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Piero Carninci
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96
Hayashizaki, Yoshihide
33
Kawai, Jun
19
Kai, Chikatoshi
10
Itoh, Masayoshi
10
Forrest, Alistair
9
Okazaki, Yasushi
9
Shiraki, Toshiyuki
9
Frith, Martin
8
Grimmond, Sean
8
Shibata, Kazuhiro
8
Kawaji, Hideya
7
Sandelin, Albin
7
Hume, David
7
Arakawa, Takahiro
7
Faulkner, Geoffrey
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All Publications
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2009: Forrest Alistair R R; Abdelhamid Rehab F; Carninci Piero
Annotating non-coding transcription using functional genomics strategies.
Briefings in functional genomics & proteomics 2009;8(6):437-43.
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2009: Faulkner Geoffrey J; Carninci Piero
Altruistic functions for selfish DNA.
Cell cycle (Georgetown, Tex.) 2009;8(18):2895-900.
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2009: Biagioli Marta; Pinto Milena; Cesselli Daniela; Zaninello Marta; Lazarevic Dejan; Roncaglia Paola; Simone Roberto; Vlachouli Christina; Plessy Charles; Bertin Nicolas; Beltrami Antonio; Kobayashi Kazuto; Gallo Vittorio; Santoro Claudio; Ferrer Isidro; Rivella Stefano; Beltrami Carlo Alberto; Carninci Piero; Raviola Elio; Gustincich Stefano
Unexpected expression of alpha- and beta-globin in mesencephalic dopaminergic neurons and glial cells.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(36):15454-9.
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2009: Taft Ryan J; Glazov Evgeny A; Lassmann Timo; Hayashizaki Yoshihide; Carninci Piero; Mattick John S
Small RNAs derived from snoRNAs.
RNA (New York, N.Y.) 2009;15(7):1233-40.
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2009: Taft Ryan J; Glazov Evgeny A; Cloonan Nicole; Simons Cas; Stephen Stuart; Faulkner Geoffrey J; Lassmann Timo; Forrest Alistair R R; Grimmond Sean M; Schroder Kate; Irvine Katharine; Arakawa Takahiro; Nakamura Mari; Kubosaki Atsutaka; Hayashida Kengo; Kawazu Chika; Murata Mitsuyoshi; Nishiyori Hiromi; Fukuda Shiro; Kawai Jun; Daub Carsten O; Hume David A; Suzuki Harukazu; Orlando Valerio; Carninci Piero; Hayashizaki Yoshihide; Mattick John S
Tiny RNAs associated with transcription start sites in animals.
Nature genetics 2009;41(5):572-8.
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2009: Faulkner Geoffrey J; Kimura Yasumasa; Daub Carsten O; Wani Shivangi; Plessy Charles; Irvine Katharine M; Schroder Kate; Cloonan Nicole; Steptoe Anita L; Lassmann Timo; Waki Kazunori; Hornig Nadine; Arakawa Takahiro; Takahashi Hazuki; Kawai Jun; Forrest Alistair R R; Suzuki Harukazu; Hayashizaki Yoshihide; Hume David A; Orlando Valerio; Grimmond Sean M; Carninci Piero
The regulated retrotransposon transcriptome of mammalian cells.
Nature genetics 2009;41(5):563-71.
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2009: Brinkmeier Michelle L; Davis Shannon W; Carninci Piero; MacDonald James W; Kawai Jun; Ghosh Debashis; Hayashizaki Yoshihide; Lyons Robert H; Camper Sally A
Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches.
Genomics 2009;93(5):449-60.
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2009: Forrest Alistair R R; Carninci Piero
Whole genome transcriptome analysis.
RNA biology 2009;6(2):107-12.
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2009: Davis Shannon W; Potok Mary Anne; Brinkmeier Michelle L; Carninci Piero; Lyons Robert H; MacDonald James W; Fleming Michelle T; Mortensen Amanda H; Egashira Noboru; Ghosh Debashis; Steel Karen P; Osamura Robert Y; Hayashizaki Yoshihide; Camper Sally A
Genetics, gene expression and bioinformatics of the pituitary gland.
Hormone research 2009;71 Suppl 2():101-15.
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2009: Olivarius Signe; Plessy Charles; Carninci Piero
High-throughput verification of transcriptional starting sites by Deep-RACE.
BioTechniques 2009;46(2):130-2.
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2009: Carninci Piero
Molecular biology: The long and short of RNAs.
Nature 2009;457(7232):974-5.
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2009: Valen Eivind; Pascarella Giovanni; Chalk Alistair; Maeda Norihiro; Kojima Miki; Kawazu Chika; Murata Mitsuyoshi; Nishiyori Hiromi; Lazarevic Dejan; Motti Dario; Marstrand Troels Torben; Tang Man-Hung Eric; Zhao Xiaobei; Krogh Anders; Winther Ole; Arakawa Takahiro; Kawai Jun; Wells Christine; Daub Carsten; Harbers Matthias; Hayashizaki Yoshihide; Gustincich Stefano; Sandelin Albin; Carninci Piero
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.
