Table of Contents: January 2009


The flower of a tulip mutant with dysfunctional class B floral homeotic genes.

Image Credit: Günter Theißen and Thorsten Lenser (University of Jena).
Issue Image

Petals and stamens are partially transformed into sepals and carpels, respectively. On the left, the graphical representations of gene regulatory networks help visualize how the obligate heterodimerization of class B floral homeotic genes may have arisen. One ancestral self-activating gene (top) is duplicated (middle), and subsequently, both transcription factors lose their homodimerization ability, leading to obligate heterodimerization (bottom) (see Lenser et al., doi:10.1371/journal.pcbi.1000264). The latter mechanism is found in Arabidopsis thaliana and other angiosperms.


A Review of 2008 for PLoS Computational Biology

Evie Browne, Rosemary Dickin, Philip E. Bourne

Message from ISCB

Microblogging the ISMB: A New Approach to Conference Reporting

Neil Saunders, Pedro Beltrão, Lars Jensen, Daniel Jurczak, Roland Krause, Michael Kuhn, Shirley Wu


A Primer on Regression Methods for Decoding cis-Regulatory Logic

Debopriya Das, Matteo Pellegrini, Joe W. Gray

Research Articles

Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae

Patrick H. Bradley, Matthew J. Brauer, Joshua D. Rabinowitz, Olga G. Troyanskaya

A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations

Charles J. Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H. Lee, Joshua M. Stuart

Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore

Dan S. Bolintineanu, Abdallah Sayyed-Ahmad, H. Ted Davis, Yiannis N. Kaznessis

Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling

Stefan Engelen, Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery, Alessandra Carbone

Astrocytic Mechanisms Explaining Neural-Activity-Induced Shrinkage of Extraneuronal Space

Ivar Østby, Leiv Øyehaug, Gaute T. Einevoll, Erlend A. Nagelhus, Erik Plahte, Thomas Zeuthen, Catherine M. Lloyd, Ole P. Ottersen, Stig W. Omholt

State Based Model of Long-Term Potentiation and Synaptic Tagging and Capture

Adam B. Barrett, Guy O. Billings, Richard G. M. Morris, Mark C. W. van Rossum

Evolutionary Sequence Modeling for Discovery of Peptide Hormones

Kemal Sonmez, Naunihal T. Zaveri, Ilan A. Kerman, Sharon Burke, Charles R. Neal, Xinmin Xie, Stanley J. Watson, Lawrence Toll

Questioning the Ubiquity of Neofunctionalization

Todd A. Gibson, Debra S. Goldberg

Polyamine Sharing between Tubulin Dimers Favours Microtubule Nucleation and Elongation via Facilitated Diffusion

Alain Mechulam, Konstantin G. Chernov, Elodie Mucher, Loic Hamon, Patrick A. Curmi, David Pastré

Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks

Adel Dayarian, Madalena Chaves, Eduardo D. Sontag, Anirvan M. Sengupta

Predicting Cellular Growth from Gene Expression Signatures

Edoardo M. Airoldi, Curtis Huttenhower, David Gresham, Charles Lu, Amy A. Caudy, Maitreya J. Dunham, James R. Broach, David Botstein, Olga G. Troyanskaya