| | Research Articles Fold Designability, Distribution, and Disease Philip Wong and Dmitrij Frishman PMCID: PMC1456317 Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays Rameen Beroukhim, Ming Lin, Yuhyun Park, Ke Hao, Xiaojun Zhao, Levi A Garraway, Edward A Fox, Ephraim P Hochberg, Ingo K Mellinghoff, Matthias D Hofer, Aurelien Descazeaud, Mark A Rubin, Matthew Meyerson, Wing Hung Wong, William R Sellers, and Cheng Li PMCID: PMC1458964 Differential Repression of Alternative Transcripts: A Screen for miRNA Targets Matthieu Legendre, William Ritchie, Fabrice Lopez, and Daniel Gautheret PMCID: PMC1458965 Spatial Regulation and the Rate of Signal Transduction Activation Nizar N Batada, Larry A Shepp, David O Siegmund, and Michael Levitt PMCID: PMC1458967 Statistics of Knots, Geometry of Conformations, and Evolution of Proteins Rhonald C Lua and Alexander Y Grosberg PMCID: PMC1463020 Genome-Wide Survey for Biologically Functional Pseudogenes Örjan Svensson, Lars Arvestad, and Jens Lagergren PMCID: PMC1456316 Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors Zhihua Zhang, Changning Liu, Geir Skogerbø, Xiaopeng Zhu, Hongchao Lu, Lan Chen, Baochen Shi, Yong Zhang, Jie Wang, Tao Wu, and Runsheng Chen PMCID: PMC1458966 Protein Family Expansions and Biological Complexity Christine Vogel and Cyrus Chothia PMCID: PMC1464810 Transcription Factor Map Alignment of Promoter Regions Enrique Blanco, Xavier Messeguer, Temple F Smith, and Roderic Guigó PMCID: PMC1464811 Reverse Engineering the Gap Gene Network of Drosophila melanogaster Theodore J Perkins, Johannes Jaeger, John Reinitz, and Leon Glass PMCID: PMC1463021 Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach Christian L Barrett and Bernhard O Palsson PMCID: PMC1463018 Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells Anthony A Philippakis, Brian W Busser, Stephen S Gisselbrecht, Fangxue Sherry He, Beatriz Estrada, Alan M Michelson, and Martha L Bulyk PMCID: PMC1464814 Predicting Shine–Dalgarno Sequence Locations Exposes Genome Annotation Errors J Starmer, A Stomp, M Vouk, and D Bitzer PMCID: PMC1463019 Evolutionary Potential of a Duplicated Repressor-Operator Pair: Simulating Pathways Using Mutation Data Frank J Poelwijk, Daniel J Kiviet, and Sander J Tans PMCID: PMC1464816 Correction Correction: Folding Very Short Peptides Using Molecular Dynamics Bosco K Ho and Ken A Dill PMCID: PMC1464817 Corrects: Bosco K Ho, et al. Folding Very Short Peptides Using Molecular Dynamics . PLoS Comput Biol. 2006 April; 2(4): e27. |
