FIND

researchers

DISCOVER

relevant articles

PROMOTE

your research

now for free

piero carninci

Research Profile

Living Beings

Mouse

Physiology

Chemicals & Drugs

Procedures

Genes & Molecular Sequences

Devices

Oligonucleotide Array Sequence Analysis

Occupations

Concepts & Ideas

Molecular Sequence Data

Co-author Network

Publications

TOP 3
Luba M Pardo; Patrizia Rizzu; Javier Simon Sanchez; Hazuki Takahashi; Wilma D J Van De Berg; Mark A van de Wiel; Morana Vitezic; piero carninci; Carsten O Daub; Margherita Francescatto; Abdullah Khamis; Gwenaël G R Leday; Yulia A Medvedeva; Peter Heutink
Regional differences in gene expression and promoter usage in aged human brains.
Ruchi Shukla; Shruti Sinha; Kyle R Upton; J Kenneth Baillie; Paul M Brennan; piero carninci; Francesca D Ciccarelli; Agnese Collino; Alexandre Dos Santos; Jamila Faivre; Malcolm E Fisher; Jose Luis Garcia-Perez; Daniel J Gerhardt; Serena Ghisletti; Catherine Guettier; Fabio Iannelli; Martin Muñoz-Lopez; Gioacchino Natoli; Thu Nguyen; Enrico Radaelli; Delphine Rapoud; Didier Samuel; Geoffrey J Faulkner
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma.
Anas Fadloun; Eduardo Gorab; Bernard Jost; Stéphanie Le Gras; Hazuki Takahashi; piero carninci; Céline Ziegler-Birling; Maria Elena Torres-Padilla
Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA.

Register for free to view:

Visualized networks:

See your personal network in
sophisticated graphical views

GeoTargeted Searches:

Locate experts around the world
and connect with global collaborators

Research Profiles:

See the research activity
of experts around the globe

Geonetwork of piero carninci (preview)

Cities where this author has publications
Cities where co-authors of this author have publications

