September 2005

Describing where genes express is an important step in understanding the function of gene products. In this slice through the mouse brain, Purkinje cell protein 4 (Pcp4) expression is shown with an associated deformed anatomical map. The amount of Pcp4 transcripts in each cell is represented by the different colors (see Carson et al).

Image Credit: Image created by James Carson from data at http://www.geneatlas.org, using Adobe Photoshop software to perform manipulations.

Research Articles

A Biophysical Model of the Mitochondrial Respiratory System and Oxidative Phosphorylation

Daniel A Beard

PLOS Computational Biology: published September 9, 2005 | https://doi.org/10.1371/journal.pcbi.0010036

Transition to Quorum Sensing in an Agrobacterium Population: A Stochastic Model

Andrew B Goryachev, Da-Jun Toh, Keng Boon Wee, Travis Lee, Hai-Bao Zhang, Lian-Hui Zhang

PLOS Computational Biology: published September 16, 2005 | https://doi.org/10.1371/journal.pcbi.0010037

Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4–5 in Splicing

Yuanyuan Xiao, Yee H Yang, Todd A Burckin, Lily Shiue, Grant A Hartzog, Mark R Segal

PLOS Computational Biology: published September 16, 2005 | https://doi.org/10.1371/journal.pcbi.0010039

Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family

Carsten Rautengarten, Dirk Steinhauser, Dirk Büssis, Annick Stintzi, Andreas Schaller, Joachim Kopka, Thomas Altmann

PLOS Computational Biology: published September 23, 2005 | https://doi.org/10.1371/journal.pcbi.0010040

A Digital Atlas to Characterize the Mouse Brain Transcriptome

James P Carson, Tao Ju, Hui-Chen Lu, Christina Thaller, Mei Xu, Sarah L Pallas, Michael C Crair, Joe Warren, Wah Chiu, Gregor Eichele

PLOS Computational Biology: published September 23, 2005 | https://doi.org/10.1371/journal.pcbi.0010041

ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun

Ruiqiang Li, Jia Ye, Songgang Li, Jing Wang, Yujun Han, Chen Ye, Jian Wang, Huanming Yang, Jun Yu, Gane Ka-Shu Wong, Jun Wang

PLOS Computational Biology: published September 23, 2005 | https://doi.org/10.1371/journal.pcbi.0010043

Modeling the Amplification Dynamics of Human Alu Retrotransposons

Dale J Hedges, Richard Cordaux, Jinchuan Xing, David J Witherspoon, Alan R Rogers, Lynn B Jorde, Mark A Batzer

PLOS Computational Biology: published September 30, 2005 | https://doi.org/10.1371/journal.pcbi.0010044

Entropic Stabilization of Proteins and Its Proteomic Consequences

Igor N Berezovsky, William W Chen, Paul J Choi, Eugene I Shakhnovich

PLOS Computational Biology: published September 30, 2005 | https://doi.org/10.1371/journal.pcbi.0010047

Cover

Purkinje cell protein 4 transcripts in mouse brain