Fast and accurate short-read alignment with hybrid hash-tree data structure by Junichiro Makino, Toshikazu Ebisuzaki, Ryutaro Himeno, Yoshihide Hayashizaki

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Aptamer-dependent full-length cDNA synthesis by overlap extension PCR by Yasumasa Mitani, Takayuki Nakayama, Matthias Harbers, Yoshihide Hayashizaki

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Constructing ORFeome resources with removable termination codons by Masayoshi Itoh, Ayako Yasunishi, Kengo Imamura, Mutsumi Kanamori-Katayama, Harukazu Suzuki, Masanori Suzuki, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki

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Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. by Daniel Carbajo, Shigeyuki Magi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair R R Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub, FANTOM consortium, Mariko Okada-Hatakeyama, Jessica C Mar

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Use of a competitive probe in assay design for genotyping of the UGT1A1*28 microsatellite polymorphism by the smart amplification process by Jun Watanabe, Yasumasa Mitani, Yuki Kawai, Takeshi Kikuchi, Yasushi Kogo, Atsuko Oguchi-Katayama, Hajime Kanamori, Kengo Usui, Masayoshi Itoh, Paul E. Cizdziel, Alexander Lezhava, Kenji Tatsumi, Yasushi Ichikawa, Shinji Togo, Hiroshi Shimada, Yoshihide Hayashizaki

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Systematic analysis of transcription start sites in avian development. by Marina Lizio, Ruslan Deviatiiarov, Hiroki Nagai, Laura Galan, Erik Arner, Masayoshi Itoh, Timo Lassmann, Takeya Kasukawa, Akira Hasegawa, Marian A Ros, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Hideya Kawaji, Oleg Gusev, Guojun Sheng

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Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer by Norihiro Maeda, Hiromi Nishiyori, Mari Nakamura, Chika Kawazu, Mitsuyoshi Murata, Hiromi Sano, Kengo Hayashida, Shiro Fukuda, Michihira Tagami, Akira Hasegawa, Kayoko Murakami, Kate Schroder, Katharine Irvine, David A. Hume, Yoshihide Hayashizaki, Piero Carninci, Harukazu Suzuki

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Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. by J Kenneth Baillie, Erik Arner, Carsten Daub, Michiel De Hoon, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Piero Carninci, Alistair R R Forrest, Yoshihide Hayashizaki, FANTOM Consortium, Geoffrey J Faulkner, Christine A Wells, Michael Rehli, Paul Pavli, Kim M Summers, David A Hume

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The reality of pervasive transcription. by Michael B Clark, Paulo P Amaral, Felix J Schlesinger, Marcel E Dinger, Ryan J Taft, John L Rinn, Chris P Ponting, Peter F Stadler, Kevin V Morris, Antonin Morillon, Joel S Rozowsky, Mark B Gerstein, Claes Wahlestedt, Yoshihide Hayashizaki, Piero Carninci, Thomas R Gingeras, John S Mattick

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Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation by James Fraser, Carmelo Ferrai, Andrea M Chiariello, Markus Schueler, Tiago Rito, Giovanni Laudanno, Mariano Barbieri, Benjamin L Moore, Dorothee CA Kraemer, Stuart Aitken, Sheila Q Xie, Kelly J Morris, Masayoshi Itoh, Hideya Kawaji, Ines Jaeger, Yoshihide Hayashizaki, Piero Carninci, Alistair RR Forrest, The FANTOM Consortium, Colin A Semple, Josée Dostie, Ana Pombo, Mario Nicodemi

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Complex Loci in human and mouse genomes. by 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

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