| | Education Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases Benjamin A Shoemaker and Anna R Panchenko PMCID: PMC1847991 Editorial Ten Simple Rules for a Successful Collaboration Quentin Vicens and Philip E Bourne PMCID: PMC1847992 Research Articles Dose Response Relationship in Anti-Stress Gene Regulatory Networks Qiang Zhang and Melvin E Andersen PMCID: PMC1808489 The Stem Cell Population of the Human Colon Crypt: Analysis via Methylation Patterns Pierre Nicolas, Kyoung-Mee Kim, Darryl Shibata, and Simon Tavaré PMCID: PMC1808490 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, and Yudong D He PMCID: PMC1808491 The (In)dependence of Alternative Splicing and Gene Duplication David Talavera, Christine Vogel, Modesto Orozco, Sarah A Teichmann, and Xavier de la Cruz PMCID: PMC1808492 A Mathematical Model for Neutrophil Gradient Sensing and Polarization Matthew Onsum and Christopher V Rao PMCID: PMC1828701 Characterization and Identification of MicroRNA Core Promoters in Four Model Species Xuefeng Zhou, Jianhua Ruan, Guandong Wang, and Weixiong Zhang PMCID: PMC1817659 Spatial Acuity and Prey Detection in Weakly Electric Fish David Babineau, John E Lewis, and André Longtin PMCID: PMC1808493 Discovering Motifs in Ranked Lists of DNA Sequences Eran Eden, Doron Lipson, Sivan Yogev, and Zohar Yakhini PMCID: PMC1829477 UV-Induced Mutagenesis in Escherichia coli SOS Response: A Quantitative Model Sandeep Krishna, Sergei Maslov, and Kim Sneppen PMCID: PMC1828700 Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation Andrea Ciliberto, Fabrizio Capuani, and John J Tyson PMCID: PMC1828705 A Look Inside HIV Resistance through Retroviral Protease Interaction Maps Aleksejs Kontijevskis, Peteris Prusis, Ramona Petrovska, Sviatlana Yahorava, Felikss Mutulis, Ilze Mutule, Jan Komorowski, and Jarl E. S Wikberg PMCID: PMC1817660 Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees Barry G Hall and Stephen J Salipante PMCID: PMC1828704 Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins Igor N Berezovsky, Konstantin B Zeldovich, and Eugene I Shakhnovich PMCID: PMC1829478 (A)Symmetric Stem Cell Replication and Cancer David Dingli, Arne Traulsen, and Franziska Michor PMCID: PMC1828703 Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, and Fernando Pereira PMCID: PMC1828702 Dynamic Simulations on the Arachidonic Acid Metabolic Network Kun Yang, Wenzhe Ma, Huanhuan Liang, Qi Ouyang, Chao Tang, and Luhua Lai PMCID: PMC1829479 Query-Dependent Banding (QDB) for Faster RNA Similarity Searches Eric P Nawrocki and Sean R Eddy PMCID: PMC1847999 Posttranscriptional Expression Regulation: What Determines Translation Rates? Regina Brockmann, Andreas Beyer, Jürgen J Heinisch, and Thomas Wilhelm PMCID: PMC1829480 Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J Low, Peter K Cheung, P. Richard Harrigan, Thomas Lengauer, and Francisco S Domingues PMCID: PMC1848001 Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch Keun-Young Kim and Jin Wang PMCID: PMC1848002 DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies Shaun Mahony, Philip E Auron, and Panayiotis V Benos PMCID: PMC1848003 Correction Correction: Specificity and Evolvability in Eukaryotic Protein Interaction Networks Pedro Beltrao and Luis Serrano PMCID: PMC1848004 Corrects: Pedro Beltrao, et al. Specificity and Evolvability in Eukaryotic Protein Interaction Networks. PLoS Comput Biol. 2007 February; 3(2): e25. |
