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Table of Contents: April 2006

Three-dimensional microCT-based virtual histology allows full assessment of an E12.5 mouse embryo (see Johnson et al.). Animations available online.

Image Credit: Image created by David Weinstein (Visual Influence), Charles Keller, and Ali Bahadur (UTHSCSA).

Technical Report

Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs

Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G Engström, Boris Lenhard, Rajith N Aturaliya, Serge Batalov, Kirk W Beisel, Carol J Bult, Colin F Fletcher, Alistair R. R Forrest, Masaaki Furuno, David Hill, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Shintaro Katayama, Masaru Katoh, Tsugumi Kawashima, John Quackenbush, Timothy Ravasi, Brian Z Ring, Kazuhiro Shibata, Koji Sugiura, Yoichi Takenaka, Rohan D Teasdale, Christine A Wells, Yunxia Zhu, Chikatoshi Kai, Jun Kawai, David A Hume, Piero Carninci, Yoshihide Hayashizaki

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Research Articles

On the Mechanism of Gene Amplification Induced under Stress in Escherichia coli

Andrew Slack, P. C Thornton, Daniel B Magner, Susan M Rosenberg, P. J Hastings

Dynamic Reprogramming of DNA Methylation at an Epigenetically Sensitive Allele in Mice

Marnie E Blewitt, Nicola K Vickaryous, Andras Paldi, Haruhiko Koseki, Emma Whitelaw

Genome-Wide Analysis of Menin Binding Provides Insights into MEN1 Tumorigenesis

Peter C Scacheri, Sean Davis, Duncan T Odom, Gregory E Crawford, Stacie Perkins, Mohamad J Halawi, Sunita K Agarwal, Stephen J Marx, Allen M Spiegel, Paul S Meltzer, Francis S Collins

Chemical Genetics Reveals an RGS/G-Protein Role in the Action of a Compound

Kevin Fitzgerald, Svetlana Tertyshnikova, Lisa Moore, Lynn Bjerke, Ben Burley, Jian Cao, Pamela Carroll, Robert Choy, Steve Doberstein, Yves Dubaquie, Yvonne Franke, Jenny Kopczynski, Hendrik Korswagen, Stanley R Krystek Jr., Nicholas J Lodge, Ronald Plasterk, John Starrett, Terry Stouch, George Thalody, Honey Wayne, Alexander van der Linden, Yongmei Zhang, Stephen G Walker, Mark Cockett, Judi Wardwell-Swanson, Petra Ross-Macdonald, Rachel M Kindt

Loss of Atrx Affects Trophoblast Development and the Pattern of X-Inactivation in Extraembryonic Tissues

David Garrick, Jackie A Sharpe, Ruth Arkell, Lorraine Dobbie, Andrew J. H Smith, William G Wood, Douglas R Higgs, Richard J Gibbons

Bayesian Estimation of the Timing and Severity of a Population Bottleneck from Ancient DNA

Yvonne L Chan, Christian N. K Anderson, Elizabeth A Hadly

DNA Methylation Supports Intrinsic Epigenetic Memory in Mammalian Cells

Yong-Qing Feng, Romain Desprat, Haiqing Fu, Emmanuel Olivier, Chii Mei Lin, Amanda Lobell, Shilpa N Gowda, Mirit I Aladjem, Eric E Bouhassira

Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping

John T Johnson, Mark S Hansen, Isabel Wu, Lindsey J Healy, Christopher R Johnson, Greg M Jones, Mario R Capecchi, Charles Keller

Pseudo–Messenger RNA: Phantoms of the Transcriptome

Martin C Frith, Laurens G Wilming, Alistair Forrest, Hideya Kawaji, Sin Lam Tan, Claes Wahlestedt, Vladimir B Bajic, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Timothy L Bailey, Lukasz Huminiecki

The Abundance of Short Proteins in the Mammalian Proteome

Martin C Frith, Alistair R Forrest, Ehsan Nourbakhsh, Ken C Pang, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Timothy L Bailey, Sean M Grimmond

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  1. Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome
  2. Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs

Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs

Masaaki Furuno, Ken C Pang, Noriko Ninomiya, Shiro Fukuda, Martin C Frith, Carol Bult, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, John S Mattick, Harukazu Suzuki

Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units

Melissa J Davis, Kelly A Hanson, Francis Clark, J. Lynn Fink, Fasheng Zhang, Takeya Kasukawa, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Rohan D Teasdale

Complex Loci in Human and Mouse Genomes

Pär G Engström, Harukazu Suzuki, Noriko Ninomiya, Altuna Akalin, Luca Sessa, Giovanni Lavorgna, Alessandro Brozzi, Lucilla Luzi, Sin Lam Tan, Liang Yang, Galih Kunarso, Edwin Lian-Chong Ng, Serge Batalov, Claes Wahlestedt, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Christine Wells, Vladimir B Bajic, Valerio Orlando, James F Reid, Boris Lenhard, Leonard Lipovich

A Method for Similarity Search of Genomic Positional Expression Using CAGE

Shigeto Seno, Yoichi Takenaka, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Hideo Matsuda

SPA: A Probabilistic Algorithm for Spliced Alignment

Erik van Nimwegen, Nicodeme Paul, Robert Sheridan, Mihaela Zavolan

A Simple Physical Model Predicts Small Exon Length Variations

Tzu-Ming Chern, Erik van Nimwegen, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Mihaela Zavolan

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

Mice and Men: Their Promoter Properties

Vladimir B Bajic, Sin Lam Tan, Alan Christoffels, Christian Schönbach, Leonard Lipovich, Liang Yang, Oliver Hofmann, Adele Kruger, Winston Hide, Chikatoshi Kai, Jun Kawai, David A Hume, Piero Carninci, Yoshihide Hayashizaki

Heterotachy in Mammalian Promoter Evolution

Martin S Taylor, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Colin A. M Semple

Correction

Correction: Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

Martin Wu, Qinghu Ren, A. Scott Durkin, Sean C Daugherty, Lauren M Brinkac, Robert J Dodson, Ramana Madupu, Steven A Sullivan, James F Kolonay, Daniel H Haft, William C Nelson, Luke J Tallon, Kristine M Jones, Luke E Ulrich, Juan M Gonzalez, Igor B Zhulin, Frank T Robb, Jonathan A Eisen

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  1. Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901