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Table of Contents: May 2006

The image depicts local fitness environments along an evolutionary path. The surfaces are based on measured data, and show the changes in fitness that can be achieved by a single base pair substitution. The first disc represents a duplicate repressor-operator pair, while the last represents a diverged pair. In this manner, a highly complex, multidimensional fitness landscape can be portrayed. The simulated paths explain why independent protein-DNA interactions can evolve rapidly (see Poelwijk et al).

Image Credit: Created by Frank Poelwijk and Daniel Kiviet using MATLAB, MOLMOL, and Jasc Paint Shop Pro.

Research Articles

Fold Designability, Distribution, and Disease

Philip Wong, Dmitrij Frishman

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, Cheng Li

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Differential Repression of Alternative Transcripts: A Screen for miRNA Targets

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Spatial Regulation and the Rate of Signal Transduction Activation

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Statistics of Knots, Geometry of Conformations, and Evolution of Proteins

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Genome-Wide Survey for Biologically Functional Pseudogenes

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Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors

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Protein Family Expansions and Biological Complexity

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Transcription Factor Map Alignment of Promoter Regions

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Reverse Engineering the Gap Gene Network of Drosophila melanogaster

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Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach

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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, Martha L Bulyk

Predicting Shine–Dalgarno Sequence Locations Exposes Genome Annotation Errors

J Starmer, A Stomp, M Vouk, D Bitzer

Evolutionary Potential of a Duplicated Repressor-Operator Pair: Simulating Pathways Using Mutation Data

Frank J Poelwijk, Daniel J Kiviet, Sander J Tans