Genome research 2009;19(2):255-65.
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2009: Balwierz Piotr J; Carninci Piero; Daub Carsten O; Kawai Jun; Hayashizaki Yoshihide; Van Belle Werner; Beisel Christian; van Nimwegen Erik
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.
Genome biology 2009;10(7):R79.
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2009: Kawaji Hideya; Severin Jessica; Lizio Marina; Waterhouse Andrew; Katayama Shintaro; Irvine Katharine M; Hume David A; Forrest Alistair R R; Suzuki Harukazu; Carninci Piero; Hayashizaki Yoshihide; Daub Carsten O
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Genome biology 2009;10(4):R40.
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2009: Severin Jessica; Waterhouse Andrew M; Kawaji Hideya; Lassmann Timo; van Nimwegen Erik; Balwierz Piotr J; de Hoon Michiel Jl; Hume David A; Carninci Piero; Hayashizaki Yoshihide; Suzuki Harukazu; Daub Carsten O; Forrest Alistair Rr
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.
Genome biology 2009;10(4):R39.
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2009: Seki Motoaki; Kamiya Asako; Carninci Piero; Hayashizaki Yoshihide; Shinozaki Kazuo
Generation of full-length cDNA libraries: focus on plants.
Methods in molecular biology (Clifton, N.J.) 2009;533():49-68.
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2008: Taylor Martin S; Massingham Tim; Hayashizaki Yoshihide; Carninci Piero; Goldman Nick; Semple Colin A M
Rapidly evolving human promoter regions.
Nature genetics 2008;40(11):1262-3; author reply 1263-4.
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2008: Shindo Yoichiro; Miura Hirohito; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Ninomiya Yuzo; Hino Akihiro; Kanda Tomomasa; Kusakabe Yuko
G alpha14 is a candidate mediator of sweet/umami signal transduction in the posterior region of the mouse tongue.
Biochemical and biophysical research communications 2008;376(3):504-8.
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2008: Centlow Magnus; Carninci Piero; Nemeth Krisztian; Mezey Eva; Brownstein Michael; Hansson Stefan R
Placental expression profiling in preeclampsia: local overproduction of hemoglobin may drive pathological changes.
Fertility and sterility 2008;90(5):1834-43.
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2008: Carninci Piero
Non-coding RNA transcription: turning on neighbours.
Nature cell biology 2008;10(9):1023-4.
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2008: Maeda Norihiro; Nishiyori Hiromi; Nakamura Mari; Kawazu Chika; Murata Mitsuyoshi; Sano Hiromi; Hayashida Kengo; Fukuda Shiro; Tagami Michihira; Hasegawa Akira; Murakami Kayoko; Schroder Kate; Irvine Katharine; Hume David; Hayashizaki Yoshihide; Carninci Piero; Suzuki Harukazu
Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.
BioTechniques 2008;45(1):95-7.
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2008: Carninci Piero
Hunting hidden transcripts.
Nature methods 2008;5(7):587-9.
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2008: Carninci Piero; Yasuda Jun; Hayashizaki Yoshihide
Multifaceted mammalian transcriptome.
Current opinion in cell biology 2008;20(3):274-80.
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2008: Faulkner Geoffrey J; Forrest Alistair R R; Chalk Alistair M; Schroder Kate; Hayashizaki Yoshihide; Carninci Piero; Hume David A; Grimmond Sean M
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.
Genomics 2008;91(3):281-8.
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2008: Frith Martin C; Valen Eivind; Krogh Anders; Hayashizaki Yoshihide; Carninci Piero; Sandelin Albin
A code for transcription initiation in mammalian genomes.
Genome research 2008;18(1):1-12.
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2008: Plessy Charles; Fagiolini Michela; Wagatsuma Akiko; Harasawa Norihiro; Kuji Takenobu; Asaka-Oba Atsuko; Kanzaki Yukari; Fujishima Sayaka; Waki Kazunori; Nakahara Hiroyuki; Hensch Takao K; Carninci Piero
A resource for transcriptomic analysis in the mouse brain.
PloS one 2008;3(8):e3012.
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2008: Kawaji Hideya; Nakamura Mari; Takahashi Yukari; Sandelin Albin; Katayama Shintaro; Fukuda Shiro; Daub Carsten O; Kai Chikatoshi; Kawai Jun; Yasuda Jun; Carninci Piero; Hayashizaki Yoshihide
Hidden layers of human small RNAs.
BMC genomics 2008;9():157.
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2007: Frith Martin C; Carninci Piero; Kai Chikatoshi; Kawai Jun; Bailey Timothy L; Hayashizaki Yoshihide; Mattick John S
Splicing bypasses 3' end formation signals to allow complex gene architectures.
Gene 2007;403(1-2):188-93.
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2007: Kawai Jun; Carninci Piero; Hayashizaki Yoshihide
Transcriptomics resources for functional genomics.
Briefings in functional genomics & proteomics 2007;6(3):171-9.
