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Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
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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
Technical Report |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020062
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Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines
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Jinfeng Liu, Julian Gough, Burkhard Rost
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020029
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SPA: A Probabilistic Algorithm for Spliced Alignment
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Erik van Nimwegen, Nicodeme Paul, Robert Sheridan, Mihaela Zavolan
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020024
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Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding
RNAs
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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
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020037
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Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome
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Yoshihide Hayashizaki, Piero Carninci
Editorial |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020063
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The Abundance of Short Proteins in the Mammalian Proteome
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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
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020052
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Pseudo–Messenger RNA: Phantoms of the Transcriptome
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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
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020023
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Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units
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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
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020046
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Mice and Men: Their Promoter Properties
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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
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020054
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Complex Loci in Human and Mouse Genomes
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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
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020047
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Heterotachy in Mammalian Promoter Evolution
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Martin S Taylor, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Colin A. M Semple
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020030
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A Method for Similarity Search of Genomic Positional Expression Using
CAGE
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Shigeto Seno, Yoichi Takenaka, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Hideo Matsuda
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020044
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A Simple Physical Model Predicts Small Exon Length Variations
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Tzu-Ming Chern, Erik van Nimwegen, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Mihaela Zavolan
Research Article |
published 28 Apr 2006
PLOS Genetics
https://doi.org/10.1371/journal.pgen.0020045
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Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain
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Jasmina Ponjavic, Peter L. Oliver, Gerton Lunter, Chris P. Ponting
Research Article |
published 21 Aug 2009
PLOS Genetics
https://doi.org/10.1371/journal.pgen.1000617