Flash Player Required

All Publications

2013: Luba M Pardo; Patrizia Rizzu; Javier Simon Sanchez; Hazuki Takahashi; Wilma D J Van De Berg; Mark A van de Wiel; Morana Vitezic; piero carninci; Carsten O Daub; Margherita Francescatto; Abdullah Khamis; Gwenaël G R Leday; Yulia A Medvedeva; Peter Heutink
Regional differences in gene expression and promoter usage in aged human brains.
Neurobiology of aging 2013;34(7):1825-36.
2013: Ruchi Shukla; Shruti Sinha; Kyle R Upton; J Kenneth Baillie; Paul M Brennan; piero carninci; Francesca D Ciccarelli; Agnese Collino; Alexandre Dos Santos; Jamila Faivre; Malcolm E Fisher; Jose Luis Garcia-Perez; Daniel J Gerhardt; Serena Ghisletti; Catherine Guettier; Fabio Iannelli; Martin Muñoz-Lopez; Gioacchino Natoli; Thu Nguyen; Enrico Radaelli; Delphine Rapoud; Didier Samuel; Geoffrey J Faulkner
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma.
Cell 2013;153(1):101-11.
2013: Anas Fadloun; Eduardo Gorab; Bernard Jost; Stéphanie Le Gras; Hazuki Takahashi; piero carninci; Céline Ziegler-Birling; Maria Elena Torres-Padilla
Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA.
Nature structural & molecular biology 2013;20(3):332-8.
2013: Charles Plessy; Linda Desbois; Teruo Fujii; piero carninci
Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types.
BioEssays : news and reviews in molecular, cellular and developmental biology 2013;35(2):131-40.
2013: Dave T P Tang; Raffaella Calligaris; Stefano Gustincich; Charles Plessy; Md Salimullah; Ana Maria Suzuki; piero carninci
Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.
Nucleic acids research 2013;41(3):e44.
2013: Philippe Batut; piero carninci; Alexander Dobin; Charles Plessy; Thomas R Gingeras
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.
Genome research 2013;23(1):169-80.
2012: Severine Durand; piero carninci; Lea Hachigian; Takao K Hensch; Annarita Patrizi; Roman Pavlyuk; Kathleen B Quast; Alka Saxena; Michela Fagiolini
NMDA receptor regulation prevents regression of visual cortical function in the absence of Mecp2.
Neuron 2012;76(6):1078-90.
2012: Claudia Carrieri; Laura Cimatti; Licio Collavin; Stefania Fedele; Isidre Ferrer; Alistair R R Forrest; Anne Beugnet; Marta Biagioli; Stefano Biffo; piero carninci; Elisa Pesce; Claudio Santoro; Elia Stupka; Silvia Zucchelli; Stefano Gustincich
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.
Nature 2012;491(7424):454-7.
2012: Alessandro Bonetti; piero carninci
Structure by sequencing: discovery of hidden messages in the noncoding RNA fraction.
Molecular cell 2012;48(2):153-5.
2012: Thomas Derrien; Sarah Djebali; Thomas R Gingeras; Jose M Gonzalez; Gregory Guernec; James B Brown; Giovanni Bussotti; piero carninci; Carrie A Davis; Jennifer Harrow; Tim J Hubbard; Rory Johnson; David G Knowles; Julien Lagarde; Timo Lassmann; Leonard Lipovich; David Martin; Angelika Merkel; Cédric Notredame; Xiaoan Ruan; Yijun Ruan; Ramin Shiekhattar; Andrea Tanzer; Mark Thomas; Hagen Tilgner; Lavanya Veeravalli; Roderic Guigó
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Genome research 2012;22(9):1775-89.
2012: Chao Cheng; Carrie A Davis; Sarah Djebali; Xianjun Dong; Roger Alexander; Ewan Birney; piero carninci; Thomas R Gingeras; Roderic Guigó; Timo Lassman; Jing Leng; Renqiang Min; Joel S Rozowsky; Yijun Ruan; Michael Snyder; Zhiping Weng; Koon-Kiu Yan; Kevin Yip; Mark Gerstein
Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Genome research 2012;22(9):1658-67.
2012: Sofia Francia; Flavia Michelini; Marina Mione; Alka Saxena; Dave Tang; Viviana Anelli; piero carninci; Michiel de Hoon; Fabrizio d'Adda di Fagagna
Site-specific DICER and DROSHA RNA products control the DNA-damage response.
Nature 2012;488(7410):231-5.
2012: Alka Saxena; Akiko Wagatsuma; Akira Watahiki; Atsuko Asaka-Oba; Michela Fagiolini; cecile gurnot; Takao K Hensch; Takenobu Kuji; Yukihiko Noro; piero carninci
Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain.
BioTechniques 2012;52(6):381-5.
2012: Kate Schroder; Colin A Semple; Harukazu Suzuki; Martin S Taylor; Altuna Akalin; John Kenneth Baillie; Nilesh J Bokil; piero carninci; Carsten O Daub; Lynsey Fairbairn; Geoffrey J Faulkner; Nick Goldman; M Milena Gongora; Sean M Grimmond; Yoshihide Hayashizaki; David A Hume; Katharine M Irvine; Ronan Kapetanovic; Hideya Kawaji; Larisa I Labzin; Kim-Anh Le Cao; Boris Lenhard; Kelly-Anne Masterman; Geoffrey J McLachlan; Matthew J Sweet
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(16):E944-53.
2012: Boris Lenhard; Albin Sandelin; piero carninci
Metazoan promoters: emerging characteristics and insights into transcriptional regulation.
Nature reviews. Genetics 2012;13(4):233-45.
2012: Hazuki Takahashi; Timo Lassmann; Mitsuyoshi Murata; piero carninci
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.
Nature protocols 2012;7(3):542-61.
2012: Charles Plessy; Jessica Severin; Roberto Simone; Anne Vassalli; Christina Vlachouli; Silvia Zucchelli; Altuna Akalin; Nicolas Bertin; Claudia Carrieri; Carsten O Daub; Geoffrey J Faulkner; Stefano Gustincich; Yoshihide Hayashizaki; Jun Kawai; Dejan Lazarevic; Boris Lenhard; Peter Mombaerts; Giovanni Pascarella; piero carninci
Promoter architecture of mouse olfactory receptor genes.
Genome research 2012;22(3):486-97.
2012: Alka Saxena; Dave Tang; piero carninci
piRNAs warrant investigation in Rett Syndrome: an omics perspective.
Disease markers 2012;33(5):261-75.
2012: Masayoshi Itoh; Ai Kaiho; Mutsumi Kanamori-Katayama; Hideya Kawaji; Miki Kojima; Timo Lassmann; Marina Lizio; Sayaka Nagao-Sato; Eri Saijo; piero carninci; Alistair R R Forrest; Yoshihide Hayashizaki
Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.
PloS one 2012;7(1):e30809.
2012: Hazuki Takahashi; Sachi Kato; Mitsuyoshi Murata; piero carninci
CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks.
Methods in molecular biology (Clifton, N.J.) 2012;786():181-200.
2011: J Kenneth Baillie; Mark W Barnett; Paul M Brennan; piero carninci; Fioravante De Sapio; Mark Fell; Thomas C Freeman; Daniel J Gerhardt; Stefano Gustincich; Peter Heutink; David A Hume; Jeffrey A Jeddeloh; John S Mattick; Richmond Todd; Patrizia Rizzu; Sarah Smith; Richard T Talbot; Kyle R Upton; Geoffrey J Faulkner
Somatic retrotransposition alters the genetic landscape of the human brain.
Nature 2011;479(7374):534-7.
2011: Alka Saxena; piero carninci
Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs.
BioEssays : news and reviews in molecular, cellular and developmental biology 2011;33(11):830-9.
2011: Alka Saxena; piero carninci
Whole transcriptome analysis: what are we still missing?
Wiley interdisciplinary reviews. Systems biology and medicine 2011;3(5):527-43.
2011: Massimiliano Caiazzo; piero carninci; Giorgia Colciago; Maria Teresa Dell'Anno; Alexander Dityatev; Elena Dvoretskova; Raul R Gainetdinov; Stefano Gustincich; Dejan Lazarevic; Damiana Leo; Andrea Menegon; Gianni Pezzoli; Paola Roncaglia; Giovanni Russo; Tatyana D Sotnikova; Stefano Taverna; Vania Broccoli
Direct generation of functional dopaminergic neurons from mouse and human fibroblasts.
Nature 2011;476(7359):224-7.
2011: Oscar Franzén; Yoshihide Hayashizaki; Daniel Nilsson; Patricia Respuela; Björn Andersson; Erik Arner; Lena Aslund; piero carninci; Marcela Ferella; Carsten O Daub
The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi.
PLoS neglected tropical diseases 2011;5(8):e1283.
2011: Michael B Clark; Marcel Dinger; Mark B Gerstein; Thomas R Gingeras; Yoshihide Hayashizaki; Paulo P Amaral; piero carninci; Antonin Morillon; Kevin V Morris; Chris P Ponting; John L Rinn; Joel S Rozowsky; Felix J Schlesinger; Peter F Stadler; Ryan J Taft; Claes Wahlestedt; John S Mattick
The reality of pervasive transcription.
PLoS biology 2011;9(7):e1000625; discussion e1001102.
2011: Mutsumi Kanamori-Katayama; Shintaro Katayama; Hideya Kawaji; Miki Kojima; Timo Lassmann; Noriko Ninomiya; Nicolas Bertin; piero carninci; Carsten O Daub; Alistair R R Forrest; Masayoshi Itoh; Ai Kaiho; Yoshihide Hayashizaki
Unamplified cap analysis of gene expression on a single-molecule sequencer.
Genome research 2011;21(7):1150-9.
2011: Roger A Hoskins; Jane M Landolin; James B Brown; Jeremy E Sandler; Hazuki Takahashi; Timo Lassmann; Charles Yu; Benjamin W Booth; Dayu Zhang; Kenneth H Wan; Li Yang; Nathan Boley; Justen Andrews; Thomas C Kaufman; Brenton R Graveley; Peter J Bickel; piero carninci; Joseph W Carlson; Susan E Celniker
Genome-wide analysis of promoter architecture in Drosophila melanogaster.
Genome research 2011;21(2):182-92.
