PUBLICATIONS

INDEX

2013

1. Pharmacogenetics of human ABC transporter ABCC11: new insights into apocrine gland growth and metabolite secretion
   Toshihisa Ishikawa, Yu Toyoda, Koh-ichiro Yoshiura, Norio Niikawa
   Frontiers in Genetics 3 Published online, (2013).
2. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
   Philippe Batut, Alexander Dobin, Charles Plessy, Piero Carninci, Thomas R. Gingeras.
   Genome Researchs 23, 169-180(2013).

2012

1. One-step detection of the 2009 pandemic influenza A(H1N1) virus by the RT-SmartAmp assay and its clinical validation.
   Yuki Kawai, Yasumasa Kimura, Alexander Lezhava, Hajime Kanamori, Kengo Usui, Takeshi Hanami, Yumiko Furuya, Takahiro Soma, Jean-Etienne Morlighem, Satomi Saga, Yuri Ishizu, Shintaro Aoki, Ryuta Endo, Atsuko Oguchi-Katayama,Yasushi Kogo, Yasumasa Mitani, Takefumi Ishidao, Chiharu kawakami, Hideshi Kurata, Takeyuki Saito, Norio Okazaki, Masatsugu Chikahira, Eiji Hayashi, Sei-ichi Tsuruoka, Tokumichi Toguchi, Yoshitomo Saito, Toshiaki Ban, Shinyu Izumi, Hideko Uryu, Koichiro Kudo, Yuko Sakai-Tagawa, Yoshihiro Kawaoka, Aizan Hirai, Yoshihide Hayashizaki, Toshihisa Ishikawa.
   PLoS One 7, e30236 (2012).
2. Emerging New Technology to Advance Personalized Medicine
   Toshihisa Ishikawa.
   Pharmacogenomics and Pharmacoproteomics 3, 1000e113 (2012).
3. Nonimmunoglobulin target loci of activation-induced cytidine deaminase (AID) share unique features with immunoglobulin genes.
   Lucia Kato, Nasim Begum, A. Maxwell Burroughs, Tomomitsu Doi, Jun Kawai, Carsten Daub, Takahisa Kawaguchi, Fumihiko Matsuda, Yoshihide Hayashizaki, Tasuku Honjo.
   Proceedings of the National Academy of Sciences of the United States of America, 109, 2479-2484 (2012).
4. Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.
   Masayoshi Itoh, Miki Kojima, Sayaka Nagao-Sato, Eri Saijo, Timo Lassmann, Mutsumi Kanamori-Katayama, Ai Kaiho, Marina Lizio, Hideya Kawaji, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki.
   PLoS One 7, e30809-e30809 (2012).
5. pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 50/30 arm variation including concomitant cleavage and polyuridylation patterns.
   A. Maxwell Burroughs, Mitsuoki Kawano, Yoshinari Ando, Carsten O. Daub, Yoshihide Hayashizaki.
   Nucleic Acids Research 40, 1424-1437 (2012).
6. Metazoan promoters: emerging characteristics and insights into transcriptional regulation.
   Boris Lenhard, Albin Sandelin, Piero Carninci.
   Nature review Genetics 13, 233-245 (2012).
7. Reconstruction of Monocyte Transcriptional Regulatory Network Accompanies Monocytic Functions in Human Fibroblasts.
   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.
   PLoS ONE 7, e33474 (2012).
8. Recent advances in pharmacogenomics of ABC transporters involved in breast cancer therapy.
   Toshihisa Ishikawa.
   Pharmacogenomics 13, 633-636 (2012).
9. RIKEN Cassava Initiative: Establishment of a Cassava Functional Genomics Platform.
   Yoshinori Utsumi, Tetsuya Sakurai, Yoshimi Umemura, Sarah Ayling, Manabu Ishitani, Jarunya Narangajavana, Punchapat Sojikul, Kanokporn Triwitayakorn, Minami Matsui, Ri-ichiroh Manabe, Kazuo Shinozaki, Motoaki Seki.
   Tropical Plant Biology 5, 110-116 (2012).
10. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
    Kate Schroder, Katharine M. Irvine, Martin S. Taylor, Nilesh J. Bokil, Kim-Anh Le Cao, Kelly-Anne Masterman, Larisa I. Labzin, Colin A. Semple, Ronan Kapetanovic, Lynsey Fairbairn, Altuna Akalin, Geoffrey J. Faulkner, John Kenneth Baillie, Milena Gongora, Carsten O. Daub, Hideya Kawaji, Geoffrey J. McLachlan, Nick Goldman, Sean M. Grimmond, Piero Carninci, Harukazu Suzuki, Yoshihide Hayashizaki, Boris Lenhard, David A. Hume, Matthew J. Sweet.
    Proceedings of the National Academy of Sciences of the United States of America 109, E944-E953 (2012).
11. Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain
    Alka Saxena, Akiko Wagatsuma, Yukihiko Noro, Takenobu Kuji, Atsuko Asaka-Oba, Akira Watahiki, Cecile Gurnot, Michela Fagiolini, Takao K. Hensch, Piero Carninci.
    BioTechniques 52, 381-385 (2012).
12. Quantitative Structure-Activity Relationship (QSAR) Analysis to Predict Drug-Drug Interactions of ABC transporter ABCG2
    Toshihisa Ishikawa, Hiroyuki Hirano, Hikaru Saito, Kazumi Sano, Yoji Ikegami, Noriyuki Yamaotsu, Syuichi Hirono.
    Mini-Reviews in Medicinal Chemistry 12, 505-514 (2012).
13. Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species
    Osamu Nishimura, Yukako Hirao, Hiroshi Tarui, Kiyokazu Agata.
    BMC Genomics 132,289 (2012).
14. Genetic variants in the human SLCO1B1 gene and individual variations in methotrexate clearance
    Toshihisa Ishikawa.
    Pharmacogenomics 13,993-995 (2012).
15. Effect of thiazole orange double-labeled thymidine on DNA duplex formation
    Yasumasa Kimura, Takeshi Hanami, Yuki Tanaka, Michiel J. L. de Hoon, Takahiro Soma, Matthias Harbers, Alexander Lezhava, Yoshihide Hayashizaki, Kengo Usui.
    Biochemistry 51, 6056-6067 (2012).
16. Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity
    Erik Arner, Niklas Mejhert, Agne Kulyte, Piotr J. Balwierz, Mikhail Pachkov, Mireille Cormont, Silvia Lorente-Cebrian, Anna Ehrlund, Jurga Laurencikiene, Per Heden, Karin Dahlman-Wright, Jean-Francois Tanti, Yoshihide Hayashizaki, Mikael Ryden, Ingrid Dahlman, Erik van Nimwegen, Carsten O. Daub, Peter Arner.
    Nucleic Acids Research 61, 1986-1993 (2012).
17. Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming
    Jay W. Shin, Takahiro Suzuki, Noriko Ninomiya, Mami Kishima, Yuki Hasegawa, Atsutaka Kubosaki, Haruka Yabukami, Yoshihide Hayashizaki, Harukazu Suzuki.
    Diabetes 40, e165 (2012).
18. Site-specific DICER and DROSHA RNA products control the DNA-damage response
    Sofia Francia, Flavia Michelini, Alka Saxena, Dave Tang, Michiel de Hoon, Viviana Anelli, Marina Mione, Piero Carninci, Fabrizio d'Adda di Fagagna.
    Nature 488, 231-235 (2012).
19. New Pyrosequencing Method to Analyze the Function of the Klenow Fragment (EXO-) for Unnatural Nucleic Acids: Pyrophosphorolysis and Incorporation Efficiency
    Takeshi Hanami, Rieko Oyama, Masayoshi Itoh, Ayako Yasunishi-Koyama,Yoshihide Hayashizaki.
    Nucleosides, Nucleotides and Nucleic Acidse 31, 608-615 (2012).
20. The SmartAmp method: Rapid Detection of SNPs in Thiopurine S-Methyltransferase and ABC Transporters ABCC4 and ABCG2.
    Wanping Aw, Alexander Lezhava, Akira Andoh, Hiroshi Tanaka, Yoshihide Hayashizaki, Toshihisa Ishikawa.
    Current Drug Metabolism 13, 968-977 (2012).
21. Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    Chao Cheng, Roger Alexander, Renqiang Min, Jing Leng, Kevin Y. Yip, Joel Rozowsky, Koon-Kiu Yan, Xianjun Dong, Sarah Djebali, Yijun Ruan, Carrie A. Davis, Piero Carninci, Timo Lassman, Thomas R. Gingeras, Roderic Guigo, Ewan Birney, Zhiping Weng, Michael Snyder, and Mark Gerstein. Genome Research 22, 1658-16679 (2012).
22. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    Thomas Derrien, Rory Johnson, Giovanni Bussotti, Andrea Tanzer, Sarah Djebali, Hagen Tilgner, Gregory Guernec, David Martin, Angelika Merkel David G. Knowles, Julien Lagarde, Lavanya Veeravalli, Xiaoan Ruan, Yijun Ruan, Timo Lassmann, Piero Carninci, James B. Brown, Leonard Lipovich, JoseM. Gonzalez, Mark Thomas, Carrie A. Davis, Ramin Shiekhattar, Thomas R. Gingeras, Tim J. Hubbard, Cedric Notredame, Jennifer Harrow, Roderic Guigo. Genome Research 22, 1775-1789 (2012).
23. An integrated encyclopedia of DNA elements in the human genome
    The ENCODE Project Consortium.
    Nature 489, 57-74 (2012).
24. Landscape of transcription in human cells
    Sarah Djebali, Carrie A. Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger, Chenghai Xue, Georgi K. Marinov, Jainab Khatun, Brian A. Williams, Chris Zaleski, Joel Rozowsky, Maik R?der, Felix Kokocinski, Rehab F. Abdelhamid, Tyler Alioto, Igor Antoshechkin, Michael T. Baer, Nadav S. Bar, Philippe Batut, Kimberly Bell, Ian Bell, Sudipto Chakrabortty, Xian Chen, Jacqueline Chrast, Joao Curado, Thomas Derrien, Jorg Drenkow, Erica Dumais, Jacqueline Dumais, Radha Duttagupta, Emilie Falconnet, Meagan Fastuca, Kata Fejes-Toth, Pedro Ferreira, Sylvain Foissac, Melissa J. Fullwood, Hui Gao, David Gonzalez, Assaf Gordon, Harsha Gunawardena, Cedric Howald, Sonali Jha, Rory Johnson, Philipp Kapranov, Brandon King, Colin Kingswood, Oscar J. Luo, Eddie Park, Kimberly Persaud, Jonathan B. Preall, Paolo Ribeca, Brian Risk, Daniel Robyr, Michael Sammeth, Lorian Schaffer, Lei-Hoon See, Atif Shahab, Jorgen Skancke, Ana Maria Suzuki, Hazuki Takahashi, Hagen Tilgner, Diane Trout, Nathalie Walters, Huaien Wang, John Wrobel, Yanbao Yu, Xiaoan Ruan, Yoshihide Hayashizaki, Jennifer Harrow, Mark Gerstein, Tim Hubbard, Alexandre Reymond, Stylianos E. Antonarakis, Gregory Hannon, Morgan C. Giddings, Yijun Ruan, Barbara Wold, Piero Carninci, Roderic Guigo, Thomas R. Gingeras.
    Nature 489, 101-108 (2012).
25. piRNAs warrant investigation in Rett Syndrome: An omics perspective
    Alka Saxena, Dave Tang, Piero Carninci
    Disease Markers 33, 261-275 (2012).
26. CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication
    Atsutaka Kubosaki, Yasuhiro Tomaru, Erina Furuhata, Takahiro Suzuki, Jay W. Shin,Christophe Simon,Yoshinari Ando, Ryota Hasegawa, Yoshihide Hayashizaki, Harukazu Suzuki
    Biochemical and Biophysical Research Communications 423, 141-147 (2012).
27. Novel small noncoding RNAs in mouse spermatozoa, zygotes and early embryos
    Mitsuoki Kawano, Hideya Kawaji, Valerie Grandjean, Jafar Kiani, Minoo Rassoulzadegan
    PloS One 79, e44542 (2012).
28. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat
    Claudia Carrieri, Laura Cimatti,Marta Biagioli, Anne Beugnet, Silvia Zucchelli, Stefania Fedele,Elisa Pesce, Isidre Ferrer, Licio Collavin, Claudio Santoro, Alistair R. R. Forrest, Piero Carninci, Stefano Biffo, Elia Stupka, Stefano Gustincich
    Nature 491, 454-457(2012).
29. Structure by Sequencing: Discovery of Hidden Messages in the Noncoding RNA Fraction
    Alessandro Bonetti, Piero Carninci
    Molecular Cell 48, 153-155 (2012).
30. Identification ofZNF395asanovelmodulator of adipogenesis
    Ryota Hasegawa, YasuhiroTomaru, MichieldeHoon, HarukazuSuzuki, Yoshihide Hayashizaki, JayW.Shin
    Experimental Cell Research Published online .
31. Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching
    Dave T. P. Tang, Charles Plessy, Md Salimullah, Ana Maria Suzuki, Raffaella Calligaris, Stefano Gustincich, Piero Carninci
    Nucleic Acid Research Published online, (2012).
32. NMDA Receptor Regulation Prevents Regression of Visual Cortical Function in the Absence of Mecp2
    Severine Durand, Annarita Patrizi, Kathleen B. Quast, Lea Hachigian, Roman Pavlyuk, Alka Saxena, Piero Carninci, Takao K. Hensch, Michela Fagiolini
    Neuron 76, 1078-1090 (2012).
33. Population transcriptomics with single-cell resolution: A new field made possible by microfluidics
    Charles Plessy, Linda Desbois, Teruo Fujii, Piero Carninci
    BioEssays Published online, (2012).

2011

1. Clinical Screening Assay for EGFR Mutations by PNA-Clamp Smart Amplification Process Version2 in Lung Adenocarcinoma
   Takuya Araki, Kimihiro Shimizu, Tomonori Nakamura, Masaru Baba, Yuki Kawai, Katsunori Nakamura, Yasumasa Mitani, Kyoko Obayashi, Tohru Aomori, Yukiyoshi Fujita, Andre Fujita, Yohei Miyamae, Seiichi Kakegawa, Kyoichi Kaira, Alexander Lezhava, Yoshihide Hayashizaki, Izumi Takeyoshi, Kojiro Yamamoto.
   Genetic Testing and Molecular Biomarkers, 26(5), 1213-1219 (2011)
2. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila
   Cernilogar Filippo M., Maria Cristina Onorati, Greg O. Kothe, Alexander Burroughs, Krisha-Mohan Parsi, Achim Breiling, Federica lo Sardo, Alka Saxena, Keita Miyoshi, Haruhiko Siomi, Mikiko C. Siomi, Piero Carninci, David S. Gilmour, Davide F.V. Corona, Valerio Orlando.
   Nature, Nov 6, 10.1038/nature10492 (2011)
3. Somatic retrotransposition alters the genetic landscape of the human brain
   Kenneth Baillie, Mark Barnett, Kyle Upton, Daniel Gerhardt, Todd Richmond, Fioravante Sapio, Paul Brennan, Patrizia Rizzu, Sarah Smith, Mark Fell, Richard Talbot, Stefano Gustincich, Tom Freeman, John Mattick, David Hume, Peter Heutink, Piero Carninci, Jeffrey Jeddeloh, Geoffrey Faulkner.
   Nature.2011, Oct 30;479(7374), 534-537 (2011)
4. LRRN4 and UPK3B are markers of primary mesothelial cells
   Mutsumi Kanamori-Katayama, Ai Kaiho, Yuri Ishizu, Yuko Okamura-Oho, Okio Hino, Masaaki Abe, Takumi Kishimoto, Hisahiko Sekihara, Yukio Nakamura, Harukazu Suzuki, Alistair Forrest, Yoshihide Hayashizaki.
   PLoS One, 6(10), e25391 (2011)
5. ADAMTSL6β rescues fibrillin-1 microfibril disorder in a Marfan syndrome mouse model through the promotion of fibrillin-1 assembly
   Masahiro Saito, Misaki Kurokawa, Masahito Oda, Masamitsu Oshima, Ko Tsutsui, Kazutaka Kosaka, Takamasa Yokoi, Kazuhisa Nakao, Miho Ogawa, Riichiro Manabe, Naoto Suda, Ganburged Ganjargal, Yasunobu Hada, Toshihide Noguchi, Toshio Teranaka, Kiyotoshi Sekiguchi, Toshi Yoneda, Tetsuji Otsuki.
   Journal of Biological Chemistry, 286, 38602-38613 (2011)
6. The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi
   Oscar Franzen, Erik Arner, Marcela Ferella, Patricia Respuela, Piero Carninci, Yoshihide Hayashizaki, Lena Aslund, Bjorn Andersson, Carsten Daub.
   PLoS Neglected Tropical Diseases, 5(8), e1283 (2011)
7. CC chemokine ligand 2 (Ccl2) enhances pluripotency of mouse iPS cells together with LIF
   Yuki Hasegawa, Naoko Takahashi, Alistair Forrest, Jay Shin, Harukazu Suzuki, Yoshihide Hayashizaki.
   Stem Cells, 29(8), 1196-1205 (2011)
8. Nuclear pore complex protein mediated nuclear localization of DICER protein in human cells
   Yoshinari Ando, Yasuhiro Tomaru, Ayako Morinaga, Alexander Burroughs, Hideya Kawaji, Atsutaka Kubosaki, Ryuichiro Kimura, Maiko Tagata, Yoko Ino, Hisashi Hirano, Joe Chiba, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki.
   PLoS One, 6(8), e23385 (2011)
9. Direct generation of functional dopaminergic neurons from mouse and human fibroblasts
   Massimiliano Caiazzo, Maria Teresa Dell’Anno, Elena Dvoretskova, Dejan Lazarevic, Stefano Taverna, Damiana Leo, Tatyana Sotnikova, Andrea Menegon, Paola Roncaglia, Giorgia Colciago, Giovanni Russo, Piero Carninci, Pezzoli Gianni, Raul R. Gainetdinov, Stefano Gustincich, Alexander Dityatev, Vania Broccoli.
   Nature, 476(7359), 224-227 (2011)
10. FXYD6, a Na,K-ATPase Regulator, Is Expressed in Type II Taste Cells
    Yoichiro Shindo, Kana Morishita, Eiichi Kotake, Hirohito Miura, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Akihiro Hino, Tomomasa Kanda, Yuko Kusakabe.
    Bioscience, Biotechnology, and Biochemistry, 75(6), 1061-1066 (2011)
11. miRNA profiling of bilateral rat hippocampal CA3 by deep-sequencing
    Yoshiaki Shinohara, Kazuko Yahagi, Mitsuoki Kawano, Hiromi Nishiyori, Chika Kawazu, Naoko Suzuki, Riichiro Manabe, Hajime Hirase.
    Biochemical and Biophysical Research Communications, 409(2), 293-298 (2011)
12. The bidirectional depolymerizer MCAK generates force by disassembling both microtubule ends
    Yusuke Oguchi, Seiichi Uchimura, Takashi Ohki, Sergey V. Mikhailenko, Shin'ichi Ishiwata.
    Nature Cell Biology, 13(7), 846-852 (2011)
13. Unamplified Cap Analysis of Gene Expression on a single molecule sequencer
    Mutsumi Kanamori, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Shintaro Katayama, Miki Kojima, Nicolas Bertin, Ai Kaiho, Noriko Ninomiya, Carsten Daub, Piero Carninci, Alistair Forrest, Yoshihide Hayashizaki.
    Genome Research, 21(7), 1150-1159 (2011)
14. Competition between a noncoding exon and a coding intron: Gomafu contains tandem UACUAAC repeats and regulates splicing kinetics
    Hitomi Tsuiji, Rei Yoshimoto, Yuko Hasegawa, Masaaki Furuno, Minoru Yoshida, Shinichi Nakagawa.
    Genes Cells, 16(5), 479-490 (2011)
15. A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
    Richard M. Myers, Piero Carninci, Yoshihide Hayashizaki, Timo Lassmann, Hazuki Takahashi, Rehab Abdelhamid, ENCODE Project Consortium.
    PLoS Biology, 9(4), e1001046 (2011)
16. Direct Genotyping of Cytochrome P450 2A6 Whole Gene Deletion from Human Blood Samples by the SmartAmp Method.
    Kenichi Azuma, Alexander Lezhava, Yasumasa Kimura, Yuri Ishizu, Toshihisa Ishikawa, Tetsuya Kamataki, Yoshihide Hayashizaki, Hiroshi Yamazaki.
    Clinica Chimica Acta, 412(13-14), 1249-1251 (2011)
17. Optimization of turn-back primers in isothermal amplification
    Yasumasa Kimura, Michiel De Hoon, Shintaro Aoki, Yuri Ishizu, Yuki Kawai, Yasushi Kogo, Carsten Daub, Alexander Lezhava, Erik Arner, Yoshihide Hayashizaki.
    Nucleic Acids Research, 39(9), e59 (2011)
18. Two-step cleavage of hairpin RNA with 5’ overhangs by human DICER
    Yoshinari Ando, Yoshiko Maida, Ayako Morinaga, Alexander Burroughs, Ryuichiro Kimura, Joe Chiba, Harukazu Suzuki, Kenkichi Masutomi, Yoshihide Hayashizaki.
    BMC Molecular Biology, 12, 6-6 (2011)
19. NanoCAGE: a high-resolution technique to discover and interrogate cells transcriptome.
    Md Salimullah, Mizuho Sakai, Charles Plessy, Piero Carninci.
    Cold Spring Harbor Protocols, 2011(2), (2011)
20. Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin
    Alexander Burroughs, Yoshinari Ando, Michiel De Hoon, Yasuhiro Tomaru, Harukazu Suzuki, Yoshihide Hayashizaki, Carsten Daub.
    RNA Biology, 8(1), 158-177 (2011)
21. Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system
    Alexander Burroughs, Lakshminarayan Iyer, L., Aravind
    Molecular BioSystem, 7(7), 2261-2277 (2011)
22. A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
    The ENCODE Project Consortium
    PLoS Biology 9(4) e1001046 (2011)
23. The Reality of Pervasive Transcription
    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. Gingera, John S. Mattick
    PLos Biology 9(7) e1000625 (2011)
24. Discovery of the "RNA continent" through a contrarian's research strategy
    Yoshihide Hayashizaki
    Genes and Genetic System 86 221-229 (2011)
25. Promoter architecture of mouse olfactory receptor genes
    Charles Plessy, Giovanni Pascarella, Nicolas Bertin, Altuna Akalin, Claudia Carrieri, Anne Vassalli, Dejan Lazarevic, Jessica Severin, Christina Vlachouli, Roberto Simone, Geoffrey J. Faulkner, Jun Kawai, Carsten O. Daub, Silvia Zucchelli, Yoshihide Hayashizaki, Peter Mombaerts, Boris Lenhard, Stefano Gustincich, Piero Carninci
    Genome Research 22 486-497 (2011)
26. Long Non coding RNA modifies chromatin
    Alka Saxena, Piero Carninci.
    Bioessays, 33(11) 830-839 (2011)
27. DNA amplification techniques in Pharmacogenomics
    Jean-Etienne Morlighem, Matthias Harbers, J Traeger-Synodinos, Alexander Lezhava.
    Pharmacogenomics, 12(6), 845-860 (2011)

