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PLOS Genetics  
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

Technical Report | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020062

Views: 9195Citations: 164Saves: 131 • Shares: 1

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

Jinfeng Liu, Julian Gough, Burkhard Rost

Research Article | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020029

Views: 12356Citations: 139Saves: 205 • Shares: 4

SPA: A Probabilistic Algorithm for Spliced Alignment

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

Views: 6242Citations: 23Saves: 0 • Shares: 0

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

Research Article | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020037

Views: 12360Citations: 153Saves: 0 • Shares: 0

Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome

Yoshihide Hayashizaki, Piero Carninci

Editorial | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020063

Views: 7382Citations: 27Saves: 0 • Shares: 0

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

Research Article | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020052

Views: 14493Citations: 200Saves: 258 • Shares: 2

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

Research Article | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020023

Views: 9819Citations: 60Saves: 102 • Shares: 3

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

Research Article | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020046

Views: 7533Citations: 34Saves: 0 • Shares: 0

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

Research Article | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020054

Views: 12879Citations: 87Saves: 0 • Shares: 0

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

Research Article | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020047

Views: 16531Citations: 276Saves: 190 • Shares: 2

Heterotachy in Mammalian Promoter Evolution

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

Views: 8732Citations: 108Saves: 0 • Shares: 0

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

Research Article | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020044

Views: 4313Citations: 4Saves: 0 • Shares: 0

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

Research Article | published 28 Apr 2006 PLOS Genetics

https://doi.org/10.1371/journal.pgen.0020045

Views: 6073Citations: 69Saves: 0 • Shares: 0

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

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

Views: 12252Citations: 356Saves: 308 • Shares: 0

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