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Table of Contents: September 2008

A growing population of digital organisms, started from one individual, colonizes an initially empty space (black). As it does so, the population evolves by random mutation and selection, based on each organism's resulting phenotype. Every colored square represents one digital organism, with different colors reflecting different fitness levels. The speed, control, and ease of data collection in the Avida digital evolution platform permits experiments that would be difficult or even impossible with natural organisms, such as the present study (Clune et al., doi:10.1371/journal.pcbi.1000187) on the evolution of mutation rates.

Image Credit: Kaben Nanlohy, Michigan State University

Education Articles

Advanced Genomic Data Mining

Xosé M. Fernández-Suárez, Ewan Birney

Reviews

Structural Biology by NMR: Structure, Dynamics, and Interactions

Phineus R. L. Markwick, Thérèse Malliavin, Michael Nilges

Research Articles

Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex

Mark A. Kramer, Anita K. Roopun, Lucy M. Carracedo, Roger D. Traub, Miles A. Whittington, Nancy J. Kopell

Insights into Protein–DNA Interactions through Structure Network Analysis

R. Sathyapriya, M. S. Vijayabaskar, Saraswathi Vishveshwara

Sizing Up Allometric Scaling Theory

Van M. Savage, Eric J. Deeds, Walter Fontana

Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae

Ji-Ping Wang, Yvonne Fondufe-Mittendorf, Liqun Xi, Guei-Feng Tsai, Eran Segal, Jonathan Widom

Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks

Neema Jamshidi, Bernhard Ø. Palsson

Identifying the Important HIV-1 Recombination Breakpoints

John Archer, John W. Pinney, Jun Fan, Etienne Simon-Loriere, Eric J. Arts, Matteo Negroni, David L. Robertson

Probabilistic Phylogenetic Inference with Insertions and Deletions

Elena Rivas, Sean R. Eddy

Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth

Roeland M. H. Merks, Erica D. Perryn, Abbas Shirinifard, James A. Glazier

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  1. Correction: Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth

Modeling Recursive RNA Interference

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A Genomewide Functional Network for the Laboratory Mouse

Yuanfang Guan, Chad L. Myers, Rong Lu, Ihor R. Lemischka, Carol J. Bult, Olga G. Troyanskaya

Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information

Kai Wang, Jeremy A. Horst, Gong Cheng, David C. Nickle, Ram Samudrala

Adaptation and Selective Information Transmission in the Cricket Auditory Neuron AN2

Klaus Wimmer, K. Jannis Hildebrandt, R. Matthias Hennig, Klaus Obermayer

Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo

Francisco J. P. Lopes, Fernando M. C. Vieira, David M. Holloway, Paulo M. Bisch, Alexander V. Spirov

A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction

Patrick Flaherty, Mala L. Radhakrishnan, Tuan Dinh, Robert A. Rebres, Tamara I. Roach, Michael I. Jordan, Adam P. Arkin

Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads

Steven L. Salzberg, Daniel D. Sommer, Daniela Puiu, Vincent T. Lee

Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes

Jeff Clune, Dusan Misevic, Charles Ofria, Richard E. Lenski, Santiago F. Elena, Rafael Sanjuán

Cavities and Atomic Packing in Protein Structures and Interfaces

Shrihari Sonavane, Pinak Chakrabarti

Organization of Excitable Dynamics in Hierarchical Biological Networks

Mark Müller-Linow, Claus C. Hilgetag, Marc-Thorsten Hütt