2010

• A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. Max Burroughs, Yoshinari Ando, Michiel De Hoon, Yasuhiro Tomaru, Takahiro Nishibu, Ryo Ukekawa, Taku Funakoshi, Tsutomu Kurokawa, Harukazu Suzuki, Yoshihide Hayashizaki, Carsten Daub. Genome Research, 10, 1398-1410 (2010) .
• A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus). Cecilia Castano-Sanchez, Kanako Fuji, Akiyuki Ozaki, Osamu Hasegawa, Takashi Sakamoto, Kagayaki Morishima, Ichiro Nakaya, A Fujiwara, Tetsuji Masaoka, H Okamoto, Kengo Hayashida, Michihira Tagami, Jun Kawai, Yoshihide Hayashizaki, Nobuaki Okamoto. BMC Genomics, 11, 554-554 (2010).
• An atlas of combinatorial transcriptional regulation in mouse and man Timothy Ravasi, Carlo Cannistraci, Shintaro Katayama, Vladimir Bajic, Kai Tan, Altuna Akalin, Sebastian Schmeier, Atanas Kamburov, Mutsumi Kanamori, Nicolas Bertin, Piero Carninci, Carsten Daub, Alistair Forrest, Julian Gough, Sean Grimmond, Jung-Hoon Han, Takehiro Hashimoto, Winston Hide, Oliver Hofmann, Mandeep Kaur, Hideya Kawaji, Atsutaka Kubosaki, Timo Lassmann, Erik van Nimwegen, Cameron MacPherson, Chihiro Ogawa, Aleksandar Radovanovic, Ariel Schwartz, Rohan Teasdale, Jesper Tegner, Boris Lenhard, Sarah Teichmann, David Hume, Trey Ideker, Takahiro Arakawa, Noriko Ninomiya, Kayoko Murakami, Michihira Tagami, Shiro Fukuda, Kengo Imamura, Chikatoshi Kai, Ryoko Ishihara, Yayoi Kitazume, Jun Kawai, Harukazu Suzuki, Yoshihide Hayashizaki. Cell, 140, 744-752 (2010).
• ADAMTSL-5 IS A NOVEL EXTRACELLULAR MATRIX PROTEIN THAT BINDS TO FIBRILLIN-1 AND PROMOTES FIBRILLIN-1 FIBRIL FORMATION. Ko Tsutsui, Riichiroh Manabe, Tomiko Yamada, Itsuko Nakano, Yasuko Oguri, Douglas Keene, Lynn Sakai, Kiyotoshi Sekiguchi. Journal of Biological Chemistry, 285, 4870-4882 (2010).
• Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. M Vitezic, T Lassmann, AR Forrest, M Suzuki, Y Tomaru, J Kawai, P Carninci, H Suzuki, Y Hayashizaki, CO Daub. Nucleic Acids Research, 38, 8141-8148 (2010)
• Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. Anton Kratz, Erik Arner, Rintaro Saito, Atsutaka Kubosaki, Jun Kawai, Harukazu Suzuki, Piero Carninci, Takahiro Arakawa, Masaru Tomita, Yoshihide Hayashizaki, Carsten Daub. BMC Genomics, 11, 257-257 (2010).
• Correlation of Axillary Osmidrosis to a SNP in the ABCC11 Gene Determined by the SMart-Amplification Process (SMAP). Yoshikazu Inoue, Terumi Mori, Aki Sakurai, Yasumasa Mitani, Yu Toyoda, Toshihisa Ishikawa, Yoshihide Hayashizaki, Koh-ichiro Yoshiura, Yohko Yoshimura, Terumi Mori, Yasuo Sakai. American Society of Plastic Surgeons, 10(7), 1187-1197 (2010).
• Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Michiel De Hoon, Ryan Taft, Takehiro Hashimoto, Mutsumi Kanamori-Katayama, Hideya Kawaji, Mitsuoki Kawano, Mami Kishima, Timo Lassmann, Geoffrey Faulkner, John Mattick, Carsten Daub, Piero Carninci, Jun Kawai, Harukazu Suzuki, Yoshihide Hayashizaki. Genome Research, 20, 257-264 (2010).
• Direct and rapid genotyping of glutathione-S-transferase M1 and T1 from human blood specimens using the SmartAmp2 method. Ran Okada, Yuri Ishizu, Ryuta Endo, Alexander Lezhava, I Ieiri, Yuichi Sugiyama, Yoshihide Hayashizaki. Drug Metab Dispos., 38(10), 1636-9 (2010).
• Effect of the turn-back primer for intermediate product generation on isothermal DNA amplification. Yuki Tanaka, Yasumasa Kimura, Yasumasa Mitani, Yuki Kawai, Alexander Lezhava, Shohei Noma, Michihira Tagami, Jun Kawai, Yoshihide Hayashizaki, Kengo Usui. BioTechniques, 49, 888-892 (2010).
• eHive: An Artificial Intelligence workflow system for genomic analysis. Jessica Severin, Kathryn Beal, Albert Vilella, Stephen Fitzgerald, Michael Schuster, Leo Gordon, Abel Ureta-Vidal, Paul Flicek, Javier Herrero. BMC Bioinformatics, 11, 240-240 (2010).
• Emerging new technologies in Pharmacogenomics: rapid SNP detection, molecular dynamic simulation, and QSAR analysis methods to validate clinically important genetic variants of human ABC Transporter ABCB1 (P-gp/MDR1). Toshihisa Ishikawa, Aki Sakurai, Hiroyuki Hirano, Alexander Lezhava, Minoru Sakurai, Yoshihide Hayashizaki. Pharmacol Ther, 126(1), 69-81 (2010).
• Enhancement of antibody response by high mobility group box protein-1-based DNA immunization. Ryuichiro Kimura, Ryota Shiibashi, Masanori Suzuki, Yoshihide Hayashizaki, Joe Chiba. Journal of Immunological Methods, 361, 21-30 (2010).
• Exciton-primer mediated real-time monitoring of Smart Amplification reactions. Alexander Lezhava, Takefumi Ishidao, Yuri Ishizu, Kana Naito, Takeshi Hanami, Atsuko Katayama, Yasushi Kogo, Takahiro Soma, Shuji Ikeda, Kayoko Murakami, Chihiro Nogawa, Masayoshi Itoh, Yasumasa Mitani, Matthias Harbers, Akimitsu Okamoto, Yoshihide Hayashizaki. Human Mutation, 31(2), 208-17 (2010).
• Genome-wide analysis of promoter architecture in Drosophila melanogaster. Roger Hoskins, Jane Landolin, James Brown, Jeremy Sandler, Hazuki Takahashi, Timo Lassmann, Charles Yu, Benjamin Booth, Dayu Zhang, Kenneth Wan, Li Yang, Nathan Boley, Justen Andrews, Thomas Kaufman, Brenton Graveley, Peter Bickel, Piero Carninci, Joseph Carlson, Susan Celniker. Genome Research, 21, 182-192 (2010).
• High sensitivity TSS prediction: Estimates of locations where TSS cannot occur. Ulf Schaefer, Rimantas Kodzius, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir Bajic. PLoS ONE, 5, e13934-e13934 (2010).
• Identification and Characterization of nCLP2, a Novel C1q Family Protein Expressed in the Central Nervous System. Chisei Shimono, Riichiroh Manabe, Tomiko Yamada, Shiro Fukuda, Jun Kawai, Yutaka Furutani, Ko Tsutsui, Kazuhiro Ikenaka, Yoshihide Hayashizaki, Kiyotoshi Sekiguchi. Journal of Biochemistry, 147, 565-579 (2010).
• Linking new promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Charles Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone, Md Salimullah, Timo Lassmann, Morana Vitezic, Jessica Severin, Signe Olivarius, Dejan Lazarevic, Nadine Hornig, Valerio Orlando, Ian Bell, Hui Gao, Jacqueline Dumais, Phil Kapranov, Huaien Wang, Carrie Davis, Thomas Gingeras, Jun Kawai, Carsten Daub, Yoshihide Hayashizaki, Stefano Gustincich, Piero Carninci. Nature Methods, 7, 528-534 (2010).
• miR-148a Is an Androgen-Responsive MicroRNA that Promotes LNCaP Prostate Cell Growth by Repressing Its Target CAND1 Transcription. Taro Murata, Kenichi Takayama, Shintaro Katayama, Tomohiko Urano, Kuniko Horie-Inoue, Kazuhiro Ikeda, Satoru Takahashi, Yasuyoshi Ouchi, Yukio Honma, Chika Kawazu, Akira Hasegawa, Yoshihide Hayashizaki, Satoshi Inoue. Prostate Cancer and Pristatic Diseases, 13, 356-361 (2010).
• Linking new promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. C Plessy, N Bertin, H Takahashi, R Simone, M Salimullah, T Lassmann, M Vitezic, J Severin, S Olivarius, D Lazarevic, N Hornig, V Orlando, I Bell, H Gao, J Dumais, P Kapranov, H Wang, CA Davis, TR Gingeras, J Kawai, CO Daub, Y Hayashizaki, S Gustincich, P Carninci. Nature Methods, 7, 528-534 (2010)
• Mutation detection of epidermal growth factor receptor and KRAS genes using the smart amplification process version 2 from formalin-fixed, paraffin-embedded lung cancer tissue. Yohei Miyamae, Kimihiro Shimizu, Yasumasa Mitani, Takuya Araki, Yuki Kawai, Masaru Baba, Seiichi Kakegawa, Masayuki Sugano, Kyoichi Kaira, Alexander Lezhava, Yoshihide Hayashizaki, Koujirou Yamamoto, Izumi Takeyoshi. Journal of Molecular Diagnostics, 12, 257-264 (2010).
• NGSView: an extendable open source editor for next-generation sequencing data. Erik Arner, Yoshihide Hayashizaki, Carsten Daub. Bioinformatics, 26, 125-126 (2010).
• Novel ELISA Using Intracellular Biotinylated Antigen for Detection of Antibody Following DNA Immunization. Ryuichiro Kimura, Yoda Ayako, Yoshihide Hayashizaki, Joe Chiba. Japanese Journal of Infectious Diseases, 63, 41-48 (2010).
• Reduction of non-insert sequence reads by “dimer eliminator” LNA oligonucleotide for small RNA deep sequencing. Mitsuoki Kawano, Chika Kawazu, Marina Lizio, Hideya Kawaji, Piero Carninci, Harukazu Suzuki, Yoshihide Hayashizaki. BioTechniques, 49, 751-755 (2010)
• Sequencing of Isotope-labeled small RNA using Femtosecond Laser Ablation Time-of-Flight Mass Spectrometry. Mizuki Nishimura, Yoshinari Ando, Tohru Kobayashi, Yukari Matsuo, Harukazu Suzuki, Yoshihide Hayashizaki, Jun Kawai. Applied Physics Express, 3, 047002-1-047002-3 (2010).
• The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. Atsutaka Kubosaki, Gabriella Lindgren, Michihira Tagami, Christophe Simon, Yasuhiro Tomaru, Hisashi Miura, Takahiro Suzuki, Erik Arner, Alistair Forrest, Katharine Irvine, Kate Schroder, Yuki Hasegawa, Mutsumi Kanamori, Michael Rehli, David Hume, Jun Kawai, Masanori Suzuki, Harukazu Suzuki, Yoshihide Hayashizaki. Molecular Immunology, 47(14), 2295-2302 (2010).
• The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Santosh Atanur, Inanc Birol, Victor Guryev, Martin Hirst, Oliver Hummel, Catherine Morrissey, Jaques Behmoaras, Xose Fernandez-Suarez, Michelle Johnson, William McLaren, Giannino Patone, Enrico Petretto, Charles Plessy, Kathleen Rockland, Charles Rockland, Kathrin Saar, Yongyum Zhao, Piero Carninci, Paul Flicek, Theodore W. Kurtz, Edwin Cuppen, Michal Pravenec, Norbert Huebner, Steven Jones, Ewan Birney, Tim Aitman. Genome Research, 20, 791-803 (2010).
• The RIKEN integrated database of mammals. Hiroshi Masuya, Yuko Makita, Norio Kobayashi, Kozo Nishikata, Yuko Yoshida, Yoshiki Mochizuki, Koji Doi, Terue Takatsuki, Kazunori Waki, Nobuhiko Tanaka, Riichiro Mizoguchi, Koji Kozaki, Teiichi Furuichi, Hideya Kawaji, Shigeharu Wakana, Kaoru Fukami-Kobayashi, Osamu Ohara, Yoshihide Hayashizaki, Yuichi Obata, Tetsuro Toyoda. Nucleic Acids Research, 39, D861-70 (2010)
• Update of FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation Hideya Kawaji, Jessica Severin, Marina Lizio, Erik van Nimwegen, Rehli Michael, Kate Shroder, Katharine Irvine, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten Daub. Nucleic Acids Research, 39, D856-D860 (2010)

2009

• Identification of DNA regions and a set of transcriptional regulatory factors involved in combinatorial regulation of several human liver-enriched transcription factor genes. Hisashi Miura, Yasuhiro Tomaru, Misato Nakanishi, Shinji Kondo, Yoshihide Hayashizaki, Masanori Suzuki. Nucleic Acids Research, 37(3), 778-792 (2009).
• Tail variation of the folding primer affects the SmartAmp2 process differently. Yasumasa Kimura, Atsuko Oguchi-Katayama, Yuki Kawai, Kana Naito, Yasumasa Mitani, Jean-Etienne Morlighem, Yoshihide Hayashizaki, Alexander Lezhava. Biochemical and Biophysical Research Communications 383, 455-459 (2009).
• Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns. Kanako Kawaura, Keiichi Mochida, Akiko Enju, Yasushi Totoki, Atsushi Toyoda, Yoshiyuki Sakaki, Chikatoshi Kai, Jun Kawai, Yoshihide Hayashizaki, Motoaki Seki, Kazuo Shinozaki, Yasunari Ogihara. BMC Genomics, 10 (271), 1-11 (2009).
• Nanoscale elongating control of the self-assembled protein filament with the cysteine-introduced building blocks. Kengo Usui, Tei Maki, Fuyu Ito, Atushi Suenaga, Satoru Kidoaki, Masayoshi Itoh, Makoto Taiji, Takehisa Matsuda, Yoshihide Hayashizaki, Harukazu Suzuki. Protein Science, 18 (5), 960-969 (2009).
• Earwax, osmidrosis, and breast cancer: why does one SNP (538G>A) in the human ABC transporter ABCC11 gene determine earwax type? Yu Toyoda, Aki Sakurai, Yasumasa Mitani, Masahiro Nakashima, Koh-ichiro Yoshiura, Hiroshi Nakagawa, Yasuo Sakai, Ikuko Ota, Alexander Lezhava, Yoshihide Hayashizaki, Norio Niikawa, Toshihisa Ishikawa. The FASEB journal, 23(6), 2001-2013 (2009).
• Data-driven normalization strategies for High-throughput quantitative RT-PCR. Jessica Mar, Yasumasa Kimura, Kate Schroder, Katharine Irvine, Harukazu Suzuki, David Hume, John Quackenbush, Yoshihide Hayashizaki. BMC Bioinformatics, 10 (110), 1-32 (2009).
• Chromatin conformation signatures of cellular differentiation. James Fraser, Mathieu Rousseau, Solomon Shenker, Maria Ferraiuolo, Yoshihide Hayashizaki, Mathieu Blanchette, Josee Dostie. Genome Biology, 10 (R37), 1-18 (2009).
• Transcriptional features of genomic regulatory blocks. Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Bryne, Harukazu Suzuki, Carsten Daub, Yoshihide Hayashizaki, Boris Lenhard. Genome Biology, 10 (R38), 1-13 (2009).
• FANTOM4 EdgeExpressDB: an integrated database of genes, microRNAs, their promoters, expression dynamics and regulatory interactions. Jessica Severin, Andrew Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr Balwierz, Michiel De Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten Daub, Alistair Forrest. Genome Biology, 10 (R39), 1-9 (2009).
• The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine Irvine, David Hume, Alistair Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten Daub. Genome Biology, 10 (R40), 1-8 (2009).
• Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation. Atsutaka Kubosaki, Yasuhiro Tomaru, Michihira Tagami, Erik Arner, Hisashi Miura, Takahiro Suzuki, Masanori Suzuki, Harukazu Suzuki, Yoshihide Hayashizaki. Genome Biology, 10 (R41), 1-14 (2009).
• The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Harukazu Suzuki, Alistair Forrest, Erik van Nimwegen, Carsten Daub, Piotr Balwierz, Katharine Irvine, Timo Lassmann, Timothy Ravasi, Yuki Hasegawa, Michiel De Hoon, Shintaro Katayama, Kate Schroder, Piero Carninci, Yasuhiro Tomaru, Mutsumi Kanamori, Atsutaka Kubosaki, Altuna Akalin, Yoshinari Ando, Erik Arner, Maki Asada, Hiroshi Asahara, Timothy Bailey, Vladimir Bajic, Denis Bauer, Anthony Beckhouse, Nicolas Bertin, Johan Bjoｨrkegren, Frank Brombacher, Erika Bulger, Alistair Chalk, Joe Chiba, Nicole Cloonan, Adam Dawe, Josee Dostie, Par Engstrom, Magbubah Essack, Geoffrey Faulkner, J Lynn Fink, David Fredman, Ko Fujimori, Masaaki Furuno, Takashi Gojyobori, Julian Gough, Sean Grimmond, Mika Gustafsson, Megumi Hashimoto, Takehiro Hashimoto, Mariko Hatakeyama, Susanne Heinzel, Winston Hide, Oliver Hofmann, Michael Hornquist, Lukasz Huminiecki, Kazuho Ikeo, Naoko Imamoto, Satoshi Inoue, Yusuke Inoue, Ryoko Ishihara, Takao Iwayanagi, Anders Jacobsen, Mandeep Kaur, Hideya Kawaji, Markus Kerr, Ryuichiro Kimura, Syuhei Kimura, Yasumasa Kimura, Hiroaki Kitano, Hisashi Koga, Toshio Kojima, Shinji Kondo, Takeshi Konno, Anders Krogh, Adele Kruger, Ajit Kumar, Boris Lenhard, Andreas Lennartsson, Morten Lindow, Marina Lizio, Cameron MacPherson, Norihiro Maeda, Christopher Maher, Monique Maqungo, Jessica Mar, Nick Matigian, Hideo Matsuda, John Mattick, Stuart Meier, Sei Miyamoto, Etsuko Miyamoto-Sato, Kazuhiko Nakabayashi, Yutaka Nakachi, Mika Nakano, Sanne Nygaard, Toshitsugu Okayama, Yasushi Okazaki, Haruka Okuda-Yabukami, Valerio Orlando, Jun Otomo, Mikhail Pachkov, Nikolai Petrovsky, Charles Plessy, John Quackenbush, Aleksandar Radovanovic, Michael Rehli, Rintaro Saito, Albin Sandelin, Sebastian Schmeier, Christian Schonbach, Ariel Schwartz, Colin Semple, Miho Sera, Jessica Severin, Katsuhiko Shirahige, Cas Simons, George St. Laurent, Masanori Suzuki, Takahiro Suzuki, Matthew Sweet, Ryan Taft, Shizu Takeda, Yoichi Takenaka, Kai Tan, Martin Taylor, Rohan Teasdale, Jesper Tegner, Sarah Teichmann, Eivind Valen, Claes Wahlestedt, Kazunori Waki, Andrew Waterhouse, Christine Wells, Ole Winther, Linda Wu, Kazumi Yamaguchi, Hiroshi Yanagawa, Jun Yasuda, Mihaela Zavolan, David Hume, Takahiro Arakawa, Shiro Fukuda, Kengo Imamura, Chikatoshi Kai, Ai Kaiho, Tsugumi Kawashima, Chika Kawazu, Yayoi Kitazume, Miki Kojima, Hisashi Miura, Kayoko Murakami, Mitsuyoshi Murata, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Chihiro Ogawa, Takuma Sano, Cristophe Simon, Michihira Tagami, Yukari Takahashi, Jun Kawai, Yoshihide Hayashizaki. Nature Genetics, 41(5), 553-562 (2009).
• The regulated retrotransposon transcriptome of mammalian cells. Geoffrey J Faulkner, Yasumasa Kimura, Carsten O Daub, Shivangi Wani, Charles Plessy, Katharine M Irvine, Kate Schroder, Nicole Cloonan, Anita L Steptoe, Timo Lassmann, Kazunori Waki, Nadine Hornig, Takahiro Arakawa, Hazuki Takahashi, Jun Kawai, Alistair R R Forrest, Harukazu Suzuki, Yoshihide Hayashizaki, David A Hume, Valerio Orlando, Sean M Grimmond, Piero Carninci. Nature Genetics, 41(5), 563-571 (2009).
• Tiny RNAs associated with transcription start sites in animals. Ryan J Taft, Evgeny A Glazov, Nicole Cloonan, Cas Simons, Stuart Stephen, Geoffrey J Faulkner, Timo Lassmann, Alistair R R Forrest, Sean M Grimmond, Kate Schroder, Katharine Irvine, Takahiro Arakawa, Mari Nakamura, Atsutaka Kubosaki, Kengo Hayashida, Chika Kawazu, Mitsuyoshi Murata, Hiromi Nishiyori, Shiro Fukuda, Jun Kawai, Carsten O Daub, David A Hume, Harukazu Suzuki, Valerio Orlando, Piero Carninci, Yoshihide Hayashizaki, John S Mattick. Nature Genetics, 41(5), 572-578 (2009).
• Genetics, gene expression, and bioinformatics of the pituitary gland. Shannon Davis, Mary Anne Potok, Michelle Brinkmeier, Piero Carninci, Robert Lyons, James MacDonald, Michelle Fleming, Amanda Mortensen, Noboru Egashira, Karen Steel, Robert Osamura, Yoshihide Hayashizaki, Sally Camper. Hormon Research , 71 (Suppl. 2), 101-115 (2009).
• SDRF2GRAPH - a visualization tool of a spreadsheet-based description of experimental processes. Hideya Kawaji, Yoshihide Hayashizaki, Carsten Daub. BMC Informatics, 10 (133), 1-9 (2009).
• Rapid and cost-effective SNP detection method: application of SmartAmp2 to pharmacogenomics research. Yasumasa Mitani, Alexander Lezhava, Aki Sakurai, Akina Horikawa, Makoto Nagakura, Yoshihide Hayashizaki, Toshihisa Ishikawa. Pharmacogenomics, 10 (7), 1187-119 (2009).
• Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Piotr Balwierz, Piero Carninci, Carsten Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen. Genome Biology, 10 (R79), 1-2 (2009).
• High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line. Naoki Adati, Ming-Chih Huang, Takahiro Suzuki, Harukazu Suzuki, Toshio Kojima. BMC Research Notes, 2, 153 (2009).
• High-throughput verification of transcriptional starting sites by Deep-RACE. Signe Olivarius, Charles Plessy, Piero Carninci. BioTechniques, 46, 130-132 (2009).
• Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi. Yasuhiro Tomaru, Misato Nakanishi, Hisashi Miura, Yasumasa Kimura, Hiroki Okawa, Yusuke Ohta, Yoshihide Hayashizaki, Masanori Suzuki. Nucleic Acids Research, 37(4), 1049-1060 (2009).
• Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. Sakiko Nakamura, Yang Cheng-Song, Naomi Sakon, Mayo Ueda, Takahiro Tougan, Akifumi Yamashita, Naohisa Goto, Kazuo Takahashi, Teruo Yasunaga, Kazuyoshi Ikuta, Tetsuya Mizutani, Yoshiko Okamoto, Michihira Tagami, Ryouji Morita, Norihiro Maeda, Jun Kawai, Yoshihide Hayashizaki, Yoshiyuki Nagai, Toshihiro Horii, Tetsuya Iida, Takaaki Nakaya. PLoS ONE, 4(1), e4219 (2009).
• Altruistic functions for selfish DNA. Geoffrey Faulkner, Piero Carninci. Cell Cycle, 8(18), 2895-2900.
• Unexpected expression of α窶驤€ and β窶暖lobin inmesencephalic dopaminergic neurons and glial cells. Marta Biagioli, Milena Pinto, Daniela Cesselli, Marta Zaninello, Dejan Lazarevic, Paola Roncaglia, Roberto Simone, Christina Vlachouli, Charles Plessy, Nicolas Bertin, Antonio Beltrami, Kazuto Kobayashi, Vittorio Gallo, Claudio Santoro, Isidro Ferrer, Stefano Rivella, Carlo Alberto Beltrami, Piero Carninci, Elio Raviola, Stefano Gustincich. Proceeding of the National Academy of Sciences of the United States of Amaerica, 106, 15446-15451.
• Whole genome transcriptome analysis. Piero Carninci, Alistair Forrest. RNA Biology, 6 (2), 1-6 (2009).
• Molecular biology: The long and short of RNAs. Piero Carninci. Nature, 457, 974-975 (2009).
• Transcriptional features of genomic regulatory blocks. Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Bryne, Harukazu Suzuki, Carsten Daub, Yoshihide Hayashizaki, Boris Lenhard. Genome Biology, 10 (R38), 1-13 (2009).
• The regulated retrotransposon transcriptome of mammalian cells. Geoffrey Faulkner, Yasumasa Kimura, Carsten Daub, Shivangi Wani, Charles Plessy, Katharine Irvine, Kate Schroder, Nicole Cloonan, Anita Steptoe, Timo Lassmann, Kazunori Waki, Nadine Hornig, Takahiro Arakawa, Hazuki Takahashi, Jun Kawai, Alistair Forrest, Harukazu Suzuki, Yoshihide Hayashizaki, David Hume, Valerio Orlando, Sean Grimmond, Piero Carninci. Nat Genet, 41(5), 563-571 (2009).
• Chromatin conformation signatures of cellular differentiation. James Fraser, Mathieu Rousseau, Solomon Shenker, Maria Ferraiuolo, Yoshihide Hayashizaki, Mathieu Blanchette, Josee Dostie. Genome Biology, 10 (R37), 1-18 (2009).
• Data-driven normalization strategies for high-throughput quantitative RT-PCR. Jessica Mar, Yasumasa Kimura, Kate Schroder, Katharine Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David Hume, John Quackenbush. BMC Bioinformatics, 10 (110), 1-9 (2009).
• Earwax, osmidrosis, and breast cancer: why does one SNP (538G>A) in the human ABC transporter ABCC11 gene determine earwax type? Yu Toyoda, Aki Sakurai, Yasumasa Mitani, Masahiro Nakashima, Koh-ichiro Yoshiura, Hiroshi Nakagawa, Yasuo Sakai, Ikuko Ota, Alexander Lezhava, Yoshihide Hayashizaki, Norio Niikawa, Toshihisa Ishikawa. FASEB J, 23(6), 2001-2013 (2009).
• Tail variation of the folding primer affects the SmartAmp2 process differently. Yasumasa Kimura, Atsuko Katayama, Yuki Kawai, Kana Naito, Yasumasa Mitani, Jean-Etienne Morlighem, Yoshihide Hayashizaki, Alexander Lezhava. Biochem Biophys Res Commun, 383, 455-459 (2009).
• Biopython: freely available Python tools for computational molecular biology and bioinformatics. Peter Cock, Iddo Friedberg, Michiel De Hoon, Tiago Antao, Brad Chapman, Cymon Cox, Thomas Hamelryck, Frank Kauff, Bartek Wilczyﾅгki, Jeffrey Chang, Andrew Dalke. Bioinformatics, 25, 1422-1423 (2009).
• Nanoscale elongating control of the self-assembled protein filament with the cysteine-introduced building blocks . Kengo Usui, Tei Maki, Fuyu Ito, Atushi Suenaga, Satoru Kidoaki, Masayoshi Itoh, Makoto Taiji, Takehisa Matsuda, Yoshihide Hayashizaki, Harukazu Suzuki. Protein Science, 18 (5), 960-969 (2009).
• High-throughput verification of transcriptional starting sites by Deep-RACE. Signe Olivarius, Charles Plessy, Piero Carninci. Biotechniques, 46, 130-132 (2009).
• Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi. Yasuhiro Tomaru, Misato Nakanishi, Hisashi Miura, Yasumasa Kimura, Hiroki Okawa, Yusuke Ohta, Yoshihide Hayashizaki, Masanori Suzuki. Nucleic Acids Res, 37(4), 1049-1060 (2009).
• Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens using an Unbiased High-throughput Sequencing Approach. Sakiko Nakamura, Yang Cheng-Song, Naomi Sakon, Mayo Ueda, Takahiro Tougan, Akifumi Yamashita, Naohisa Goto, Kazuo Takahashi, Teruo Yasunaga, Kazuyoshi Ikuta, Tetsuya Mizutani, Yoshiko Okamoto, Michihira Tagami, Ryouji Morita, Norihiro Maeda, Jun Kawai, Yoshihide Hayashizaki, Yoshiyuki Nagai, Toshihiro Horii, Tetsuya Iida, Takaaki Nakaya. PLoS ONE, 4(1), e4219-e4219 (2009).

