| | Education An Introduction to Bioinformatics for Glycomics Research Kiyoko F. Aoki-Kinoshita PMCID: PMC2398734 Editorial Ten Simple Rules for Aspiring Scientists in a Low-Income Country Edgardo Moreno and José-María Gutiérrez PMCID: PMC2268008 Review Why Are Computational Neuroscience and Systems Biology So Separate? Erik De Schutter PMCID: PMC2367448 Research Articles A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number Arbel D. Tadmor and Tsvi Tlusty PMCID: PMC2320978 Estimating Cell Depth from Somatic Mutations Adam Wasserstrom, Dan Frumkin, Rivka Adar, Shalev Itzkovitz, Tomer Stern, Shai Kaplan, Gabi Shefer, Irena Shur, Lior Zangi, Yitzhak Reizel, Alon Harmelin, Yuval Dor, Nava Dekel, Yair Reisner, Dafna Benayahu, Eldad Tzahor, Eran Segal, and Ehud Shapiro PMCID: PMC2275312 Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins Nan Song, Jacob M. Joseph, George B. Davis, and Dannie Durand PMCID: PMC2377100 Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation Sean M. Cory and Theodore J. Perkins PMCID: PMC2330068 A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation Sean R. Eddy PMCID: PMC2396288 The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures Diego U. Ferreiro, Aleksandra M. Walczak, Elizabeth A. Komives, and Peter G. Wolynes PMCID: PMC2366061 Discovering Sequence Motifs with Arbitrary Insertions and Deletions Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe, and Timothy L. Bailey PMCID: PMC2323616 Transient Cognitive Dynamics, Metastability, and Decision Making Mikhail I. Rabinovich, Ramón Huerta, Pablo Varona, and Valentin S. Afraimovich PMCID: PMC2358972 Short-Term Memory Trace in Rapidly Adapting Synapses of Inferior Temporal Cortex Yasuko Sugase-Miyamoto, Zheng Liu, Matthew C. Wiener, Lance M. Optican, and Barry J. Richmond PMCID: PMC2366068 Viral Population Estimation Using Pyrosequencing Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, and Niko Beerenwinkel PMCID: PMC2323617 An Allosteric Mechanism for Switching between Parallel Tracks in Mammalian Sulfur Metabolism Tatyana K. Korendyaseva, Denis N. Kuvatov, Vladimir A. Volkov, Michael V. Martinov, Victor M. Vitvitsky, Ruma Banerjee, and Fazoil I. Ataullakhanov PMCID: PMC2346559 Measuring Global Credibility with Application to Local Sequence Alignment Bobbie-Jo M. Webb-Robertson, Lee Ann McCue, and Charles E. Lawrence PMCID: PMC2367447 Computational Lipidology: Predicting Lipoprotein Density Profiles in Human Blood Plasma Katrin Hübner, Thomas Schwager, Karl Winkler, Jens-Georg Reich, and Hermann-Georg Holzhütter PMCID: PMC2361219 Context-Specific Metabolic Networks Are Consistent with Experiments Scott A. Becker and Bernhard O. Palsson PMCID: PMC2366062 Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments Lies Baeten, Joke Reumers, Vicente Tur, François Stricher, Tom Lenaerts, Luis Serrano, Frederic Rousseau, and Joost Schymkowitz PMCID: PMC2367438 Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics Richard A. Goldstein and Orkun S. Soyer PMCID: PMC2386285 Silent Synapses, LTP, and the Indirect Parallel-Fibre Pathway: Computational Consequences of Optimal Cerebellar Noise-Processing John Porrill and Paul Dean PMCID: PMC2377154 Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, and Jason A. Papin PMCID: PMC2377155 Uncovering Interactions in the Frequency Domain Shuixia Guo, Jianhua Wu, Mingzhou Ding, and Jianfeng Feng PMCID: PMC2398781 Astrocytes Optimize the Synaptic Transmission of Information Suhita Nadkarni, Peter Jung, and Herbert Levine PMCID: PMC2390854 |