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2007: Baxter Laura L; Hsu Benjamin J; Umayam Lowell; Wolfsberg Tyra G; Larson Denise M; Frith Martin C; Kawai Jun; Hayashizaki Yoshihide; Carninci Piero; Pavan William J
Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function.
Pigment cell research / sponsored by the European Society for Pigment Cell Research and the International Pigment Cell Society 2007;20(3):201-9.
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2007: Sandelin Albin; Carninci Piero; Lenhard Boris; Ponjavic Jasmina; Hayashizaki Yoshihide; Hume David A
Mammalian RNA polymerase II core promoters: insights from genome-wide studies.
Nature reviews. Genetics 2007;8(6):424-36.
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2007: Carninci Piero
Constructing the landscape of the mammalian transcriptome.
The Journal of experimental biology 2007;210(Pt 9):1497-506.
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2007: Purmann Antje; Toedling Joern; Schueler Markus; Carninci Piero; Lehrach Hans; Hayashizaki Yoshihide; Huber Wolfgang; Sperling Silke
Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality.
Genomics 2007;89(5):580-7.
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2007: Carninci Piero; Hayashizaki Yoshihide
Noncoding RNA transcription beyond annotated genes.
Current opinion in genetics & development 2007;17(2):139-44.
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2007: Beisel Kirk W; Rocha-Sanchez Sonia M; Ziegenbein Sylvia J; Morris Ken A; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Davis Robin L
Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells.
Gene 2007;386(1-2):11-23.
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2007: Kruger Adele; Hofmann Oliver; Carninci Piero; Hayashizaki Yoshihide; Hide Winston
Simplified ontologies allowing comparison of developmental mammalian gene expression.
Genome biology 2007;8(10):R229.
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2007: Shimokawa Kazuro; Okamura-Oho Yuko; Kurita Takio; Frith Martin C; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide
Large-scale clustering of CAGE tag expression data.
BMC bioinformatics 2007;8():161.
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2006: Wada Kazuhiro; Howard Jason T; McConnell Patrick; Whitney Osceola; Lints Thierry; Rivas Miriam V; Horita Haruhito; Patterson Michael A; White Stephanie A; Scharff Constance; Haesler Sebastian; Zhao Shengli; Sakaguchi Hironobu; Hagiwara Masatoshi; Shiraki Toshiyuki; Hirozane-Kishikawa Tomoko; Skene Pate; Hayashizaki Yoshihide; Carninci Piero; Jarvis Erich D
A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(41):15212-7.
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2006: Carninci Piero
Tagging mammalian transcription complexity.
Trends in genetics : TIG 2006;22(9):501-10.
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2006: Gustincich Stefano; Sandelin Albin; Plessy Charles; Katayama Shintaro; Simone Roberto; Lazarevic Dejan; Hayashizaki Yoshihide; Carninci Piero
The complexity of the mammalian transcriptome.
The Journal of physiology 2006;575(Pt 2):321-32.
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2006: Nilsson Roland; Bajic Vladimir B; Suzuki Harukazu; di Bernardo Diego; Björkegren Johan; Katayama Shintaro; Reid James F; Sweet Matthew J; Gariboldi Manuela; Carninci Piero; Hayashizaki Yosihide; Hume David A; Tegner Jesper; Ravasi Timothy
Transcriptional network dynamics in macrophage activation.
Genomics 2006;88(2):133-42.
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2006: Itoh Masayoshi; Yasunishi Ayako; Imamura Kengo; Kanamori-Katayama Mutsumi; Suzuki Harukazu; Suzuki Masanori; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide
Constructing ORFeome resources with removable termination codons.
BioTechniques 2006;41(1):44, 46, 48 passim.
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2006: Frith Martin C; Ponjavic Jasmina; Fredman David; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Sandelin Albin
Evolutionary turnover of mammalian transcription start sites.
Genome research 2006;16(6):713-22.
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2006: Aturaliya Rajith N; Fink J Lynn; Davis Melissa J; Teasdale Melvena S; Hanson Kelly A; Miranda Kevin C; Forrest Alistair R R; Grimmond Sean M; Suzuki Harukazu; Kanamori Mutsumi; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Teasdale Rohan D
Subcellular localization of mammalian type II membrane proteins.
Traffic (Copenhagen, Denmark) 2006;7(5):613-25.
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2006: Hayashizaki Yoshihide; Carninci Piero
Genome Network and FANTOM3: assessing the complexity of the transcriptome.
PLoS genetics 2006;2(4):e63.
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2006: Bajic Vladimir B; Tan Sin Lam; Christoffels Alan; Schönbach Christian; Lipovich Leonard; Yang Liang; Hofmann Oliver; Kruger Adele; Hide Winston; Kai Chikatoshi; Kawai Jun; Hume David A; Carninci Piero; Hayashizaki Yoshihide
Mice and men: their promoter properties.
PLoS genetics 2006;2(4):e54.
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2006: Frith Martin C; Forrest Alistair R; Nourbakhsh Ehsan; Pang Ken C; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Bailey Timothy L; Grimmond Sean M
The abundance of short proteins in the mammalian proteome.