2009

• Identification of DNA regions and a set of transcriptional regulatory factors involved in combinatorial regulation of several human liver-enriched transcription factor genes. Hisashi Miura, Yasuhiro Tomaru, Misato Nakanishi, Shinji Kondo, Yoshihide Hayashizaki, Masanori Suzuki. Nucleic Acids Research, 37(3), 778-792.
• Tail variation of the folding primer affects the SmartAmp2 process differently. Yasumasa Kimura, Atsuko Oguchi-Katayama, Yuki Kawai, Kana Naito, Yasumasa Mitani, Jean-Etienne Morlighem, Yoshihide Hayashizaki, Alexander Lezhava. Biochemical and Biophysical Research Communications 383, 455-459.
• Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns. Kanako Kawaura, Keiichi Mochida, Akiko Enju, Yasushi Totoki, Atsushi Toyoda, Yoshiyuki Sakaki, Chikatoshi Kai, Jun Kawai, Yoshihide Hayashizaki, Motoaki Seki, Kazuo Shinozaki, Yasunari Ogihara. BMC Genomics, 10 (271), 1-11.
• Nanoscale elongating control of the self-assembled protein filament with the cysteine-introduced building blocks. Kengo Usui, Tei Maki, Fuyu Ito, Atushi Suenaga, Satoru Kidoaki, Masayoshi Itoh, Makoto Taiji, Takehisa Matsuda, Yoshihide Hayashizaki, Harukazu Suzuki. Protein Science, 18 (5), 960-969.
• Earwax, osmidrosis, and breast cancer: why does one SNP (538G>A) in the human ABC transporter ABCC11 gene determine earwax type? Yu Toyoda, Aki Sakurai, Yasumasa Mitani, Masahiro Nakashima, Koh-ichiro Yoshiura, Hiroshi Nakagawa, Yasuo Sakai, Ikuko Ota, Alexander Lezhava, Yoshihide Hayashizaki, Norio Niikawa, Toshihisa Ishikawa. The FASEB journal, 23(6), 2001-2013.
• Data-driven normalization strategies for High-throughput quantitative RT-PCR. Jessica Mar, Yasumasa Kimura, Kate Schroder, Katharine Irvine, Harukazu Suzuki, David Hume, John Quackenbush, Yoshihide Hayashizaki. BMC Bioinformatics, 10 (110), 1-32.
• Chromatin conformation signatures of cellular differentiation. James Fraser, Mathieu Rousseau, Solomon Shenker, Maria Ferraiuolo, Yoshihide Hayashizaki, Mathieu Blanchette, Josee Dostie. Genome Biology, 10 (R37), 1-18.
• Transcriptional features of genomic regulatory blocks. Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Bryne, Harukazu Suzuki, Carsten Daub, Yoshihide Hayashizaki, Boris Lenhard. Genome Biology, 10 (R38), 1-13.
• FANTOM4 EdgeExpressDB: an integrated database of genes, microRNAs, their promoters, expression dynamics and regulatory interactions. Jessica Severin, Andrew Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr Balwierz, Michiel De Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten Daub, Alistair Forrest. Genome Biology, 10 (R39), 1-9.
• The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine Irvine, David Hume, Alistair Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten Daub. Genome Biology, 10 (R40), 1-8.
• Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation. Atsutaka Kubosaki, Yasuhiro Tomaru, Michihira Tagami, Erik Arner, Hisashi Miura, Takahiro Suzuki, Masanori Suzuki, Harukazu Suzuki, Yoshihide Hayashizaki. Genome Biology, 10 (R41), 1-14.
• The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Harukazu Suzuki, Alistair Forrest, Erik van Nimwegen, Carsten Daub, Piotr Balwierz, Katharine Irvine, Timo Lassmann, Timothy Ravasi, Yuki Hasegawa, Michiel De Hoon, Shintaro Katayama, Kate Schroder, Piero Carninci, Yasuhiro Tomaru, Mutsumi Kanamori, Atsutaka Kubosaki, Altuna Akalin, Yoshinari Ando, Erik Arner, Maki Asada, Hiroshi Asahara, Timothy Bailey, Vladimir Bajic, Denis Bauer, Anthony Beckhouse, Nicolas Bertin, Johan Bjoｨrkegren, Frank Brombacher, Erika Bulger, Alistair Chalk, Joe Chiba, Nicole Cloonan, Adam Dawe, Josee Dostie, Par Engstrom, Magbubah Essack, Geoffrey Faulkner, J Lynn Fink, David Fredman, Ko Fujimori, Masaaki Furuno, Takashi Gojyobori, Julian Gough, Sean Grimmond, Mika Gustafsson, Megumi Hashimoto, Takehiro Hashimoto, Mariko Hatakeyama, Susanne Heinzel, Winston Hide, Oliver Hofmann, Michael Hornquist, Lukasz Huminiecki, Kazuho Ikeo, Naoko Imamoto, Satoshi Inoue, Yusuke Inoue, Ryoko Ishihara, Takao Iwayanagi, Anders Jacobsen, Mandeep Kaur, Hideya Kawaji, Markus Kerr, Ryuichiro Kimura, Syuhei Kimura, Yasumasa Kimura, Hiroaki Kitano, Hisashi Koga, Toshio Kojima, Shinji Kondo, Takeshi Konno, Anders Krogh, Adele Kruger, Ajit Kumar, Boris Lenhard, Andreas Lennartsson, Morten Lindow, Marina Lizio, Cameron MacPherson, Norihiro Maeda, Christopher Maher, Monique Maqungo, Jessica Mar, Nick Matigian, Hideo Matsuda, John Mattick, Stuart Meier, Sei Miyamoto, Etsuko Miyamoto-Sato, Kazuhiko Nakabayashi, Yutaka Nakachi, Mika Nakano, Sanne Nygaard, Toshitsugu Okayama, Yasushi Okazaki, Haruka Okuda-Yabukami, Valerio Orlando, Jun Otomo, Mikhail Pachkov, Nikolai Petrovsky, Charles Plessy, John Quackenbush, Aleksandar Radovanovic, Michael Rehli, Rintaro Saito, Albin Sandelin, Sebastian Schmeier, Christian Schonbach, Ariel Schwartz, Colin Semple, Miho Sera, Jessica Severin, Katsuhiko Shirahige, Cas Simons, George St. Laurent, Masanori Suzuki, Takahiro Suzuki, Matthew Sweet, Ryan Taft, Shizu Takeda, Yoichi Takenaka, Kai Tan, Martin Taylor, Rohan Teasdale, Jesper Tegner, Sarah Teichmann, Eivind Valen, Claes Wahlestedt, Kazunori Waki, Andrew Waterhouse, Christine Wells, Ole Winther, Linda Wu, Kazumi Yamaguchi, Hiroshi Yanagawa, Jun Yasuda, Mihaela Zavolan, David Hume, Takahiro Arakawa, Shiro Fukuda, Kengo Imamura, Chikatoshi Kai, Ai Kaiho, Tsugumi Kawashima, Chika Kawazu, Yayoi Kitazume, Miki Kojima, Hisashi Miura, Kayoko Murakami, Mitsuyoshi Murata, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Chihiro Ogawa, Takuma Sano, Cristophe Simon, Michihira Tagami, Yukari Takahashi, Jun Kawai, Yoshihide Hayashizaki. Nature Genetics, 41(5), 553-562.
• The regulated retrotransposon transcriptome of mammalian cells. Geoffrey J Faulkner, Yasumasa Kimura, Carsten O Daub, Shivangi Wani, Charles Plessy, Katharine M Irvine, Kate Schroder, Nicole Cloonan, Anita L Steptoe, Timo Lassmann, Kazunori Waki, Nadine Hornig, Takahiro Arakawa, Hazuki Takahashi, Jun Kawai, Alistair R R Forrest, Harukazu Suzuki, Yoshihide Hayashizaki, David A Hume, Valerio Orlando, Sean M Grimmond, Piero Carninci. Nature Genetics, 41(5), 563-571.
• Tiny RNAs associated with transcription start sites in animals. Ryan J Taft, Evgeny A Glazov, Nicole Cloonan, Cas Simons, Stuart Stephen, Geoffrey J Faulkner, Timo Lassmann, Alistair R R Forrest, Sean M Grimmond, Kate Schroder, Katharine Irvine, Takahiro Arakawa, Mari Nakamura, Atsutaka Kubosaki, Kengo Hayashida, Chika Kawazu, Mitsuyoshi Murata, Hiromi Nishiyori, Shiro Fukuda, Jun Kawai, Carsten O Daub, David A Hume, Harukazu Suzuki, Valerio Orlando, Piero Carninci, Yoshihide Hayashizaki, John S Mattick. Nature Genetics, 41(5), 572-578.
• Genetics, gene expression, and bioinformatics of the pituitary gland. Shannon Davis, Mary Anne Potok, Michelle Brinkmeier, Piero Carninci, Robert Lyons, James MacDonald, Michelle Fleming, Amanda Mortensen, Noboru Egashira, Karen Steel, Robert Osamura, Yoshihide Hayashizaki, Sally Camper. Hormon Research , 71 (Suppl. 2), 101-115.
• SDRF2GRAPH - a visualization tool of a spreadsheet-based description of experimental processes. Hideya Kawaji, Yoshihide Hayashizaki, Carsten Daub. BMC Informatics, 10 (133), 1-9.
• Rapid and cost-effective SNP detection method: application of SmartAmp2 to pharmacogenomics research. Yasumasa Mitani, Alexander Lezhava, Aki Sakurai, Akina Horikawa, Makoto Nagakura, Yoshihide Hayashizaki, Toshihisa Ishikawa. Pharmacogenomics, 10 (7), 1187-119.
• Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Piotr Balwierz, Piero Carninci, Carsten Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen. Genome Biology, 10 (R79), 1-2.
• High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line. Naoki Adati, Ming-Chih Huang, Takahiro Suzuki, Harukazu Suzuki, Toshio Kojima. BMC Research Notes, 2, 153.
• High-throughput verification of transcriptional starting sites by Deep-RACE. Signe Olivarius, Charles Plessy, Piero Carninci. BioTechniques, 46, 130-132 (2009).
• Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi. Yasuhiro Tomaru, Misato Nakanishi, Hisashi Miura, Yasumasa Kimura, Hiroki Okawa, Yusuke Ohta, Yoshihide Hayashizaki, Masanori Suzuki. Nucleic Acids Research, 37(4), 1049-1060 (2009).
• Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. Sakiko Nakamura, Yang Cheng-Song, Naomi Sakon, Mayo Ueda, Takahiro Tougan, Akifumi Yamashita, Naohisa Goto, Kazuo Takahashi, Teruo Yasunaga, Kazuyoshi Ikuta, Tetsuya Mizutani, Yoshiko Okamoto, Michihira Tagami, Ryouji Morita, Norihiro Maeda, Jun Kawai, Yoshihide Hayashizaki, Yoshiyuki Nagai, Toshihiro Horii, Tetsuya Iida, Takaaki Nakaya. PLoS ONE, 4(1), e4219 (2009).
• Altruistic functions for selfish DNA. Geoffrey Faulkner, Piero Carninci. Cell Cycle, 8(18), 2895-2900.
• Unexpected expression of α窶驤€ and β窶暖lobin inmesencephalic dopaminergic neurons and glial cells. Marta Biagioli, Milena Pinto, Daniela Cesselli, Marta Zaninello, Dejan Lazarevic, Paola Roncaglia, Roberto Simone, Christina Vlachouli, Charles Plessy, Nicolas Bertin, Antonio Beltrami, Kazuto Kobayashi, Vittorio Gallo, Claudio Santoro, Isidro Ferrer, Stefano Rivella, Carlo Alberto Beltrami, Piero Carninci, Elio Raviola, Stefano Gustincich. Proceeding of the National Academy of Sciences of the United States of Amaerica, 106, 15446-15451.
• Whole genome transcriptome analysis. Piero Carninci, Alistair Forrest. RNA Biology, 6 (2), 1-6 (2009).
• Molecular biology: The long and short of RNAs. Piero Carninci. Nature, 457, 974-975 (2009).

2008

• Rapidly evolving human promoter regions. Martin S Taylor Yoshihide Hayashizaki Piero Carninci Colin A M Semple. Nature Genetics, 40, 1262-1263 (2008).
• Rapid screening assay for K-ras mutations by the modified SMart Amplification Process. Kenji Tatsumi, Yasumasa Mitani, Jun Watanabe, Hideki Takakura, Kanako Hoshi, Yuki Kawai, Takeshi Kikuchi, Yasushi Kogo, Atsuko Oguchi-Katayama, Yasuhiro Tomaru, Hajime Kanamori, Kengo Usui, Masayoshi Itoh, Paul E. Cizdziel, Alexander Lezhava, Michio Ueda, Yasushi Ichikawa, Itaru Endo, Shinji Togo, Hiroshi Shimada, Yoshihide Hayashizaki. Journal of Molecular Diagnostics, 10, 520-526 (2008).
• Oliver Hofmann, Otavia Caballero, Tzeela Cohen, Ramon Chua, Christopher Maher, Sumir Panji, Ulf Schaefer, Minna Lehvaslaiho Adele Kruger, Brian Stevenson, Piero Carninci, Yoshihide Hayashizaki, Victor Jongeneel, Andy Simpson, Lloyd Old Winston Hide. Genome-wide analysis of cancer/testis gene expression, Proceedings of the National Academy of Sciences of the United States of America (PNAS), 105, 20428-20433 (2008).
• A resource for transcriptomic analysis in the mouse brain. Charles Plessy, Michela Fagiolini, Akiko Wagastuma, Norihiro Harasawa, Takenobu Kuji, Atsuko Asaka-Oba, Yukari Kanzaki Kazunori Waki, Hiroyuki Nakahara, Takao K. Hensch, Piero Carninci. PloS ONE, 3, 1-10 (2008).
• Metagenomic Diagnosis of Bacterial Infections: Direct Detection of Bacterial Pathogen in Human Specimens by Means of High-Throughput DNA Sequencing. Shota Nakamura Norihiro Maeda Ionut Mihai Miron Myonsun Yoh Kaori Izutsu Chidoh Kataoka Takeshi Honda Takaaki Nakaya Jun Kawai Yoshihide Hayashizaki Toshihiro Horii Tetsuya Iida. Emerging Infectious Diseases, 14, 1784-1786 (2008).
• Nkx2.2 antisense RNA overexpression enhanced oligodendrocytic differentiation. Shiro Tochitani, Yoshihide Hayashizaki. Biochemical and Biophysical Research Communications, 372, 691-696 (2008).
• An epigenetic aberration increased in intergenic regions of cloned mice. Hiromi Nishida, Takahiro Suzuki, Yuki Tsujimura, Shunsuke Komatsu, Yoshihide Hayashizaki. Mammalian Genome, 19, 667-674 (2008).
• Dynamics of Ablation Plasma Produced with a Femtosecond Laser Pulse in Electric Fields. Mizuki Nishimura, Yukari Matsuo, Tohru Kobayashi, Jun Kawai, Yoshihide Hayashizaki. Applied Surface Science (2008).
• Transcriptome-based systematic identification of extracellular matrix proteins Riichiroh Manabe, Ko Tsutsui, Tomiko Yamada, Mina Kimura, Chisei Shimono, Noriko Sanzen, Yutaka Furutani, Tomohiko Fukuda, Yasuko Oguri, Keiko Shimamoto, Daiji Kiyozumi, Yuya Sato, Yoshikazu Sado, Haruki Senoo, Shohei Yamashina, Shiro Fukuda, Jun Kawai, Nobuo Sugiura, Koji Kimata, Yoshihide Hayashizaki, Kiyotoshi Sekiguchi, Itsuko Nakano. Proceedings of the National Academy of Sciences of the United States of America, 105, 12849-12854 (2008).
• Non-coding RNA transcription: turning on neighbours. Piero Carninci. Nature Cell Biology, 10, 1023-1024 (2008)
• Structure of the C-terminal phosphotyrosineinteraction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding Mode. Hua Li, Seizou Kosiba, Fumiaki Hayashi, Naoya Tochino, Tadashi Tomozawa, Takuma Kasai, Takashi Yabuki, Yoko Motoda, Takushi Harada, Satoru Watanabe, Yoshihide Hayashizaki, Makoto Inoue, Akiko Tanaka, Takanori Kigawa, Shigeyuki Yokoyama. The Journal of biological chemistry, 283, 27165-27178 (2008).
• Gα14 is a candidate mediator of sweet/umami signal transduction in the posterior region of the mouse tongue. Yoichiro Shindo, Hirohito Miura, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Yuzo Ninomiya, Akihiro Hino, Tomomasa Kanda, Yuko Kusakabe. Biochemical and Biophysical Research Communications, 376, 504-508 (2008).
• Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Elizabeth Fozo, Mitsuoki Kawano, Yusuf Kaya, Kathy Mendieta, Kristi Jones, Alejandro Ocampo, Kenneth Rudd, Gisela Storz. Molecular Microbiology, 70, 1076-1093 (2008).
• Structure of the C-terminal PID domain of Fe65L1 complexed with the cytoplasmic tail of APP reveals a novel peptide binding Mode. Li H, Koshiba S, Hayashi F, Tochio N, Tomozawa T, Kasai T, Yabuki T, Motoda Y, Harada T, Watanabe S, Inoue M, Hayashizaki Y, Tanaka A, Kigawa T, Yokoyama S. J Biol Chem. Epub 2008 Jul 23.
• The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition. Nagata T, Suzuki S, Endo R, Shirouzu M, Terada T, Inoue M, Kigawa T, Kobayashi N, Guntert P, Tanaka A, Hayashizaki Y, Muto Y, Yokoyama S. Nucleic Acids Res. Epub 2008 Jul 19.
• FOXP1 is an androgen-responsive transcription factor that negatively regulates androgen receptor signaling in prostate cancer cells. Takayama K, Horie-Inoue K, Ikeda K, Urano T, Murakami K, Hayashizaki Y, Ouchi Y, Inoue S. Biochem Biophys Res Commun. Epub 2008 Jul 18.
• Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. Maeda N, Nishiyori H, Nakamura M, Kawazu C, Murata M, Sano H, Hayashida K, Fukuda S, Tagami M, Hasegawa A, Murakami K, Schroder K, Irvine K, Hume D, Hayashizaki Y, Carninci P, Suzuki H. Biotechniques. 2008 Jul;45(1):95-7.
• Hunting hidden transcripts. Carninci P. Nat Methods. 2008 Jul;5(7):587-9.
• Genome annotation. Kawaji H, Hayashizaki Y. Methods Mol Biol. 2008;452:125-39.
• Nkx2.2 antisense RNA overexpression enhanced oligodendrocytic differentiation. Tochitani S, Hayashizaki Y. Biochem Biophys Res Commun. 2008 Aug 8;372(4):691-6. Epub 2008 Jun 4.
• Solution Structure of the Second RNA Recognition Motif (RRM) Domain of Murine T Cell Intracellular Antigen-1 (TIA-1) and Its RNA Recognition Mode. Kuwasako K, Takahashi M, Tochio N, Abe C, Tsuda K, Inoue M, Terada T, Shirouzu M, Kobayashi N, Kigawa T, Taguchi S, Tanaka A, Hayashizaki Y, Guntert P, Muto Y, Yokoyama S. Biochemistry. 2008 May 24.
• Multifaceted mammalian transcriptome. Carninci P, Yasuda J, Hayashizaki Y. Curr Opin Cell Biol. 2008 May 9.
• Mutation of Dock5, a member of the guanine exchange factor Dock180 superfamily, in the rupture of lens cataract mouse. Omi N, Kiyokawa E, Matsuda M, Kinoshita K, Yamada S, Yamada K, Matsushima Y, Wang Y, Kawai J, Suzuki M, Hayashizaki Y, Hiai H. Exp Eye Res. 2008 May;86(5):828-34.
• Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference. de Hoon M, Hayashizaki Y. Biotechniques. 2008 Apr;44(5):627-8, 630, 632.
• Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells. Nakanishi M, Tomaru Y, Miura H, Hayashizaki Y, Suzuki M. Nucleic Acids Res. 2008 Apr 29.
• Sensitive detection of EGFR mutations using a competitive probe to suppress background in the SMart Amplification Process. Kawai Y, Kikuchi T, Mitani Y, Kogo Y, Itoh M, Usui K, Kanamori H, Kaiho A, Takakura H, Hoshi K, Cizdziel PE, Hayashizaki Y. Biologicals. 2008 Apr 25.
• Hidden layers of human small RNAs. Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y. BMC Genomics. 2008 Apr 10;9:157.
• Genome-wide analysis of abnormal H3K9 acetylation in cloned mice. Suzuki T, Kondo S, Wakayama T, Cizdziel PE, Hayashizaki Y. PLoS ONE. 2008 Apr 9;3(4):e1905.
• Role of nitric oxide synthesized by nitric oxide synthase 2 in liver regeneration. Kumamoto T, Togo S, Ishibe A, Morioka D, Watanabe K, Takahashi T, Shimizu T, Matsuo KI, Kubota T, Tanaka K, Nagashima Y, Kawai J, Hayashizaki Y, Shimada H. Liver Int. 2008 Apr 1.
• Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in heregulin-stimulated MCF-7 cells. Nagashima T, Suzuki T, Kondo S, Kuroki Y, Takahashi K, Ide K, Yumoto N, Hasegawa A, Toyoda T, Kojima T, Konagaya A, Suzuki H, Hayashizaki Y, Sakaki Y, Hatakeyama M. PLoS ONE. 2008 Mar 19;3(3):e1803.
• Expression profiling of transcriptional start sites. Kanamori-Katayama M, Katayama S, Suzuki H, Hayashizaki Y. DNA microarrays-methods express. 2008 Jan.
• Methods for increasing the utility of microarray data. Shimokawa K, Kodzius R, Matsumura Y, Hayashizaki Y. DNA microarrays-methods express. 2008 Jan.
• Time-of-flight detection of monoatomic ions generated by femtosecond laser ablation from large molecules. Kato T, Kobayashi T, Kurata-Nishimura M, Matsuo Y, Okamura-OhoY, Sano T, Oyama R, Kawai J, Hayashizaki Y. Nuclear Instruments and Methods in Physics Research. 2008 Jan 26:266: 992-997.
• Gene Expression During Liver Regeneration After Partial Hepatectomy in Mice Lacking Type 1 Tumor Necrosis Factor Receptor. Shimizu T, Togo S, Kumamoto T, Makino H, Morita T, Tanaka K, Kubota T, Ichikawa Y, Nagasima Y, Okazaki Y, Hayashizaki Y, Shimada H. J Surg Res. Epub 2008 Jan 31
• The RNA continent. J. Yasuda and Y. Hayashizaki. Adv Cancer Res, 99, 77-112 (2008)
• The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. C. Yamasaki and K. Murakami and Y. Fujii and Y. Sato and E. Harada and J. Takeda and T. Taniya and R. Sakate and S. Kikugawa and M. Shimada and M. Tanino and K. O. Koyanagi and R. A. Barrero and C. Gough and H. W. Chun and T. Habara and H. Hanaoka and Y. Hayakawa and P. B. Hilton and Y. Kaneko and M. Kanno and Y. Kawahara and T. Kawamura and A. Matsuya and N. Nagata and K. Nishikata and A. O. Noda and S. Nurimoto and N. Saichi and H. Sakai and R. Sanbonmatsu and R. Shiba and M. Suzuki and K. Takabayashi and A. Takahashi and T. Tamura and M. Tanaka and S. Tanaka and F. Todokoro and K. Yamaguchi and N. Yamamoto and T. Okido and J. Mashima and A. Hashizume and L. Jin and K. B. Lee and Y. C. Lin and A. Nozaki and K. Sakai and M. Tada and S. Miyazaki and T. Makino and H. Ohyanagi and N. Osato and N. Tanaka and Y. Suzuki and K. Ikeo and N. Saitou and H. Sugawara and C. O'Donovan and T. Kulikova and E. Whitfield and B. Halligan and M. Shimoyama and S. Twigger and K. Yura and K. Kimura and T. Yasuda and T. Nishikawa and Y. Akiyama and C. Motono and Y. Mukai and H. Nagasaki and M. Suwa and P. Horton and R. Kikuno and O. Ohara and D. Lancet and E. Eveno and E. Graudens and S. Imbeaud and M. A. Debily and Y. Hayashizaki and C. Amid and M. Han and A. Osanger and T. Endo and M. A. Thomas and M. Hirakawa and W. Makalowski and M. Nakao and N. S. Kim and H. S. Yoo and S. J. De Souza and F. Bonaldo Mde and Y. Niimura and V. Kuryshev and I. Schupp and S. Wiemann and M. Bellgard and M. Shionyu and L. Jia and D. Thierry-Mieg and J. Thierry-Mieg and L. Wagner and Q. Zhang and M. Go and S. Minoshima and M. Ohtsubo and K. Hanada and P. Tonellato and T. Isogai and J. Zhang and B. Lenhard and S. Kim and Z. Chen and U. Hinz and A. Estreicher and K. Nakai and I. Makalowska and W. Hide and N. Tiffin and L. Wilming and R. Chakraborty and M. B. Soares and M. L. Chiusano and Y. Suzuki and C. Auffray and Y. Yamaguchi-Kabata and T. Itoh and T. Hishiki and S. Fukuchi and K. Nishikawa and S. Sugano and N. Nomura and Y. Tateno and T. Imanishi and T. Gojobori. Nucleic Acids Res, 36, D793-799 (2008)
• Exploration of small RNAs. H. Kawaji and Y. Hayashizaki. PLoS Genet, 4, e22 (2008)
• Expression analysis for inverted effects of serotonin transporter inactivation. M. Ichikawa, Y. Okamura-Oho, K. Shimokawa, S. Kondo, S. Nakamura, H. Yokota, R. Himeno, K. P. Lesch, and Y. Hayashizaki. Biochem Biophys Res Commun, (2008)
• A code for transcription initiation in mammalian genomes. M. C. Frith, E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci, and A. Sandelin. Genome Res, 18, 1-12 (2008)
• Towards defining the nuclear proteome. J. L. Fink, S. Karunaratne, A. Mittal, D. M. Gardiner, N. Hamilton, D. Mahony, C. Kai, H. Suzuki, Y. Hayashizaki, and R. D. Teasdale. Genome Biol, 9, R15 (2008)
• A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. G. J. Faulkner, A. R. Forrest, A. M. Chalk, K. Schroder, Y. Hayashizaki, P. Carninci, D. A. Hume, and S. M. Grimmond. Genomics, (2008)