2011: Yoshinari Ando; A Maxwell Burroughs; piero carninci; Joe Chiba; Hisashi Hirano; Yoko Ino; Hideya Kawaji; Ryuichiro Kimura; Atsutaka Kubosaki; Ayako Morinaga; Harukazu Suzuki; Maiko Tagata; Yasuhiro Tomaru; Yoshihide Hayashizaki
Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells.
PloS one 2011;6(8):e23385.
2011: Yoichiro Shindo; hirohito miura; Kana Morishita; piero carninci; Yoshihide Hayashizaki; Akihiro Hino; Tomomasa Kanda; Jun Kawai; Eiichi Kotake; Yuko Kusakabe
FXYD6, a Na,K-ATPase regulator, is expressed in type II taste cells.
Bioscience, biotechnology, and biochemistry 2011;75(6):1061-6.
2011: Md Salimullah; Sakai Mizuho; Charles Plessy; Mizuho Sakai; piero carninci
NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes.
Cold Spring Harbor protocols 2011;2011(1):pdb.prot5559.
2011: Hideya Kawaji; Jessica Severin; Marina Lizio; Alistair R R Forrest; Erik van Nimwegen; Michael Rehli; Kate Schroder; Katharine Irvine; Harukazu Suzuki; piero carninci; Yoshihide Hayashizaki; Carsten O Daub
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Nucleic acids research 2011;39(Database issue):D856-60.
2010: Morana Vitezic; Timo Lassmann; Alistair R R Forrest; Masanori Suzuki; Yasuhiro Tomaru; Jun Kawai; piero carninci; Harukazu Suzuki; Yoshihide Hayashizaki; Carsten O Daub
Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.
Nucleic acids research 2010;38(22):8141-8.
2010: Mitsuoki Kawano; Chika Kawazu; Marina Lizio; Hideya Kawaji; piero carninci; Harukazu Suzuki; Yoshihide Hayashizaki
Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing.
BioTechniques 2010;49(4):751-5.
2010: Shannon W Davis; F Castinetti; L R Carvalho; Buffy Ellsworth; Mary Anne Potok; Robert H Lyons Jr; Michelle L Brinkmeier; Lori T Raetzman; piero carninci; A H Mortensen; Yoshihide Hayashizaki; I J P Arnhold; B B Mendonça; T Brue; Sally A Camper
Molecular mechanisms of pituitary organogenesis: In search of novel regulatory genes.
Molecular and cellular endocrinology 2010;323(1):4-19.
2010: 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; Philipp Kapranov; Huaien Wang; Carrie A Davis; Thomas Gingeras; Jun Kawai; Carsten O Daub; Yoshihide Hayashizaki; Stefano Gustincich; piero carninci
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
Nature methods 2010;7(7):528-34.
2010: Santosh S Atanur; Inanç Birol; Victor Guryev; Martin Hirst; Oliver Hummel; Catherine Morrissey; Jacques Behmoaras; Xose M. Fernandez; Michelle D Johnson; William M McLaren; Giannino Patone; Enrico Petretto; Charles Plessy; Kathleen S Rockland; Charles Rockland; Kathrin Saar; Yongjun Zhao; piero carninci; Paul Flicek; Ted Kurtz; Edwin Cuppen; Michal Pravenec; Norbert Hubner; Steven J M Jones; Ewan Birney; Timothy J Aitman
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Genome research 2010;20(6):791-803.
2010: piero carninci
RNA dust: where are the genes?
DNA research : an international journal for rapid publication of reports on genes and genomes 2010;17(2):51-9.
2010: Michiel J L de Hoon; Ryan J Taft; Takehiro Hashimoto; Mutsumi Kanamori-Katayama; Hideya Kawaji; Mitsuoki Kawano; Mami Kishima; Timo Lassmann; Geoffrey J Faulkner; John S Mattick; Carsten O Daub; piero carninci; Jun Kawai; Harukazu Suzuki; Yoshihide Hayashizaki
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries.
Genome research 2010;20(2):257-64.
2010: Ulf Schaefer; Rimantas Kodzius; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Vladimir B Bajic
High sensitivity TSS prediction: estimates of locations where TSS cannot occur.
PloS one 2010;5(11):e13934.
2010: Anton Kratz; Erik Arner; Rintaro Saito; Atsutaka Kubosaki; Jun Kawai; Harukazu Suzuki; piero carninci; Takahiro Arakawa; Masaru Tomita; Yoshihide Hayashizaki; Carsten O Daub
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns.
BMC genomics 2010;11():257.
2009: Md Salimullah; Sachiko Kato; Mitsuyoshi Murata; Chika Kawazu; Charles Plessy; piero carninci
Tunable fractionation of nucleic acids.
BioTechniques 2009;47(6):1041-3.
2009: Alistair Forrest; Rehab F Abdelhamid; piero carninci
Annotating non-coding transcription using functional genomics strategies.
Briefings in functional genomics & proteomics 2009;8(6):437-43.
2009: piero carninci
Is sequencing enlightenment ending the dark age of the transcriptome?
Nature methods 2009;6(10):711-13.
2009: Geoffrey J Faulkner; piero carninci
Altruistic functions for selfish DNA.
Cell cycle (Georgetown, Tex.) 2009;8(18):2895-900.
2009: 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
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.
2009: Ryan J Taft; Evgeny Glazov; Timo Lassmann; Yoshihide Hayashizaki; piero carninci; John S Mattick
Small RNAs derived from snoRNAs.
RNA (New York, N.Y.) 2009;15(7):1233-40.
2009: Ryan J Taft; Evgeny Glazov; Nicole Cloonan; Cas Simons; Stuart Stephen; Geoffrey J Faulkner; Timo Lassmann; Alistair Forrest; Sean M Grimmond; Kate Schroder; Katharine M 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
Tiny RNAs associated with transcription start sites in animals.
Nature genetics 2009;41(5):572-8.
2009: 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 Forrest; Harukazu Suzuki; Yoshihide Hayashizaki; David A Hume; Valerio Orlando; Sean M Grimmond; piero carninci
The regulated retrotransposon transcriptome of mammalian cells.
Nature genetics 2009;41(5):563-71.
2009: Christian Schönbach; Alistair Forrest; Erik van Nimwegen; Carsten O Daub; Piotr J Balwierz; Katharine M Irvine; Timo Lassmann; Timothy Ravasi; Yuki Hasegawa; Michiel J L de Hoon; Shintaro Katayama; Kate Schroder; piero carninci; Yasuhiro Tomaru; Mutsumi Kanamori-Katayama; Atsutaka Kubosaki; Altuna Akalin; Yoshinari Ando; Erik Arner; Maki Asada; Hiroshi Asahara; Timothy Bailey; Vladimir Bajic; Denis Bauer; Anthony Beckhouse; Nicolas Bertin; Johan Björkegren; Frank Brombacher; Erika Bulger; Alistair Chalk; Joe Chiba; Nicole Cloonan; Adam Dawe; Josee Dostie; Pär G Engström; Magbubah Essack; Geoffrey J Faulkner; J Lynn Fink; David Fredman; Ko Fujimori; Masaaki Furuno; Takashi Gojobori; Julian Gough; Sean M Grimmond; Mika Gustafsson; Megumi Hashimoto; Takehiro Hashimoto; Mariko Hatakeyama; Susanne Heinzel; Winston Hide; Oliver Hofmann; Michael Hörnquist; Lukasz Huminiecki; Kazuho Ikeo; Naoko Imamoto; Satoshi Inoue; Yusuke Inoue; Ryoko Ishihara; Takao Iwayanagi; Anders Jacobsen; Mandeep Kaur; Hideya Kawaji; Markus C 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 A. Maher; Monique Maqungo; Jessica Mar; Nicholas A Matigian; Hideo Matsuda; John S 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 Schönbach; Ariel S Schwartz; Colin A Semple; Miho Sera; Jessica Severin; Katsuhiko Shirahige; Cas Simons; George St Laurent; Masanori Suzuki; Takahiro Suzuki; Matthew J Sweet; Ryan J Taft; Shizu Takeda; Yoichi Takenaka; Kai Tan; Martin S Taylor; Rohan D Teasdale; Jesper Tegnér; Sarah Teichmann; Eivind Valen; Claes Wahlestedt; Kazunori Waki; Andrew Waterhouse; Christine A Wells; Ole Winther; Linda Wu; Kazumi Yamaguchi; Hiroshi Yanagawa; Jun Yasuda; Mihaela Zavolan; David A 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; Christophe Simon; Michihira Tagami; Yukari Takahashi; Jun Kawai; Yoshihide Hayashizaki
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Nature genetics 2009;41(5):553-62.
2009: Michelle L Brinkmeier; Shannon W Davis; piero carninci; James W MacDonald; Jun Kawai; Debashis Ghosh; Yoshihide Hayashizaki; Robert H Lyons Jr; Sally A Camper
Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches.
Genomics 2009;93(5):449-60.
2009: Alistair Forrest; piero carninci
Whole genome transcriptome analysis.
RNA biology 2009;6(2):107-12.
2009: Shannon W Davis; Mary Anne Potok; Michelle L Brinkmeier; piero carninci; Robert H Lyons Jr; James W MacDonald; Michelle T Fleming; Amanda H Mortensen; Noboru Egashira; Debashis Ghosh; Karen P Steel; Robert Y Osamura; Yoshihide Hayashizaki; Sally A Camper
Genetics, gene expression and bioinformatics of the pituitary gland.
Hormone research 2009;71 Suppl 2():101-15.
2009: piero carninci
Molecular biology: The long and short of RNAs.
Nature 2009;457(7232):974-5.
2009: Signe Olivarius; Charles Plessy; piero carninci
High-throughput verification of transcriptional starting sites by Deep-RACE.
BioTechniques 2009;46(2):130-2.
2009: Eivind Valen; Giovanni Pascarella; Alistair Chalk; Norihiro Maeda; Miki Kojima; Chika Kawazu; Mitsuyoshi Murata; Hiromi Nishiyori; Dejan Lazarevic; Dario Motti; Troels Torben Marstrand; Man-Hung Eric Tang; Xiaobei Zhao; Anders Krogh; Ole Winther; Takahiro Arakawa; Jun Kawai; Christine Wells; Carsten Daub; Matthias Harbers; Yoshihide Hayashizaki; Stefano Gustincich; Albin Sandelin; piero carninci