PLoS genetics 2006;2(4):e52.
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2006: Engström Pär G; Suzuki Harukazu; Ninomiya Noriko; Akalin Altuna; Sessa Luca; Lavorgna Giovanni; Brozzi Alessandro; Luzi Lucilla; Tan Sin Lam; Yang Liang; Kunarso Galih; Ng Edwin Lian-Chong; Batalov Serge; Wahlestedt Claes; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Wells Christine; Bajic Vladimir B; Orlando Valerio; Reid James F; Lenhard Boris; Lipovich Leonard
Complex Loci in human and mouse genomes.
PLoS genetics 2006;2(4):e47.
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2006: Davis Melissa J; Hanson Kelly A; Clark Francis; Fink J Lynn; Zhang Fasheng; Kasukawa Takeya; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Teasdale Rohan D
Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units.
PLoS genetics 2006;2(4):e46.
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2006: Chern Tzu-Ming; van Nimwegen Erik; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Zavolan Mihaela
A simple physical model predicts small exon length variations.
PLoS genetics 2006;2(4):e45.
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2006: Seno Shigeto; Takenaka Yoichi; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Matsuda Hideo
A method for similarity search of genomic positional expression using CAGE.
PLoS genetics 2006;2(4):e44.
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2006: Furuno Masaaki; Pang Ken C; Ninomiya Noriko; Fukuda Shiro; Frith Martin C; Bult Carol; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Mattick John S; Suzuki Harukazu
Clusters of internally primed transcripts reveal novel long noncoding RNAs.
PLoS genetics 2006;2(4):e37.
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2006: Taylor Martin S; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Semple Colin A M
Heterotachy in mammalian promoter evolution.
PLoS genetics 2006;2(4):e30.
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2006: Frith Martin C; Wilming Laurens G; Forrest Alistair; Kawaji Hideya; Tan Sin Lam; Wahlestedt Claes; Bajic Vladimir B; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Bailey Timothy L; Huminiecki Lukasz
Pseudo-messenger RNA: phantoms of the transcriptome.
PLoS genetics 2006;2(4):e23.
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2006: Kodzius Rimantas; Kojima Miki; Nishiyori Hiromi; Nakamura Mari; Fukuda Shiro; Tagami Michihira; Sasaki Daisuke; Imamura Kengo; Kai Chikatoshi; Harbers Matthias; Hayashizaki Yoshihide; Carninci Piero
CAGE: cap analysis of gene expression.
Nature methods 2006;3(3):211-22.
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2006: Frith Martin C; Bailey Timothy L; Kasukawa Takeya; Mignone Flavio; Kummerfeld Sarah K; Madera Martin; Sunkara Sirisha; Furuno Masaaki; Bult Carol J; Quackenbush John; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Pesole Graziano; Mattick John S
Discrimination of non-protein-coding transcripts from protein-coding mRNA.
RNA biology 2006;3(1):40-8.
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2006: Kawaji Hideya; Kasukawa Takeya; Fukuda Shiro; Katayama Shintaro; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.
Nucleic acids research 2006;34(Database issue):D632-6.
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2006: Fink J Lynn; Aturaliya Rajith N; Davis Melissa J; Zhang Fasheng; Hanson Kelly; Teasdale Melvena S; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Teasdale Rohan D
LOCATE: a mouse protein subcellular localization database.
Nucleic acids research 2006;34(Database issue):D213-7.
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2006: Brahmachary Manisha; Schönbach Christian; Yang Liang; Huang Enli; Tan Sin Lam; Chowdhary Rajesh; Krishnan S P T; Lin Chin-Yo; Hume David A; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Bajic Vladimir B
Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes.
BMC bioinformatics 2006;7 Suppl 5():S8.
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2006: Kawaji Hideya; Frith Martin C; Katayama Shintaro; Sandelin Albin; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide
Dynamic usage of transcription start sites within core promoters.
Genome biology 2006;7(12):R118.
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2006: Ponjavic Jasmina; Lenhard Boris; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Sandelin Albin
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters.
Genome biology 2006;7(8):R78.
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2006: Wells Christine A; Chalk Alistair M; Forrest Alistair; Taylor Darrin; Waddell Nic; Schroder Kate; Himes S Roy; Faulkner Geoffrey; Lo Sandra; Kasukawa Takeya; Kawaji Hideya; Kai Chikatoshi; Kawai Jun; Katayama Shintaro; Carninci Piero; Hayashizaki Yoshihide; Hume David A; Grimmond Sean M
Alternate transcription of the Toll-like receptor signaling cascade.
Genome biology 2006;7(2):R10.
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2006: Forrest Alistair R R; Taylor Darrin F; Crowe Mark L; Chalk Alistair M; Waddell Nic J; Kolle Gabriel; Faulkner Geoffrey J; Kodzius Rimantas; Katayama Shintaro; Wells Christine; Kai Chikatoshi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Grimmond Sean M
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases.
Genome biology 2006;7(1):R5.