2007

• Structural and functional differences of SWIRM domain subtypes. M. Yoneyama, N. Tochio, T. Umehara, S. Koshiba, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, S. Watanabe, Y. Tomo, Y. Nishimura, T. Harada, T. Terada, M. Shirouzu, Y. Hayashizaki, O. Ohara, A. Tanaka, T. Kigawa, and S. Yokoyama. J Mol Biol, 369, 222-238 (2007)
• Use of a competitive probe in assay design for genotyping of the UGT1A1 *28 microsatellite polymorphism by the smart amplification process. J. Watanabe, Y. Mitani, Y. Kawai, T. Kikuchi, Y. Kogo, A. Oguchi-Katayama, H. Kanamori, K. Usui, M. Itoh, P. E. Cizdziel, A. Lezhava, K. Tatsumi, Y. Ichikawa, S. Togo, H. Shimada, and Y. Hayashizaki. Biotechniques, 43, 479-484 (2007)
• Environmental cDNA analysis of the genes involved in lignocellulose digestion in the symbiotic protist community of Reticulitermes speratus. N. Todaka, S. Moriya, K. Saita, T. Hondo, I. Kiuchi, H. Takasu, M. Ohkuma, C. Piero, Y. Hayashizaki, and T. Kudo. FEMS Microbiol Ecol, 59, 592-599 (2007)
• Functional screening revisited in the postgenomic era. S. Tochitani and Y. Hayashizaki. Mol Biosyst, 3, 195-207 (2007)
• Isolation of a novel mouse gene, mSVS-1/SUSD2, reversing tumorigenic phenotypes of cancer cells in vitro. T. Sugahara, Y. Yamashita, M. Shinomi, B. Yamanoha, H. Iseki, A. Takeda, Y. Okazaki, Y. Hayashizaki, K. Kawai, H. Suemizu, and T. Andoh. Cancer Sci, 98, 900-908 (2007)
• Large-scale clustering of CAGE tag expression data. K. Shimokawa, Y. Okamura-Oho, T. Kurita, M. C. Frith, J. Kawai, P. Carninci, and Y. Hayashizaki. BMC Bioinformatics, 8, 161 (2007)
• Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray. K. Satoh, K. Doi, T. Nagata, N. Kishimoto, K. Suzuki, Y. Otomo, J. Kawai, M. Nakamura, T. Hirozane-Kishikawa, S. Kanagawa, T. Arakawa, J. Takahashi-Iida, M. Murata, N. Ninomiya, D. Sasaki, S. Fukuda, M. Tagami, H. Yamagata, K. Kurita, K. Kamiya, M. Yamamoto, A. Kikuta, T. Bito, N. Fujitsuka, K. Ito, H. Kanamori, I. R. Choi, Y. Nagamura, T. Matsumoto, K. Murakami, K. Matsubara, P. Carninci, Y. Hayashizaki, and S. Kikuchi. PLoS ONE, 2, e1235 (2007)
• Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: causes of signal variation and false positive signals. D. Sasaki, S. Kondo, N. Maeda, T. R. Gingeras, Y. Hasegawa, and Y. Hayashizaki. Genomics, 89, 541-551 (2007)
• Mammalian RNA polymerase II core promoters: insights from genome-wide studies. A. Sandelin, P. Carninci, B. Lenhard, J. Ponjavic, Y. Hayashizaki, and D. A. Hume. Nat Rev Genet, 8, 424-436 (2007)
• Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. A. Purmann, J. Toedling, M. Schueler, P. Carninci, H. Lehrach, Y. Hayashizaki, W. Huber, and S. Sperling. Genomics, 89, 580-587 (2007)
• Correlating purity by microdissection with gene expression in gastric cancer tissue. Y. Otsuka, Y. Ichikawa, C. Kunisaki, G. Matsuda, H. Akiyama, M. Nomura, S. Togo, Y. Hayashizaki, and H. Shimada. Scand J Clin Lab Invest, 67, 367-379 (2007)
• Gemin2 plays an important role in stabilizing the survival of motor neuron complex. C. Ogawa, K. Usui, M. Aoki, F. Ito, M. Itoh, C. Kai, M. Kanamori-Katayama, Y. Hayashizaki, and H. Suzuki. J Biol Chem, 282, 11122-11134 (2007)
• Crystal structure analysis of the PHD domain of the transcription co-activator Pygopus. Y. Nakamura, T. Umehara, H. Hamana, Y. Hayashizaki, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, A. Tanaka, B. Padmanabhan, and S. Yokoyama. J Mol Biol, 370, 80-92 (2007)?
• Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome. Y. Nakamura, K. Nakano, T. Umehara, M. Kimura, Y. Hayashizaki, A. Tanaka, M. Horikoshi, B. Padmanabhan, and S. Yokoyama. Structure, 15, 179-189 (2007)
• Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology. Y. Mitani, A. Lezhava, Y. Kawai, T. Kikuchi, A. Oguchi-Katayama, Y. Kogo, M. Itoh, T. Miyagi, H. Takakura, K. Hoshi, C. Kato, T. Arakawa, K. Shibata, K. Fukui, R. Masui, S. Kuramitsu, K. Kiyotani, A. Chalk, K. Tsunekawa, M. Murakami, T. Kamataki, T. Oka, H. Shimada, P. E. Cizdziel, and Y. Hayashizaki. Nat Methods, 4, 257-262 (2007)
• Dynamic force spectroscopy of the specific interaction between the PDZ domain and its recognition peptides. T. Maki, S. Kidoaki, K. Usui, H. Suzuki, M. Ito, F. Ito, Y. Hayashizaki, and T. Matsuda. Langmuir, 23, 2668-2673 (2007)
• Simplified ontologies allowing comparison of developmental mammalian gene expression. A. Kruger, O. Hofmann, P. Carninci, Y. Hayashizaki, and W. Hide. Genome Biol, 8, R229 (2007)
• Ionization and fragmentation of solid C60 by femtosecond laser ablation. T. Kobayashi, T. Kato, Y. Matsuo, M. Kurata-Nishimura, J. Kawai, and Y. Hayashizaki. J Chem Phys, 126, 061101 (2007)
• Wavelength-dependent fragmentation and clustering observed after femtosecond laser ablation of solid C60. T. Kobayashi, T. Kato, Y. Matsuo, M. Kurata-Nishimura, Y. Hayashizaki, and J. Kawai. J Chem Phys, 127, 111101 (2007)
• Transcriptomics resources for functional genomics. J. Kawai, P. Carninci, and Y. Hayashizaki. Brief Funct Genomic Proteomic, 6, 171-179 (2007)
• CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts. S. Katayama, M. Kanamori-Katayama, K. Yamaguchi, P. Carninci, and Y. Hayashizaki. Genome Biol, 8, R42 (2007)
• Rapid detection of epidermal growth factor receptor mutations in lung cancer by the SMart-Amplification Process. K. Hoshi, H. Takakura, Y. Mitani, K. Tatsumi, N. Momiyama, Y. Ichikawa, S. Togo, T. Miyagi, Y. Kawai, Y. Kogo, T. Kikuchi, C. Kato, T. Arakawa, S. Uno, P. E. Cizdziel, A. Lezhava, N. Ogawa, Y. Hayashizaki, and H. Shimada. Clin Cancer Res, 13, 4974-4983 (2007)
• New phase of the transcriptome analysis. Y. Hayashizaki. Rinsho Ketsueki, 48, 1277-1280 (2007)
• Splicing bypasses 3' end formation signals to allow complex gene architectures. M. C. Frith, P. Carninci, C. Kai, J. Kawai, T. L. Bailey, Y. Hayashizaki, and J. S. Mattick. Gene, 403, 188-193 (2007)
• Solution structure of the general transcription factor 2I domain in mouse TFII-I protein. Y. Doi-Katayama, F. Hayashi, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, T. Kigawa, M. Yoshida, M. Shirouzu, T. Terada, Y. Hayashizaki, S. Yokoyama, and H. Hirota. Protein Sci, 16, 1788-1792 (2007)
• A set of polymorphic trinucleotide and tetranucleotide microsatellite markers for the Japanese flounder (Paralichthys olivaceus). C. Castano-Sanchez, K. Fuji, K. Hayashida, M. Tagami, A. Ozaki, O. Hasegawa, T. Sakamoto, J. Kawai, Y. Hayashizaki, and N. Okamoto. Anim Genet, 38, 75-76 (2007)
• Noncoding RNA transcription beyond annotated genes. P. Carninci and Y. Hayashizaki. Curr Opin Genet Dev, 17, 139-144 (2007)?
• Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. E. Birney and J. A. Stamatoyannopoulos and A. Dutta and R. Guigo and T. R. Gingeras and E. H. Margulies and Z. Weng and M. Snyder and E. T. Dermitzakis and R. E. Thurman and M. S. Kuehn and C. M. Taylor and S. Neph and C. M. Koch and S. Asthana and A. Malhotra and I. Adzhubei and J. A. Greenbaum and R. M. Andrews and P. Flicek and P. J. Boyle and H. Cao and N. P. Carter and G. K. Clelland and S. Davis and N. Day and P. Dhami and S. C. Dillon and M. O. Dorschner and H. Fiegler and P. G. Giresi and J. Goldy and M. Hawrylycz and A. Haydock and R. Humbert and K. D. James and B. E. Johnson and E. M. Johnson and T. T. Frum and E. R. Rosenzweig and N. Karnani and K. Lee and G. C. Lefebvre and P. A. Navas and F. Neri and S. C. Parker and P. J. Sabo and R. Sandstrom and A. Shafer and D. Vetrie and M. Weaver and S. Wilcox and M. Yu and F. S. Collins and J. Dekker and J. D. Lieb and T. D. Tullius and G. E. Crawford and S. Sunyaev and W. S. Noble and I. Dunham and F. Denoeud and A. Reymond and P. Kapranov and J. Rozowsky and D. Zheng and R. Castelo and A. Frankish and J. Harrow and S. Ghosh and A. Sandelin and I. L. Hofacker and R. Baertsch and D. Keefe and S. Dike and J. Cheng and H. A. Hirsch and E. A. Sekinger and J. Lagarde and J. F. Abril and A. Shahab and C. Flamm and C. Fried and J. Hackermuller and J. Hertel and M. Lindemeyer and K. Missal and A. Tanzer and S. Washietl and J. Korbel and O. Emanuelsson and J. S. Pedersen and N. Holroyd and R. Taylor and D. Swarbreck and N. Matthews and M. C. Dickson and D. J. Thomas and M. T. Weirauch and J. Gilbert and J. Drenkow and I. Bell and X. Zhao and K. G. Srinivasan and W. K. Sung and H. S. Ooi and K. P. Chiu and S. Foissac and T. Alioto and M. Brent and L. Pachter and M. L. Tress and A. Valencia and S. W. Choo and C. Y. Choo and C. Ucla and C. Manzano and C. Wyss and E. Cheung and T. G. Clark and J. B. Brown and M. Ganesh and S. Patel and H. Tammana and J. Chrast and C. N. Henrichsen and C. Kai and J. Kawai and U. Nagalakshmi and J. Wu and Z. Lian and J. Lian and P. Newburger and X. Zhang and P. Bickel and J. S. Mattick and P. Carninci and Y. Hayashizaki and S. Weissman and T. Hubbard and R. M. Myers and J. Rogers and P. F. Stadler and T. M. Lowe and C. L. Wei and Y. Ruan and K. Struhl and M. Gerstein and S. E. Antonarakis and Y. Fu and E. D. Green and U. Karaoz and A. Siepel and J. Taylor and L. A. Liefer and K. A. Wetterstrand and P. J. Good and E. A. Feingold and M. S. Guyer and G. M. Cooper and G. Asimenos and C. N. Dewey and M. Hou and S. Nikolaev and J. I. Montoya-Burgos and A. Loytynoja and S. Whelan and F. Pardi and T. Massingham and H. Huang and N. R. Zhang and I. Holmes and J. C. Mullikin and A. Ureta-Vidal and B. Paten and M. Seringhaus and D. Church and K. Rosenbloom and W. J. Kent and E. A. Stone and S. Batzoglou and N. Goldman and R. C. Hardison and D. Haussler and W. Miller and A. Sidow and N. D. Trinklein and Z. D. Zhang and L. Barrera and R. Stuart and D. C. King and A. Ameur and S. Enroth and M. C. Bieda and J. Kim and A. A. Bhinge and N. Jiang and J. Liu and F. Yao and V. B. Vega and C. W. Lee and P. Ng and A. Shahab and A. Yang and Z. Moqtaderi and Z. Zhu and X. Xu and S. Squazzo and M. J. Oberley and D. Inman and M. A. Singer and T. A. Richmond and K. J. Munn and A. Rada-Iglesias and O. Wallerman and J. Komorowski and J. C. Fowler and P. Couttet and A. W. Bruce and O. M. Dovey and P. D. Ellis and C. F. Langford and D. A. Nix and G. Euskirchen and S. Hartman and A. E. Urban and P. Kraus and S. Van Calcar and N. Heintzman and T. H. Kim and K. Wang and C. Qu and G. Hon and R. Luna and C. K. Glass and M. G. Rosenfeld and S. F. Aldred and S. J. Cooper and A. Halees and J. M. Lin and H. P. Shulha and X. Zhang and M. Xu and J. N. Haidar and Y. Yu and Y. Ruan and V. R. Iyer and R. D. Green and C. Wadelius and P. J. Farnham and B. Ren and R. A. Harte and A. S. Hinrichs and H. Trumbower and H. Clawson and J. Hillman-Jackson and A. S. Zweig and K. Smith and A. Thakkapallayil and G. Barber and R. M. Kuhn and D. Karolchik and L. Armengol and C. P. Bird and P. I. de Bakker and A. D. Kern and N. Lopez-Bigas and J. D. Martin and B. E. Stranger and A. Woodroffe and E. Davydov and A. Dimas and E. Eyras and I. B. Hallgrimsdottir and J. Huppert and M. C. Zody and G. R. Abecasis and X. Estivill and G. G. Bouffard and X. Guan and N. F. Hansen and J. R. Idol and V. V. Maduro and B. Maskeri and J. C. McDowell and M. Park and P. J. Thomas and A. C. Young and R. W. Blakesley and D. M. Muzny and E. Sodergren and D. A. Wheeler and K. C. Worley and H. Jiang and G. M. Weinstock and R. A. Gibbs and T. Graves and R. Fulton and E. R. Mardis and R. K. Wilson and M. Clamp and J. Cuff and S. Gnerre and D. B. Jaffe and J. L. Chang and K. Lindblad-Toh and E. S. Lander and M. Koriabine and M. Nefedov and K. Osoegawa and Y. Yoshinaga and B. Zhu and P. J. de Jong. Nature, 447, 799-816 (2007)
• Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells. K. W. Beisel, S. M. Rocha-Sanchez, S. J. Ziegenbein, K. A. Morris, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and R. L. Davis. Gene, 386, 11-23 (2007)
• Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function. L. L. Baxter, B. J. Hsu, L. Umayam, T. G. Wolfsberg, D. M. Larson, M. C. Frith, J. Kawai, Y. Hayashizaki, P. Carninci, and W. J. Pavan. Pigment Cell Res, 20, 201-209 (2007)

2006

• Alternate transcription of the Toll-like receptor signaling cascade. C. A. Wells, A. M. Chalk, A. Forrest, D. Taylor, N. Waddell, K. Schroder, S. R. Himes, G. Faulkner, S. Lo, T. Kasukawa, H. Kawaji, C. Kai, J. Kawai, S. Katayama, P. Carninci, Y. Hayashizaki, D. A. Hume, and S. M. Grimmond. Genome Biol, 7, R10 (2006)
• A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. K. Wada, J. T. Howard, P. McConnell, O. Whitney, T. Lints, M. V. Rivas, H. Horita, M. A. Patterson, S. A. White, C. Scharff, S. Haesler, S. Zhao, H. Sakaguchi, M. Hagiwara, T. Shiraki, T. Hirozane-Kishikawa, P. Skene, Y. Hayashizaki, P. Carninci, and E. D. Jarvis. Proc Natl Acad Sci U S A, 103, 15212-15217 (2006)
• Cancer research with non-coding RNA. Y. Tomaru and Y. Hayashizaki. Cancer Sci, 97, 1285-1290 (2006)
• Solution structure of the kinase-associated domain 1 of mouse microtubule-associated protein/microtubule affinity-regulating kinase 3. N. Tochio, S. Koshiba, N. Kobayashi, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, Y. Tomo, Y. Motoda, A. Kobayashi, A. Tanaka, Y. Hayashizaki, T. Terada, M. Shirouzu, T. Kigawa, and S. Yokoyama. Protein Sci, 15, 2534-2543 (2006)
• Heterotachy in mammalian promoter evolution. M. S. Taylor, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and C. A. Semple. PLoS Genet, 2, e30 (2006)
• Chemosensitivity prediction in esophageal squamous cell carcinoma: novel marker genes and efficacy-prediction formulae using their expression data. T. Shimokuni, K. Tanimoto, K. Hiyama, K. Otani, M. Ohtaki, J. Hihara, K. Yoshida, T. Noguchi, K. Kawahara, S. Natsugoe, T. Aikou, Y. Okazaki, Y. Hayashizaki, Y. Sato, S. Todo, E. Hiyama, and M. Nishiyama. Int J Oncol, 28, 1153-1162 (2006)
• A method for similarity search of genomic positional expression using CAGE. S. Seno, Y. Takenaka, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and H. Matsuda. PLoS Genet, 2, e44 (2006)
• Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. T. Ravasi, H. Suzuki, K. C. Pang, S. Katayama, M. Furuno, R. Okunishi, S. Fukuda, K. Ru, M. C. Frith, M. M. Gongora, S. M. Grimmond, D. A. Hume, Y. Hayashizaki, and J. S. Mattick. Genome Res, 16, 11-19 (2006)
• Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. J. Ponjavic, B. Lenhard, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and A. Sandelin. Genome Biol, 7, R78 (2006)
• Use of the SST-REX method for the identification of genes expressed at the condensation stage of chondrogenic cell line ATDC5. A. Noguchi, N. Watanabe, R. Fujimaki, T. Kitamura, Y. Hayashizaki, S. Miyaki, K. Tezuka, and N. Hozumi. J Bone Miner Metab, 24, 153-157 (2006)
• Histone H3 acetylated at lysine 9 in promoter is? associated with low nucleosome density in the vicinity of transcription start site in human cell. H. Nishida, T. Suzuki, S. Kondo, H. Miura, Y. Fujimura, and Y. Hayashizaki. Chromosome Res, 14, 203-211 (2006)?
• Transcriptional network dynamics in macrophage activation. R. Nilsson, V. B. Bajic, H. Suzuki, D. di Bernardo, J. Bjorkegren, S. Katayama, J. F. Reid, M. J. Sweet, M. Gariboldi, P. Carninci, Y. Hayashizaki, D. A. Hume, J. Tegner, and T. Ravasi. Genomics, 88, 133-142 (2006)
• Innovation of transcriptome analysis. H. Miura, Y. Tomaru, and Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 51, 2413-2419 (2006)
• Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. N. Maeda, T. Kasukawa, R. Oyama, J. Gough, M. Frith, P. G. Engstrom, B. Lenhard, R. N. Aturaliya, S. Batalov, K. W. Beisel, C. J. Bult, C. F. Fletcher, A. R. Forrest, M. Furuno, D. Hill, M. Itoh, M. Kanamori-Katayama, S. Katayama, M. Katoh, T. Kawashima, J. Quackenbush, T. Ravasi, B. Z. Ring, K. Shibata, K. Sugiura, Y. Takenaka, R. D. Teasdale, C. A. Wells, Y. Zhu, C. Kai, J. Kawai, D. A. Hume, P. Carninci, and Y. Hayashizaki. PLoS Genet, 2, e62 (2006)?
• Genome-wide survey of imprinted genes. N. Maeda and Y. Hayashizaki. Cytogenet Genome Res, 113, 144-152 (2006)
• Crystal structure of the RUN domain of the RAP2-interacting protein x. M. Kukimoto-Niino, T. Takagi, R. Akasaka, K. Murayama, T. Uchikubo-Kamo, T. Terada, M. Inoue, S. Watanabe, A. Tanaka, Y. Hayashizaki, T. Kigawa, M. Shirouzu, and S. Yokoyama. J Biol Chem, 281, 31843-31853 (2006)
• CAGE: cap analysis of gene expression. R. Kodzius, M. Kojima, H. Nishiyori, M. Nakamura, S. Fukuda, M. Tagami, D. Sasaki, K. Imamura, C. Kai, M. Harbers, Y. Hayashizaki, and P. Carninci. Nat Methods, 3, 211-222 (2006)
• CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. H. Kawaji, T. Kasukawa, S. Fukuda, S. Katayama, C. Kai, J. Kawai, P. Carninci, and Y. Hayashizaki. Nucleic Acids Res, 34, D632-636 (2006)
• Dynamic usage of transcription start sites within core promoters. H. Kawaji, M. C. Frith, S. Katayama, A. Sandelin, C. Kai, J. Kawai, P. Carninci, and Y. Hayashizaki. Genome Biol, 7, R118 (2006)
• Constructing ORFeome resources with removable termination codons. M. Itoh, A. Yasunishi, K. Imamura, M. Kanamori-Katayama, H. Suzuki, M. Suzuki, P. Carninci, J. Kawai, and Y. Hayashizaki. Biotechniques, 41, 44, 46, 48 passim (2006)
• Genome Network and FANTOM3: assessing the complexity of the transcriptome. Y. Hayashizaki and P. Carninci. PLoS Genet, 2, e63 (2006)
• A RecA-mediated exon profiling method. Y. Hasegawa, S. Fukuda, K. Shimokawa, S. Kondo, N. Maeda, and Y. Hayashizaki. Nucleic Acids Res, 34, e97 (2006)
• Structure of the UNC5H2 death domain. N. Handa, M. Kukimoto-Niino, R. Akasaka, K. Murayama, T. Terada, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, E. Nunokawa, A. Tanaka, Y. Hayashizaki, T. Kigawa, M. Shirouzu, and S. Yokoyama. Acta Crystallogr D Biol Crystallogr, 62, 1502-1509 (2006)
• The crystal structure of mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain. N. Handa, M. Kukimoto-Niino, R. Akasaka, S. Kishishita, K. Murayama, T. Terada, M. Inoue, T. Kigawa, S. Kose, N. Imamoto, A. Tanaka, Y. Hayashizaki, M. Shirouzu, and S. Yokoyama. J Mol Biol, 363, 114-124 (2006)
• The complexity of the mammalian transcriptome. S. Gustincich, A. Sandelin, C. Plessy, S. Katayama, R. Simone, D. Lazarevic, Y. Hayashizaki, and P. Carninci. J Physiol, 575, 321-332 (2006)
• Clusters of internally primed transcripts reveal novel long noncoding RNAs. M. Furuno, K. C. Pang, N. Ninomiya, S. Fukuda, M. C. Frith, C. Bult, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, J. S. Mattick, and H. Suzuki. PLoS Genet, 2, e37 (2006)
• Pseudo-messenger RNA: phantoms of the transcriptome. M. C. Frith, L. G. Wilming, A. Forrest, H. Kawaji, S. L. Tan, C. Wahlestedt, V. B. Bajic, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, T. L. Bailey, and L. Huminiecki. PLoS Genet, 2, e23 (2006)
• Evolutionary turnover of mammalian transcription start sites. M. C. Frith, J. Ponjavic, D. Fredman, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and A. Sandelin. Genome Res, 16, 713-722 (2006)
• The abundance of short proteins in the mammalian proteome. M. C. Frith, A. R. Forrest, E. Nourbakhsh, K. C. Pang, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, T. L. Bailey, and S. M. Grimmond. PLoS Genet, 2, e52 (2006)
• Discrimination of non-protein-coding transcripts from protein-coding mRNA. M. C. Frith, T. L. Bailey, T. Kasukawa, F. Mignone, S. K. Kummerfeld, M. Madera, S. Sunkara, M. Furuno, C. J. Bult, J. Quackenbush, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, G. Pesole, and J. S. Mattick. RNA Biol, 3, 40-48 (2006)
• PhosphoregDB: the tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. A. R. Forrest, D. F. Taylor, J. L. Fink, M. M. Gongora, C. Flegg, R. D. Teasdale, H. Suzuki, M. Kanamori, C. Kai, Y. Hayashizaki, and S. M. Grimmond. BMC Bioinformatics, 7, 82 (2006)
• Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. A. R. Forrest, D. F. Taylor, M. L. Crowe, A. M. Chalk, N. J. Waddell, G. Kolle, G. J. Faulkner, R. Kodzius, S. Katayama, C. Wells, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and S. M. Grimmond. Genome Biol, 7, R5 (2006)
• LOCATE: a mouse protein subcellular localization database. J. L. Fink, R. N. Aturaliya, M. J. Davis, F. Zhang, K. Hanson, M. S. Teasdale, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and R. D. Teasdale. Nucleic Acids Res, 34, D213-217 (2006)?
• Complex Loci in human and mouse genomes. P. G. Engstrom, H. Suzuki, N. Ninomiya, A. Akalin, L. Sessa, G. Lavorgna, A. Brozzi, L. Luzi, S. L. Tan, L. Yang, G. Kunarso, E. L. Ng, S. Batalov, C. Wahlestedt, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, C. Wells, V. B. Bajic, V. Orlando, J. F. Reid, B. Lenhard, and L. Lipovich. PLoS Genet, 2, e47 (2006)
• Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. M. J. Davis, K. A. Hanson, F. Clark, J. L. Fink, F. Zhang, T. Kasukawa, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and R. D. Teasdale. PLoS Genet, 2, e46 (2006)
• Insights into social insects from the genome of the honeybee Apis mellifera. International Honeybee Genome Consortium. Nature, 443, 931-949 (2006)
• A simple physical model predicts small exon length variations. T. M. Chern, E. van Nimwegen, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and M. Zavolan. PLoS Genet, 2, e45 (2006)
• Genome-wide analysis of mammalian promoter architecture and evolution. P. Carninci, A. Sandelin, B. Lenhard, S. Katayama, K. Shimokawa, J. Ponjavic, C. A. Semple, M. S. Taylor, P. G. Engstrom, M. C. Frith, A. R. Forrest, W. B. Alkema, S. L. Tan, C. Plessy, R. Kodzius, T. Ravasi, T. Kasukawa, S. Fukuda, M. Kanamori-Katayama, Y. Kitazume, H. Kawaji, C. Kai, M. Nakamura, H. Konno, K. Nakano, S. Mottagui-Tabar, P. Arner, A. Chesi, S. Gustincich, F. Persichetti, H. Suzuki, S. M. Grimmond, C. A. Wells, V. Orlando, C. Wahlestedt, E. T. Liu, M. Harbers, J. Kawai, V. B. Bajic, D. A. Hume, and Y. Hayashizaki. Nat Genet, 38, 626-635 (2006)
• Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. M. Brahmachary, C. Schonbach, L. Yang, E. Huang, S. L. Tan, R. Chowdhary, S. P. Krishnan, C. Y. Lin, D. A. Hume, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and V. B. Bajic. BMC Bioinformatics, 7 Suppl 5, S8 (2006)
• Mice and men: their promoter properties. V. B. Bajic, S. L. Tan, A. Christoffels, C. Schonbach, L. Lipovich, L. Yang, O. Hofmann, A. Kruger, W. Hide, C. Kai, J. Kawai, D. A. Hume, P. Carninci, and Y. Hayashizaki. PLoS Genet, 2, e54 (2006)
• LPS regulates proinflammatory gene expression in macrophages by altering histone deacetylase expression. H. T. Aung, K. Schroder, S. R. Himes, K. Brion, W. van Zuylen, A. Trieu, H. Suzuki, Y. Hayashizaki, D. A. Hume, M. J. Sweet, and T. Ravasi. Faseb J, 20, 1315-1327 (2006)
• Subcellular localization of mammalian type II membrane proteins. R. N. Aturaliya, J. L. Fink, M. J. Davis, M. S. Teasdale, K. A. Hanson, K. C. Miranda, A. R. Forrest, S. M. Grimmond, H. Suzuki, M. Kanamori, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, and R. D. Teasdale. Traffic, 7, 613-625 (2006)
• Restriction landmark genomic scanning. Y. Ando and Y. Hayashizaki. Nat Protoc, 1, 2774-2783 (2006)

