Table of Contents: May 2009


DNA damage induces phase advances in the circadian clock.

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

Messages from ISCB


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

How to Get the Most out of Your Curation Effort

Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur

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

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

Prediction of Protein Binding Regions in Disordered Proteins

Bálint Mészáros, István Simon, Zsuzsanna Dosztányi

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