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

Related Articles

  1. Correction: Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays

Differential Repression of Alternative Transcripts: A Screen for miRNA Targets

Matthieu Legendre, William Ritchie, Fabrice Lopez, Daniel Gautheret

Spatial Regulation and the Rate of Signal Transduction Activation

Nizar N Batada, Larry A Shepp, David O Siegmund, Michael Levitt

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

Rhonald C Lua, Alexander Y Grosberg

Genome-Wide Survey for Biologically Functional Pseudogenes

Örjan Svensson, Lars Arvestad, Jens Lagergren

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, Runsheng Chen

Protein Family Expansions and Biological Complexity

Christine Vogel, Cyrus Chothia

Transcription Factor Map Alignment of Promoter Regions

Enrique Blanco, Xavier Messeguer, Temple F Smith, Roderic Guigó

Reverse Engineering the Gap Gene Network of Drosophila melanogaster

Theodore J Perkins, Johannes Jaeger, John Reinitz, Leon Glass

Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach

Christian L Barrett, Bernhard O Palsson

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