| | Education Introduction to Computational Proteomics Jacques Colinge and Keiryn L Bennett PMCID: PMC1933459 Review Quantitative Analysis of Cell Nucleus Organisation Carol Shiels, Niall M Adams, Suhail A Islam, David A Stephens, and Paul S Freemont PMCID: PMC1933473 Research Articles Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle Bertrand C. W Tanner, Thomas L Daniel, and Michael Regnier PMCID: PMC1914368 Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution Fereydoun Hormozdiari, Petra Berenbrink, Nataša Pržulj, and S. Cenk Sahinalp PMCID: PMC1913096 Protein–Protein Interaction Hotspots Carved into Sequences Yanay Ofran and Burkhard Rost PMCID: PMC1914369 Evolution of Function in the “Two Dinucleotide Binding Domains” Flavoproteins Sunil Ojha, Elaine C Meng, and Patricia C Babbitt PMCID: PMC1924876 Efficiency, Selectivity, and Robustness of Nucleocytoplasmic Transport Anton Zilman, Stefano Di Talia, Brian T Chait, Michael P Rout, and Marcelo O Magnasco PMCID: PMC1914370 A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes Zizhen Yao, Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald Breaker, Martin Tompa, and Walter L Ruzzo PMCID: PMC1913097 Sensitivity Analysis of Intracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control Alborz Mahdavi, Ryan E Davey, Patrick Bhola, Ting Yin, and Peter W Zandstra PMCID: PMC1913098 Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network Reut Shalgi, Daniel Lieber, Moshe Oren, and Yitzhak Pilpel PMCID: PMC1914371 Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes Patricia A Ryan, Brian W Kirk, Chad W Euler, Raymond Schuch, and Vincent A Fischetti PMCID: PMC1913099 Optimal Timing and Duration of Induction Therapy for HIV-1 Infection Marcel E Curlin, Shyamala Iyer, and John E Mittler PMCID: PMC1914372 Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning Poramate Manoonpong, Tao Geng, Tomas Kulvicius, Bernd Porr, and Florentin Wörgötter PMCID: PMC1914373 Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation Joti Giordano, Yongchao Ge, Yevgeniy Gelfand, György Abrusán, Gary Benson, and Peter E Warburton PMCID: PMC1914374 A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds Konstantin B Zeldovich, Peiqiu Chen, Boris E Shakhnovich, and Eugene I Shakhnovich PMCID: PMC1914367 Natively Unstructured Loops Differ from Other Loops Avner Schlessinger, Jinfeng Liu, and Burkhard Rost PMCID: PMC1924875 Computationally Derived Points of Fragility of a Human Cascade Are Consistent with Current Therapeutic Strategies Deyan Luan, Michael Zai, and Jeffrey D Varner PMCID: PMC1924874 Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster Anastasia A Samsonova, Mahesan Niranjan, Steven Russell, and Alvis Brazma PMCID: PMC1924873 Detecting Emerging Transmissibility of Avian Influenza Virus in Human Households Michiel van Boven, Marion Koopmans, Mirna Du Ry van Beest Holle, Adam Meijer, Don Klinkenberg, Christl A Donnelly, and Hans (J. A. P.) Heesterbeek PMCID: PMC1933478 Chemotaxis Receptor Complexes: From Signaling to Assembly Robert G Endres, Joseph J Falke, and Ned S Wingreen PMCID: PMC1933480 Corrections Correction: Computational Model Explains High Activity and Rapid Cycling of Rho GTPases within Protein Complexes Andrew B Goryachev and Alexandra V Pokhilko PMCID: PMC1933471 Corrects: Andrew B Goryachev, et al. Computational Model Explains High Activity and Rapid Cycling of Rho GTPases within Protein Complexes. PLoS Comput Biol. 2006 December; 2(12): e172. Correction: In Search of the Biological Significance of Modular Structures in Protein Networks Zhi Wang and Jianzhi Zhang PMCID: PMC1933479 Corrects: Zhi Wang, et al. In Search of the Biological Significance of Modular Structures in Protein Networks. PLoS Comput Biol. 2007 June; 3(6): e107. Retraction: Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees Barry G Hall and Stephen J Salipante PMCID: PMC1924872 Corrects: Barry G Hall, et al. Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees. PLoS Comput Biol. 2007 March; 3(3): e51. |