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2005: Aidinis Vassilis; Carninci Piero; Armaka Maria; Witke Walter; Harokopos Vaggelis; Pavelka Norman; Koczan Dirk; Argyropoulos Christos; Thwin Maung-Maung; Möller Steffen; Waki Kazunori; Gopalakrishnakone Ponnampalam; Ricciardi-Castagnoli Paola; Thiesen Hans-Jürgen; Hayashizaki Yoshihide; Kollias George
Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis.
PLoS genetics 2005;1(4):e48.
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2005: Harbers Matthias; Carninci Piero
Tag-based approaches for transcriptome research and genome annotation.
Nature methods 2005;2(7):495-502.
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2005: Kitagawa Noriyuki; Washio Takanori; Kosugi Shunichi; Yamashita Tomoya; Higashi Kenji; Yanagawa Hiroshi; Higo Kenichi; Satoh Koji; Ohtomo Yasuhiro; Sunako Tomomi; Murakami Kazuo; Matsubara Kenichi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Kikuchi Shoshi; Tomita Masaru
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).
Bioinformatics (Oxford, England) 2005;21(9):1758-63.
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2005: Nakabachi Atsushi; Shigenobu Shuji; Sakazume Naoko; Shiraki Toshiyuki; Hayashizaki Yoshihide; Carninci Piero; Ishikawa Hajime; Kudo Toshiaki; Fukatsu Takema
Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(15):5477-82.
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2005: Morris Ken A; Snir Einat; Pompeia Celine; Koroleva Irina V; Kachar Bechara; Hayashizaki Yoshihide; Carninci Piero; Soares M Bento; Beisel Kirk W
Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray.
Journal of the Association for Research in Otolaryngology : JARO 2005;6(1):75-89.
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2005: Usui Kengo; Katayama Shintaro; Kanamori-Katayama Mutsumi; Ogawa Chihiro; Kai Chikatoshi; Okada Makiko; Kawai Jun; Arakawa Takahiro; Carninci Piero; Itoh Masayoshi; Takio Koji; Miyano Masashi; Kidoaki Satoru; Matsuda Takehisa; Hayashizaki Yoshihide; Suzuki Harukazu
Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
Genome biology 2005;6(12):R98.
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2005: Caldwell Randolph B; Kierzek Andrzej M; Arakawa Hiroshi; Bezzubov Yuri; Zaim Jolanta; Fiedler Petra; Kutter Stefan; Blagodatski Artem; Kostovska Diyana; Koter Marek; Plachy Jiri; Carninci Piero; Hayashizaki Yoshihide; Buerstedde Jean-Marie
Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis.
Genome biology 2005;6(1):R6.
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2004: Watahiki Akira; Waki Kazunori; Hayatsu Norihito; Shiraki Toshiyuki; Kondo Shinji; Nakamura Mari; Sasaki Daisuke; Arakawa Takahiro; Kawai Jun; Harbers Matthias; Hayashizaki Yoshihide; Carninci Piero
Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas.
Nature methods 2004;1(3):233-9.
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2004: Nakamura Mari; Carninci Piero
[Cap analysis gene expression: CAGE]
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 2004;49(17 Suppl):2688-93.
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2004: Nagata Toshifumi; Iizumi Shigemi; Satoh Kouji; Ooka Hisako; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Otomo Yasuhiro; Murakami Kazuo; Matsubara Kenichi; Kikuchi Shoshi
Comparative analysis of plant and animal calcium signal transduction element using plant full-length cDNA data.
Molecular biology and evolution 2004;21(10):1855-70.
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2004: Ogihara Yasunari; Mochida Keiichi; Kawaura Kanako; Murai Koji; Seki Motoaki; Kamiya Asako; Shinozaki Kazuo; Carninci Piero; Hayashizaki Yoshihide; Shin-I Tadasu; Kohara Yuji; Yamazaki Yukiko
Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags.
Genes & genetic systems 2004;79(4):227-32.
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2004: Nameki Nobukazu; Yoneyama Misao; Koshiba Seizo; Tochio Naoya; Inoue Makoto; Seki Eiko; Matsuda Takayoshi; Tomo Yasuko; Harada Takushi; Saito Kohei; Kobayashi Naohiro; Yabuki Takashi; Aoki Masaaki; Nunokawa Emi; Matsuda Natsuko; Sakagami Noriko; Terada Takaho; Shirouzu Mikako; Yoshida Mayumi; Hirota Hiroshi; Osanai Takashi; Tanaka Akiko; Arakawa Takahiro; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Kinoshita Kengo; Güntert Peter; Kigawa Takanori; Yokoyama Shigeyuki
Solution structure of the RWD domain of the mouse GCN2 protein.
Protein science : a publication of the Protein Society 2004;13(8):2089-100.
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2004: Beisel Kirk W; Shiraki Toshiyuki; Morris Ken A; Pompeia Celine; Kachar Bechara; Arakawa Takahiro; Bono Hidemasa; Kawai Jun; Hayashizaki Yoshihide; Carninci Piero
Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library.
Genomics 2004;83(6):1012-23.