2005

• Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3. K. Usui, S. Katayama, M. Kanamori-Katayama, C. Ogawa, C. Kai, M. Okada, J. Kawai, T. Arakawa, P. Carninci, M. Itoh, K. Takio, M. Miyano, S. Kidoaki, T. Matsuda, Y. Hayashizaki, and H. Suzuki. Genome Biol, 6, R98 (2005)
• Dextran sulfate suppresses cell adhesion and cell cycle progression of melanoma cells. T. Takagi, C. Sakakura, S. Kin, Y. Nakase, K. Fukuda, K. Shimomura, T. Ito, J. Fujiyama, J. Yamasaki, H. Tsujimoto, Y. Okazaki, Y. Hayashizaki, H. Yamagishi, and A. Hagiwara. Anticancer Res, 25, 895-902 (2005)
• Human genome research enters a new phase. H. Suzuki and Y. Hayashizaki. Genome Biol, 6, 337 (2005)
• LPS regulates a set of genes in primary murine macrophages by antagonising CSF-1 action. D. P. Sester, A. Trieu, K. Brion, K. Schroder, T. Ravasi, J. A. Robinson, R. C. McDonald, V. Ripoll, C. A. Wells, H. Suzuki, Y. Hayashizaki, K. J. Stacey, D. A. Hume, and M. J. Sweet. Immunobiology, 210, 97-107 (2005)
• RNAdb--a comprehensive mammalian noncoding RNA database. K. C. Pang, S. Stephen, P. G. Engstrom, K. Tajul-Arifin, W. Chen, C. Wahlestedt, B. Lenhard, Y. Hayashizaki, and J. S. Mattick. Nucleic Acids Res, 33, D125-130 (2005)
• Ssdp1 regulates head morphogenesis of mouse embryos by activating the Lim1-Ldb1 complex. N. Nishioka, S. Nagano, R. Nakayama, H. Kiyonari, T. Ijiri, K. Taniguchi, W. Shawlot, Y. Hayashizaki, H. Westphal, R. R. Behringer, Y. Matsuda, S. Sakoda, H. Kondoh, and H. Sasaki. Development, 132, 2535-2546 (2005)
• Naturally occurring antisense RNA of histone H2a in mouse cultured cell lines. H. Nishida, Y. Tomaru, Y. Oho, and Y. Hayashizaki. BMC Genet, 6, 23 (2005)
• A novel replication-independent histone H2a gene in mouse. H. Nishida, T. Suzuki, Y. Tomaru, and Y. Hayashizaki. BMC Genet, 6, 10 (2005)
• Comparative analysis of expression of histone H2a genes in mouse. H. Nishida, T. Suzuki, H. Ookawa, Y. Tomaru, and Y. Hayashizaki. BMC Genomics, 6, 108 (2005)
• Solution structure of the PWWP domain of the hepatoma-derived growth factor family. N. Nameki, N. Tochio, S. Koshiba, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, Y. Fujikura, M. Saito, M. Ikari, M. Watanabe, T. Terada, M. Shirouzu, M. Yoshida, H. Hirota, A. Tanaka, Y. Hayashizaki, P. Guntert, T. Kigawa, and S. Yokoyama. Protein Sci, 14, 756-764 (2005)
• Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. A. Nakabachi, S. Shigenobu, N. Sakazume, T. Shiraki, Y. Hayashizaki, P. Carninci, H. Ishikawa, T. Kudo, and T. Fukatsu. Proc Natl Acad Sci U S A, 102, 5477-5482 (2005)
• Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray. K. A. Morris, E. Snir, C. Pompeia, I. V. Koroleva, B. Kachar, Y. Hayashizaki, P. Carninci, M. B. Soares, and K. W. Beisel. J Assoc Res Otolaryngol, 6, 75-89 (2005)?
• Analysis of Reg IV expression in peritoneal dissemination of gastric cancer using real-time RT-PCR. K. Miyagawa, C. Sakakura, S. Nakashima, T. Yoshikawa, S. Kin, Y. Nakase, K. Fukuda, A. Hagiwara, Y. Okazaki, Y. Hayashizaki, and H. Yamagishi. Gan To Kagaku Ryoho, 32, 1707-1708 (2005)
• Pharmacologic preconditioning effects: prostaglandin E1 induces heat-shock proteins immediately after ischemia/reperfusion of the mouse liver. K. Matsuo, S. Togo, H. Sekido, T. Morita, M. Kamiyama, D. Morioka, T. Kubota, Y. Miura, K. Tanaka, T. Ishikawa, Y. Ichikawa, I. Endo, H. Goto, H. Nitanda, Y. Okazaki, Y. Hayashizaki, and H. Shimada. J Gastrointest Surg, 9, 758-768 (2005)
• Development of a spot reliability evaluation score for DNA microarrays. Y. Matsumura, K. Shimokawa, Y. Hayashizaki, K. Ikeo, Y. Tateno, and J. Kawai. Gene, 350, 149-160 (2005)
• Solution structure of the mouse enhancer of rudimentary protein reveals a novel fold. H. Li, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, E. Nunokawa, Y. Motoda, A. Kobayashi, T. Terada, M. Shirouzu, S. Koshiba, Y. J. Lin, P. Guntert, H. Suzuki, Y. Hayashizaki, T. Kigawa, and S. Yokoyama. J Biomol NMR, 32, 329-334 (2005)
• Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. H. Kiyosawa, N. Mise, S. Iwase, Y. Hayashizaki, and K. Abe. Genome Res, 15, 463-474 (2005)
• Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). N. Kitagawa, T. Washio, S. Kosugi, T. Yamashita, K. Higashi, H. Yanagawa, K. Higo, K. Satoh, Y. Ohtomo, T. Sunako, K. Murakami, K. Matsubara, J. Kawai, P. Carninci, Y. Hayashizaki, S. Kikuchi, and M. Tomita. Bioinformatics, 21, 1758-1763 (2005)?
• Antisense transcription in the mammalian transcriptome. S. Katayama, Y. Tomaru, T. Kasukawa, K. Waki, M. Nakanishi, M. Nakamura, H. Nishida, C. C. Yap, M. Suzuki, J. Kawai, H. Suzuki, P. Carninci, Y. Hayashizaki, C. Wells, M. Frith, T. Ravasi, K. C. Pang, J. Hallinan, J. Mattick, D. A. Hume, L. Lipovich, S. Batalov, P. G. Engstrom, Y. Mizuno, M. A. Faghihi, A. Sandelin, A. M. Chalk, S. Mottagui-Tabar, Z. Liang, B. Lenhard, and C. Wahlestedt. Science, 309, 1564-1566 (2005)
• Force measurement for antigen-antibody interaction by atomic force microscopy using a photograft-polymer spacer. A. Idiris, S. Kidoaki, K. Usui, T. Maki, H. Suzuki, M. Ito, M. Aoki, Y. Hayashizaki, and T. Matsuda. Biomacromolecules, 6, 2776-2784 (2005)
• Expression analysis of genes responsible for serotonin signaling in the brain. M. Ichikawa, Y. Okamura-Oho, R. Okunishi, M. Kanamori, H. Suzuki, A. Ritani, H. Nitta, N. Eguchi, Y. Urade, and Y. Hayashizaki. Neurobiol Dis, 19, 378-385 (2005)
• Differentially expressed genes throughout the cellular immortalization processes are quite different between normal human fibroblasts and endothelial cells. K. Hiyama, K. Otani, M. Ohtaki, K. Satoh, T. Kumazaki, T. Takahashi, Y. Mitsui, Y. Okazaki, Y. Hayashizaki, H. Omatsu, T. Noguchi, K. Tanimoto, and M. Nishiyama. Int J Oncol, 27, 87-95 (2005)
• Identification and characterization of photomedins: novel olfactomedin-domain-containing proteins with chondroitin sulphate-E-binding activity. Y. Furutani, R. Manabe, K. Tsutsui, T. Yamada, N. Sugimoto, S. Fukuda, J. Kawai, N. Sugiura, K. Kimata, Y. Hayashizaki, and K. Sekiguchi. Biochem J, 389, 675-684 (2005)
• The transcriptional landscape of the mammalian genome. P. Carninci and T. Kasukawa and S. Katayama and J. Gough and M. C. Frith and N. Maeda and R. Oyama and T. Ravasi and B. Lenhard and C. Wells and R. Kodzius and K. Shimokawa and V. B. Bajic and S. E. Brenner and S. Batalov and A. R. Forrest and M. Zavolan and M. J. Davis and L. G. Wilming and V. Aidinis and J. E. Allen and A. Ambesi-Impiombato and R. Apweiler and R. N. Aturaliya and T. L. Bailey and M. Bansal and L. Baxter and K. W. Beisel and T. Bersano and H. Bono and A. M. Chalk and K. P. Chiu and V. Choudhary and A. Christoffels and D. R. Clutterbuck and M. L. Crowe and E. Dalla and B. P. Dalrymple and B. de Bono and G. Della Gatta and D. di Bernardo and T. Down and P. Engstrom and M. Fagiolini and G. Faulkner and C. F. Fletcher and T. Fukushima and M. Furuno and S. Futaki and M. Gariboldi and P. Georgii-Hemming and T. R. Gingeras and T. Gojobori and R. E. Green and S. Gustincich and M. Harbers and Y. Hayashi and T. K. Hensch and N. Hirokawa and D. Hill and L. Huminiecki and M. Iacono and K. Ikeo and A. Iwama and T. Ishikawa and M. Jakt and A. Kanapin and M. Katoh and Y. Kawasawa and J. Kelso and H. Kitamura and H. Kitano and G. Kollias and S. P. Krishnan and A. Kruger and S. K. Kummerfeld and I. V. Kurochkin and L. F. Lareau and D. Lazarevic and L. Lipovich and J. Liu and S. Liuni and S. McWilliam and M. Madan Babu and M. Madera and L. Marchionni and H. Matsuda and S. Matsuzawa and H. Miki and F. Mignone and S. Miyake and K. Morris and S. Mottagui-Tabar and N. Mulder and N. Nakano and H. Nakauchi and P. Ng and R. Nilsson and S. Nishiguchi and S. Nishikawa and F. Nori and O. Ohara and Y. Okazaki and V. Orlando and K. C. Pang and W. J. Pavan and G. Pavesi and G. Pesole and N. Petrovsky and S. Piazza and J. Reed and J. F. Reid and B. Z. Ring and M. Ringwald and B. Rost and Y. Ruan and S. L. Salzberg and A. Sandelin and C. Schneider and C. Schonbach and K. Sekiguchi and C. A. Semple and S. Seno and L. Sessa and Y. Sheng and Y. Shibata and H. Shimada and K. Shimada and D. Silva and B. Sinclair and S. Sperling and E. Stupka and K. Sugiura and R. Sultana and Y. Takenaka and K. Taki and K. Tammoja and S. L. Tan and S. Tang and M. S. Taylor and J. Tegner and S. A. Teichmann and H. R. Ueda and E. van Nimwegen and R. Verardo and C. L. Wei and K. Yagi and H. Yamanishi and E. Zabarovsky and S. Zhu and A. Zimmer and W. Hide and C. Bult and S. M. Grimmond and R. D. Teasdale and E. T. Liu and V. Brusic and J. Quackenbush and C. Wahlestedt and J. S. Mattick and D. A. Hume and C. Kai and D. Sasaki and Y. Tomaru and S. Fukuda and M. Kanamori-Katayama and M. Suzuki and J. Aoki and T. Arakawa and J. Iida and K. Imamura and M. Itoh and T. Kato and H. Kawaji and N. Kawagashira and T. Kawashima and M. Kojima and S. Kondo and H. Konno and K. Nakano and N. Ninomiya and T. Nishio and M. Okada and C. Plessy and K. Shibata and T. Shiraki and S. Suzuki and M. Tagami and K. Waki and A. Watahiki and Y. Okamura-Oho and H. Suzuki and J. Kawai and Y. Hayashizaki. Science, 309, 1559-1563 (2005)
• Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. R. B. Caldwell, A. M. Kierzek, H. Arakawa, Y. Bezzubov, J. Zaim, P. Fiedler, S. Kutter, A. Blagodatski, D. Kostovska, M. Koter, J. Plachy, P. Carninci, Y. Hayashizaki, and J. M. Buerstedde. Genome Biol, 6, R6 (2005)
• High-throughput mapping of a dynamic signaling network in mammalian cells. M. Barrios-Rodiles, K. R. Brown, B. Ozdamar, R. Bose, Z. Liu, R. S. Donovan, F. Shinjo, Y. Liu, J. Dembowy, I. W. Taylor, V. Luga, N. Przulj, M. Robinson, H. Suzuki, Y. Hayashizaki, I. Jurisica, and J. L. Wrana. Science, 307, 1621-1625 (2005)
• Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Angstroms resolution. R. Arai, M. Kukimoto-Niino, H. Uda-Tochio, S. Morita, T. Uchikubo-Kamo, R. Akasaka, Y. Etou, Y. Hayashizaki, T. Kigawa, T. Terada, M. Shirouzu, and S. Yokoyama. Protein Sci, 14, 1888-1893 (2005)
• Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis. V. Aidinis, P. Carninci, M. Armaka, W. Witke, V. Harokopos, N. Pavelka, D. Koczan, C. Argyropoulos, M. M. Thwin, S. Moller, K. Waki, P. Gopalakrishnakone, P. Ricciardi-Castagnoli, H. J. Thiesen, Y. Hayashizaki, and G. Kollias. PLoS Genet, 1, e48 (2005)

2004

• Structure and regulation of the mDot1 gene, a mouse histone H3 methyltransferase. W. Zhang, Y. Hayashizaki, and B. C. Kone. Biochem J, 377, 641-651 (2004)
• The responsibility to share: sharing the responsibility. M. Yuille, B. Korn, T. Moore, A. A. Farmer, J. Carrino, C. Prange, and Y. Hayashizaki. Genome Res, 14, 2015-2019 (2004)
• Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. J. Yazaki, Z. Shimatani, A. Hashimoto, Y. Nagata, F. Fujii, K. Kojima, K. Suzuki, T. Taya, M. Tonouchi, C. Nelson, A. Nakagawa, Y. Otomo, K. Murakami, K. Matsubara, J. Kawai, P. Carninci, Y. Hayashizaki, and S. Kikuchi. Physiol Genomics, 17, 87-100 (2004)
• Sharing genomes: an integrated approach to funding, managing and distributing genomic clone resources. T. Weaver, J. Maurer, and Y. Hayashizaki. Nat Rev Genet, 5, 861-866 (2004)
• Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. A. Watahiki, K. Waki, N. Hayatsu, T. Shiraki, S. Kondo, M. Nakamura, D. Sasaki, T. Arakawa, J. Kawai, M. Harbers, Y. Hayashizaki, and P. Carninci. Nat Methods, 1, 233-239 (2004)
• Mechanism of liver regeneration after partial hepatectomy using mouse cDNA microarray. S. Togo, H. Makino, T. Kobayashi, T. Morita, T. Shimizu, T. Kubota, Y. Ichikawa, T. Ishikawa, Y. Okazaki, Y. Hayashizaki, and H.? Shimada. J Hepatol, 40, 464-471 (2004)
• Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi. T. Tanaka, Y. Tomaru, Y. Nomura, H. Miura, M. Suzuki, and Y. Hayashizaki. Nucleic Acids Res, 32, 2740-2750 (2004)
• Concise prediction models of anticancer efficacy of 8 drugs using expression data from 12 selected genes. T. Tanaka, K. Tanimoto, K. Otani, K. Satoh, M. Ohtaki, K. Yoshida, T. Toge, H. Yahata, S. Tanaka, K. Chayama, Y. Okazaki, Y. Hayashizaki, K. Hiyama, and M. Nishiyama. Int J Cancer, 111, 617-626 (2004)
• Large-scale collection and characterization of promoters of human and mouse genes. Y. Suzuki, R. Yamashita, M. Shirota, Y. Sakakibara, J. Chiba, J. Mizushima-Sugano, A. E. Kel, T. Arakawa, P. Carninci, J. Kawai, Y. Hayashizaki, T. Takagi, K. Nakai, and S. Sugano. In Silico Biol, 4, 429-444 (2004)
• Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs. M. Suzuki and Y. Hayashizaki. Bioessays, 26, 833-843 (2004)
• Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR. H. Suzuki, R. Okunishi, W. Hashizume, S. Katayama, N. Ninomiya, N. Osato, K. Sato, M. Nakamura, J. Iida, M. Kanamori, and Y. Hayashizaki. FEBS Lett, 573, 214-218 (2004)
• In vitro pull-down assay without expression constructs. H. Suzuki, C. Ogawa, K. Usui, and Y. Hayashizaki. Biotechniques, 37, 918, 920 (2004)
• Combination of L-3-phosphoserine phosphatase and CEA using real-time RT-PCR improves accuracy in detection of peritoneal micrometastasis of gastric cancer. K. Shimomura, C. Sakakura, M. Takemura, T. Takagi, K. Fukuda, S. Kin, Y. Nakase, K. Miyagawa, M. Ohgaki, J. Fujiyama, Y. Fujita, M. Nakanishi, A. Hagiwara, M. Shirane, Y. Okazaki, Y. Hayashizaki, and H. Yamagishi. Anticancer Res, 24, 1113-1120 (2004)
• Clinico-molecular study of dedifferentiation in well-differentiated liposarcoma. T. Shimoji, H. Kanda, T. Kitagawa, K. Kadota, R. Asai, K. Takahashi, N. Kawaguchi, S. Matsumoto, Y. Hayashizaki, Y. Okazaki, and K. Shinomiya. Biochem Biophys Res Commun, 314, 1133-1140 (2004)
• Genome wide analysis of TNF-inducible genes reveals that antioxidant enzymes are induced by TNF and responsible for elimination of ROS. T. Sasazuki, T. Okazaki, K. Tada, S. Sakon-Komazawa, M. Katano, M. Tanaka, H. Yagita, K. Okumura, N. Tominaga, Y. Hayashizaki, Y. Okazaki, and H. Nakano. Mol Immunol, 41, 547-551 (2004)
• Utility of dopa decarboxylase as a novel marker for the detection of peritoneal micro-metastases of gastric cancer with realtime RT-PCR. C. Sakakura, M. Takemura, K. Miyagawa, K. Fukuda, K. Shimomura, S. Kin, Y. Nakase, Y. Kuriu, S. Nakashima, T. Yoshikawa, Y. Ueda, J. Fujiyama, T. Sonoyama, Y. Okazaki, Y. Hayashizaki, A. Hagiwara, and H. Yamagishi. Gan To Kagaku Ryoho, 31, 1906-1908 (2004)
• Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. Y. Ogihara, K. Mochida, K. Kawaura, K. Murai, M. Seki, A. Kamiya, K. Shinozaki, P. Carninci, Y. Hayashizaki, I. T. Shin, Y. Kohara, and Y. Yamazaki. Genes Genet Syst, 79, 227-232 (2004)
• Significance of RNAi in biology. M. Nishikawa and Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 49, 2832-2836 (2004)
• EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. I. Nikaido, C. Saito, A. Wakamoto, Y. Tomaru, T. Arakawa, Y. Hayashizaki, and Y. Okazaki. Nucleic Acids Res, 32, D548-551 (2004)
• Solution structure of the RWD domain of the mouse GCN2 protein. N. Nameki, M. Yoneyama, S. Koshiba, N. Tochio, M. Inoue, E. Seki, T. Matsuda, Y. Tomo, T. Harada, K. Saito, N. Kobayashi, T. Yabuki, M. Aoki, E. Nunokawa, N. Matsuda, N. Sakagami, T. Terada, M. Shirouzu, M. Yoshida, H. Hirota, T. Osanai, A. Tanaka, T. Arakawa, P. Carninci, J. Kawai, Y. Hayashizaki, K. Kinoshita, P. Guntert, T. Kigawa, and S. Yokoyama. Protein Sci, 13, 2089-2100 (2004)
• Comparative analysis of plant and animal calcium signal transduction element using plant full-length cDNA data. T. Nagata, S. Iizumi, K. Satoh, H. Ooka, J. Kawai, P. Carninci, Y. Hayashizaki, Y. Otomo, K. Murakami, K. Matsubara, and S. Kikuchi. Mol Biol Evol, 21, 1855-1870 (2004)
• FREP: a database of functional repeats in mouse cDNAs. T. Nagashima, H. Matsuda, D. G. Silva, N. Petrovsky, A. Konagaya, C. Schonbach, T. Kasukawa, T. Arakawa, P. Carninci, J. Kawai, and Y. Hayashizaki. Nucleic Acids Res, 32, D471-475 (2004)
• Gene expression profile analysis of regenerating liver after portal vein ligation in rats by a cDNA microarray system. Y. Nagano, K. Nagahori, F. Yoshiro, Y. Hamaguchi, T. Ishikawa, Y. Ichikawa, S. Togo, Y. Okazaki, Y. Hayashizaki, and H. Shimada. Liver Int, 24, 253-258 (2004)
• Over expression of Reg IV in peritoneal dissemination of gastric cancer. K. Miyagawa, C. Sakakura, S. Kin, Y. Nakase, K. Fukuda, A. Hagiwara, Y. Okazaki, Y. Hayashizaki, and H. Yamagishi. Gan To Kagaku Ryoho, 31, 1909-1911 (2004)
• Aptamer-dependent full-length cDNA synthesis by overlap extension PCR. Y. Mitani, T. Nakayama, M. Harbers, and Y. Hayashizaki. Biotechniques, 37, 124, 126, 128-129 (2004)
• Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16). T. Maeda, M. Inoue, S. Koshiba, T. Yabuki, M. Aoki, E. Nunokawa, E. Seki, T. Matsuda, Y. Motoda, A. Kobayashi, F. Hiroyasu, M. Shirouzu, T. Terada, N. Hayami, Y. Ishizuka, N. Shinya, A. Tatsuguchi, M. Yoshida, H. Hirota, Y. Matsuo, K. Tani, T. Arakawa, P. Carninci, J. Kawai, Y. Hayashizaki, T. Kigawa, and S. Yokoyama. J Biol Chem, 279, 13174-13182 (2004)
• Spatial patterns of gene expression in the olfactory bulb. D. M. Lin, Y. H. Yang, J. A. Scolnick, L. J. Brunet, H. Marsh, V. Peng, Y. Okazaki, Y. Hayashizaki, T. P. Speed, and J. Ngai. Proc Natl Acad Sci U S A, 101, 12718-12723 (2004)
• Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags. R. Kodzius, Y. Matsumura, T. Kasukawa, K. Shimokawa, S. Fukuda, T. Shiraki, M. Nakamura, T. Arakawa, D. Sasaki, J. Kawai, M. Harbers, P. Carninci, and Y. Hayashizaki. FEBS Lett, 559, 22-26 (2004)
• Systematic genome-wide approach to positional candidate cloning for identification of novel human disease genes. H. Kiyosawa, T. Kawashima, D. Silva, N. Petrovsky, Y. Hasegawa, K. Sakai, and Y. Hayashizaki. Intern Med J, 34, 79-90 (2004)
• Integrated analysis of the genome and the transcriptome by FANTOM. S. Katayama, M. Kanamori, and Y. Hayashizaki. Brief Bioinform, 5, 249-258 (2004)
• Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis. T. Kasukawa, S. Katayama, H. Kawaji, H. Suzuki, D. A. Hume, and Y. Hayashizaki. Genomics, 84, 913-921 (2004)?
• MaXML: mouse annotation XML. T. Kasukawa, H. Bono, Y. Hayashizaki, Y. Okazaki, and H. Matsuda. In Silico Biol, 4, 7-15 (2004)
• Solution structure of a BolA-like protein from Mus musculus. T. Kasai, M. Inoue, S. Koshiba, T. Yabuki, M. Aoki, E. Nunokawa, E. Seki, T. Matsuda, N. Matsuda, Y. Tomo, M. Shirouzu, T. Terada, N. Obayashi, H. Hamana, N. Shinya, A. Tatsuguchi, S. Yasuda, M. Yoshida, H. Hirota, Y. Matsuo, K. Tani, H. Suzuki, T. Arakawa, P. Carninci, J. Kawai, Y. Hayashizaki, T. Kigawa, and S. Yokoyama. Protein Sci, 13, 545-548 (2004)
• A genome-wide and nonredundant mouse transcription factor database. M. Kanamori, H. Konno, N. Osato, J. Kawai, Y. Hayashizaki, and H. Suzuki. Biochem Biophys Res Commun, 322, 787-793 (2004)
• Integrative annotation of 21,037 human genes validated by full-length cDNA clones. T. Imanishi and T. Itoh and Y. Suzuki and C. O'Donovan and S. Fukuchi and K. O. Koyanagi and R. A. Barrero and T. Tamura and Y. Yamaguchi-Kabata and M. Tanino and K. Yura and S. Miyazaki and K. Ikeo and K. Homma and A. Kasprzyk and T. Nishikawa and M. Hirakawa and J. Thierry-Mieg and D. Thierry-Mieg and J. Ashurst and L. Jia and M. Nakao and M. A. Thomas and N. Mulder and Y. Karavidopoulou and L. Jin and S. Kim and T. Yasuda and B. Lenhard and E. Eveno and Y. Suzuki and C. Yamasaki and J. Takeda and C. Gough and P. Hilton and Y. Fujii and H. Sakai and S. Tanaka and C. Amid and M. Bellgard and F. Bonaldo Mde and H. Bono and S. K. Bromberg and A. J. Brookes and E. Bruford and P. Carninci and C. Chelala and C. Couillault and S. J. de Souza and M. A. Debily and M. D. Devignes and I. Dubchak and T. Endo and A. Estreicher and E. Eyras and K. Fukami-Kobayashi and G. R. Gopinath and E. Graudens and Y. Hahn and M. Han and Z. G. Han and K. Hanada and H. Hanaoka and E. Harada and K. Hashimoto and U. Hinz and M. Hirai and T. Hishiki and I. Hopkinson and S. Imbeaud and H. Inoko and A. Kanapin and Y. Kaneko and T. Kasukawa and J. Kelso and P. Kersey and R. Kikuno and K. Kimura and B. Korn and V. Kuryshev and I. Makalowska and T. Makino and S. Mano and R. Mariage-Samson and J. Mashima and H. Matsuda and H. W. Mewes and S. Minoshima and K. Nagai and H. Nagasaki and N. Nagata and R. Nigam and O. Ogasawara and O. Ohara and M. Ohtsubo and N. Okada and T. Okido and S. Oota and M. Ota and T. Ota and T. Otsuki and D. Piatier-Tonneau and A. Poustka and S. X. Ren and N. Saitou and K. Sakai and S. Sakamoto and R. Sakate and I. Schupp and F. Servant and S. Sherry and R. Shiba and N. Shimizu and M. Shimoyama and A. J. Simpson and B. Soares and C. Steward and M. Suwa and M. Suzuki and A. Takahashi and G. Tamiya and H. Tanaka and T. Taylor and J. D. Terwilliger and P. Unneberg and V. Veeramachaneni and S. Watanabe and L. Wilming and N. Yasuda and H. S. Yoo and M. Stodolsky and W. Makalowski and M. Go and K. Nakai and T. Takagi and M. Kanehisa and Y. Sakaki and J. Quackenbush and Y. Okazaki and Y. Hayashizaki and W. Hide and R. Chakraborty and K. Nishikawa and H. Sugawara and Y. Tateno and Z. Chen and M. Oishi and P. Tonellato and R. Apweiler and K. Okubo and L. Wagner and S. Wiemann and R. L. Strausberg and T. Isogai and C. Auffray and N. Nomura and T. Gojobori and S. Sugano. PLoS Biol, 2, e162 (2004)
• Identification of a novel left-right asymmetrically expressed gene in the mouse belonging to the BPI/PLUNC superfamily. J. Hou, K. Yashiro, Y. Okazaki, Y. Saijoh, Y. Hayashizaki, and H. Hamada. Dev Dyn, 229, 373-379 (2004)
• Genomic project network and the patents (discussion). Y. Hayashizaki, T. Oinuma, and S. Kohtsuki. Tanpakushitsu Kakusan Koso, 49, 3001-3016 (2004)
• A new approach to the distribution and storage of genetic resources. Y. Hayashizaki and J. Kawai. Nat Rev Genet, 5, 223-228 (2004)
• Dynamic transcriptome of mice. Y. Hayashizaki and M. Kanamori. Trends Biotechnol, 22, 161-167 (2004)
• Genome network: the new researching style. Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 49, 2617-2619 (2004)
• Future views on genome network projects. Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 49, 3017 (2004)
• Gene discovery in genetically labeled single dopaminergic neurons of the retina. S. Gustincich, M. Contini, M. Gariboldi, M. Puopolo, K. Kadota, H. Bono, J. LeMieux, P. Walsh, P. Carninci, Y. Hayashizaki, Y. Okazaki, and E. Raviola. Proc Natl Acad Sci U S A, 101, 5069-5074 (2004)
• Differential gene expression profiles of radioresistant oesophageal cancer cell lines established by continuous fractionated irradiation. K. Fukuda, C. Sakakura, K. Miyagawa, Y. Kuriu, S. Kin, Y. Nakase, A. Hagiwara, S. Mitsufuji, Y. Okazaki, Y. Hayashizaki, and H. Yamagishi. Br J Cancer, 91, 1543-1550 (2004)
• Mammalian class E Vps proteins, SBP1 and mVps2/CHMP2A, interact with and regulate the function of an AAA-ATPase SKD1/Vps4B. H. Fujita, Y. Umezuki, K. Imamura, D. Ishikawa, S. Uchimura, A. Nara, T. Yoshimori, Y. Hayashizaki, J. Kawai, K. Ishidoh, Y. Tanaka, and M. Himeno. J Cell Sci, 117, 2997-3009 (2004)
• Identification of a developmentally regulated striatum-enriched zinc-finger gene, Nolz-1, in the mammalian brain. C. W. Chang, C. W. Tsai, H. F. Wang, H. C. Tsai, H. Y. Chen, T. F. Tsai, H. Takahashi, H. Y. Li, M. J. Fann, C. W. Yang, Y. Hayashizaki, T. Saito, and F. C. Liu. Proc Natl Acad Sci U S A, 101, 2613-2618 (2004)
• Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library. K. W. Beisel, T. Shiraki, K. A. Morris, C. Pompeia, B. Kachar, T. Arakawa, H. Bono, J. Kawai, Y. Hayashizaki, and P. Carninci. Genomics, 83, 1012-1023 (2004)
• Establishment of stable hFis1 knockdown cells with an siRNA expression vector. R. Arai, K. Ito, M. Wakiyama, E. Matsumoto, A. Sakamoto, Y. Etou, M. Otsuki, M. Inoue, Y. Hayashizaki, M. Miyagishi, K. Taira, M. Shirouzu, and S. Yokoyama. J Biochem, 136, 421-425 (2004)

