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Table of Contents: March 2007

Sequence changes introduced by alternative splicing and gene duplication are usually different. Shown here is the location and nature (using a hydrophobicity scale) of the differences between alternative splicing isoforms of MAPK9 (left), and between MAPK9 and the paralogs MAPK10 (center) and MAPK13 (right) (see Talavera et al).

Image Credit: Image created by David Talavera, Christine Vogel, and Xavier de la Cruz with PyMOL

Editorials

Ten Simple Rules for a Successful Collaboration

Quentin Vicens, Philip E Bourne

Education Articles

Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases

Benjamin A Shoemaker, Anna R Panchenko

Research Articles

Dose Response Relationship in Anti-Stress Gene Regulatory Networks

Qiang Zhang, Melvin E Andersen

The Stem Cell Population of the Human Colon Crypt: Analysis via Methylation Patterns

Pierre Nicolas, Kyoung-Mee Kim, Darryl Shibata, Simon Tavaré

PPARα siRNA–Treated Expression Profiles Uncover the Causal Sufficiency Network for Compound-Induced Liver Hypertrophy

Xudong Dai, Angus T. De Souza, Hongyue Dai, David L Lewis, Chang-kyu Lee, Andy G Spencer, Hans Herweijer, Jim E Hagstrom, Peter S Linsley, Douglas E Bassett, Roger G Ulrich, Yudong D He

The (In)dependence of Alternative Splicing and Gene Duplication

David Talavera, Christine Vogel, Modesto Orozco, Sarah A Teichmann, Xavier de la Cruz

A Mathematical Model for Neutrophil Gradient Sensing and Polarization

Matthew Onsum, Christopher V Rao

Characterization and Identification of MicroRNA Core Promoters in Four Model Species

Xuefeng Zhou, Jianhua Ruan, Guandong Wang, Weixiong Zhang

Spatial Acuity and Prey Detection in Weakly Electric Fish

David Babineau, John E Lewis, André Longtin

Discovering Motifs in Ranked Lists of DNA Sequences

Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini

UV-Induced Mutagenesis in Escherichia coli SOS Response: A Quantitative Model

Sandeep Krishna, Sergei Maslov, Kim Sneppen

Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation

Andrea Ciliberto, Fabrizio Capuani, John J Tyson

A Look Inside HIV Resistance through Retroviral Protease Interaction Maps

Aleksejs Kontijevskis, Peteris Prusis, Ramona Petrovska, Sviatlana Yahorava, Felikss Mutulis, Ilze Mutule, Jan Komorowski, Jarl E. S Wikberg

Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins

Igor N Berezovsky, Konstantin B Zeldovich, Eugene I Shakhnovich

(A)Symmetric Stem Cell Replication and Cancer

David Dingli, Arne Traulsen, Franziska Michor

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Query-Dependent Banding (QDB) for Faster RNA Similarity Searches

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Posttranscriptional Expression Regulation: What Determines Translation Rates?

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Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage

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DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies

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