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2004: Lagonigro M Stefania; De Cecco Loris; Carninci Piero; Di Stasi Delia; Ranzani Tiziana; Rodolfo Monica; Gariboldi Manuela
CTAB-urea method purifies RNA from melanin for cDNA microarray analysis.
Pigment cell research / sponsored by the European Society for Pigment Cell Research and the International Pigment Cell Society 2004;17(3):312-5.
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2004: Gustincich Stefano; Contini Massimo; Gariboldi Manuela; Puopolo Michelino; Kadota Koji; Bono Hidemasa; LeMieux Julianna; Walsh Pamela; Carninci Piero; Hayashizaki Yoshihide; Okazaki Yasushi; Raviola Elio
Gene discovery in genetically labeled single dopaminergic neurons of the retina.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(14):5069-74.
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2004: Yazaki Junshi; Shimatani Zenpei; Hashimoto Akiko; Nagata Yuko; Fujii Fumiko; Kojima Keiichi; Suzuki Kohji; Taya Toshiki; Tonouchi Mio; Nelson Charles; Nakagawa Allen; Otomo Yasuhiro; Murakami Kazuo; Matsubara Kenichi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Kikuchi Shoshi
Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
Physiological genomics 2004;17(2):87-100.
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2004: Maeda Takeshi; Inoue Makoto; Koshiba Seizo; Yabuki Takashi; Aoki Masaaki; Nunokawa Emi; Seki Eiko; Matsuda Takayoshi; Motoda Yoko; Kobayashi Atsuo; Hiroyasu Fumiko; Shirouzu Mikako; Terada Takaho; Hayami Nobuhiro; Ishizuka Yoshiko; Shinya Naoko; Tatsuguchi Ayako; Yoshida Mayumi; Hirota Hiroshi; Matsuo Yo; Tani Kazutoshi; Arakawa Takahiro; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Kigawa Takanori; Yokoyama Shigeyuki
Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16).
The Journal of biological chemistry 2004;279(13):13174-82.
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2004: Kodzius Rimantas; Matsumura Yonehiro; Kasukawa Takeya; Shimokawa Kazuro; Fukuda Shiro; Shiraki Toshiyuki; Nakamura Mari; Arakawa Takahiro; Sasaki Daisuke; Kawai Jun; Harbers Matthias; Carninci Piero; Hayashizaki Yoshihide
Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags.
FEBS letters 2004;559(1-3):22-6.
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2004: Kasai Takuma; Inoue Makoto; Koshiba Seizo; Yabuki Takashi; Aoki Masaaki; Nunokawa Emi; Seki Eiko; Matsuda Takayoshi; Matsuda Natsuko; Tomo Yasuko; Shirouzu Mikako; Terada Takaho; Obayashi Naomi; Hamana Hiroaki; Shinya Naoko; Tatsuguchi Ayako; Yasuda Satoko; Yoshida Mayumi; Hirota Hiroshi; Matsuo Yo; Tani Kazutoshi; Suzuki Harukazu; Arakawa Takahiro; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Kigawa Takanori; Yokoyama Shigeyuki
Solution structure of a BolA-like protein from Mus musculus.
Protein science : a publication of the Protein Society 2004;13(2):545-8.
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2004: Nagashima Takeshi; Matsuda Hideo; Silva Diego G; Petrovsky Nikolai; Konagaya Akihiko; Schönbach Christian; Kasukawa Takeya; Arakawa Takahiro; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide;
FREP: a database of functional repeats in mouse cDNAs.
Nucleic acids research 2004;32(Database issue):D471-5.
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2004: Suzuki Yutaka; Yamashita Riu; Shirota Matsuyuki; Sakakibara Yuta; Chiba Joe; Mizushima-Sugano Junko; Kel Alexander E; Arakawa Takahiro; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Takagi Toshihisa; Nakai Kenta; Sugano Sumio
Large-scale collection and characterization of promoters of human and mouse genes.
In silico biology 2004;4(4):429-44.
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2003: Ooka Hisako; Satoh Kouji; Doi Koji; Nagata Toshifumi; Otomo Yasuhiro; Murakami Kazuo; Matsubara Kenichi; Osato Naoki; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Suzuki Koji; Kojima Keiichi; Takahara Yoshinori; Yamamoto Koji; Kikuchi Shoshi
Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana.
DNA research : an international journal for rapid publication of reports on genes and genomes 2003;10(6):239-47.
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2003: Shiraki Toshiyuki; Kondo Shinji; Katayama Shintaro; Waki Kazunori; Kasukawa Takeya; Kawaji Hideya; Kodzius Rimantas; Watahiki Akira; Nakamura Mari; Arakawa Takahiro; Fukuda Shiro; Sasaki Daisuke; Podhajska Anna; Harbers Matthias; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(26):15776-81.
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2003: Fujimori Shigeo; Washio Takanori; Higo Kenichi; Ohtomo Yasuhiro; Murakami Kazuo; Matsubara Kenichi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Kikuchi Shoshi; Tomita Masaru
A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription.
