Table of Contents

May 2009

DNA damage in mammalian cells leads to activation of the cell cycle regulator Chk2, which triggers downstream degradations of a core clock component, PER (i.e., PER1 in mice). This, in turn, creates unique phase shifts (mostly advances) in the circadian clock. Computational analyses from Hong et al. (doi:10.1371/journal.pcbi.1000384) recapitulate a phase advance (dashed curve) when DNA damage occurs around the peak of PER abundance, but minimum phase shifts around the trough (dots). The model proposes a molecular mechanism behind this phenomenon: differential degradation of PER in the presence of an essential positive feedback loop in the circadian system.

Image Credit: Judit Zámborszky (CoSBi, Microsoft Research-University of Trento Centre for Computational and Systems Biology, Italy).


Hypergraphs and Cellular Networks

Steffen Klamt, Utz-Uwe Haus, Fabian Theis

Research Articles

Fast Statistical Alignment

Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes, Lior Pachter

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

Gregory D. Friedland, Nils-Alexander Lakomek, Christian Griesinger, Jens Meiler, Tanja Kortemme

Structural Adaptation and Heterogeneity of Normal and Tumor Microvascular Networks

Axel R. Pries, Annemiek J. M. Cornelissen, Anoek A. Sloot, Marlene Hinkeldey, Matthew R. Dreher, Michael Höpfner, Mark W. Dewhirst, Timothy W. Secomb

Brain Anatomical Network and Intelligence

Yonghui Li, Yong Liu, Jun Li, Wen Qin, Kuncheng Li, Chunshui Yu, Tianzi Jiang

SHRiMP: Accurate Mapping of Short Color-space Reads

Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno

Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling

Smita Agrawal, Colin Archer, David V. Schaffer

How to Get the Most out of Your Curation Effort

Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur

Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior

Javad Golji, Robert Collins, Mohammad R. K. Mofrad

Differential Affinity and Catalytic Activity of CheZ in E. coli Chemotaxis

Siebe B. van Albada, Pieter Rein ten Wolde

Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings

Quentin J. M. Huys, Liam Paninski

Minimum Criteria for DNA Damage-Induced Phase Advances in Circadian Rhythms

Christian I. Hong, Judit Zámborszky, Attila Csikász-Nagy

Representation of Time-Varying Stimuli by a Network Exhibiting Oscillations on a Faster Time Scale

Maoz Shamir, Oded Ghitza, Steven Epstein, Nancy Kopell

Predictive Feedback Can Account for Biphasic Responses in the Lateral Geniculate Nucleus

Janneke F. M. Jehee, Dana H. Ballard

Prediction of Protein Binding Regions in Disordered Proteins

Bálint Mészáros, István Simon, Zsuzsanna Dosztányi

Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2

Joel O. Wertheim, Michael Worobey

Functional Brain Networks Develop from a “Local to Distributed” Organization

Damien A. Fair, Alexander L. Cohen, Jonathan D. Power, Nico U. F. Dosenbach, Jessica A. Church, Francis M. Miezin, Bradley L. Schlaggar, Steven E. Petersen

A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation

Nicholas J. Hudson, Antonio Reverter, Brian P. Dalrymple