Table of Contents

January 2009

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.

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


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

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

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

An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors

Katherine V. Wendelsdorf, Zhuo Song, Yang Cao, David C. Samuels

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

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

Adrian M. Altenhoff, Christophe Dessimoz

Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins

Thorsten Lenser, Günter Theißen, Peter Dittrich

Action Potential Initiation in the Hodgkin-Huxley Model

Lucy J. Colwell, Michael P. Brenner

Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties

Wenxu Tong, Ying Wei, Leonel F. Murga, Mary Jo Ondrechen, Ronald J. Williams

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

Model-Based Therapeutic Correction of Hypothalamic-Pituitary-Adrenal Axis Dysfunction

Amos Ben-Zvi, Suzanne D. Vernon, Gordon Broderick

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

Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes

Like Fokkens, Berend Snel

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

Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests

Mile Šikić, Sanja Tomić, Kristian Vlahoviček

Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures

Dirk Müller, Jörg Stelling