2003

• Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. M. Zavolan, S. Kondo, C. Schonbach, J. Adachi, D. A. Hume, Y. Hayashizaki, and T. Gaasterland. Genome Res, 13, 1290-1300 (2003)
• Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. J. Yazaki, N. Kishimoto, Y. Nagata, M. Ishikawa, F. Fujii, A. Hashimoto, K. Shimbo, Z. Shimatani, K. Kojima, K. Suzuki, M. Yamamoto, S. Honda, A. Endo, Y. Yoshida, Y. Sato, K. Takeuchi, K. Toyoshima, C. Miyamoto, J. Wu, T. Sasaki, K. Sakata, K. Yamamoto, K. Iba, T. Oda, Y. Otomo, K. Murakami, K. Matsubara, J. Kawai, P. Carninci, Y. Hayashizaki, and S. Kikuchi. DNA Res, 10, 249-261 (2003)
• Empirical analysis of transcriptional activity in the Arabidopsis genome. K. Yamada, J. Lim, J. M. Dale, H. Chen, P. Shinn, C. J. Palm, A. M. Southwick, H. C. Wu, C. Kim, M. Nguyen, P. Pham, R. Cheuk, G. Karlin-Newmann, S. X. Liu, B. Lam, H. Sakano, T. Wu, G. Yu, M. Miranda, H. L. Quach, M. Tripp, C. H. Chang, J. M. Lee, M. Toriumi, M. M. Chan, C. C. Tang, C. S. Onodera, J. M. Deng, K. Akiyama, Y. Ansari, T. Arakawa, J. Banh, F. Banno, L. Bowser, S. Brooks, P. Carninci, Q. Chao, N. Choy, A. Enju, A. D. Goldsmith, M. Gurjal, N. F. Hansen, Y. Hayashizaki, C. Johnson-Hopson, V. W. Hsuan, K. Iida, M. Karnes, S. Khan, E. Koesema, J. Ishida, P. X. Jiang, T. Jones, J. Kawai, A. Kamiya, C. Meyers, M. Nakajima, M. Narusaka, M. Seki, T. Sakurai, M. Satou, R. Tamse, M. Vaysberg, E. K. Wallender, C. Wong, Y. Yamamura, S. Yuan, K. Shinozaki, R. W. Davis, A. Theologis, and J. R. Ecker. Science, 302, 842-846 (2003)
• Genetic control of the innate immune response. C. A. Wells, T. Ravasi, G. J. Faulkner, P. Carninci, Y. Okazaki, Y. Hayashizaki, M. Sweet, B. J. Wainwright, and D. A. Hume. BMC Immunol, 4, 5 (2003)
• Multiple tissue-specific promoters control expression of the murine tartrate-resistant acid phosphatase gene. N. C. Walsh, M. Cahill, P. Carninci, J. Kawai, Y. Okazaki, Y. Hayashizaki, D. A. Hume, and A. I. Cassady. Gene, 307, 111-123 (2003)
• A comprehensive search for HNF-3alpha-regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysis. Y. Tomaru, S. Kondo, M. Suzuki, and Y. Hayashizaki. Biochem Biophys Res Commun, 310, 667-674 (2003)
• Identification of genes by mouse genome and transcriptome analysis. S. Suzuki, S. Kondo, and Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 48, 747-759 (2003)
• The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer. H. Suzuki, R. Saito, M. Kanamori, C. Kai, C. Schonbach, T. Nagashima, J. Hosaka, and Y. Hayashizaki. Genome Res, 13, 1534-1541 (2003)?
• Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. T. Shiraki, S. Kondo, S. Katayama, K. Waki, T. Kasukawa, H. Kawaji, R. Kodzius, A. Watahiki, M. Nakamura, T. Arakawa, S. Fukuda, D. Sasaki, A. Podhajska, M. Harbers, J. Kawai, P. Carninci, and Y. Hayashizaki. Proc Natl Acad Sci U S A, 100, 15776-15781 (2003)
• Characterization of the mouse Abcc12 gene and its transcript encoding an ATP-binding cassette transporter, an orthologue of human ABCC12. H. Shimizu, H. Taniguchi, Y. Hippo, Y. Hayashizaki, H. Aburatani, and T. Ishikawa. Gene, 310, 17-28 (2003)
• Practical application of transcriptional sequencing for GC-rich templates. K. Shibata, M. Izawa, Y. Hayashizaki, and M. Watahiki. J Struct Funct Genomics, 4, 35-39 (2003)
• Possible involvement of inositol 1, 4, 5-trisphosphate receptor type 3 (IP3R3) in the peritoneal dissemination of gastric cancers. C. Sakakura, K. Miyagawa, K. Fukuda, K. Shimomura, M. Takemura, T. Takagi, S. Kin, Y. Nakase, J. Fujiyama, K. Mikoshiba, Y. Okazaki, Y. Hayashizaki, A. Hagiwara, and H. Yamagishi. Gan To Kagaku Ryoho, 30, 1784-1787 (2003)
• Global insights into protein complexes through integrated analysis of the reliable interactome and knockout lethality. R. Saito, H. Suzuki, and Y. Hayashizaki. Biochem Biophys Res Commun, 301, 633-640 (2003)
• Construction of reliable protein-protein interaction networks with a new interaction generality measure. R. Saito, H. Suzuki, and Y. Hayashizaki. Bioinformatics, 19, 756-763 (2003)
• Antisense transcripts with rice full-length cDNAs. N. Osato, H. Yamada, K. Satoh, H. Ooka, M. Yamamoto, K. Suzuki, J. Kawai, P. Carninci, Y. Ohtomo, K. Murakami, K. Matsubara, S. Kikuchi, and Y. Hayashizaki. Genome Biol, 5, R5 (2003)
• Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. H. Ooka, K. Satoh, K. Doi, T. Nagata, Y. Otomo, K. Murakami, K. Matsubara, N. Osato, J. Kawai, P. Carninci, Y. Hayashizaki, K. Suzuki, K. Kojima, Y. Takahara, K. Yamamoto, and S. Kikuchi. DNA Res, 10, 239-247 (2003)
• K. Numata, A. Kanai, R. Saito, S. Kondo, J. Adachi, L. G. Wilming, D. A. Hume, Y. Hayashizaki, and M. Tomita. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res, 13, 1301-1306 (2003)
• Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. T. Nishiyama, T. Fujita, I. T. Shin, M. Seki, H. Nishide, I. Uchiyama, A. Kamiya, P. Carninci, Y. Hayashizaki, K. Shinozaki, Y. Kohara, and M. Hasebe. Proc Natl Acad Sci U S A, 100, 8007-8012 (2003)
• Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. I. Nikaido, C. Saito, Y. Mizuno, M. Meguro, H. Bono, M. Kadomura, T. Kono, G. A. Morris, P. A. Lyons, M. Oshimura, Y. Hayashizaki, and Y. Okazaki. Genome Res, 13, 1402-1409 (2003)
• Undulated short-tail deletion mutation in the mouse ablates Pax1 and leads to ectopic activation of neighboring Nkx2-2 in domains that normally express Pax1. C. Kokubu, B. Wilm, T. Kokubu, M. Wahl, I. Rodrigo, N. Sakai, F. Santagati, Y. Hayashizaki, M. Suzuki, K. Yamamura, K. Abe, and K. Imai. Genetics, 165, 299-307 (2003)
• Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. H. Kiyosawa, I. Yamanaka, N. Osato, S. Kondo, and Y. Hayashizaki. Genome Res, 13, 1324-1334 (2003)
• Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. S. Kikuchi, K. Satoh, T. Nagata, N. Kawagashira, K. Doi, N. Kishimoto, J. Yazaki, M. Ishikawa, H. Yamada, H. Ooka, I. Hotta, K. Kojima, T. Namiki, E. Ohneda, W. Yahagi, K. Suzuki, C. J. Li, K. Ohtsuki, T. Shishiki, Y. Otomo, K. Murakami, Y. Iida, S. Sugano, T. Fujimura, Y. Suzuki, Y. Tsunoda, T. Kurosaki, T. Kodama, H. Masuda, M. Kobayashi, Q. Xie, M. Lu, R. Narikawa, A. Sugiyama, K. Mizuno, S. Yokomizo, J. Niikura, R. Ikeda, J. Ishibiki, M. Kawamata, A. Yoshimura, J. Miura, T. Kusumegi, M. Oka, R. Ryu, M. Ueda, K. Matsubara, J. Kawai, P. Carninci, J. Adachi, K. Aizawa, T. Arakawa, S. Fukuda, A. Hara, W. Hashizume, N. Hayatsu, K. Imotani, Y. Ishii, M. Itoh, I. Kagawa, S. Kondo, H. Konno, A. Miyazaki, N. Osato, Y. Ota, R. Saito, D. Sasaki, K. Sato, K. Shibata, A. Shinagawa, T. Shiraki, M. Yoshino, Y. Hayashizaki, and A. Yasunishi. Science, 301, 376-379 (2003)
• DNA book. J. Kawai and Y. Hayashizaki. Genome Res, 13, 1488-1495 (2003)
• Development and evaluation of an automated annotation pipeline and cDNA annotation system. T. Kasukawa, M. Furuno, I. Nikaido, H. Bono, D. A. Hume, C. Bult, D. P. Hill, R. Baldarelli, J. Gough, A. Kanapin, H. Matsuda, L. M. Schriml, Y. Hayashizaki, Y. Okazaki, and J. Quackenbush. Genome Res, 13, 1542-1551 (2003)
• The PDZ protein tax-interacting protein-1 inhibits beta-catenin transcriptional activity and growth of colorectal cancer cells. M. Kanamori, P. Sandy, S. Marzinotto, R. Benetti, C. Kai, Y. Hayashizaki, C. Schneider, and H. Suzuki. J Biol Chem, 278, 38758-38764 (2003)
• Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure. K. Kadota, S. Nishimura, H. Bono, S. Nakamura, Y. Hayashizaki, Y. Okazaki, and K. Takahashi. Physiol Genomics, 12, 251-259 (2003)
• Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts. T. Hirozane-Kishikawa, T. Shiraki, K. Waki, M. Nakamura, T. Arakawa, J. Kawai, M. Fagiolini, T. K. Hensch, Y. Hayashizaki, and P. Carninci. Biotechniques, 35, 510-516, 518 (2003)
• RIKEN mouse genome encyclopedia. Y. Hayashizaki. Mech Ageing Dev, 124, 93-102 (2003)
• The Riken mouse genome encyclopedia project. Y. Hayashizaki. C R Biol, 326, 923-929 (2003)
• Mouse Genome Encyclopedia Project. Y. Hayashizaki. Cold Spring Harb Symp Quant Biol, 68, 195-204 (2003)
• Analysis of the mouse transcriptome for genes involved in the function of the nervous system. S. Gustincich, S. Batalov, K. W. Beisel, H. Bono, P. Carninci, C. F. Fletcher, S. Grimmond, N. Hirokawa, E. D. Jarvis, T. Jegla, Y. Kawasawa, J. LeMieux, H. Miki, E. Raviola, R. D. Teasdale, N. Tominaga, K. Yagi, A. Zimmer, Y. Hayashizaki, and Y. Okazaki. Genome Res, 13, 1395-1401 (2003)
• The mouse secretome: functional classification of the proteins secreted into the extracellular environment. S. M. Grimmond, K. C. Miranda, Z. Yuan, M. J. Davis, D. A. Hume, K. Yagi, N. Tominaga, H. Bono, Y. Hayashizaki, Y. Okazaki, and R. D. Teasdale. Genome Res, 13, 1350-1359 (2003)
• Gene expression profile of normal lungs predicts genetic predisposition to lung cancer in mice. M. Gariboldi, M. Spinola, S. Milani, C. Pignatiello, K. Kadota, H. Bono, Y. Hayashizaki, T. A. Dragani, and Y. Okazaki. Carcinogenesis, 24, 1819-1826 (2003)
• SCCA2-like serpins mediate genetic predisposition to skin tumors. M. Gariboldi, B. Peissel, A. Fabbri, A. Saran, D. Zaffaroni, F. S. Falvella, M. Spinola, J. Tanuma, S. Pazzaglia, M. T. Mancuso, A. Maurichi, C. Bartoli, S. Cataltepe, G. A. Silverman, S. Pilotti, Y. Hayashizaki, Y. Okazaki, and T. A. Dragani. Cancer Res, 63, 1871-1875 (2003)
• Molecular basis of constitutive production of basement membrane components. Gene expression profiles of Engelbreth-Holm-Swarm tumor and F9 embryonal carcinoma cells. S. Futaki, Y. Hayashi, M. Yamashita, K. Yagi, H. Bono, Y. Hayashizaki, Y. Okazaki, and K. Sekiguchi. J Biol Chem, 278, 50691-50701 (2003)
• CDS annotation in full-length cDNA sequence. M. Furuno, T. Kasukawa, R. Saito, J. Adachi, H. Suzuki, R. Baldarelli, Y. Hayashizaki, and Y. Okazaki. Genome Res, 13, 1478-1487 (2003)
• A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. S. Fujimori, T. Washio, K. Higo, Y. Ohtomo, K. Murakami, K. Matsubara, J. Kawai, P. Carninci, Y. Hayashizaki, S. Kikuchi, and M. Tomita. FEBS Lett, 554, 17-22 (2003)
• Analysis of gene expression in the developing mouse retina. E. Diaz, Y. H. Yang, T. Ferreira, K. C. Loh, Y. Okazaki, Y. Hayashizaki, M. Tessier-Lavigne, T. P. Speed, and J. Ngai. Proc Natl Acad Sci U S A, 100, 5491-5496 (2003)
• Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. P. Carninci, K. Waki, T. Shiraki, H. Konno, K. Shibata, M. Itoh, K. Aizawa, T. Arakawa, Y. Ishii, D. Sasaki, H. Bono, S. Kondo, Y. Sugahara, R. Saito, N. Osato, S. Fukuda, K. Sato, A. Watahiki, T. Hirozane-Kishikawa, M. Nakamura, Y. Shibata, A. Yasunishi, N. Kikuchi, A. Yoshiki, M. Kusakabe, S. Gustincich, K. Beisel, W. Pavan, V. Aidinis, A. Nakagawara, W. A. Held, H. Iwata, T. Kono, H. Nakauchi, P. Lyons, C. Wells, D. A. Hume, M. Fagiolini, T. K. Hensch, M. Brinkmeier, S. Camper, J. Hirota, P. Mombaerts, M. Muramatsu, Y. Okazaki, J. Kawai, and Y. Hayashizaki. Genome Res, 13, 1273-1289 (2003)
• Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. H. Bono, K. Yagi, T. Kasukawa, I. Nikaido, N. Tominaga, R. Miki, Y. Mizuno, Y. Tomaru, H. Goto, H. Nitanda, D. Shimizu, H. Makino, T. Morita, J. Fujiyama, T. Sakai, T. Shimoji, D. A. Hume, Y. Hayashizaki, and Y. Okazaki. Genome Res, 13, 1318-1323 (2003)
• Comprehensive analysis of the mouse metabolome based on the transcriptome. H. Bono, I. Nikaido, T. Kasukawa, Y. Hayashizaki, and Y. Okazaki. Genome Res, 13, 1345-1349 (2003)
• FANTOM-DB: database of functional annotation of RIKEN mouse cDNA clones. H. Bono, T. Kasukawa, M. Furuno, Y. Hayashizaki, and Y. Okazaki. Seikagaku, 75, 149-152 (2003)

