| | This journal provides immediate access to some articles. 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, and Yoshihide Hayashizaki PMCID: PMC1449903 Editorial Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome Yoshihide Hayashizaki and Piero Carninci PMCID: PMC1449904 Review Balancing Selection and Its Effects on Sequences in Nearby Genome Regions Deborah Charlesworth PMCID: PMC1449905 Research Articles 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, and Lukasz Huminiecki PMCID: PMC1449882 SPA: A Probabilistic Algorithm for Spliced Alignment Erik van Nimwegen, Nicodeme Paul, Robert Sheridan, and Mihaela Zavolan PMCID: PMC1449883 Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines Jinfeng Liu, Julian Gough, and Burkhard Rost PMCID: PMC1449884 Heterotachy in Mammalian Promoter Evolution Martin S Taylor, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, and Colin A. M Semple PMCID: PMC1449885 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, and Harukazu Suzuki PMCID: PMC1449886 A Method for Similarity Search of Genomic Positional Expression Using CAGE Shigeto Seno, Yoichi Takenaka, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, and Hideo Matsuda PMCID: PMC1449887 A Simple Physical Model Predicts Small Exon Length Variations Tzu-Ming Chern, Erik van Nimwegen, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, and Mihaela Zavolan PMCID: PMC1449888 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, and Rohan D Teasdale PMCID: PMC1449889 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, and Leonard Lipovich PMCID: PMC1449890 On the Mechanism of Gene Amplification Induced under Stress in Escherichia coli Andrew Slack, P. C Thornton, Daniel B Magner, Susan M Rosenberg, and P. J Hastings PMCID: PMC1428787 Dynamic Reprogramming of DNA Methylation at an Epigenetically Sensitive Allele in Mice Marnie E Blewitt, Nicola K Vickaryous, Andras Paldi, Haruhiko Koseki, and Emma Whitelaw PMCID: PMC1428789 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, and Francis S Collins PMCID: PMC1428788 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, and Sean M Grimmond PMCID: PMC1449894 Global Patterns in Human Mitochondrial DNA and Y-Chromosome Variation Caused by Spatial Instability of the Local Cultural Processes Vikrant Kumar, Banrida T Langstieh, Komal V Madhavi, Vegi M Naidu, Hardeep Pal Singh, Silpak Biswas, Kumarasamy Thangaraj, Lalji Singh, and B. Mohan Reddy PMCID: PMC1435684 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, and Yoshihide Hayashizaki PMCID: PMC1449896 Multiple Mechanisms Promote the Retained Expression of Gene Duplicates in the Tetraploid Frog Xenopus laevis Frédéric J. J Chain and Ben J Evans PMCID: PMC1449897 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, and Rachel M Kindt PMCID: PMC1440875 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, and Richard J Gibbons PMCID: PMC1440874 Bayesian Estimation of the Timing and Severity of a Population Bottleneck from Ancient DNA Yvonne L Chan, Christian N. K Anderson, and Elizabeth A Hadly PMCID: PMC1440876 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, and Charles Keller PMCID: PMC1449902 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, and Eric E Bouhassira PMCID: PMC1449906 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, and Jonathan A Eisen PMCID: PMC1449901 Corrects: Martin Wu, et al. Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet. 2005 November; 1(5): e65. |
