Table of Contents: May 2008

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).

Image Credit: Genia Brodsky, Weizmann Institute of Science


Ten Simple Rules for Aspiring Scientists in a Low-Income Country

Edgardo Moreno, José-María Gutiérrez


An Introduction to Bioinformatics for Glycomics Research

Kiyoko F. Aoki-Kinoshita


Research Articles

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

Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins

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

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, Peter G. Wolynes

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

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

Transient Cognitive Dynamics, Metastability, and Decision Making

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

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

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

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

Measuring Global Credibility with Application to Local Sequence Alignment

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

Computational Lipidology: Predicting Lipoprotein Density Profiles in Human Blood Plasma

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

Context-Specific Metabolic Networks Are Consistent with Experiments

Scott A. Becker, Bernhard O. Palsson

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

Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics

Richard A. Goldstein, Orkun S. Soyer

Uncovering Interactions in the Frequency Domain

Shuixia Guo, Jianhua Wu, Mingzhou Ding, Jianfeng Feng