2002

• Mapping of 19032 mouse cDNAs on mouse chromosomes. I. Yamanaka, H. Kiyosawa, S. Kondo, T. Saito, P. Carninci, A. Shinagawa, K. Aizawa, S. Fukuda, A. Hara, M. Itoh, J. Kawai, K. Shibata, T. Arakawa, Y. Ishii, and Y. Hayashizaki. J Struct Funct Genomics, 2, 23-28 (2002)
• Initial sequencing and comparative analysis of the mouse genome. R. H. Waterston and K. Lindblad-Toh and E. Birney and J. Rogers and J. F. Abril and P. Agarwal and R. Agarwala and R. Ainscough and M. Alexandersson and P. An and S. E. Antonarakis and J. Attwood and R. Baertsch and J. Bailey and K. Barlow and S. Beck and E. Berry and B. Birren and T. Bloom and P. Bork and M. Botcherby and N. Bray and M. R. Brent and D. G. Brown and S. D. Brown and C. Bult and J. Burton and J. Butler and R. D. Campbell and P. Carninci and S. Cawley and F. Chiaromonte and A. T. Chinwalla and D. M. Church and M. Clamp and C. Clee and F. S. Collins and L. L. Cook and R. R. Copley and A. Coulson and O. Couronne and J. Cuff and V. Curwen and T. Cutts and M. Daly and R. David and J. Davies and K. D. Delehaunty and J. Deri and E. T. Dermitzakis and C. Dewey and N. J. Dickens and M. Diekhans and S. Dodge and I. Dubchak and D. M. Dunn and S. R. Eddy and L. Elnitski and R. D. Emes and P. Eswara and E. Eyras and A. Felsenfeld and G. A. Fewell and P. Flicek and K. Foley and W. N. Frankel and L. A. Fulton and R. S. Fulton and T. S. Furey and D. Gage and R. A. Gibbs and G. Glusman and S. Gnerre and N. Goldman and L. Goodstadt and D. Grafham and T. A. Graves and E. D. Green and S. Gregory and R. Guigo and M. Guyer and R. C. Hardison and D. Haussler and Y. Hayashizaki and L. W. Hillier and A. Hinrichs and W. Hlavina and T. Holzer and F. Hsu and A. Hua and T. Hubbard and A. Hunt and I. Jackson and D. B. Jaffe and L. S. Johnson and M. Jones and T. A. Jones and A. Joy and M. Kamal and E. K. Karlsson and D. Karolchik and A. Kasprzyk and J. Kawai and E. Keibler and C. Kells and W. J. Kent and A. Kirby and D. L. Kolbe and I. Korf and R. S. Kucherlapati and E. J. Kulbokas and D. Kulp and T. Landers and J. P. Leger and S. Leonard and I. Letunic and R. Levine and J. Li and M. Li and C. Lloyd and S. Lucas and B. Ma and D. R. Maglott and E. R. Mardis and L. Matthews and E. Mauceli and J. H. Mayer and M. McCarthy and W. R. McCombie and S. McLaren and K. McLay and J. D. McPherson and J. Meldrim and B. Meredith and J. P. Mesirov and W. Miller and T. L. Miner and E. Mongin and K. T. Montgomery and M. Morgan and R. Mott and J. C. Mullikin and D. M. Muzny and W. E. Nash and J. O. Nelson and M. N. Nhan and R. Nicol and Z. Ning and C. Nusbaum and M. J. O'Connor and Y. Okazaki and K. Oliver and E. Overton-Larty and L. Pachter and G. Parra and K. H. Pepin and J. Peterson and P. Pevzner and R. Plumb and C. S. Pohl and A. Poliakov and T. C. Ponce and C. P. Ponting and S. Potter and M. Quail and A. Reymond and B. A. Roe and K. M. Roskin and E. M. Rubin and A. G. Rust and R. Santos and V. Sapojnikov and B. Schultz and J. Schultz and M. S. Schwartz and S. Schwartz and C. Scott and S. Seaman and S. Searle and T. Sharpe and A. Sheridan and R. Shownkeen and S. Sims and J. B. Singer and G. Slater and A. Smit and D. R. Smith and B. Spencer and A. Stabenau and N. Stange-Thomann and C. Sugnet and M. Suyama and G. Tesler and J. Thompson and D. Torrents and E. Trevaskis and J. Tromp and C. Ucla and A. Ureta-Vidal and J. P. Vinson and A. C. Von Niederhausern and C. M. Wade and M. Wall and R. J. Weber and R. B. Weiss and M. C. Wendl and A. P. West and K. Wetterstrand and R. Wheeler and S. Whelan and J. Wierzbowski and D. Willey and S. Williams and R. K. Wilson and E. Winter and K. C. Worley and D. Wyman and S. Yang and S. P. Yang and E. M. Zdobnov and M. C. Zody and E. S. Lander. Nature, 420, 520-562 (2002)
• The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. M. Stapleton, G. Liao, P. Brokstein, L. Hong, P. Carninci, T. Shiraki, Y. Hayashizaki, M. Champe, J. Pacleb, K. Wan, C. Yu, J. Carlson, R. George, S. Celniker, and G. M. Rubin. Genome Res, 12, 1294-1300 (2002)
• Functional annotation of a full-length Arabidopsis cDNA collection. M. Seki, M. Narusaka, A. Kamiya, J. Ishida, M. Satou, T. Sakurai, M. Nakajima, A. Enju, K. Akiyama, Y. Oono, M. Muramatsu, Y. Hayashizaki, J. Kawai, P. Carninci, M. Itoh, Y. Ishii, T. Arakawa, K. Shibata, A. Shinagawa, and K. Shinozaki. Science, 296, 141-145 (2002)
• Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. M. Seki, M. Narusaka, J. Ishida, T. Nanjo, M. Fujita, Y. Oono, A. Kamiya, M. Nakajima, A. Enju, T. Sakurai, M. Satou, K. Akiyama, T. Taji, K. Yamaguchi-Shinozaki, P. Carninci, J. Kawai, Y. Hayashizaki, and K. Shinozaki. Plant J, 31, 279-292 (2002)
• Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. M. Seki, J. Ishida, M. Narusaka, M. Fujita, T. Nanjo, T. Umezawa, A. Kamiya, M. Nakajima, A. Enju, T. Sakurai, M. Satou, K. Akiyama, K. Yamaguchi-Shinozaki, P. Carninci, J. Kawai, Y. Hayashizaki, and K. Shinozaki. Funct Integr Genomics, 2, 282-291 (2002)
• On biased distribution of introns in various eukaryotes. A. Sakurai, S. Fujimori, H. Kochiwa, S. Kitamura-Abe, T. Washio, R. Saito, P. Carninci, Y. Hayashizaki, and M. Tomita. Gene, 300, 89-95 (2002)
• Differential gene expression profiles of gastric cancer cells established from primary tumour and malignant ascites. C. Sakakura, A. Hagiwara, M. Nakanishi, K. Shimomura, T. Takagi, R. Yasuoka, Y. Fujita, T. Abe, Y. Ichikawa, S. Takahashi, T. Ishikawa, I. Nishizuka, T. Morita, H. Shimada, Y. Okazaki, Y. Hayashizaki, and H. Yamagishi. Br J Cancer, 87, 1153-1161 (2002)
• Interaction generality, a measurement to assess the reliability of a protein-protein interaction. R. Saito, H. Suzuki, and Y. Hayashizaki. Nucleic Acids Res, 30, 1163-1168 (2002)
• Comprehensive sequence analysis of translation termination sites in various eukaryotes. Y. Ozawa, S. Hanaoka, R. Saito, T. Washio, S. Nakano, A. Shinagawa, M. Itoh, K. Shibata, P. Carninci, H. Konno, J. Kawai, Y. Hayashizaki, and M. Tomita. Gene, 300, 79-87 (2002)
• A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs. N. Osato, M. Itoh, H. Konno, S. Kondo, K. Shibata, P. Carninci, T. Shiraki, A. Shinagawa, T. Arakawa, S. Kikuchi, K. Sato, J. Kawai, and Y. Hayashizaki. Genome Res, 12, 1127-1134 (2002)
• Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Y. Okazaki and M. Furuno and T. Kasukawa and J. Adachi and H. Bono and S. Kondo and I. Nikaido and N. Osato and R. Saito and H. Suzuki and I. Yamanaka and H. Kiyosawa and K. Yagi and Y. Tomaru and Y. Hasegawa and A. Nogami and C. Schonbach and T. Gojobori and R. Baldarelli and D. P. Hill and C. Bult and D. A. Hume and J. Quackenbush and L. M. Schriml and A. Kanapin and H. Matsuda and S. Batalov and K. W. Beisel and J. A. Blake and D. Bradt and V. Brusic and C. Chothia and L. E. Corbani and S. Cousins and E. Dalla and T. A. Dragani and C. F. Fletcher and A. Forrest and K. S. Frazer and T. Gaasterland and M. Gariboldi and C. Gissi and A. Godzik and J. Gough and S. Grimmond and S. Gustincich and N. Hirokawa and I. J. Jackson and E. D. Jarvis and A. Kanai and H. Kawaji and Y. Kawasawa and R. M. Kedzierski and B. L. King and A. Konagaya and I. V. Kurochkin and Y. Lee and B. Lenhard and P. A. Lyons and D. R. Maglott and L. Maltais and L. Marchionni and L. McKenzie and H. Miki and T. Nagashima and K. Numata and T. Okido and W. J. Pavan and G. Pertea and G. Pesole and N. Petrovsky and R. Pillai and J. U. Pontius and D. Qi and S. Ramachandran and T. Ravasi and J. C. Reed and D. J. Reed and J. Reid and B. Z. Ring and M. Ringwald and A. Sandelin and C. Schneider and C. A. Semple and M. Setou and K. Shimada and R. Sultana and Y. Takenaka and M. S. Taylor and R. D. Teasdale and M. Tomita and R. Verardo and L. Wagner and C. Wahlestedt and Y. Wang and Y. Watanabe and C. Wells and L. G. Wilming and A. Wynshaw-Boris and M. Yanagisawa and I. Yang and L. Yang and Z. Yuan and M. Zavolan and Y. Zhu and A. Zimmer and P. Carninci and N. Hayatsu and T. Hirozane-Kishikawa and H. Konno and M. Nakamura and N. Sakazume and K. Sato and T. Shiraki and K. Waki and J. Kawai and K. Aizawa and T. Arakawa and S. Fukuda and A. Hara and W. Hashizume and K. Imotani and Y. Ishii and M. Itoh and I. Kagawa and A. Miyazaki and K. Sakai and D. Sasaki and K. Shibata and A. Shinagawa and A. Yasunishi and M. Yoshino and R. Waterston and E. S. Lander and J. Rogers and E. Birney and Y. Hayashizaki. Nature, 420, 563-573 (2002)
• Analysis of gene expression involved in brain metastasis from breast cancer using cDNA microarray. I. Nishizuka, T. Ishikawa, Y. Hamaguchi, M. Kamiyama, Y. Ichikawa, K. Kadota, R. Miki, Y. Tomaru, Y. Mizuno, N. Tominaga, R. Yano, H. Goto, H. Nitanda, S. Togo, Y. Okazaki, Y. Hayashizaki, and H. Shimada. Breast Cancer, 9, 26-32 (2002)
• Mechanism of postoperative liver failure after excessive hepatectomy investigated using a cDNA microarray. T. Morita, S. Togo, T. Kubota, N. Kamimukai, I. Nishizuka, T. Kobayashi, Y. Ichikawa, T. Ishikawa, S. Takahashi, K. Matsuo, Y. Tomaru, Y. Okazaki, Y. Hayashizaki, and H. Shimada. J Hepatobiliary Pancreat Surg, 9, 352-359 (2002)
• Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray. Y. Mizuno, Y. Sotomaru, Y. Katsuzawa, T. Kono, M. Meguro, M. Oshimura, J. Kawai, Y. Tomaru, H. Kiyosawa, I. Nikaido, H. Amanuma, Y. Hayashizaki, and Y. Okazaki. Biochem Biophys Res Commun, 290, 1499-1505 (2002)
• Identification of seven loci for static glucokinesis and dynamic glucokinesis in mice. S. Komatsu, H. Kiyosawa, A. Yoshiki, Y. Okazaki, M. Yoshino, Y. Tomaru, S. Watanabe, M. Muramatsu, M. Kusakabe, and Y. Hayashizaki. Mamm Genome, 13, 293-298 (2002)?
• Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. H. Kochiwa, R. Suzuki, T. Washio, R. Saito, H. Bono, P. Carninci, Y. Okazaki, R. Miki, Y. Hayashizaki, and M. Tomita. Genome Res, 12, 1286-1293 (2002)
• Exploration of novel motifs derived from mouse cDNA sequences. H. Kawaji, C. Schonbach, Y. Matsuo, J. Kawai, Y. Okazaki, Y. Hayashizaki, and H. Matsuda. Genome Res, 12, 367-378 (2002)
• T2BP, a novel TRAF2 binding protein, can activate NF-kappaB and AP-1 without TNF stimulation. M. Kanamori, H. Suzuki, R. Saito, M. Muramatsu, and Y. Hayashizaki. Biochem Biophys Res Commun, 290, 1108-1113 (2002)
• NF-kappaB activator Act1 associates with IL-1/Toll pathway adaptor molecule TRAF6. M. Kanamori, C. Kai, Y. Hayashizaki, and H. Suzuki. FEBS Lett, 532, 241-246 (2002)
• A framework for integrating the songbird brain. E. D. Jarvis, V. A. Smith, K. Wada, M. V. Rivas, M. McElroy, T. V. Smulders, P. Carninci, Y. Hayashizaki, F. Dietrich, X. Wu, P. McConnell, J. Yu, P. P. Wang, A. J. Hartemink, and S. Lin. J Comp Physiol A Neuroethol Sens Neural Behav Physiol, 188, 961-980 (2002)
• Identification of a novel mouse membrane-bound family 1 glycosidase-like protein, which carries an atypical active site structure. S. Ito, T. Fujimori, Y. Hayashizaki, and Y. Nabeshima. Biochim Biophys Acta, 1576, 341-345 (2002)
• Identification of genes regulating colorectal carcinogenesis by using the algorithm for diagnosing malignant state method. Y. Ichikawa, T. Ishikawa, S. Takahashi, Y. Hamaguchi, T. Morita, I. Nishizuka, S. Yamaguchi, I. Endo, H. Ike, S. Togo, S. Oki, H. Shimada, K. Kadota, S. Nakamura, H. Goto, H. Nitanda, S. Satomi, T. Sakai, I. Narita, F. Gejyo, Y. Tomaru, K. Shimizu, Y. Hayashizaki, and Y. Okazaki. Biochem Biophys Res Commun, 296, 497-506 (2002)
• Molecular analysis of gene expression in the developing pontocerebellar projection system. E. Diaz, Y. Ge, Y. H. Yang, K. C. Loh, T. A. Serafini, Y. Okazaki, Y. Hayashizaki, T. P. Speed, J. Ngai, and P. Scheiffele. Neuron, 36, 417-434 (2002)
• Extra-long first-strand cDNA synthesis. P. Carninci, T. Shiraki, Y. Mizuno, M. Muramatsu, and Y. Hayashizaki. Biotechniques, 32, 984-985 (2002)
• Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. P. Carninci, M. Nakamura, K. Sato, Y. Hayashizaki, and M. J. Brownstein. Biotechniques, 33, 306-309 (2002)
• The DT40 web site: sampling and connecting the genes of a B cell line. J. M. Buerstedde, H. Arakawa, A. Watahiki, P. P. Carninci, Y. Y. Hayashizaki, B. Korn, and J. Plachy. Nucleic Acids Res, 30, 230-231 (2002)
• READ: RIKEN Expression Array Database. H. Bono, T. Kasukawa, Y. Hayashizaki, and Y. Okazaki. Nucleic Acids Res, 30, 211-213 (2002)
• FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones. H. Bono, T. Kasukawa, M. Furuno, Y. Hayashizaki, and Y. Okazaki. Nucleic Acids Res, 30, 116-118 (2002)

2001

• Cloning and characterization of a novel mouse AP-2 transcription factor, AP-2delta, with unique DNA binding and transactivation properties. F. Zhao, M. Satoda, J. D. Licht, Y. Hayashizaki, and B. D. Gelb. J Biol Chem, 276, 40755-40760 (2001)
• Identification of a novel member of the snail/Gfi-1 repressor family, mlt 1, which is methylated and silenced in liver tumors of SV40 T antigen transgenic mice. M. Tateno, Y. Fukunishi, S. Komatsu, Y. Okazaki, J. Kawai, K. Shibata, M. Itoh, M. Muramatsu, W. A. Held, and Y. Hayashizaki. Cancer Res, 61, 1144-1153 (2001)
• Protein-protein interaction panel using mouse full-length cDNAs. H. Suzuki, Y. Fukunishi, I. Kagawa, R. Saito, H. Oda, T. Endo, S. Kondo, H. Bono, Y. Okazaki, and Y. Hayashizaki. Genome Res, 11, 1758-1765 (2001)
• Comparative evaluation of 5'-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries. Y. Sugahara, P. Carninci, M. Itoh, K. Shibata, H. Konno, T. Endo, M. Muramatsu, and Y. Hayashizaki. Gene, 263, 93-102 (2001)
• Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method. Y. Shibata, P. Carninci, A. Watahiki, T. Shiraki, H. Konno, M. Muramatsu, and Y. Hayashizaki. Biotechniques, 30, 1250-1254 (2001)
• Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing. Y. Shibata, P. Carninci, K. Sato, N. Hayatsu, T. Shiraki, Y. Ishii, T. Arakawa, A. Hara, N. Ohsato, M. Izawa, K. Aizawa, M. Itoh, K. Shibata, A. Shinagawa, J. Kawai, Y. Ota, S. Kikuchi, N. Kishimoto, M. Muramatsu, and Y. Hayashizaki. Biotechniques, 31, 1042, 1044, 1048-1049 (2001)
• Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. M. Seki, M. Narusaka, H. Abe, M. Kasuga, K. Yamaguchi-Shinozaki, P. Carninci, Y. Hayashizaki, and K. Shinozaki. Plant Cell, 13, 61-72 (2001)
• Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes. H. Sakai, T. Washio, R. Saito, A. Shinagawa, M. Itoh, K. Shibata, P. Carninci, H. Konno, J. Kawai, Y. Hayashizaki, and M. Tomita. Gene, 276, 101-105 (2001)
• The present situation and significance in mouse genome sequencing. T. Okido, K. Sakai, M. Furuno, and Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 46, 1277-1282 (2001)
• Targeting oncogenesis by introduction of a 5.2-kbp segment of the 5' regulatory region of the human thyrotropin beta-subunit gene. I. Miyoshi, K. Maki, Y. Kon, T. Yamashita, S. Aoyama, Y. Hayashizaki, and N. Kasai. Endocr Res, 27, 387-398 (2001)
• Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. R. Miki, K. Kadota, H. Bono, Y. Mizuno, Y. Tomaru, P. Carninci, M. Itoh, K. Shibata, J. Kawai, H. Konno, S. Watanabe, K. Sato, Y. Tokusumi, N. Kikuchi, Y. Ishii, Y. Hamaguchi, I. Nishizuka, H. Goto, H. Nitanda, S. Satomi, A. Yoshiki, M. Kusakabe, J. L. DeRisi, M. B. Eisen, V. R. Iyer, P. O. Brown, M. Muramatsu, H. Shimada, Y. Okazaki, and Y. Hayashizaki. Proc Natl Acad Sci U S A, 98, 2199-2204 (2001)
• Initial sequencing and analysis of the human genome. E. S. Lander and L. M. Linton and B. Birren and C. Nusbaum and M. C. Zody and J. Baldwin and K. Devon and K. Dewar and M. Doyle and W. FitzHugh and R. Funke and D. Gage and K. Harris and A. Heaford and J. Howland and L. Kann and J. Lehoczky and R. LeVine and P. McEwan and K. McKernan and J. Meldrim and J. P. Mesirov and C. Miranda and W. Morris and J. Naylor and C. Raymond and M. Rosetti and R. Santos and A. Sheridan and C. Sougnez and N. Stange-Thomann and N. Stojanovic and A. Subramanian and D. Wyman and J. Rogers and J. Sulston and R. Ainscough and S. Beck and D. Bentley and J. Burton and C. Clee and N. Carter and A. Coulson and R. Deadman and P. Deloukas and A. Dunham and I. Dunham and R. Durbin and L. French and D. Grafham and S. Gregory and T. Hubbard and S. Humphray and A. Hunt and M. Jones and C. Lloyd and A. McMurray and L. Matthews and S. Mercer and S. Milne and J. C. Mullikin and A. Mungall and R. Plumb and M. Ross and R. Shownkeen and S. Sims and R. H. Waterston and R. K. Wilson and L. W. Hillier and J. D. McPherson and M. A. Marra and E. R. Mardis and L. A. Fulton and A. T. Chinwalla and K. H. Pepin and W. R. Gish and S. L. Chissoe and M. C. Wendl and K. D. Delehaunty and T. L. Miner and A. Delehaunty and J. B. Kramer and L. L. Cook and R. S. Fulton and D. L. Johnson and P. J. Minx and S. W. Clifton and T. Hawkins and E. Branscomb and P. Predki and P. Richardson and S. Wenning and T. Slezak and N. Doggett and J. F. Cheng and A. Olsen and S. Lucas and C. Elkin and E. Uberbacher and M. Frazier and R. A. Gibbs and D. M. Muzny and S. E. Scherer and J. B. Bouck and E. J. Sodergren and K. C. Worley and C. M. Rives and J. H. Gorrell and M. L. Metzker and S. L. Naylor and R. S. Kucherlapati and D. L. Nelson and G. M. Weinstock and Y. Sakaki and A. Fujiyama and M. Hattori and T. Yada and A. Toyoda and T. Itoh and C. Kawagoe and H. Watanabe and Y. Totoki and T. Taylor and J. Weissenbach and R. Heilig and W. Saurin and F. Artiguenave and P. Brottier and T. Bruls and E. Pelletier and C. Robert and P. Wincker and D. R. Smith and L. Doucette-Stamm and M. Rubenfield and K. Weinstock and H. M. Lee and J. Dubois and A. Rosenthal and M. Platzer and G. Nyakatura and S. Taudien and A. Rump and H. Yang and J. Yu and J. Wang and G. Huang and J. Gu and L. Hood and L. Rowen and A. Madan and S. Qin and R. W. Davis and N. A. Federspiel and A. P. Abola and M. J. Proctor and R. M. Myers and J. Schmutz and M. Dickson and J. Grimwood and D. R. Cox and M. V. Olson and R. Kaul and C. Raymond and N. Shimizu and K. Kawasaki and S. Minoshima and G. A. Evans and M. Athanasiou and R. Schultz and B. A. Roe and F. Chen and H. Pan and J. Ramser and H. Lehrach and R. Reinhardt and W. R. McCombie and M. de la Bastide and N. Dedhia and H. Blocker and K. Hornischer and G. Nordsiek and R. Agarwala and L. Aravind and J. A. Bailey and A. Bateman and S. Batzoglou and E. Birney and P. Bork and D. G. Brown and C. B. Burge and L. Cerutti and H. C. Chen and D. Church and M. Clamp and R. R. Copley and T. Doerks and S. R. Eddy and E. E. Eichler and T. S. Furey and J. Galagan and J. G. Gilbert and C. Harmon and Y. Hayashizaki and D. Haussler and H. Hermjakob and K. Hokamp and W. Jang and L. S. Johnson and T. A. Jones and S. Kasif and A. Kaspryzk and S. Kennedy and W. J. Kent and P. Kitts and E. V. Koonin and I. Korf and D. Kulp and D. Lancet and T. M. Lowe and A. McLysaght and T. Mikkelsen and J. V. Moran and N. Mulder and V. J. Pollara and C. P. Ponting and G. Schuler and J. Schultz and G. Slater and A. F. Smit and E. Stupka and J. Szustakowski and D. Thierry-Mieg and J. Thierry-Mieg and L. Wagner and J. Wallis and R. Wheeler and A. Williams and Y. I. Wolf and K. H. Wolfe and S. P. Yang and R. F. Yeh and F. Collins and M. S. Guyer and J. Peterson and A. Felsenfeld and K. A. Wetterstrand and A. Patrinos and M. J. Morgan and P. de Jong and J. J. Catanese and K. Osoegawa and H. Shizuya and S. Choi and Y. J. Chen. Nature, 409, 860-921 (2001)
• Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library. H. Konno, Y. Fukunishi, K. Shibata, M. Itoh, P. Carninci, Y. Sugahara, and Y. Hayashizaki. Genome Res, 11, 281-289 (2001)
• Computational analysis of full-length mouse cDNAs compared with human genome sequences. S. Kondo, A. Shinagawa, T. Saito, H. Kiyosawa, I. Yamanaka, K. Aizawa, S. Fukuda, A. Hara, M. Itoh, J. Kawai, K. Shibata, and Y. Hayashizaki. Mamm Genome, 12, 673-677 (2001)
• Mouse gene encyclopedia project: identification of the genes responsible for diseases. H. Kiyosawa and Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 46, 2365-2370 (2001)
• Functional annotation of a full-length mouse cDNA collection. J. Kawai, A. Shinagawa, K. Shibata, M. Yoshino, M. Itoh, Y. Ishii, T. Arakawa, A. Hara, Y. Fukunishi, H. Konno, J. Adachi, S. Fukuda, K. Aizawa, M. Izawa, K. Nishi, H. Kiyosawa, S. Kondo, I. Yamanaka, T. Saito, Y. Okazaki, T. Gojobori, H. Bono, T. Kasukawa, R. Saito, K. Kadota, H. Matsuda, M. Ashburner, S. Batalov, T. Casavant, W. Fleischmann, T. Gaasterland, C. Gissi, B. King, H. Kochiwa, P. Kuehl, S. Lewis, Y. Matsuo, I. Nikaido, G. Pesole, J. Quackenbush, L. M. Schriml, F. Staubli, R. Suzuki, M. Tomita, L. Wagner, T. Washio, K. Sakai, T. Okido, M. Furuno, H. Aono, R. Baldarelli, G. Barsh, J. Blake, D. Boffelli, N. Bojunga, P. Carninci, M. F. de Bonaldo, M. J. Brownstein, C. Bult, C. Fletcher, M. Fujita, M. Gariboldi, S. Gustincich, D. Hill, M. Hofmann, D. A. Hume, M. Kamiya, N. H. Lee, P. Lyons, L. Marchionni, J. Mashima, J. Mazzarelli, P. Mombaerts, P. Nordone, B. Ring, M. Ringwald, I. Rodriguez, N. Sakamoto, H. Sasaki, K. Sato, C. Schonbach, T. Seya, Y. Shibata, K. F. Storch, H. Suzuki, K. Toyo-oka, K. H. Wang, C. Weitz, C. Whittaker, L. Wilming, A. Wynshaw-Boris, K. Yoshida, Y. Hasegawa, H. Kawaji, S. Kohtsuki, and Y. Hayashizaki. Nature, 409, 685-690 (2001)
• Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data. K. Kadota, R. Miki, H. Bono, K. Shimizu, Y. Okazaki, and Y. Hayashizaki. Physiol Genomics, 4, 183-188 (2001)
• Molecular cloning, genetic mapping, and expression of the mouse Sf3b1 (SAP155) gene for the U2 snRNP component of spliceosome. K. Isono, K. Abe, Y. Tomaru, Y. Okazaki, Y. Hayashizaki, and H. Koseki. Mamm Genome, 12, 192-198 (2001)
• Amino acid translation program for full-length cDNA sequences with frameshift errors. Y. Fukunishi and Y. Hayashizaki. Physiol Genomics, 5, 81-87 (2001)
• Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. P. Carninci, Y. Shibata, N. Hayatsu, M. Itoh, T. Shiraki, T. Hirozane, A. Watahiki, K. Shibata, H. Konno, M. Muramatsu, and Y. Hayashizaki. Genomics, 77, 79-90 (2001)

2000

• The paternal methylation imprint of the mouse H19 locus is acquired in the gonocyte stage during foetal testis development. T. Ueda, K. Abe, A. Miura, M. Yuzuriha, M. Zubair, M. Noguchi, K. Niwa, Y. Kawase, T. Kono, Y. Matsuda, H. Fujimoto, H. Shibata, Y. Hayashizaki, and H. Sasaki. Genes Cells, 5, 649-659 (2000)
• Bacterial artificial chromosome libraries for mouse sequencing and functional analysis. K. Osoegawa, M. Tateno, P. Y. Woon, E. Frengen, A. G. Mammoser, J. J. Catanese, Y. Hayashizaki, and P. J. de Jong. Genome Res, 10, 116-128 (2000)
• Methylation and downregulated expression of mac25/insulin-like growth factor binding protein-7 is associated with liver tumorigenesis in SV40T/t antigen transgenic mice, screened by restriction landmark genomic scanning for methylation (RLGS-M). S. Komatsu, Y. Okazaki, M. Tateno, J. Kawai, H. Konno, M. Kusakabe, A. Yoshiki, M. Muramatsu, W. A. Held, and Y. Hayashizaki. Biochem Biophys Res Commun, 267, 109-117 (2000)
• Characterization of the promoter of the murine mac25 gene. N. Kanemitsu, M. V. Kato, T. Miki, S. Komatsu, Y. Okazaki, Y. Hayashizaki, and T. Sakai. Biochem Biophys Res Commun, 279, 251-257 (2000)
• The cell cycle control gene ZAC/PLAGL1 is imprinted--a strong candidate gene for transient neonatal diabetes. M. Kamiya, H. Judson, Y. Okazaki, M. Kusakabe, M. Muramatsu, S. Takada, N. Takagi, T. Arima, N. Wake, K. Kamimura, K. Satomura, R. Hermann, D. T. Bonthron, and Y. Hayashizaki. Hum Mol Genet, 9, 453-460 (2000)
• T7 RNA polymerase activation and improvement of the transcriptional sequencing by polyamines. M. Iwata, M. Izawa, N. Sasaki, Y. Nagumo, H. Sasabe, and Y. Hayashizaki. Bioorg Med Chem, 8, 2185-2194 (2000)
• Corrigendum to: prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database. Y. Fukunishi, H. Suzuki, M. Yoshino, H. Konno, and Y. Hayashizaki. FEBS Lett, 471, 261 (2000)
• Single-strand conformation polymorphism analysis on the delta-sarcoglycan gene in Japanese patients with hypertrophic cardiomyopathy. M. Date, K. Otsu, K. Nishida, T. Toyofuku, Y. Matsumura, T. Morita, S. Hirotani, Y. Okazaki, Y. Hayashizaki, V. Nigro, T. Kuzuya, M. Tada, and M. Hori. Am J Cardiol, 85, 1315-1318 (2000)
• Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. P. Carninci, Y. Shibata, N. Hayatsu, Y. Sugahara, K. Shibata, M. Itoh, H. Konno, Y. Okazaki, M. Muramatsu, and Y. Hayashizaki. Genome Res, 10, 1617-1630 (2000)
• A genetic linkage map of the MSM Japanese wild mouse strain with restriction landmark genomic scanning (RLGS). S. Akiyoshi, H. Kanda, Y. Okazaki, T. Akama, K. Nomura, Y. Hayashizaki, and T. Kitagawa. Mamm Genome, 11, 356-359 (2000)

