Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome

Yoshihide Hayashizaki, Piero Carninci

PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020063

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Balancing Selection and Its Effects on Sequences in Nearby Genome Regions

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PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020064

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

PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020062

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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

PLOS Genetics: published April 7, 2006 | https://doi.org/10.1371/journal.pgen.0020048

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

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

PLOS Genetics: published April 7, 2006 | https://doi.org/10.1371/journal.pgen.0020049

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

PLOS Genetics: published April 7, 2006 | https://doi.org/10.1371/journal.pgen.0020051

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, B. Mohan Reddy

PLOS Genetics: published April 14, 2006 | https://doi.org/10.1371/journal.pgen.0020053

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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

PLOS Genetics: published April 21, 2006 | https://doi.org/10.1371/journal.pgen.0020057

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

PLOS Genetics: published April 21, 2006 | https://doi.org/10.1371/journal.pgen.0020058

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

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

PLOS Genetics: published April 21, 2006 | https://doi.org/10.1371/journal.pgen.0020059

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

PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020065

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

PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020061

Multiple Mechanisms Promote the Retained Expression of Gene Duplicates in the Tetraploid Frog Xenopus laevis

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PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020056

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

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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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Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines

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PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020029

Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs

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PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020037

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

PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020046

Complex Loci in Human and Mouse Genomes

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A Method for Similarity Search of Genomic Positional Expression Using CAGE

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PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020044

SPA: A Probabilistic Algorithm for Spliced Alignment

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A Simple Physical Model Predicts Small Exon Length Variations

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PLOS Genetics: published April 28, 2006 | https://doi.org/10.1371/journal.pgen.0020045

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Heterotachy in Mammalian Promoter Evolution

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

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