Table of Contents: November 2007

A trinucleotide disease is like a genetic time bomb. A patient with such a disease inherits a DNA region consisting of a three-letter code repeated abnormally many times. The age at which the disease strikes the patient is encoded by the number of repeats. A universal mechanism by which this molecular time bomb operates in this broad family of hereditary diseases has been suggested (see Kaplan et al, e235).

Image Credit: Genia Brodsky, Weizmann Institute of Science


Ten Simple Rules for Graduate Students

Jenny Gu, Philip E Bourne


A Primer on Python for Life Science Researchers

Sebastian Bassi


Computational Biology in Cuba: An Opportunity to Promote Science in a Developing Country

Tirso Pons, Luis A Montero, Juan P Febles

Research Articles

Phenotypic Mutation Rates and the Abundance of Abnormal Proteins in Yeast

Martin Willensdorfer, Reinhard Bürger, Martin A Nowak

From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses

Sven Zenker, Jonathan Rubin, Gilles Clermont

Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes

Kevin P Keegan, Suraj Pradhan, Ji-Ping Wang, Ravi Allada

Are There Rearrangement Hotspots in the Human Genome?

Max A Alekseyev, Pavel A Pevzner

Self-Assembly and DNA Binding of the Blocking Factor in X Chromosome Inactivation

Mario Nicodemi, Antonella Prisco

Detecting Coevolution in and among Protein Domains

Chen-Hsiang Yeang, David Haussler

Self-organizing Mechanism for Development of Space-filling Neuronal Dendrites

Kaoru Sugimura, Kohei Shimono, Tadashi Uemura, Atsushi Mochizuki

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps

Hailiang Huang, Bruno M Jedynak, Joel S Bader

A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast

Leelavati Narlikar, Raluca Gordân, Alexander J Hartemink

Stochastic Noise and Synchronisation during Dictyostelium Aggregation Make cAMP Oscillations Robust

Jongrae Kim, Pat Heslop-Harrison, Ian Postlethwaite, Declan G Bates

STDP in a Bistable Synapse Model Based on CaMKII and Associated Signaling Pathways

Michael Graupner, Nicolas Brunel

Computational Analysis of Mouse piRNA Sequence and Biogenesis

Doron Betel, Robert Sheridan, Debora S Marks, Chris Sander

Genetic Progression and the Waiting Time to Cancer

Niko Beerenwinkel, Tibor Antal, David Dingli, Arne Traulsen, Kenneth W Kinzler, Victor E Velculescu, Bert Vogelstein, Martin A Nowak

A Dynamical Systems Hypothesis of Schizophrenia

Marco Loh, Edmund T Rolls, Gustavo Deco

Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum

Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael Stumpf, Sylvia Richardson, Carsten Wiuf

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope

Art F. Y Poon, Fraser I Lewis, Sergei L. Kosakovsky Pond, Simon D. W Frost

CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures

Oliver C Redfern, Andrew Harrison, Tim Dallman, Frances M. G Pearl, Christine A Orengo

Small Regulatory RNAs May Sharpen Spatial Expression Patterns

Erel Levine, Peter McHale, Herbert Levine

A Universal Mechanism Ties Genotype to Phenotype in Trinucleotide Diseases

Shai Kaplan, Shalev Itzkovitz, Ehud Shapiro

Gamma Oscillations of Spiking Neural Populations Enhance Signal Discrimination

Naoki Masuda, Brent Doiron

Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes

Juan A. G Ranea, Corin Yeats, Alastair Grant, Christine A Orengo

Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants

Morten Lindow, Anders Jacobsen, Sanne Nygaard, Yuan Mang, Anders Krogh

Predicting Gene Expression from Sequence: A Reexamination

Yuan Yuan, Lei Guo, Lei Shen, Jun S Liu

Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection

Xiaohong Li, Steven G Self, Patricia C Galipeau, Thomas G Paulson, Brian J Reid

Retinal Wave Behavior through Activity-Dependent Refractory Periods

Keith B Godfrey, Nicholas V Swindale