Table of Contents: August 2007

In contrast to biophysical predictions, this image illustrates that "DNA damage sensing proteins" (green signal) form foci along primary cosmic rays in a regular self-excluding manner (see Costes et al, e155). Upper panel: the white dashed arrow indicates the traversal of one Fe particle in a human cell (DNA shown in blue). Middle panel: the relative position of foci (green spheres) is shown with respect to the DNA dye intensity profile visualized by a three-dimensional topographic surface. Lower panel: foci preferentially locate within low DNA nuclear density regions, or at the interface between high and low nuclear DNA densities.

Image Credit: Image by Sylvain Costes.

Education Articles

Recent Evolutions of Multiple Sequence Alignment Algorithms

Cédric Notredame

A Primer on Learning in Bayesian Networks for Computational Biology

Chris J Needham, James R Bradford, Andrew J Bulpitt, David R Westhead

Research Articles

Automated Discovery of Functional Generality of Human Gene Expression Programs

Georg K Gerber, Robin D Dowell, Tommi S Jaakkola, David K Gifford

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, Awdhesh Kalia

PERIOD–TIMELESS Interval Timer May Require an Additional Feedback Loop

Robert S Kuczenski, Kevin C Hong, Jordi García-Ojalvo, Kelvin H Lee

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, Mary Helen Barcellos-Hoff

Mechanisms of Firing Patterns in Fast-Spiking Cortical Interneurons

David Golomb, Karnit Donner, Liron Shacham, Dan Shlosberg, Yael Amitai, David Hansel

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, Jonathan Dushoff

Automated Protein Subfamily Identification and Classification

Duncan P Brown, Nandini Krishnamurthy, Kimmen Sjölander

Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis

Andrew E Teschendorff, Michel Journée, Pierre A Absil, Rodolphe Sepulchre, Carlos Caldas

Inferring Function Using Patterns of Native Disorder in Proteins

Anna Lobley, Mark B Swindells, Christine A Orengo, David T Jones

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, Burkhart Schraven

Design of Multi-Specificity in Protein Interfaces

Elisabeth L Humphris, Tanja Kortemme

Perceptual Learning via Modification of Cortical Top-Down Signals

Roland Schäfer, Eleni Vasilaki, Walter Senn

Slowness and Sparseness Lead to Place, Head-Direction, and Spatial-View Cells

Mathias Franzius, Henning Sprekeler, Laurenz Wiskott

Functional Representation of Enzymes by Specific Peptides

Vered Kunik, Yasmine Meroz, Zach Solan, Ben Sandbank, Uri Weingart, Eytan Ruppin, David Horn

Buffering Mechanisms in Aging: A Systems Approach Toward Uncovering the Genetic Component of Aging

Aviv Bergman, Gil Atzmon, Kenny Ye, Thomas MacCarthy, Nir Barzilai

Pathway Switching Explains the Sharp Response Characteristic of Hypoxia Response Network

Yihai Yu, Guanyu Wang, Rahul Simha, Weiqun Peng, Frank Turano, Chen Zeng