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.
Genome research 2009;19(2):255-65.
2009: Piotr J Balwierz; piero carninci; Carsten O Daub; Jun Kawai; Yoshihide Hayashizaki; Werner Van Belle; Christian Beisel; Erik van Nimwegen
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.
Genome biology 2009;10(7):R79.
2009: Hideya Kawaji; Jessica Severin; Marina Lizio; Andrew Waterhouse; Shintaro Katayama; Katharine M Irvine; David A Hume; Alistair Forrest; Harukazu Suzuki; piero carninci; Yoshihide Hayashizaki; Carsten O Daub
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Genome biology 2009;10(4):R40.
2009: Jessica Severin; Andrew M Waterhouse; Hideya Kawaji; Timo Lassmann; Erik van Nimwegen; Piotr J Balwierz; Michiel Jl de Hoon; David A Hume; piero carninci; Yoshihide Hayashizaki; Harukazu Suzuki; Carsten O Daub; Alistair Forrest
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.
Genome biology 2009;10(4):R39.
2009: Motoaki Seki; Asako Kamiya; piero carninci; Yoshihide Hayashizaki; Kazuo Shinozaki
Generation of full-length cDNA libraries: focus on plants.
Methods in molecular biology (Clifton, N.J.) 2009;533():49-68.
2008: Oliver Hofmann; Otavia L Caballero; Brian J Stevenson; Yao-Tseng Chen; Tzeela Cohen; Ramon Chua; Christopher A. Maher; Sumir Panji; Ulf Schaefer; Adele Kruger; Minna Lehvaslaiho; piero carninci; Yoshihide Hayashizaki; Victor Jongeneel; Andrew J G Simpson; Lloyd J Old; Winston Hide
Genome-wide analysis of cancer/testis gene expression.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(51):20422-7.
2008: Yoichiro Shindo; Hirohito Miura; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Yuzo Ninomiya; Akihiro Hino; Tomomasa Kanda; Yuko Kusakabe
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.
2008: Martin Taylor; Tim Massingham; Yoshihide Hayashizaki; piero carninci; Nick Goldman; Colin A M Semple
Rapidly evolving human promoter regions.
Nature genetics 2008;40(11):1262-3; author reply 1263-4.
2008: Magnus Centlow; piero carninci; Krisztian Nemeth; Eva Mezey; Michael Brownstein; Stefan R Hansson
Placental expression profiling in preeclampsia: local overproduction of hemoglobin may drive pathological changes.
Fertility and sterility 2008;90(5):1834-43.
2008: piero carninci
Non-coding RNA transcription: turning on neighbours.
Nature cell biology 2008;10(9):1023-4.
2008: Norihiro Maeda; Hiromi Nishiyori; Mari Nakamura; Chika Kawazu; Mitsuyoshi Murata; Hiromi Sano; Kengo Hayashida; Shiro Fukuda; Michihira Tagami; Akira Hasegawa; Kayoko Murakami; Kate Schroder; Katharine Irvine; David Hume; Yoshihide Hayashizaki; piero carninci; Harukazu Suzuki
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.
2008: piero carninci
Hunting hidden transcripts.
Nature methods 2008;5(7):587-9.
2008: piero carninci; Jun Yasuda; Yoshihide Hayashizaki
Multifaceted mammalian transcriptome.
Current opinion in cell biology 2008;20(3):274-80.
2008: Geoffrey J Faulkner; Alistair Forrest; Alistair Chalk; Kate Schroder; Yoshihide Hayashizaki; piero carninci; David A Hume; Sean M Grimmond
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.
Genomics 2008;91(3):281-8.
2008: Charles Plessy; Michela Fagiolini; Akiko Wagatsuma; Norihiro Harasawa; Takenobu Kuji; Atsuko Asaka-Oba; Yukari Kanzaki; Sayaka Fujishima; Kazunori Waki; Hiroyuki Nakahara; Takao K Hensch; piero carninci
A resource for transcriptomic analysis in the mouse brain.
PloS one 2008;3(8):e3012.
2008: Hideya Kawaji; Mari Nakamura; Yukari Takahashi; Albin Sandelin; Shintaro Katayama; Shiro Fukuda; Carsten O Daub; Chikatoshi Kai; Jun Kawai; Jun Yasuda; piero carninci; Yoshihide Hayashizaki
Hidden layers of human small RNAs.
BMC genomics 2008;9():157.
2008: Martin C Frith; Eivind Valen; Anders Krogh; Yoshihide Hayashizaki; piero carninci; Albin Sandelin
A code for transcription initiation in mammalian genomes.
Genome research 2008;18(1):1-12.
2007: Martin C Frith; piero carninci; Chikatoshi Kai; Jun Kawai; Timothy Lawrence Bailey; Yoshihide Hayashizaki; John S Mattick
Splicing bypasses 3' end formation signals to allow complex gene architectures.
Gene 2007;403(1-2):188-93.
2007: Jun Kawai; piero carninci; Yoshihide Hayashizaki
Transcriptomics resources for functional genomics.
Briefings in functional genomics & proteomics 2007;6(3):171-9.
2007: Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason Dillon Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A. Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jorg Hackermuller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; piero carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos Antonarakis; Yutao Fu; Eric Green; Ulaş Karaöz; Adam Siepel; James TAYLOR; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Richmond Todd; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Goncalo Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature 2007;447(7146):799-816.
2007: Laura L Baxter; Benjamin J Hsu; Lowell Umayam; Tyra G Wolfsberg; Denise M Larson; Martin C Frith; Jun Kawai; Yoshihide Hayashizaki; piero carninci; William J Pavan
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.
2007: Albin Sandelin; piero carninci; Boris Lenhard; Jasmina Ponjavic; Yoshihide Hayashizaki; David A Hume
Mammalian RNA polymerase II core promoters: insights from genome-wide studies.
Nature reviews. Genetics 2007;8(6):424-36.
2007: piero carninci
Constructing the landscape of the mammalian transcriptome.
The Journal of experimental biology 2007;210(Pt 9):1497-506.
2007: Antje Purmann; Joern Toedling; Markus Schueler; piero carninci; Hans Lehrach; Yoshihide Hayashizaki; Wolfgang Huber; Silke Sperling
Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality.
Genomics 2007;89(5):580-7.
2007: piero carninci; Yoshihide Hayashizaki
Noncoding RNA transcription beyond annotated genes.
Current opinion in genetics & development 2007;17(2):139-44.
2007: Kirk W Beisel; Sonia M S Rocha-Sanchez; Sylvia J Ziegenbein; Ken A Morris; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Robin L Davis
Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells.
Gene 2007;386(1-2):11-23.
2007: Kouji Satoh; Koji Doi; Toshifumi Nagata; Naoki Kishimoto; Kohji Suzuki; Yasuhiro Otomo; Jun Kawai; Mari Nakamura; Tomoko Hirozane-Kishikawa; Saeko Kanagawa; Takahiro Arakawa; Juri Takahashi-Iida; Mitsuyoshi Murata; Noriko Ninomiya; Daisuke Sasaki; Shiro Fukuda; Michihira Tagami; Harumi Yamagata; Kanako Kurita; Kozue Kamiya; Mayu Yamamoto; Ari Kikuta; Takahito Bito; Nahoko Fujitsuka; Kazue Ito; Hiroyuki Kanamori; Il-Ryong Choi; Yoshiaki Nagamura; Takashi Matsumoto; Kazuo Murakami; Ken-ichi Matsubara; piero carninci; Yoshihide Hayashizaki; Shoshi Kikuchi
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.
PloS one 2007;2(11):e1235.
2007: Adele Kruger; Oliver Hofmann; piero carninci; Yoshihide Hayashizaki; Winston Hide
Simplified ontologies allowing comparison of developmental mammalian gene expression.
Genome biology 2007;8(10):R229.
2007: Kazuro Shimokawa; Yuko Okamura-Oho; Takio Kurita; Martin C Frith; Jun Kawai; piero carninci; Yoshihide Hayashizaki
Large-scale clustering of CAGE tag expression data.
BMC bioinformatics 2007;8():161.
2006: Kazuhiro Wada; Jason T Howard; Patrick McConnell; Osceola Whitney; Thierry Lints; Miriam V Rivas; Haruhito Horita; Michael A Patterson; Stephanie A White; Constance Scharff; Sebastian Haesler; Shengli Zhao; Hironobu Sakaguchi; Masatoshi Hagiwara; Toshiyuki Shiraki; Tomoko Hirozane-Kishikawa; Pate Skene; Yoshihide Hayashizaki; piero carninci; Erich D Jarvis
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.
2006: piero carninci
Tagging mammalian transcription complexity.
Trends in genetics : TIG 2006;22(9):501-10.
2006: Stefano Gustincich; Albin Sandelin; Charles Plessy; Shintaro Katayama; Roberto Simone; Dejan Lazarevic; Yoshihide Hayashizaki; piero carninci
The complexity of the mammalian transcriptome.
The Journal of physiology 2006;575(Pt 2):321-32.
2006: Roland Nilsson; Vladimir Bajic; Harukazu Suzuki; Diego di Bernardo; Johan Björkegren; Shintaro Katayama; James F Reid; Matthew J Sweet; manuela gariboldi; piero carninci; Yosihide Hayashizaki; David A Hume; Jesper Tegner; Timothy Ravasi
Transcriptional network dynamics in macrophage activation.
Genomics 2006;88(2):133-42.
2006: Masayoshi Itoh; Ayako Yasunishi; Kengo Imamura; Mutsumi Kanamori-Katayama; Harukazu Suzuki; Masanori Suzuki; piero carninci; Jun Kawai; Yoshihide Hayashizaki
