Yu, Guanyu Wang, Rahul Simha, Weiqun Peng, Frank Turano, and Chen Zeng PMCID: PMC1963493 |