1983-1999

• Detection and cloning of an X-linked locus associated with a NotI site that is not methylated on mouse inactivated X chromosome by the RLGS-M method. S. Takada, M. Kamiya, T. Arima, H. Kagebayashi, H. Shibata, M. Muramatsu, V. M. Chapman, N. Wake, Y. Hayashizaki, and N. Takagi. Genomics, 61, 92-100 (1999)
• Application of the RLGS image analysis tool (RAT) to the construction of a genetic linkage map of recombinant inbred strain SMXA. Y. Sugahara, S. Akiyoshi, Y. Okazaki, I. Tanihata, Y. Hayashizaki, and M. Nishimura. Mamm Genome, 10, 611-616 (1999)
• A direct repeat sequence at the Rasgrf1 locus and imprinted expression. R. S. Pearsall, C. Plass, M. A. Romano, M. D. Garrick, H. Shibata, Y. Hayashizaki, and W. A. Held. Genomics, 55, 194-201 (1999)
• Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display. Y. Mizuno, P. Carninci, Y. Okazaki, M. Tateno, J. Kawai, H. Amanuma, M. Muramatsu, and Y. Hayashizaki. Nucleic Acids Res, 27, 1345-1349 (1999)
• Automated filtration-based high-throughput plasmid preparation system. M. Itoh, T. Kitsunai, J. Akiyama, K. Shibata, M. Izawa, J. Kawai, Y. Tomaru, P. Carninci, Y. Shibata, Y. Ozawa, M. Muramatsu, Y. Okazaki, and Y. Hayashizaki. Genome Res, 9, 463-470 (1999)?
• Prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database. Y. Fukunishi, H. Suzuki, M. Yoshino, H. Konno, and Y. Hayashizaki. FEBS Lett, 464, 129-132 (1999)
• High-efficiency full-length cDNA cloning. P. Carninci and Y. Hayashizaki. Methods Enzymol, 303, 19-44 (1999)
• An automatic image analysis system for RLGS films. Y. Sugahara, S. Akiyoshi, Y. Okazaki, Y. Hayashizaki, and I. Tanihata. Mamm Genome, 9, 643-651 (1998)
• A methylation imprint mark in the mouse imprinted gene Grf1/Cdc25Mm locus shares a common feature with the U2afbp-rs gene: an association with a short tandem repeat and a hypermethylated region. H. Shibata, Y. Yoda, R. Kato, T. Ueda, M. Kamiya, N. Hiraiwa, A. Yoshiki, C. Plass, R. S. Pearsall, W. A. Held, M. Muramatsu, H. Sasaki, M. Kusakabe, and Y. Hayashizaki. Genomics, 49, 30-37 (1998)
• High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper. M. Seki, P. Carninci, Y. Nishiyama, Y. Hayashizaki, and K. Shinozaki. Plant J, 15, 707-720 (1998)
• Characterization of gene expression in mouse blastocyst using single-pass sequencing of 3995 clones. N. Sasaki, S. Nagaoka, M. Itoh, M. Izawa, H. Konno, P. Carninci, A. Yoshiki, M. Kusakabe, T. Moriuchi, M. Muramatsu, Y. Okazaki, and Y. Hayashizaki. Genomics, 49, 167-179 (1998)
• Transcriptional sequencing: A method for DNA sequencing using RNA polymerase. N. Sasaki, M. Izawa, M. Watahiki, K. Ozawa, T. Tanaka, Y. Yoneda, S. Matsuura, P. Carninci, M. Muramatsu, Y. Okazaki, and Y. Hayashizaki. Proc Natl Acad Sci U S A, 95, 3455-3460 (1998)
• Identification of stable RNA hairpins causing band compression in transcriptional sequencing and their elimination by use of inosine triphosphate. N. Sasaki, M. Izawa, Y. Sugahara, T. Tanaka, M. Watahiki, K. Ozawa, E. Ohara, H. Funaki, Y. Yoneda, S. Matsuura, M. Muramatsu, Y. Okazaki, and Y. Hayashizaki. Gene, 222, 17-23 (1998)
• The Rasgrf1-repeat sequence (D9Ncvs53) maps between Mod1 and Rbp1 on mouse chromosome 9 and may define a putative imprinted region. R. S. Pearsall, K. Imai, H. Shibata, Y. Hayashizaki, V. M. Chapman, W. A. Held, and C. Plass. Mamm Genome, 9, 261-262 (1998)
• An actively retrotransposing, novel subfamily of mouse L1 elements. T. P. Naas, R. J. DeBerardinis, J. V. Moran, E. M. Ostertag, S. F. Kingsmore, M. F. Seldin, Y. Hayashizaki, S. L. Martin, and H. H. Kazazian. Embo J, 17, 590-597 (1998)
• Genetic profile of the SMXA recombinant inbred mouse strains revealed with restriction landmark genomic scanning. M. Mori, S. Akiyoshi, Y. Mizuno, H. Okuizumi, Y. Okazaki, Y. Hayashizaki, and M. Nishimura. Mamm Genome, 9, 695-709 (1998)
• Paternal imprinting of mouse serotonin receptor 2A gene Htr2 in embryonic eye: a conserved imprinting regulation on the RB/Rb locus. M. V. Kato, Y. Ikawa, Y. Hayashizaki, and H. Shibata. Genomics, 47, 146-148 (1998)
• Recognition sites of 3'-OH group by T7 RNA polymerase and its application to transcriptional sequencing. M. Izawa, N. Sasaki, M. Watahiki, E. Ohara, Y. Yoneda, M. Muramatsu, Y. Okazaki, and Y. Hayashizaki. J Biol Chem, 273, 14242-14246 (1998)
• The human GNAS1 gene is imprinted and encodes distinct paternally and biallelically expressed G proteins. B. E. Hayward, M. Kamiya, L. Strain, V. Moran, R. Campbell, Y. Hayashizaki, and D. T. Bonthron. Proc Natl Acad Sci U S A, 95, 10038-10043 (1998)
• Association of a redefined proximal mouse chromosome 11 imprinting region and U2afbp-rs/U2af1-rs1 expression. B. M. Cattanach, H. Shibata, Y. Hayashizaki, K. M. Townsend, S. Ball, and C. V. Beechey. Cytogenet Cell Genet, 80, 41-47 (1998)
• Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA. P. Carninci, Y. Nishiyama, A. Westover, M. Itoh, S. Nagaoka, N. Sasaki, Y. Okazaki, M. Muramatsu, and Y. Hayashizaki. Proc Natl Acad Sci U S A, 95, 520-524 (1998)
• An oocyte-specific methylation imprint center in the mouse U2afbp-rs/U2af1-rs1 gene marks the establishment of allele-specific methylation during preimplantation development. H. Shibata, T. Ueda, M. Kamiya, A. Yoshiki, M. Kusakabe, C. Plass, W. A. Held, S. Sunahara, M. Katsuki, M. Muramatsu, and Y. Hayashizaki. Genomics, 44, 171-178 (1997)
• A novel control system for polymerase chain reaction using a RIKEN GS384 thermalcycler. N. Sasaki, M. Izawa, M. Shimojo, K. Shibata, J. Akiyama, M. Itoh, S. Nagaoka, P. Carninci, Y. Okazaki, T. Moriuchi, M. Muramatsu, S. Watanabe, and Y. Hayashizaki. DNA Res, 4, 387-391 (1997)
• Linkage map of Syrian hamster with restriction landmark genomic scanning. H. Okuizumi, T. Ohsumi, N. Sakaki, H. Imoto, Y. Mizuno, T. Hanami, H. Yamashita, M. Kamiya, S. Takada, A. Kitamura, M. Muramatsu, M. Nishimura, M. Mori, Y. Matsuda, O. Tagaya, Y. Okazaki, and Y. Hayashizaki. Mamm Genome, 8, 121-128 (1997)
• The role of the laboratory mouse and the application of RLGS to the mouse genome. Y. Okazaki, M. Muramatsu, and Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 42, 2887-2896 (1997)
• High-speed positional cloning based on restriction landmark genome scanning. Y. Okazaki and Y. Hayashizaki. Methods, 13, 359-377 (1997)
• New approach for an analysis of full-length cDNA library. Y. Nishiyama, P. Carninci, S. Yoneya, and Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 42, 2858-2863 (1997)
• Identification of the Syrian hamster cardiomyopathy gene. V. Nigro, Y. Okazaki, A. Belsito, G. Piluso, Y. Matsuda, L. Politano, G. Nigro, C. Ventura, C. Abbondanza, A. M. Molinari, D. Acampora, M. Nishimura, Y. Hayashizaki, and G. A. Puca. Hum Mol Genet, 6, 601-607 (1997)
• A unique downregulation of h2-calponin gene expression in Down syndrome: a possible attenuation mechanism for fetal survival by methylation at the CpG island in the trisomic chromosome 21. J. Kuromitsu, H. Yamashita, H. Kataoka, T. Takahara, M. Muramatsu, T. Sekine, N. Okamoto, Y. Furuichi, and Y. Hayashizaki. Mol Cell Biol, 17, 707-712 (1997)
• Morphological study of pituitary tumorigenesis in transgenic mice induced by hybrid oncogene of the thyrotropin beta-subunit and the simian virus 40 large T-antigen. Y. Kon, I. Miyoshi, K. Maki, T. Yamashita, S. Aoyama, T. Watanabe, Y. Hayashizaki, and N. Kasai. Histol Histopathol, 12, 981-990 (1997)
• Simple and rapid preparation of plasmid template by a filtration method using microtiter filter plates. M. Itoh, P. Carninci, S. Nagaoka, N. Sasaki, Y. Okazaki, T. Ohsumi, M. Muramatsu, and Y. Hayashizaki. Nucleic Acids Res, 25, 1315-1316 (1997)
• High efficiency selection of full-length cDNA by improved biotinylated cap trapper. P. Carninci, A. Westover, Y. Nishiyama, T. Ohsumi, M. Itoh, S. Nagaoka, N. Sasaki, Y. Okazaki, M. Muramatsu, C. Schneider, and Y. Hayashizaki. DNA Res, 4, 61-66 (1997)
• Restriction landmark genomic scanning (RLGS-M)-based genome-wide scanning of mouse liver tumors for alterations in DNA methylation status. T. O. Akama, Y. Okazaki, M. Ito, H. Okuizumi, H. Konno, M. Muramatsu, C. Plass, W. A. Held, and Y. Hayashizaki. Cancer Res, 57, 3294-3299 (1997)
• Dysfunction of the Orleans reeler gene arising from exon skipping due to transposition of a full-length copy of an active L1 sequence into the skipped exon. T. Takahara, T. Ohsumi, J. Kuromitsu, K. Shibata, N. Sasaki, Y. Okazaki, H. Shibata, S. Sato, A. Yoshiki, M. Kusakabe, M. Muramatsu, M. Ueki, K. Okuda, and Y. Hayashizaki. Hum Mol Genet, 5, 989-993 (1996)
• Five candidate genes for hamster cardiomyopathy did not map to the cardiomyopathy locus by FISH analysis. S. Takada, Y. Okazaki, M. Kamiya, T. Ohsumi, O. Nomura, H. Okuizumi, N. Sasaki, H. Shibata, M. Mori, M. Nishimura, M. Muramatsu, Y. Hayashizaki, and Y. Matsuda. DNA Res, 3, 273-276 (1996)
• Stac, a novel neuron-specific protein with cysteine-rich and SH3 domains. H. Suzuki, J. Kawai, C. Taga, T. Yaoi, A. Hara, K. Hirose, Y. Hayashizaki, and S. Watanabe. Biochem Biophys Res Commun, 229, 902-909 (1996)
• Inactive allele-specific methylation and chromatin structure of the imprinted gene U2af1-rs1 on mouse chromosome 11. H. Shibata, K. Yoshino, S. Sunahara, Y. Gondo, M. Katsuki, T. Ueda, M. Kamiya, M. Muramatsu, Y. Murakami, I. Kalcheva, C. Plass, V. M. Chapman, and Y. Hayashizaki. Genomics, 35, 248-252 (1996)
• Identification of Grf1 on mouse chromosome 9 as an imprinted gene by RLGS-M. C. Plass, H. Shibata, I. Kalcheva, L. Mullins, N. Kotelevtseva, J. Mullins, R. Kato, H. Sasaki, S. Hirotsune, Y. Okazaki, W. A. Held, Y. Hayashizaki, and V. M. Chapman. Nat Genet, 14, 106-109 (1996)
• Absence of imprinting in U2AFBPL, a human homologue of the imprinted mouse gene U2afbp-rs. R. S. Pearsall, H. Shibata, A. Brozowska, K. Yoshino, K. Okuda, P. J. deJong, C. Plass, V. M. Chapman, Y. Hayashizaki, and W. A. Held. Biochem Biophys Res Commun, 222, 171-177 (1996)
• A genetic linkage map of the Syrian hamster and localization of cardiomyopathy locus on chromosome 9qa2.1-b1 using RLGS spot-mapping. Y. Okazaki, H. Okuizumi, T. Ohsumi, O. Nomura, S. Takada, M. Kamiya, N. Sasaki, Y. Matsuda, M. Nishimura, O. Tagaya, M. Muramatsu, and Y. Hayashizaki. Nat Genet, 13, 87-90 (1996)
• Isolation of DNA sequences amplified at chromosome 19q13.1-q13.2 including the AKT2 locus in human pancreatic cancer. W. Miwa, J. Yasuda, Y. Murakami, K. Yashima, K. Sugano, T. Sekine, A. Kono, S. Egawa, K. Yamaguchi, Y. Hayashizaki, and T. Sekiya. Biochem Biophys Res Commun, 225, 968-974 (1996)
• Comparative mapping of the reeler gene on human chromosome 7q22, rat chromosome 4q11.2, and mouse chromosome 5 A3-B1. Y. Matsuda, T. Takahara, M. Kusakabe, and Y. Hayashizaki. Mamm Genome, 7, 468-469 (1996)
• Construction of high-resolution physical maps from yeast artificial chromosomes using restriction landmark genomic scanning (RLGS). S. Hirotsune, T. Takahara, N. Sasaki, H. Imoto, Y. Okazaki, T. Eki, Y. Murakami, M. Abe, K. Furuya, M. Muramatsu, Y. Eto, V. M. Chapman, and Y. Hayashizaki. Genomics, 37, 87-95 (1996)
• High-efficiency full-length cDNA cloning by biotinylated CAP trapper. P. Carninci, C. Kvam, A. Kitamura, T. Ohsumi, Y. Okazaki, M. Itoh, M. Kamiya, K. Shibata, N. Sasaki, M. Izawa, M. Muramatsu, Y. Hayashizaki, and C. Schneider. Genomics, 37, 327-336 (1996)
• Identification and characterization of Zic4, a new member of the mouse Zic gene family. J. Aruga, A. Yozu, Y. Hayashizaki, Y. Okazaki, V. M. Chapman, and K. Mikoshiba. Gene, 172, 291-294 (1996)
• The mouse zic gene family. Homologues of the Drosophila pair-rule gene odd-paired. J. Aruga, T. Nagai, T. Tokuyama, Y. Hayashizaki, Y. Okazaki, V. M. Chapman, and K. Mikoshiba. J Biol Chem, 271, 1043-1047 (1996)
• Accessibility to tissue-specific genes from methylation profiles of mouse brain genomic DNA. S. Watanabe, J. Kawai, S. Hirotsune, H. Suzuki, K. Hirose, C. Taga, N. Ozawa, S. Fushiki, and Y. Hayashizaki. Electrophoresis, 16, 218-226 (1995)
• The use of restriction landmark genomic scanning to scan the mouse genome for endogenous loci with imprinted patterns of methylation. H. Shibata, K. Yoshino, M. Muramatsu, C. Plass, V. M. Chapman, and Y. Hayashizaki. Electrophoresis, 16, 210-217 (1995)?
• Comparative analysis of mouse NotI linking clones with mouse and human genomic sequences and transcripts. C. Plass, J. Kawai, I. Kalcheva, L. Davis, S. Watanabe, Y. Hayashizaki, and V. Chapman. DNA Res, 2, 27-35 (1995)
• Genetic mapping of restriction landmark genomic scanning loci in the mouse. H. Okuizumi, Y. Okazaki, T. Ohsumi, Y. Hayashizaki, C. Plass, and V. M. Chapman. Electrophoresis, 16, 233-240 (1995)
• A single gel analysis of 575 dominant and codominant restriction landmark genomic scanning loci in mice interspecific backcross progeny. H. Okuizumi, Y. Okazaki, T. Ohsumi, T. Hanami, Y. Mizuno, M. Muramatsu, Y. Hayashizaki, C. Plass, and V. M. Chapman. Electrophoresis, 16, 253-260 (1995)
• An expanded system of restriction landmark genomic scanning (RLGS Ver. 1.8). Y. Okazaki, H. Okuizumi, N. Sasaki, T. Ohsumi, J. Kuromitsu, N. Hirota, M. Muramatsu, and Y. Hayashizaki. Electrophoresis, 16, 197-202 (1995)
• A spot cloning method for restriction landmark genomic scanning. T. Ohsumi, Y. Okazaki, S. Hirotsune, H. Shibata, M. Muramatsu, H. Suzuki, C. Taga, S. Watanabe, and Y. Hayashizaki. Electrophoresis, 16, 203-209 (1995)
• Stage-specific induction and regulation by genomic imprinting of the mouse U2afbp-rs gene during preimplantation development. K. E. Latham, L. Rambhatla, Y. Hayashizaki, and V. M. Chapman. Dev Biol, 168, 670-676 (1995)
• Reproducible alterations of DNA methylation at a specific population of CpG islands during blast formation of peripheral blood lymphocytes. J. Kuromitsu, H. Kataoka, H. Yamashita, M. Muramatsu, Y. Furuichi, T. Sekine, and Y. Hayashizaki. DNA Res, 2, 263-267 (1995)
• Localization of mouse imprinted gene U2af1-rs1 to A3.2-4 band of chromosome 11 by FISH. M. Tada, T. Tada, N. Takagi, Y. Hayashizaki, H. Shibata, S. Hirotsune, Y. Okazaki, M. Muramatsu, H. Sasaki, T. Ueda, and et al.. Mamm Genome, 5, 655 (1994)
• The gene responsible for LEC hepatitis, located on rat chromosome 16, is the homolog to the human Wilson disease gene. N. Sasaki, Y. Hayashizaki, M. Muramatsu, Y. Matsuda, Y. Ando, T. Kuramoto, T. Serikawa, T. Azuma, A. Naito, T. Agui, and et al.. Biochem Biophys Res Commun, 202, 512-518 (1994)
• Application of the RLGS method to large-size genomes using a restriction trapper. H. Okuizumi, Y. Okazaki, N. Sasaki, M. Muramatsu, K. Nakashima, K. Fan, H. Tano, K. Ohba, and Y. Hayashizaki. DNA Res, 1, 99-102 (1994)
• Structure and regulation of human thyroid-stimulating hormone (TSH) gene. I. Miyoshi, N. Kasai, and Y. Hayashizaki. Nippon Rinsho, 52, 940-947 (1994)
• Targeted pituitary tumorigenesis using the human thyrotropin beta-subunit chain promoter in transgenic mice. K. Maki, I. Miyoshi, Y. Kon, T. Yamashita, N. Sasaki, S. Aoyama, E. Takahashi, S. Namioka, Y. Hayashizaki, and N. Kasai. Mol Cell Endocrinol, 105, 147-154 (1994)
• Comparison of DNA methylation patterns among mouse cell lines by restriction landmark genomic scanning. J. Kawai, K. Hirose, S. Fushiki, S. Hirotsune, N. Ozawa, A. Hara, Y. Hayashizaki, and S. Watanabe. Mol Cell Biol, 14, 7421-7427 (1994)
• Direct determination of NotI cleavage sites in the genomic DNA of adult mouse kidney and human trophoblast using whole-range restriction landmark genomic scanning. H. Imoto, S. Hirotsune, M. Muramatsu, K. Okuda, O. Sugimoto, V. M. Chapman, and Y. Hayashizaki. DNA Res, 1, 239-243 (1994)
• Spot mapping on the standard profile of restriction landmark genomic scanning (RLGS) of sorted chromosome 20 using methylation-insensitive enzyme. S. Hirotsune, K. Hirose, H. Kataoka, J. Kuromitsu, Y. Furuichi, M. Muramatsu, Y. Matsuda, and Y. Hayashizaki. Genomics, 24, 593-596 (1994)
• Identification of an imprinted U2af binding protein related sequence on mouse chromosome 11 using the RLGS method. Y. Hayashizaki, H. Shibata, S. Hirotsune, H. Sugino, Y. Okazaki, N. Sasaki, K. Hirose, H. Imoto, H. Okuizumi, M. Muramatsu, and et al.. Nat Genet, 6, 33-40 (1994)
• A genetic linkage map of the mouse using restriction landmark genomic scanning (RLGS). Y. Hayashizaki, S. Hirotsune, Y. Okazaki, H. Shibata, A. Akasako, M. Muramatsu, J. Kawai, T. Hirasawa, S. Watanabe, T. Shiroishi, and et al.. Genetics, 138, 1207-1238 (1994)
• Absence of linkage between the retinoblastoma gene and hts gene in the LEC rat: a model of human Wilson's disease. N. Sasaki, Y. Hayashizaki, and N. Kasai. Jpn J Cancer Res, 84, 1019-1022 (1993)
• Genomic analysis of human hepatocellular carcinomas using Restriction Landmark Genomic Scanning. H. Nagai, S. Hirotsune, H. Komatsubara, I. Hatada, T. Mukai, Y. Hayashizaki, and K. Matsubara. Cancer Detect Prev, 17, 399-404 (1993)
• Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method. J. Kawai, S. Hirotsune, K. Hirose, S. Fushiki, S. Watanabe, and Y. Hayashizaki. Nucleic Acids Res, 21, 5604-5608 (1993)
• Restriction landmark genomic scanning method and its various applications. Y. Hayashizaki, S. Hirotsune, Y. Okazaki, I. Hatada, H. Shibata, J. Kawai, K. Hirose, S. Watanabe, S. Fushiki, S. Wada, and et al.. Electrophoresis, 14, 251-258 (1993)
• Restriction landmark genomic scanning (RLGS) method and its application. Y. Hayashizaki, I. Hatada, S. Hirotsune, Y. Okazaki, H. Shibata, and T. Mukai. Seikagaku, 65, 109-115 (1993)
• Genomic scanning method--restriction landmark genomic scanning. Y. Hayashizaki, I. Hatada, S. Hirotsune, and T. Mukai. Tanpakushitsu Kakusan Koso, 38, 573-580 (1993)
• A new method for constructing NotI linking and boundary libraries using a restriction trapper. Y. Hayashizaki, S. Hirotsune, I. Hatada, S. Tamatsukuri, C. Miyamoto, Y. Furuichi, and T. Mukai. Genomics, 14, 733-739 (1992)
• A genomic scanning method for higher organisms using restriction sites as landmarks. I. Hatada, Y. Hayashizaki, S. Hirotsune, H. Komatsubara, and T. Mukai. Proc Natl Acad Sci U S A, 88, 9523-9527 (1991)
• Chromosome regional mapping for the human thyroid stimulating hormone beta subunit (TSHB) gene. T. Tokino, Y. Hayashizaki, K. I. Takata, M. C. Yoshida, and K. Matsubara. Cytogenet Cell Genet, 53, 140-143 (1990)
• Deoxyribonucleic acid analyses of five families with familial inherited thyroid stimulating hormone deficiency. Y. Hayashizaki, Y. Hiraoka, K. Tatsumi, T. Hashimoto, J. Furuyama, K. Miyai, K. Nishijo, M. Matsuura, H. Kohno, A. Labbe, and et al.. J Clin Endocrinol Metab, 71, 792-796 (1990)
• The role of the carboxyl-terminal 6 amino acid extension of human TSH beta subunit. K. Takata, S. Watanabe, M. Hirono, M. Tamaki, H. Teraoka, and Y. Hayashizaki. Biochem Biophys Res Commun, 165, 1035-1042 (1989)
• Thyroid-stimulating hormone (TSH) deficiency caused by a single base substitution in the CAGYC region of the beta-subunit. Y. Hayashizaki, Y. Hiraoka, Y. Endo, K. Miyai, and K. Matsubara. Embo J, 8, 2291-2296 (1989)
• The structure of the human thyrotropin beta-subunit gene. K. Tatsumi, Y. Hayashizaki, Y. Hiraoka, K. Miyai, and K. Matsubara. Gene, 73, 489-497 (1988)
• Serum free thyrotropin subunit in congenital isolated thyrotropin deficiency. K. Miyai, Y. Endo, Y. Iijima, O. Kabutomori, and Y. Hayashizaki. Endocrinol Jpn, 35, 517-521 (1988)
• Congenital thyrotropin abnormalities. K. Miyai, Y. Endo, and Y. Hayashizaki. Tanpakushitsu Kakusan Koso, 33, 884-889 (1988)
• The dysfunction of human thyroid stimulating hormone (hTSH) due to TSH beta subunit gene abnormality. Y. Hayashizaki, K. Matsubara, and K. Miyai. Rinsho Byori, 36, 538-540 (1988)
• The production of active human thyroid-stimulating hormone from alpha and beta mRNAs in Xenopus laevis oocytes. Y. Hayashizaki, Y. Endo, K. Miyai, and K. Matsubara. Biochem Biophys Res Commun, 152, 703-710 (1988)
• Production of human thyroid-stimulating hormone in Chinese hamster ovary cells. S. Watanabe, Y. Hayashizaki, Y. Endo, M. Hirono, N. Takimoto, M. Tamaki, H. Teraoka, K. Miyai, and K. Matsubara. Biochem Biophys Res Commun, 149, 1149-1155 (1987)
• Revision of consensus sequence of human Alu repeats--a review. Y. Kariya, K. Kato, Y. Hayashizaki, S. Himeno, S. Tarui, and K. Matsubara. Gene, 53, 1-10 (1987)
• Expression of human gastrin gene in normal and gastrinoma tissues. Y. Kariya, K. Kato, Y. Hayashizaki, S. Himeno, S. Tarui, and K. Matsubara. Gene, 50, 345-352 (1986)
• Effects of corticotropin releasing factor and growth hormone releasing factor on pituitary hormone secretion in patients with congenital thyrotropin deficiency. Abnormal response of growth hormone to corticotropin releasing factor. Y. Hayashizaki, K. Miyai, T. Onishi, and Y. Kumahara. Horm Metab Res, 18, 849-853 (1986)
• Anterior pituitary hormone genes. Y. Hayashizaki and K. Miyai. Nippon Sanka Fujinka Gakkai Zasshi, 38, 2293-2300 (1986)?
• Molecular cloning of the human cholecystokinin gene by use of a synthetic probe containing deoxyinosine. Y. Takahashi, K. Kato, Y. Hayashizaki, T. Wakabayashi, E. Ohtsuka, S. Matsuki, M. Ikehara, and K. Matsubara. Proc Natl Acad Sci U S A, 82, 1931-1935 (1985)
• Molecular cloning of the human thyrotropin-beta subunit gene. Y. Hayashizaki, K. Miyai, K. Kato, and K. Matsubara. FEBS Lett, 188, 394-400 (1985)
• Molecular cloning of the human gastrin gene. K. Kato, Y. Hayashizaki, Y. Takahashi, S. Himeno, and K. Matsubara. Nucleic Acids Res, 11, 8197-8203 (1983)