Constructing ORFeome resources with removable termination codons.
BioTechniques 2006;41(1):44, 46, 48 passim.
2006: Martin C Frith; Jasmina Ponjavic; David Fredman; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Yoshihide Hayshizaki; Albin Sandelin
Evolutionary turnover of mammalian transcription start sites.
Genome research 2006;16(6):713-22.
2006: piero carninci; Albin Sandelin; Boris Lenhard; Shintaro Katayama; Kazuro Shimokawa; Jasmina Ponjavic; Colin Semple; Martin Taylor; Pär G Engström; Martin C Frith; Alistair Forrest; Wynand B Alkema; Sin Lam Tan; Charles Plessy; Rimantas Kodzius; Timothy Ravasi; Takeya Kasukawa; Shiro Fukuda; Mutsumi Kanamori-Katayama; Yayoi Kitazume; Hideya Kawaji; Chikatoshi Kai; Mari Nakamura; Hideaki Konno; Kenji Nakano; Salim Mottagui-Tabar; Peter Arner; Alessandra Chesi; Stefano Gustincich; Francesca Persichetti; Harukazu Suzuki; Sean M Grimmond; Christine A Wells; Valerio Orlando; Claes Wahlestedt; Edison Liu; Matthias Harbers; Jun Kawai; Vladimir Bajic; David A Hume; Yoshihide Hayashizaki
Genome-wide analysis of mammalian promoter architecture and evolution.
Nature genetics 2006;38(6):626-35.
2006: Rajith N Aturaliya; J Lynn Fink; Melissa J Davis; Melvena S Teasdale; Kelly A Hanson; Kevin C Miranda; Alistair Forrest; Sean M Grimmond; Harukazu Suzuki; Mutsumi Kanamori; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Rohan Teasdale
Subcellular localization of mammalian type II membrane proteins.
Traffic (Copenhagen, Denmark) 2006;7(5):613-25.
2006: Yoshihide Hayashizaki; piero carninci
Genome Network and FANTOM3: assessing the complexity of the transcriptome.
PLoS genetics 2006;2(4):e63.
2006: Norihiro Maeda; Takeya Kasukawa; Rieko Oyama; Julian Gough; Martin Frith; Pär G Engström; Boris Lenhard; Rajith N Aturaliya; Serge Batalov; Kirk W Beisel; Carol Bult; Colin F Fletcher; Alistair Forrest; Masaaki Furuno; David Hill; Masayoshi Itoh; Mutsumi Kanamori-Katayama; Shintaro Katayama; Masaru Katoh; Tsugumi Kawashima; John Quackenbush; Timothy Ravasi; Brian Z Ring; Kazuhiro Shibata; Koji Sugiura; Yoichi Takenaka; Rohan Teasdale; Christine A Wells; Yunxia Zhu; Chikatoshi Kai; Jun Kawai; David A Hume; piero carninci; Yoshihide Hayashizaki
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
PLoS genetics 2006;2(4):e62.
2006: Vladimir Bajic; Sin Lam Tan; Alan Christoffels; Christian Schönbach; Leonard Lipovich; Liang Yang; Oliver Hofmann; Adele Kruger; Winston Hide; Chikatoshi Kai; Jun Kawai; David A Hume; piero carninci; Yoshihide Hayashizaki
Mice and men: their promoter properties.
PLoS genetics 2006;2(4):e54.
2006: Martin C Frith; Alistair Forrest; Ehsan Nourbakhsh; Ken C Pang; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Timothy Lawrence Bailey; Sean M Grimmond
The abundance of short proteins in the mammalian proteome.
PLoS genetics 2006;2(4):e52.
2006: Pär G Engström; Harukazu Suzuki; Noriko Ninomiya; Altuna Akalin; Luca Sessa; Giovanni Lavorgna; Alessandro Brozzi; Lucilla Luzi; Sin Lam Tan; Liang Yang; Galih Kunarso; Edwin Lian-Chong Ng; Serge Batalov; Claes Wahlestedt; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Christine Wells; Vladimir Bajic; Valerio Orlando; James F Reid; Boris Lenhard; Leonard Lipovich
Complex Loci in human and mouse genomes.
PLoS genetics 2006;2(4):e47.
2006: Melissa J Davis; Kelly A Hanson; Francis Clark; J Lynn Fink; Fasheng Zhang; Takeya Kasukawa; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Rohan Teasdale
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.
2006: Tzu-Ming Chern; Erik van Nimwegen; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Mihaela Zavolan
A simple physical model predicts small exon length variations.
PLoS genetics 2006;2(4):e45.
2006: Shigeto Seno; Yoichi Takenaka; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Hideo Matsuda
A method for similarity search of genomic positional expression using CAGE.
PLoS genetics 2006;2(4):e44.
2006: Masaaki Furuno; Ken C Pang; Noriko Ninomiya; Shiro Fukuda; Martin C Frith; Carol Bult; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; John S Mattick; Harukazu Suzuki
Clusters of internally primed transcripts reveal novel long noncoding RNAs.
PLoS genetics 2006;2(4):e37.
2006: Martin Taylor; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Colin Semple
Heterotachy in mammalian promoter evolution.
PLoS genetics 2006;2(4):e30.
2006: Martin C Frith; Laurens G Wilming; Alistair Forrest; Hideya Kawaji; Sin Lam Tan; Claes Wahlestedt; Vladimir Bajic; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Timothy Lawrence Bailey; Lukasz Huminiecki
Pseudo-messenger RNA: phantoms of the transcriptome.
PLoS genetics 2006;2(4):e23.
2006: Rimantas Kodzius; Miki Kojima; Hiromi Nishiyori; Mari Nakamura; Shiro Fukuda; Michihira Tagami; Daisuke Sasaki; Kengo Imamura; Chikatoshi Kai; Matthias Harbers; Yoshihide Hayashizaki; piero carninci
CAGE: cap analysis of gene expression.
Nature methods 2006;3(3):211-22.
2006: Manisha Brahmachary; Christian Schönbach; Liang Yang; Enli Huang; Sin Lam Tan; Rajesh Chowdhary; S P T Krishnan; Chin-Yo Lin; David A Hume; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Vladimir Bajic
Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes.
BMC bioinformatics 2006;7 Suppl 5():S8.
2006: Hideya Kawaji; Martin C Frith; Shintaro Katayama; Albin Sandelin; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki
Dynamic usage of transcription start sites within core promoters.
Genome biology 2006;7(12):R118.
2006: Martin C Frith; Timothy Lawrence Bailey; Takeya Kasukawa; Flavio Mignone; Sarah K Kummerfeld; Martin Madera; Sirisha Sunkara; Masaaki Furuno; Carol Bult; John Quackenbush; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Graziano Pesole; John S Mattick
Discrimination of non-protein-coding transcripts from protein-coding mRNA.
RNA biology 2006;3(1):40-8.
2006: Jasmina Ponjavic; Boris Lenhard; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Albin Sandelin
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters.
Genome biology 2006;7(8):R78.
2006: Christine A Wells; Alistair Chalk; Alistair Forrest; Darrin Taylor; Nic Waddell; Kate Schroder; S Roy Himes; Geoffrey J Faulkner; Sandra Lo; Takeya Kasukawa; Hideya Kawaji; Chikatoshi Kai; Jun Kawai; Shintaro Katayama; piero carninci; Yoshihide Hayashizaki; David A Hume; Sean M Grimmond
Alternate transcription of the Toll-like receptor signaling cascade.
Genome biology 2006;7(2):R10.
2006: Alistair Forrest; Darrin F Taylor; Mark L Crowe; Alistair Chalk; Nic J Waddell; Gabriel Kolle; Geoffrey J Faulkner; Rimantas Kodzius; Shintaro Katayama; Christine Wells; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Sean M Grimmond
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases.
Genome biology 2006;7(1):R5.
2006: Hideya Kawaji; Takeya Kasukawa; Shiro Fukuda; Shintaro Katayama; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.
Nucleic acids research 2006;34(Database issue):D632-6.
2006: J Lynn Fink; Rajith N Aturaliya; Melissa J Davis; Fasheng Zhang; Kelly Hanson; Melvena S Teasdale; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Rohan Teasdale
LOCATE: a mouse protein subcellular localization database.
Nucleic acids research 2006;34(Database issue):D213-7.
2005: Vassilis Aidinis; piero carninci; Maria Armaka; Walter Witke; Vaggelis Harokopos; Norman Pavelka; Dirk Koczan; Christos Argyropoulos; Maung-Maung Thwin; Steffen Möller; Kazunori Waki; Waki Kazunori; Ponnampalam Gopalakrishnakone; Paola Ricciardi-Castagnoli; Hans-Jürgen Thiesen; Yoshihide Hayashizaki; george kollias
Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis.
PLoS genetics 2005;1(4):e48.
2005: S Katayama; Y Tomaru; T Kasukawa; Kazunori Waki; M Nakanishi; M Nakamura; H Nishida; C C Yap; M Suzuki; J Kawai; H Suzuki; piero carninci; Y Hayashizaki; C Wells; M Frith; T Ravasi; K C Pang; J Hallinan; J Mattick; D A Hume; Leonard Lipovich; S Batalov; P G Engström; Y Mizuno; Mohammad Faghihi; A Sandelin; Alistair Chalk; S Mottagui-Tabar; Z Liang; B Lenhard; Claes Wahlestedt
Antisense transcription in the mammalian transcriptome.
Science (New York, N.Y.) 2005;309(5740):1564-6.
