Exploration of small RNAs. by Hideya Kawaji, Yoshihide Hayashizaki

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Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference by Michiel de Hoon, Yoshihide Hayashizaki

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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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In vitro pull-down assay without expression constructs by Harukazu Suzuki, Chihiro Ogawa, Kengo Usui, Yoshihide Hayashizaki

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Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing by Mitsuoki Kawano, Chika Kawazu, Marina Lizio, Hideya Kawaji, Piero Carninci, Harukazu Suzuki, Yoshihide Hayashizaki

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Heterotachy in mammalian promoter evolution. by Martin S Taylor, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Colin A M Semple

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A simple physical model predicts small exon length variations. by Tzu-Ming Chern, Erik van Nimwegen, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Mihaela Zavolan

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RUNX1 regulates site specificity of DNA demethylation by recruitment of DNA demethylation machineries in hematopoietic cells by Takahiro Suzuki, Yuri Shimizu, Erina Furuhata, Shiori Maeda, Mami Kishima, Hajime Nishimura, Saaya Enomoto, Yoshihide Hayashizaki, Harukazu Suzuki

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Hotspots of De Novo Point Mutations in Induced Pluripotent Stem Cells by Masahito Yoshihara, Ryoko Araki, Yasuji Kasama, Misato Sunayama, Masumi Abe, Kohji Nishida, Hideya Kawaji, Yoshihide Hayashizaki, Yasuhiro Murakawa

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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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Discovery of molecular markers to discriminate corneal endothelial cells in the human body. by Masahito Yoshihara, Hiroko Ohmiya, Susumu Hara, Satoshi Kawasaki, FANTOM consortium, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji, Motokazu Tsujikawa, Kohji Nishida

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Effects of the turn-back primer on intermediate product generation in isothermal DNA amplification by Yuki Tanaka, Yasumasa Kimura, Yasumasa Mitani, Yuki Kawai, Alexander Lezhava, Shohei Noma, Michihira Tagami, Jun Kawai, Yoshihide Hayashizaki, Kengo Usui

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Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts by Tomoko Hirozane-Kishikawa, Toshiyuki Shiraki, Kazunori Waki, Mari Nakamura, Takahiro Arakawa, Jun Kawai, Michela Fagiolini, Takao K. Hensch, Yoshihide Hayashizaki, Piero Carninci

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Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays. by Yasumasa Kimura, Takahiro Soma, Naoko Kasahara, Diane Delobel, Takeshi Hanami, Yuki Tanaka, Michiel J L de Hoon, Yoshihide Hayashizaki, Kengo Usui, Matthias Harbers

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Development of a Tet-On Inducible Expression System for the Anhydrobiotic Cell Line, Pv11 by Shoko Tokumoto, Yugo Miyata, Kengo Usui, Ruslan Deviatiiarov, Takahiro Ohkawa, Sabina Kondratieva, Elena Shagimardanova, Oleg Gusev, Richard Cornette, Masayoshi Itoh, Yoshihide Hayashizaki, Takahiro Kikawada

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Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. by 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

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Metagenomic Diagnosis of Bacterial Infections by Shota Nakamura, Norihiro Maeda, Ionut Mihai Miron, Myonsun Yoh, Kaori Izutsu, Chidoh Kataoka, Takeshi Honda, Teruo Yasunaga, Takaaki Nakaya, Jun Kawai, Yoshihide Hayashizaki, Toshihiro Horii, Tetsuya Iida

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Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts. by Takahiro Suzuki, Mika Nakano-Ikegaya, Haruka Yabukami-Okuda, Michiel de Hoon, Jessica Severin, Satomi Saga-Hatano, Jay W Shin, Atsutaka Kubosaki, Christophe Simon, Yuki Hasegawa, Yoshihide Hayashizaki, Harukazu Suzuki

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Mice and men: their promoter properties. by 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

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