FEBS letters 2003;554(1-2):17-22.
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2003: Hirozane-Kishikawa Tomoko; Shiraki Toshiyuki; Waki Kazunori; Nakamura Mari; Arakawa Takahiro; Kawai Jun; Fagiolini Michela; Hensch Takao K; Hayashizaki Yoshihide; Carninci Piero
Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.
BioTechniques 2003;35(3):510-6, 518.
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2003: Wells Christine A; Ravasi Timothy; Faulkner Geoffrey J; Carninci Piero; Okazaki Yasushi; Hayashizaki Yoshihide; Sweet Matthew; Wainwright Brandon J; Hume David A
Genetic control of the innate immune response.
BMC immunology 2003;4():5.
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2003: Gustincich Stefano; Batalov Serge; Beisel Kirk W; Bono Hidemasa; Carninci Piero; Fletcher Colin F; Grimmond Sean; Hirokawa Nobutaka; Jarvis Erich D; Jegla Tim; Kawasawa Yuka; LeMieux Julianna; Miki Harukata; Raviola Elio; Teasdale Rohan D; Tominaga Naoko; Yagi Ken; Zimmer Andreas; Hayashizaki Yoshihide; Okazaki Yasushi;
Analysis of the mouse transcriptome for genes involved in the function of the nervous system.
Genome research 2003;13(6B):1395-401.
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2003: Wells Christine A; Ravasi Timothy; Sultana Razvan; Yagi Ken; Carninci Piero; Bono Hidemasa; Faulkner Geoffrey; Okazaki Yasushi; Quackenbush John; Hume David A; Lyons Paul A;
Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage.
Genome research 2003;13(6B):1360-5.
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2003: Nishiyama Tomoaki; Fujita Tomomichi; Shin-I Tadasu; Seki Motoaki; Nishide Hiroyo; Uchiyama Ikuo; Kamiya Asako; Carninci Piero; Hayashizaki Yoshihide; Shinozaki Kazuo; Kohara Yuji; Hasebe Mitsuyasu
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(13):8007-12.
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2003: Walsh Nicole C; Cahill Marian; Carninci Piero; Kawai Jun; Okazaki Yasushi; Hayashizaki Yoshihide; Hume David A; Cassady A Ian
Multiple tissue-specific promoters control expression of the murine tartrate-resistant acid phosphatase gene.
Gene 2003;307():111-23.
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2003: Osato Naoki; Yamada Hitomi; Satoh Kouji; Ooka Hisako; Yamamoto Makoto; Suzuki Kohji; Kawai Jun; Carninci Piero; Ohtomo Yasuhiro; Murakami Kazuo; Matsubara Kenichi; Kikuchi Shoshi; Hayashizaki Yoshihide
Antisense transcripts with rice full-length cDNAs.
Genome biology 2003;5(1):R5.
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2002: Jarvis E D; Smith V A; Wada K; Rivas M V; McElroy M; Smulders T V; Carninci P; Hayashizaki Y; Dietrich F; Wu X; McConnell P; Yu J; Wang P P; Hartemink A J; Lin S
A framework for integrating the songbird brain.
Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology 2002;188(11-12):961-80.
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2002: Seki Motoaki; Ishida Junko; Narusaka Mari; Fujita Miki; Nanjo Tokihiko; Umezawa Taishi; Kamiya Asako; Nakajima Maiko; Enju Akiko; Sakurai Tetsuya; Satou Masakazu; Akiyama Kenji; Yamaguchi-Shinozaki Kazuko; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Shinozaki Kazuo
Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray.
Functional & integrative genomics 2002;2(6):282-91.
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2002: Sakurai A; Fujimori S; Kochiwa H; Kitamura-Abe S; Washio T; Saito R; Carninci P; Hayashizaki Y; Tomita M
On biased distribution of introns in various eukaryotes.
Gene 2002;300(1-2):89-95.
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2002: Ozawa Y; Hanaoka S; Saito R; Washio T; Nakano S; Shinagawa A; Itoh M; Shibata K; Carninci P; Konno H; Kawai J; Hayashizaki Y; Tomita M
Comprehensive sequence analysis of translation termination sites in various eukaryotes.
Gene 2002;300(1-2):79-87.
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2002: Stapleton Mark; Liao Guochun; Brokstein Peter; Hong Ling; Carninci Piero; Shiraki Toshiyuki; Hayashizaki Yoshihide; Champe Mark; Pacleb Joanne; Wan Ken; Yu Charles; Carlson Joe; George Reed; Celniker Susan; Rubin Gerald M
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes.
Genome research 2002;12(8):1294-300.
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2002: Kochiwa Hiromi; Suzuki Ryosuke; Washio Takanori; Saito Rintaro; Bono Hidemasa; Carninci Piero; Okazaki Yasushi; Miki Rika; Hayashizaki Yoshihide; Tomita Masaru;
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data.
Genome research 2002;12(8):1286-93.