2005: piero carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; Vladimir Bajic; S E Brenner; S Batalov; Alistair Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; Timothy Lawrence Bailey; M Bansal; L Baxter; K W Beisel; Tom Bersano; H Bono; Alistair Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; manuela gariboldi; P Georgii-Hemming; Thomas Gingeras; Takashi Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; Kazuho Ikeo; A Iwama; T Ishikawa; M Jakt; Alexander Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; george kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; Leonard Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; LUIGI MARCHIONNI; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Yasushi Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; Nikolai Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; Steven L Salzberg; A Sandelin; C Schneider; Christian Schönbach; K Sekiguchi; Colin Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; Elia Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; Martin Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; Winston Hide; Carol Bult; S M Grimmond; Rohan Teasdale; Edison Liu; V Brusic; John Quackenbush; Claes Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; Masayoshi Itoh; T Kato; Hideya Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; Kazunori Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
The transcriptional landscape of the mammalian genome.
Science (New York, N.Y.) 2005;309(5740):1559-63.
2005: Matthias Harbers; piero carninci
Tag-based approaches for transcriptome research and genome annotation.
Nature methods 2005;2(7):495-502.
2005: Noriyuki Kitagawa; Takanori Washio; Shunichi Kosugi; Tomoya Yamashita; Kenji Higashi; Hiroshi Yanagawa; Kenichi Higo; Koji Satoh; Yasuhiro Ohtomo; Tomomi Sunako; Kazuo Murakami; Kenichi Matsubara; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Shoshi Kikuchi; Masaru Tomita
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.
2005: Atsushi Nakabachi; Shuji Shigenobu; Naoko Sakazume; Toshiyuki Shiraki; Yoshihide Hayashizaki; piero carninci; Hajime Ishikawa; Toshiaki Kudo; Takema Fukatsu
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.
2005: Ken A Morris; Einat Snir; Celine Pompeia; Irina V Koroleva; Anne E White-Olson; Yoshihide Hayashizaki; piero carninci; M Bento Soares; Kirk W Beisel
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.
2005: Kengo Usui; Shintaro Katayama; Mutsumi Kanamori-Katayama; Chihiro Ogawa; Chikatoshi Kai; Makiko Okada; Jun Kawai; Takahiro Arakawa; piero carninci; Masayoshi Itoh; Koji Takio; Masashi Miyano; Satoru Kidoaki; Takehisa Matsuda; Yoshihide Hayashizaki; Harukazu Suzuki
Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
Genome biology 2005;6(12):R98.
2005: Randolph B Caldwell; Andrzej M Kierzek; Hiroshi Arakawa; Yuri Bezzubov; Jolanta Zaim; Petra Fiedler; Stefan Kutter; Artem Blagodatski; Diyana Kostovska; Marek Koter; Jiri Plachy; piero carninci; Yoshihide Hayashizaki; Jean-Marie Buerstedde
Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis.
Genome biology 2005;6(1):R6.
2004: Akira Watahiki; Kazunori Waki; Norihito Hayatsu; Toshiyuki Shiraki; Shinji Kondo; Mari Nakamura; Daisuke Sasaki; Takahiro Arakawa; Jun Kawai; Matthias Harbers; Yoshihide Hayashizaki; piero carninci
Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas.
Nature methods 2004;1(3):233-9.
2004: Mari Nakamura; piero carninci
[Cap analysis gene expression: CAGE].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 2004;49(17 Suppl):2688-93.
2004: Daniela S Gerhard; Lukas Wagner; Elise A Feingold; Carolyn M Shenmen; Lynette H Grouse; Greg Schuler; Steven L Klein; Susan Old; Rebekah Rasooly; Peter Good; Mark Guyer; Allison M Peck; Jeffery G Derge; David Lipman; Francis S Collins; Wonhee Jang; Steven Sherry; Michael Feolo; Leonie Misquitta; Eduardo Lee; Kirill Rotmistrovsky; Susan F Greenhut; Carl F Schaefer; Kenneth Buetow; Tom I Bonner; David Haussler; Jim Kent; Mark Kiekhaus; Terry Furey; Michael Brent; Christa Prange; Kirsten Schreiber; Nicole Shapiro; Narayan K Bhat; Ralph F Hopkins; Florence Hsie; Tom Driscoll; M Bento Soares; Tom L Casavant; Todd E Scheetz; Michael J Brown-stein; Ted B Usdin; Shiraki Toshiyuki; piero carninci; Yulan Piao; Dawood B Dudekula; Minoru S H Ko; Koichi Kawakami; Yutaka Suzuki; Sumio Sugano; C E Gruber; M R Smith; Blake Simmons; Troy Moore; Richard Waterman; Stephen L Johnson; Yijun Ruan; Chia Lin Wei; S Mathavan; Preethi H Gunaratne; Jiaqian Wu; Angela M Garcia; Stephen W Hulyk; Edwin Fuh; Ye Yuan; Anna Sneed; Carla Kowis; Anne Hodgson; Donna M Muzny; John McPherson; Richard A Gibbs; Jessica Fahey; Erin Helton; Mark Ketteman; Anuradha Madan; Stephanie Rodrigues; Amy Sanchez; Michelle Whiting; Anup Madari; Alice C Young; Keith D Wetherby; Steven J Granite; Peggy N Kwong; Charles P Brinkley; Russell L Pearson; Gerard G Bouffard; Robert W Blakesly; Eric Green; Mark C Dickson; Alex C Rodriguez; Jane Grimwood; Jeremy Schmutz; Richard Myers; Yaron S N Butterfield; Malachi Griffith; Obi L Griffith; Martin I Krzywinski; Nancy Liao; Ryan Morin; Ryan Morrin; Diana Palmquist; Anca S Petrescu; Ursula Skalska; Duane E Smailus; Jeff M Stott; Angelique Schnerch; Jacqueline E Schein; Steven J M Jones; Robert A Holt; Agnes Baross; Marco A Marra; Sandra Clifton; Kathryn A Makowski; Stephanie Bosak; Joel Malek
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
Genome research 2004;14(10B):2121-7.
2004: Toshifumi Nagata; Shigemi Iizumi; Kouji Satoh; Hisako Ooka; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Yasuhiro Otomo; Kazuo Murakami; Kenichi Matsubara; Shoshi Kikuchi
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.
2004: Yasunari Ogihara; Keiichi Mochida; Kanako Kawaura; Koji Murai; Motoaki Seki; Asako Kamiya; Kazuo Shinozaki; piero carninci; Yoshihide Hayashizaki; Tadasu Shin-i; Yuji Kohara; Yukiko Yamazaki
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.
2004: Nobukazu Nameki; Misao Yoneyama; Seizo Koshiba; Naoya Tochio; Makoto Inoue; Eiko Seki; Takayoshi Matsuda; Yasuko Tomo; Takushi Harada; Kohei Saito; Naohiro Kobayashi; Takashi Yabuki; Masaaki Aoki; Emi Nunokawa; Natsuko Matsuda; Noriko Sakagami; Takaho Terada; Mikako Shirouzu; Mayumi Yoshida; Hiroshi Hirota; Takashi Osanai; Akiko Tanaka; Takahiro Arakawa; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Kengo Kinoshita; Peter Güntert; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of the RWD domain of the mouse GCN2 protein.
Protein science : a publication of the Protein Society 2004;13(8):2089-100.
2004: Kirk W Beisel; Toshiyuki Shiraki; Ken A Morris; Celine Pompeia; Anne E White-Olson; Takahiro Arakawa; Hidemasa Bono; Jun Kawai; Yoshihide Hayashizaki; piero carninci
Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library.
Genomics 2004;83(6):1012-23.
2004: M Stefania Lagonigro; Loris De Cecco; piero carninci; Delia Di Stasi; Tiziana Ranzani; Monica Rodolfo; manuela gariboldi
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.
2004: Tadashi Imanishi; Takeshi Itoh; Yutaka Suzuki; Claire O'Donovan; Satoshi Fukuchi; Kanako O Koyanagi; Roberto A Barrero; Takuro Tamura; Yumi Yamaguchi-Kabata; Motohiko Tanino; Kei Yura; Satoru Miyazaki; Kazuho Ikeo; Keiichi Homma; Arek Kasprzyk; Tetsuo Nishikawa; Mika Hirakawa; Jean Thierry-Mieg; Danielle Thierry-Mieg; Jennifer Ashurst; Libin Jia; Mitsuteru Nakao; Michael A Thomas; Nicola Mulder; Youla Karavidopoulou; Lihua Jin; Sangsoo Kim; Tomohiro Yasuda; Boris Lenhard; Eric Eveno; Yoshiyuki Suzuki; Chisato Yamasaki; Jun-ichi Takeda; Craig Gough; Phillip Hilton; Yasuyuki Fujii; Hiroaki Sakai; Susumu Tanaka; Clara Amid; Matthew Bellgard; Maria de Fatima Bonaldo; Hidemasa Bono; Susan K Bromberg; Anthony J Brookes; Elspeth Bruford; piero carninci; Claude Chelala; Christine Couillault; Sandro J de Souza; Marie-Anne Debily; Marie-Dominique Devignes; Inna Dubchak; Toshinori Endo; Anne Estreicher; Eduardo Eyras; Kaoru Fukami-Kobayashi; Gopal R Gopinath; Esther Graudens; Yoonsoo Hahn; Michael Han; Ze-Guang Han; Kousuke Hanada; Hideki Hanaoka; Erimi Harada; Katsuyuki Hashimoto; Ursula Hinz; Momoki Hirai; Teruyoshi Hishiki; Ian Hopkinson; Sandrine Imbeaud; Hidetoshi Inoko; Alexander Kanapin; Yayoi Kaneko; Takeya Kasukawa; Janet Kelso; Paul Kersey; Reiko Kikuno; Kouichi Kimura; Bernhard Korn; Vladimir Kuryshev; Izabela Makalowska; Takashi Makino; Shuhei Mano; Regine Mariage-Samson; Jun Mashima; Hideo Matsuda; Hans-Werner Mewes; Shinsei Minoshima; Keiichi Nagai; Hideki Nagasaki; Naoki Nagata; Rajni Nigam; Osamu Ogasawara; Osamu Ohara; Masafumi Ohtsubo; Norihiro Okada; Toshihisa Okido; Satoshi Oota; Motonori Ota; Toshio Ota; Tetsuji Otsuki; Dominique Piatier-Tonneau; Annemarie Poustka; Shuang-Xi Ren; Naruya Saitou; Katsunaga Sakai; Shigetaka Sakamoto; Ryuichi Sakate; Ingo Schupp; Florence Servant; Stephen Sherry; Rie Shiba; Nobuyoshi Shimizu; Mary Shimoyama; Andrew J Simpson; Bento Soares; Charles Steward; Makiko Suwa; Mami Suzuki; Aiko Takahashi; Gen Tamiya; Hiroshi Tanaka; Todd Taylor; Joseph D Terwilliger; Per Unneberg; Vamsi Veeramachaneni; Shinya Watanabe; Laurens Wilming; Norikazu Yasuda; Hyang-Sook Yoo; Marvin Stodolsky; Wojciech Makalowski; Mitiko Go; Kenta Nakai; Toshihisa Takagi; Minoru Kanehisa; Yoshiyuki Sakaki; John Quackenbush; Yasushi Okazaki; Yoshihide Hayashizaki; Winston Hide; Ranajit Chakraborty; Ken Nishikawa; Hideaki Sugawara; Yoshio Tateno; Zhu Chen; Michio Oishi; Peter Tonellato; Rolf Apweiler; Kousaku Okubo; Lukas Wagner; Stefan Wiemann; Robert L Strausberg; Takao Isogai; Charles Auffray; Nobuo Nomura; Takashi Gojobori; Sumio Sugano
