Table of Contents: May 2008


Image Credit: Genia Brodsky, Weizmann Institute of Science
Issue Image
A coarse-grained view of E. coli.

Much like the "Ford-T assembly line," Escherichia coli can be thought of as a factory producing RNA polymerase, ribosomes, and other molecular machinery, all inside the crowded cytoplasm of the cell. In this simplified picture, genes and proteins of similar function are lumped together, resulting in an effective, coarse-grained representation of the cell (see Tadmor, Tlusty, doi:10.1371/journal.pcbi.1000038).




Research Articles

Uncovering Interactions in the Frequency Domain

Shuixia Guo, Jianhua Wu, Mingzhou Ding, Jianfeng Feng

Astrocytes Optimize the Synaptic Transmission of Information

Suhita Nadkarni, Peter Jung, Herbert Levine

Computational Lipidology: Predicting Lipoprotein Density Profiles in Human Blood Plasma

Katrin Hübner, Thomas Schwager, Karl Winkler, Jens-Georg Reich, Hermann-Georg Holzhütter

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, Joost Schymkowitz

Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

Jong Min Lee, Erwin P. Gianchandani, James A. Eddy, Jason A. Papin

Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins

Nan Song, Jacob M. Joseph, George B. Davis, Dannie Durand

Short-Term Memory Trace in Rapidly Adapting Synapses of Inferior Temporal Cortex

Yasuko Sugase-Miyamoto, Zheng Liu, Matthew C. Wiener, Lance M. Optican, Barry J. Richmond

Measuring Global Credibility with Application to Local Sequence Alignment

Bobbie-Jo M. Webb-Robertson, Lee Ann McCue, Charles E. Lawrence

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, Ehud Shapiro

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe, Timothy L. Bailey

Viral Population Estimation Using Pyrosequencing

Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel

Transient Cognitive Dynamics, Metastability, and Decision Making

Mikhail I. Rabinovich, Ramón Huerta, Pablo Varona, Valentin S. Afraimovich

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, Fazoil I. Ataullakhanov