June 2005

The image shows predicted functional linkage gene networks for large and small cytoplasmic ribosomal subunits in eukaryotes, derived from phylogenetic analysis of whole genomes. Each point represents a gene, and each line a functional link. Colors represent protein functional classes. (See Barker and Pagel)

Image Credit: Drawn by Barker and Pagel using BioLayout software.

Editorial

PLoS Computational Biology: A New Community Journal

Philip E Bourne, Steven E Brenner, Michael B Eisen

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010004

Message from ISCB

An Open Forum for Computational Biology

Michael Gribskov

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010005

Perspective

“Antedisciplinary” Science

Sean R Eddy

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010006

Review

The Human Connectome: A Structural Description of the Human Brain

Olaf Sporns, Giulio Tononi, Rolf Kötter

PLOS Computational Biology: published September 30, 2005 | https://doi.org/10.1371/journal.pcbi.0010042

Research Articles

Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge

Tommy Kaplan, Nir Friedman, Hanah Margalit

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010001

What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation?

Johan Elf, Måns Ehrenberg

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010002

Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes

Daniel Barker, Mark Pagel

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010003

Susceptibility to Superhelically Driven DNA Duplex Destabilization: A Highly Conserved Property of Yeast Replication Origins

Prashanth Ak, Craig J Benham

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010007

Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a β-Hairpin

Laxmi Parida, Ruhong Zhou

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010008

Improving the Precision of the Structure–Function Relationship by Considering Phylogenetic Context

Boris E Shakhnovich

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010009

Extraction of Transcript Diversity from Scientific Literature

Parantu K Shah, Lars J Jensen, Stéphanie Boué, Peer Bork

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010010

A Phenomenological Theory of Spatially Structured Local Synaptic Connectivity

Bagrat Amirikian

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010011

The Genomic Pattern of tDNA Operon Expression in E. coli

David H Ardell, Leif A Kirsebom

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010012

microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets

Dominic Grün, Yi-Lu Wang, David Langenberger, Kristin C Gunsalus, Nikolaus Rajewsky

PLOS Computational Biology: published June 24, 2005 | https://doi.org/10.1371/journal.pcbi.0010013

Cover

Predicted functional linkage gene networks