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
PLoS biology 2004;2(6):e162.
2004: Junshi Yazaki; Zenpei Shimatani; Akiko Hashimoto; Yuko Nagata; Fumiko Fujii; Keiichi Kojima; Kohji Suzuki; Toshiki Taya; Mio Tonouchi; Charles Nelson; Allen Nakagawa; Yasuhiro Otomo; Kazuo Murakami; Kenichi Matsubara; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Shoshi Kikuchi
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.
2004: Stefano Gustincich; Massimo Contini; manuela gariboldi; Michelino Puopolo; Koji Kadota; Hidemasa Bono; Julianna LeMieux; Pamela Walsh; piero carninci; Yoshihide Hayashizaki; Yasushi Okazaki; Elio Raviola
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.
2004: Takeshi Maeda; Makoto Inoue; Seizo Koshiba; Takashi Yabuki; Masaaki Aoki; Emi Nunokawa; Eiko Seki; Takayoshi Matsuda; Yoko Motoda; Atsuo Kobayashi; Fumiko Hiroyasu; Mikako Shirouzu; Takaho Terada; Nobuhiro Hayami; Yoshiko Ishizuka; Naoko Shinya; Ayako Tatsuguchi; Mayumi Yoshida; Hiroshi Hirota; Yo Matsuo; Kazutoshi Tani; Takahiro Arakawa; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Takanori Kigawa; Shigeyuki Yokoyama
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.
2004: Rimantas Kodzius; Yonehiro Matsumura; Takeya Kasukawa; Kazuro Shimokawa; Shiro Fukuda; Toshiyuki Shiraki; Mari Nakamura; Takahiro Arakawa; Daisuke Sasaki; Jun Kawai; Matthias Harbers; piero carninci; Yoshihide Hayashizaki
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.
2004: Takuma Kasai; Makoto Inoue; Seizo Koshiba; Takashi Yabuki; Masaaki Aoki; Emi Nunokawa; Eiko Seki; Takayoshi Matsuda; Natsuko Matsuda; Yasuko Tomo; Mikako Shirouzu; Takaho Terada; Naomi Obayashi; Hiroaki Hamana; Naoko Shinya; Ayako Tatsuguchi; Satoko Yasuda; Mayumi Yoshida; Hiroshi Hirota; Yo Matsuo; Kazutoshi Tani; Harukazu Suzuki; Takahiro Arakawa; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Takanori Kigawa; Shigeyuki Yokoyama
Solution structure of a BolA-like protein from Mus musculus.
Protein science : a publication of the Protein Society 2004;13(2):545-8.
2004: Yutaka Suzuki; Riu Yamashita; Matsuyuki Shirota; Yuta Sakakibara; Joe Chiba; Junko Mizushima-Sugano; Alexander Kel; Takahiro Arakawa; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Toshihisa Takagi; Kenta Nakai; Sumio Sugano
Large-scale collection and characterization of promoters of human and mouse genes.
In silico biology 2004;4(4):429-44.
2004: Takeshi Nagashima; Hideo Matsuda; Diego G Silva; Nikolai Petrovsky; Akihiko Konagaya; Christian Schönbach; Takeya Kasukawa; Takahiro Arakawa; piero carninci; Jun Kawai; Yoshihide Hayashizaki
FREP: a database of functional repeats in mouse cDNAs.
Nucleic acids research 2004;32(Database issue):D471-5.
2003: Junshi Yazaki; Naoki Kishimoto; Yuko Nagata; Masahiro Ishikawa; Fumiko Fujii; Akiko Hashimoto; Kanako Shimbo; Zenpei Shimatani; Keiichi Kojima; Kouji Suzuki; Makoto Yamamoto; Sachiko Honda; Ayano Endo; Yumiko Yoshida; Yuki Sato; Keiko Takeuchi; Kazuko Toyoshima; Chikako Miyamoto; Jianzhong Wu; Takuji Sasaki; Katsumi Sakata; Kimiko Yamamoto; Koh Iba; Takahiro Oda; Yasuhiro Otomo; Kazuo Murakami; Kenichi Matsubara; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Shoshi Kikuchi
Genomics approach to abscisic acid- and gibberellin-responsive genes in rice.
DNA research : an international journal for rapid publication of reports on genes and genomes 2003;10(6):249-61.
2003: Hisako Ooka; Kouji Satoh; Koji Doi; Toshifumi Nagata; Yasuhiro Otomo; Kazuo Murakami; Kenichi Matsubara; Naoki Osato; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Koji Suzuki; Keiichi Kojima; Yoshinori Takahara; Koji Yamamoto; Shoshi Kikuchi
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.
2003: Toshiyuki Shiraki; Shinji Kondo; Shintaro Katayama; Kazunori Waki; Takeya Kasukawa; Hideya Kawaji; Rimantas Kodzius; Akira Watahiki; Mari Nakamura; Takahiro Arakawa; Shiro Fukuda; Daisuke Sasaki; Anna J Podhajska; Matthias Harbers; Jun Kawai; piero carninci; Yoshihide Hayashizaki
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.
2003: Shigeo Fujimori; Takanori Washio; Kenichi Higo; Yasuhiro Ohtomo; Kazuo Murakami; Kenichi Matsubara; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Shoshi Kikuchi; Masaru Tomita
A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription.
FEBS letters 2003;554(1-2):17-22.
2003: Kayoko Yamada; Jun Lim; Joseph M Dale; Huaming Chen; Paul Shinn; Curtis J Palm; Audrey M Southwick; Hank C Wu; Christopher Kim; Michelle Nguyen; Paul Pham; Rosa Cheuk; George Karlin-Newmann; Shirley X Liu; Bao Lam; Hitomi Sakano; Troy Wu; Guixia Yu; Molly Miranda; Hong L Quach; Matthew Tripp; Charlie H Chang; Jeong M Lee; Mitsue Toriumi; Marie M H Chan; Carolyn C Tang; Courtney S Onodera; Justine M Deng; Kenji Akiyama; Yasser Ansari; Takahiro Arakawa; Jenny Banh; Fumika Banno; Leah Bowser; Shelise Brooks; piero carninci; Qimin Chao; Nathan Choy; Akiko Enju; Andrew D Goldsmith; Mani Gurjal; Nancy F Hansen; Yoshihide Hayashizaki; Chanda Johnson-Hopson; Vickie W Hsuan; Kei Iida; Meagan Karnes; Shehnaz Khan; Eric Koesema; Junko Ishida; Paul X Jiang; Ted Jones; Jun Kawai; Asako Kamiya; Cristina Meyers; Maiko Nakajima; Mari Narusaka; Motoaki Seki; Tetsuya Sakurai; Masakazu Satou; Racquel Tamse; Maria Vaysberg; Erika K Wallender; Cecilia Wong; Yuki Yamamura; Shiaulou Yuan; Kazuo Shinozaki; Ronald W Davis; Athanasios Theologis; Joseph R Ecker
Empirical analysis of transcriptional activity in the Arabidopsis genome.
Science (New York, N.Y.) 2003;302(5646):842-6.
2003: Tomoko Hirozane-Kishikawa; Toshiyuki Shiraki; Kazunori Waki; Mari Nakamura; Takahiro Arakawa; Jun Kawai; Michela Fagiolini; Takao K Hensch; Yoshihide Hayashizaki; piero carninci
Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.
BioTechniques 2003;35(3):510-6, 518.
2003: Shoshi Kikuchi; Kouji Satoh; Toshifumi Nagata; Nobuyuki Kawagashira; Koji Doi; Naoki Kishimoto; Junshi Yazaki; Masahiro Ishikawa; Hitomi Yamada; Hisako Ooka; Isamu Hotta; Keiichi Kojima; Takahiro Namiki; Eisuke Ohneda; Wataru Yahagi; Kohji Suzuki; Chao Jie Li; Kenji Ohtsuki; Toru Shishiki; Yasuhiro Otomo; Kazuo Murakami; Yoshiharu Iida; Sumio Sugano; Tatsuto Fujimura; Yutaka Suzuki; Yuki Tsunoda; Takashi Kurosaki; Takeko Kodama; Hiromi Masuda; Michie Kobayashi; Quihong Xie; Min Lu; Ryuya Narikawa; Akio Sugiyama; Kouichi Mizuno; Satoko Yokomizo; Junko Niikura; Rieko Ikeda; Junya Ishibiki; Midori Kawamata; Akemi Yoshimura; Junichirou Miura; Takahiro Kusumegi; Mitsuru Oka; Risa Ryu; Mariko Ueda; Kenichi Matsubara; Jun Kawai; piero carninci; Jun Adachi; Katsunori Aizawa; Takahiro Arakawa; Shiro Fukuda; Ayako Hara; Wataru Hashizume; Norihito Hayatsu; Koichi Imotani; Yoshiyuki Ishii; Masayoshi Itoh; Ikuko Kagawa; Shinji Kondo; Hideaki Konno; Ai Miyazaki; Naoki Osato; Yoshimi Ota; Rintaro Saito; Daisuke Sasaki; Kenjiro Sato; Kazuhiro Shibata; Akira Shinagawa; Toshiyuki Shiraki; Masayasu Yoshino; Yoshihide Hayashizaki; Ayako Yasunishi
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
Science (New York, N.Y.) 2003;301(5631):376-9.
2003: Christine A Wells; Timothy Ravasi; Geoffrey J Faulkner; piero carninci; Yasushi Okazaki; Yoshihide Hayashizaki; Matthew J Sweet; Brandon J Wainwright; David A Hume
Genetic control of the innate immune response.
BMC immunology 2003;4():5.
2003: Tomoaki Nishiyama; Tomomichi Fujita; Tadasu Shin-i; Motoaki Seki; Hiroyo Nishide; Ikuo Uchiyama; Asako Kamiya; piero carninci; Yoshihide Hayashizaki; Kazuo Shinozaki; Yuji Kohara; Mitsuyasu Hasebe
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.
2003: Stefano Gustincich; Serge Batalov; Kirk W Beisel; Hidemasa Bono; piero carninci; Colin F Fletcher; Sean M Grimmond; Nobutaka Hirokawa; Erich D Jarvis; Tim Jegla; Yuka Kawasawa; Julianna LeMieux; Harukata Miki; Elio Raviola; Rohan Teasdale; Naoko Tominaga; Ken Yagi; Andreas Zimmer; Yoshihide Hayashizaki; Yasushi Okazaki
