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Table of Contents: November 2006

COVER

Projections of hexamer sequence space in the vicinity of the sequences GAAGAA and TATATT

Image Credit: Created by Michael Stadler, using GraphViz.
Issue Image

Neighboring sequences are predictive of splicing regulatory element activity. Shown here are projections of hexamer sequence space in the vicinity of the sequences GAAGAA (left blue circle) and TATATT (right blue circle), with known exonic splicing enhancer and silencers indicated as green and red circles, respectively. (See Stadler et al., e191.)

Review

Research Articles

Inference of Splicing Regulatory Activities by Sequence Neighborhood Analysis

Michael B Stadler, Noam Shomron, Gene W Yeo, Aniket Schneider, Xinshu Xiao, Christopher B Burge

Pigment Pattern in jaguar/obelix Zebrafish Is Caused by a Kir7.1 Mutation: Implications for the Regulation of Melanosome Movement

Motoko Iwashita, Masakatsu Watanabe, Masaru Ishii, Tim Chen, Stephen L Johnson, Yoshihisa Kurachi, Norihiro Okada, Shigeru Kondo

Opposite Root Growth Phenotypes of hy5 versus hy5 hyh Mutants Correlate with Increased Constitutive Auxin Signaling

Richard Sibout, Poornima Sukumar, Chamari Hettiarachchi, Magnus Holm, Gloria K Muday, Christian S Hardtke

Impact of Nonsense-Mediated mRNA Decay on the Global Expression Profile of Budding Yeast

Qiaoning Guan, Wei Zheng, Shijie Tang, Xiaosong Liu, Robert A Zinkel, Kam-Wah Tsui, Brian S Yandell, Michael R Culbertson

Genomic Selective Constraints in Murid Noncoding DNA

Daniel J Gaffney, Peter D Keightley

Four Linked Genes Participate in Controlling Sporulation Efficiency in Budding Yeast

Giora Ben-Ari, Drora Zenvirth, Amir Sherman, Lior David, Michael Klutstein, Uri Lavi, Jossi Hillel, Giora Simchen

Functional Identification of Api5 as a Suppressor of E2F-Dependent Apoptosis In Vivo

Erick J Morris, William A Michaud, Jun-Yuan Ji, Nam-Sung Moon, James W Rocco, Nicholas J Dyson

Genomic Variation in Rice: Genesis of Highly Polymorphic Linkage Blocks during Domestication

Tian Tang, Jian Lu, Jianzi Huang, Jinghong He, Susan R McCouch, Yang Shen, Zeng Kai, Michael D Purugganan, Suhua Shi, Chung-I Wu

Harnessing a High Cargo-Capacity Transposon for Genetic Applications in Vertebrates

Darius Balciunas, Kirk J Wangensteen, Andrew Wilber, Jason Bell, Aron Geurts, Sridhar Sivasubbu, Xin Wang, Perry B Hackett, David A Largaespada, R. Scott McIvor, Stephen C Ekker

p38 MAPK Regulates Expression of Immune Response Genes and Contributes to Longevity in C. elegans

Emily R Troemel, Stephanie W Chu, Valerie Reinke, Siu Sylvia Lee, Frederick M Ausubel, Dennis H Kim

Selection for Unequal Densities of σ70 Promoter-Like Signals in Different Regions of Large Bacterial Genomes

Araceli M Huerta, M. Pilar Francino, Enrique Morett, Julio Collado-Vides

The Role of DNA Double-Strand Breaks in Spontaneous Homologous Recombination in S. cerevisiae

Gaëlle Lettier, Qi Feng, Adriana Antúnez de Mayolo, Naz Erdeniz, Robert J. D Reid, Michael Lisby, Uffe H Mortensen, Rodney Rothstein

CAF-1 Is Essential for Heterochromatin Organization in Pluripotent Embryonic Cells

Martin Houlard, Soizik Berlivet, Aline V Probst, Jean-Pierre Quivy, Patrick Héry, Geneviève Almouzni, Matthieu Gérard

Correspondence

Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More?

Michael Hiller, Karol Szafranski, Rolf Backofen, Matthias Platzer

Authors' Reply

Erik van Nimwegen, Mihaela Zavolan

Correction

Correction: Evidence for Diversity in Transcriptional Profiles of Single Hematopoietic Stem Cells

Carlos A Ramos, Teresa A Bowman, Nathan C Boles, Akil A Merchant, Yayun Zheng, Irma Parra, Suzanne A. W Fuqua, Chad A Shaw, Margaret A Goodell