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2002: Seki Motoaki; Narusaka Mari; Ishida Junko; Nanjo Tokihiko; Fujita Miki; Oono Youko; Kamiya Asako; Nakajima Maiko; Enju Akiko; Sakurai Tetsuya; Satou Masakazu; Akiyama Kenji; Taji Teruaki; Yamaguchi-Shinozaki Kazuko; Carninci Piero; Kawai Jun; Hayashizaki Yoshihide; Shinozaki Kazuo
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray.
The Plant journal : for cell and molecular biology 2002;31(3):279-92.
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2002: Osato Naoki; Itoh Masayoshi; Konno Hideaki; Kondo Shinji; Shibata Kazuhiro; Carninci Piero; Shiraki Toshiyuki; Shinagawa Akira; Arakawa Takahiro; Kikuchi Shoshi; Sato Kouji; Kawai Jun; Hayashizaki Yoshihide
A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs.
Genome research 2002;12(7):1127-34.
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2002: Seki Motoaki; Narusaka Mari; Kamiya Asako; Ishida Junko; Satou Masakazu; Sakurai Tetsuya; Nakajima Maiko; Enju Akiko; Akiyama Kenji; Oono Youko; Muramatsu Masami; Hayashizaki Yoshihide; Kawai Jun; Carninci Piero; Itoh Masayoshi; Ishii Yoshiyuki; Arakawa Takahiro; Shibata Kazuhiro; Shinagawa Akira; Shinozaki Kazuo
Functional annotation of a full-length Arabidopsis cDNA collection.
Science (New York, N.Y.) 2002;296(5565):141-5.
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2002: Buerstedde Jean-Marie; Arakawa Hiroshi; Watahiki Akira; Carninci Piere Piero; Hayashizaki Y Yoshihide; Korn Bernhard; Plachy Jiri
The DT40 web site: sampling and connecting the genes of a B cell line.
Nucleic acids research 2002;30(1):230-1.
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2002: Yamanaka Itaru; Kiyosawa Hidenori; Kondo Shinji; Saito Tetsuya; Carninci Piero; Shinagawa Akira; Aizawa Katsunori; Fukuda Shiro; Hara Ayako; Itoh Masayoshi; Kawai Jun; Shibata Kazuhiro; Arakawa Takahiro; Ishii Yoshiyuki; Hayashizaki Yoshihide
Mapping of 19032 mouse cDNAs on mouse chromosomes.
Journal of structural and functional genomics 2002;2(1):23-8.
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2001: Shibata Y; Carninci P; Sato K; Hayatsu N; Shiraki T; Ishii Y; Arakawa T; Hara A; Ohsato N; Izawa M; Aizawa K; Itoh M; Shibata K; Shinagawa A; Kawai J; Ota Y; Kikuchi S; Kishimoto N; Muramatsu M; Hayashizaki Y
Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing.
BioTechniques 2001;31(5):1042, 1044, 1048-9.
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2001: Sakai H; Washio T; Saito R; Shinagawa A; Itoh M; Shibata K; Carninci P; Konno H; Kawai J; Hayashizaki Y; Tomita M
Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes.
Gene 2001;276(1-2):101-5.
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2001: Carninci P; Shibata Y; Hayatsu N; Itoh M; Shiraki T; Hirozane T; Watahiki A; Shibata K; Konno H; Muramatsu M; Hayashizaki Y
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.
Genomics 2001;77(1-2):79-90.
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2001: Shibata Y; Carninci P; Watahiki A; Shiraki T; Konno H; Muramatsu M; Hayashizaki Y
Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method.
BioTechniques 2001;30(6):1250-4.
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2001: Miki R; Kadota K; Bono H; Mizuno Y; Tomaru Y; Carninci P; Itoh M; Shibata K; Kawai J; Konno H; Watanabe S; Sato K; Tokusumi Y; Kikuchi N; Ishii Y; Hamaguchi Y; Nishizuka I; Goto H; Nitanda H; Satomi S; Yoshiki A; Kusakabe M; DeRisi J L; Eisen M B; Iyer V R; Brown P O; Muramatsu M; Shimada H; Okazaki Y; Hayashizaki Y
Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(5):2199-204.
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2001: Konno H; Fukunishi Y; Shibata K; Itoh M; Carninci P; Sugahara Y; Hayashizaki Y
Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library.
Genome research 2001;11(2):281-9.
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2001: Seki M; Narusaka M; Abe H; Kasuga M; Yamaguchi-Shinozaki K; Carninci P; Hayashizaki Y; Shinozaki K
Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray.
The Plant cell 2001;13(1):61-72.
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2000: Carninci P; Shibata Y; Hayatsu N; Sugahara Y; Shibata K; Itoh M; Konno H; Okazaki Y; Muramatsu M; Hayashizaki Y
Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes.
Genome research 2000;10(10):1617-30.
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1999: Itoh M; Kitsunai T; Akiyama J; Shibata K; Izawa M; Kawai J; Tomaru Y; Carninci P; Shibata Y; Ozawa Y; Muramatsu M; Okazaki Y; Hayashizaki Y
Automated filtration-based high-throughput plasmid preparation system.
Genome research 1999;9(5):463-70.
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