Analysis of the mouse transcriptome for genes involved in the function of the nervous system.
Genome research 2003;13(6B):1395-401.
2003: Christine A Wells; Timothy Ravasi; Razvan Sultana; Ken Yagi; piero carninci; Hidemasa Bono; Geoffrey J Faulkner; Yasushi Okazaki; John Quackenbush; David A Hume; Paul A Lyons
Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage.
Genome research 2003;13(6B):1360-5.
2003: piero carninci; Kazunori Waki; Toshiyuki Shiraki; Hideaki Konno; Kazuhiro Shibata; Masayoshi Itoh; Katsunori Aizawa; Takahiro Arakawa; Yoshiyuki Ishii; Daisuke Sasaki; Hidemasa Bono; Shinji Kondo; Yuichi Sugahara; Rintaro Saito; Naoki Osato; Shiro Fukuda; Kenjiro Sato; Akira Watahiki; Tomoko Hirozane-Kishikawa; Mari Nakamura; Yuko Shibata; Ayako Yasunishi; Noriko Kikuchi; Atsushi Yoshiki; Moriaki Kusakabe; Stefano Gustincich; Kirk Beisel; William Pavan; Vassilis Aidinis; Akira Nakagawara; William A Held; Hiroo Iwata; Tomohiro Kono; Hiromitsu Nakauchi; Paul Lyons; Christine Wells; David A Hume; Michela Fagiolini; Takao K Hensch; Michelle Brinkmeier; Sally A Camper; Junji Hirota; Peter Mombaerts; Masami Muramatsu; Yasushi Okazaki; Jun Kawai; Yoshihide Hayashizaki
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.
Genome research 2003;13(6B):1273-89.
2003: Nicole C Walsh; Marian Cahill; piero carninci; Jun Kawai; Yasushi Okazaki; Yoshihide Hayashizaki; David A Hume; A Ian Cassady
Multiple tissue-specific promoters control expression of the murine tartrate-resistant acid phosphatase gene.
Gene 2003;307():111-23.
2003: Naoki Osato; Hitomi Yamada; Kouji Satoh; Hisako Ooka; Makoto Yamamoto; Kohji Suzuki; Jun Kawai; piero carninci; Yasuhiro Ohtomo; Kazuo Murakami; Kenichi Matsubara; Shoshi Kikuchi; Yoshihide Hayashizaki
Antisense transcripts with rice full-length cDNAs.
Genome biology 2003;5(1):R5.
2002: Robert L Strausberg; Elise A Feingold; Lynette H Grouse; Jeffery G Derge; Richard D Klausner; Francis S Collins; Lukas Wagner; Carolyn M Shenmen; Gregory D Schuler; Stephen F Altschul; Barry Zeeberg; Kenneth H Buetow; Carl F Schaefer; Narayan K Bhat; Ralph F Hopkins; Heather Jordan; Troy Moore; Steve I Max; Jun Wang; Florence Hsieh; Luda Diatchenko; Kate Marusina; Andrew A Farmer; Gerald M Rubin; Ling Hong; Mark Stapleton; M Bento Soares; Maria F Bonaldo; Tom L Casavant; Todd E Scheetz; Michael J Brownstein; Ted B Usdin; Shiraki Toshiyuki; piero carninci; Christa Prange; Sam S Raha; Naomi A Loquellano; Garrick J Peters; Rick D Abramson; Sara J Mullahy; Stephanie A Bosak; Paul J McEwan; Kevin J McKernan; Joel A Malek; Preethi H Gunaratne; Stephen Richards; Kim C Worley; Sarah Hale; Angela M Garcia; Laura J Gay; Stephen W Hulyk; Debbie K Villalon; Donna M Muzny; Erica J Sodergren; Xiuhua Lu; Richard A Gibbs; Jessica Fahey; Erin Helton; Mark Ketteman; Anuradha Madan; Stephanie Rodrigues; Amy Sanchez; Michelle Whiting; Anup Madan; Alice C Young; Yuriy Shevchenko; Gerard G Bouffard; Robert W Blakesley; Jeffrey W Touchman; Eric Green; Mark C Dickson; Alex C Rodriguez; Jane Grimwood; Jeremy Schmutz; Richard Myers; Yaron S N Butterfield; Martin I Krzywinski; Ursula Skalska; Duane E Smailus; Angelique Schnerch; Jacqueline E Schein; Steven J M Jones; Marco A Marra
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(26):16899-903.
2002: Yasushi Okazaki; M Furuno; T Kasukawa; J Adachi; H Bono; S Kondo; I Nikaido; N Osato; R Saito; H Suzuki; I Yamanaka; H Kiyosawa; K Yagi; Y Tomaru; Y Hasegawa; A Nogami; Christian Schönbach; Takashi Gojobori; R Baldarelli; D P Hill; Carol Bult; D A Hume; John Quackenbush; Lynn M Schriml; Alexander Kanapin; H Matsuda; S Batalov; K W Beisel; J A Blake; D Bradt; V Brusic; C Chothia; L E Corbani; S Cousins; E Dalla; T A Dragani; C F Fletcher; Alistair Forrest; K S Frazer; T Gaasterland; manuela gariboldi; C Gissi; A Godzik; J Gough; S Grimmond; S Gustincich; N Hirokawa; I J Jackson; E D Jarvis; A Kanai; Hideya Kawaji; Y Kawasawa; R M Kedzierski; B L King; A Konagaya; I V Kurochkin; Y Lee; B Lenhard; P A Lyons; D R Maglott; L Maltais; LUIGI MARCHIONNI; L McKenzie; H Miki; T Nagashima; K Numata; T Okido; W J Pavan; G Pertea; G Pesole; Nikolai Petrovsky; R Pillai; J U Pontius; D Qi; S Ramachandran; T Ravasi; J C Reed; D J Reed; J Reid; B Z Ring; M Ringwald; A Sandelin; C Schneider; Colin Semple; M Setou; K Shimada; R Sultana; Y Takenaka; Martin Taylor; Rohan Teasdale; M Tomita; R Verardo; L Wagner; Claes Wahlestedt; Y Wang; Y Watanabe; C Wells; L G Wilming; A Wynshaw-Boris; M Yanagisawa; I Yang; L Yang; Z Yuan; M Zavolan; Y Zhu; A Zimmer; piero carninci; N Hayatsu; T Hirozane-Kishikawa; H Konno; M Nakamura; N Sakazume; K Sato; T Shiraki; Kazunori Waki; J Kawai; K Aizawa; T Arakawa; S Fukuda; A Hara; W Hashizume; K Imotani; Y Ishii; Masayoshi Itoh; I Kagawa; A Miyazaki; K Sakai; D Sasaki; K Shibata; A Shinagawa; A Yasunishi; M Yoshino; R Waterston; E S Lander; J Rogers; E Birney; Y Hayashizaki
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
Nature 2002;420(6915):563-73.
2002: Robert H Waterston; Kerstin Lindblad-Toh; Ewan Birney; Jane Rogers; Josep F Abril; Pankaj Agarwal; Richa Agarwala; Rachel Ainscough; Marina Alexandersson; Peter An; Stylianos Antonarakis; John Attwood; Robert Baertsch; Jonathon Bailey; Karen Barlow; Stephan Beck; Eric Berry; Bruce Birren; Toby Bloom; Peer Bork; Marc Botcherby; Nicolas Bray; Michael R Brent; Daniel G Brown; Stephen D Brown; Carol Bult; John Burton; Jonathan Butler; Robert D Campbell; piero carninci; Simon Cawley; Francesca Chiaromonte; Asif T Chinwalla; Deanna M Church; Michele Clamp; Christopher Clee; Francis S Collins; Lisa L Cook; Richard R Copley; Alan Coulson; Olivier Couronne; James Cuff; Val Curwen; Tim Cutts; Mark J Daly; Robert David; Joy Davies; Kimberly D Delehaunty; Justin Deri; Emmanouil T Dermitzakis; Colin Dewey; Nicholas J Dickens; Mark Diekhans; Sheila Dodge; Inna Dubchak; Diane M Dunn; Sean R Eddy; Laura Elnitski; Richard Emes; Pallavi Eswara; Eduardo Eyras; Adam Felsenfeld; Ginger A Fewell; Paul Flicek; Karen Foley; Wayne N Frankel; Lucinda A Fulton; Robert S Fulton; Terrence S Furey; Diane Gage; Richard A Gibbs; Gustavo Glusman; Sante Gnerre; Nick Goldman; Leo Goodstadt; Darren Grafham; Tina A Graves; Eric Green; Simon Gregory; Roderic Guigó; Mark Guyer; Ross C Hardison; David Haussler; Yoshihide Hayashizaki; LaDeana W Hillier; Angela Hinrichs; Wratko Hlavina; Timothy Holzer; Fan Hsu; Axin Hua; Tim Hubbard; Adrienne Hunt; Ian Jackson; David B Jaffe; L Steven Johnson; Matthew Jones; Thomas A Jones; Ann Joy; Michael Kamal; Elinor K. Karlsson; Donna Karolchik; Arkadiusz Kasprzyk; Jun Kawai; Evan Keibler; Cristyn Kells; W James Kent; Andrew Kirby; Diana L Kolbe; Ian F Korf; Raju S Kucherlapati; Edward J Kulbokas; David Kulp; Tom Landers; J P Leger; Steven Leonard; Ivica Letunic; Rosie Levine; Jia Li; Ming Li; Christine Lloyd; Susan Lucas; Bin Ma; Donna R Maglott; Elaine R Mardis; Lucy Matthews; Evan Mauceli; John H Mayer; Megan McCarthy; W Richard McCombie; Stuart McLaren; Kirsten McLay; John D McPherson; Jim Meldrim; Beverley Meredith; Jill P Mesirov; Webb Miller; Tracie L Miner; Emmanuel Mongin; Kate T Montgomery; Michael Morgan; Richard Mott; James C Mullikin; Donna M Muzny; William E Nash; Joanne O Nelson; Michael N Nhan; Robert Nicol; Zemin Ning; Chad Nusbaum; Michael J O'Connor; Yasushi Okazaki; Karen Oliver; Emma Overton-Larty; Lior Pachter; Genís Parra; Kymberlie H Pepin; Jane Peterson; Pavel Pevzner; Robert Plumb; Craig S Pohl; Alex Poliakov; Tracy C Ponce; Chris P Ponting; Simon Potter; Michael Quail; Alexandre Reymond; Bruce A Roe; Krishna M Roskin; Edward M Rubin; Alistair G Rust; Ralph Santos; Victor Sapojnikov; Brian Schultz; Jörg Schultz; Matthias S Schwartz; Scott Schwartz; Carol Scott; Steven Seaman; Steve Searle; Ted Sharpe; Andrew Sheridan; Ratna Shownkeen; Sarah Sims; Jonathan B Singer; Guy Slater; Arian Smit; Douglas R Smith; Brian Spencer; Arne Stabenau; Nicole Stange-Thomann; Charles Sugnet; Mikita Suyama; Glenn Tesler; Johanna Thompson; David Torrents; Evanne Trevaskis; John Tromp; Catherine Ucla; Abel Ureta-Vidal; Jade P Vinson; Andrew C Von Niederhausern; Claire M Wade; Melanie Wall; Ryan J Weber; Robert B Weiss; Michael Wendl; Anthony P West; Kris Wetterstrand; Raymond Wheeler; Simon Whelan; Jamey Wierzbowski; David Willey; Sophie Williams; Richard K Wilson; Eitan Winter; Kim C Worley; Dudley Wyman; Shan Yang; Shiaw-Pyng Yang; Evgeny M Zdobnov; Michael C Zody; Eric S Lander
Initial sequencing and comparative analysis of the mouse genome.
Nature 2002;420(6915):520-62.
2002: Erich D Jarvis; V Anne Smith; Kazuhiro Wada; Miriam V Rivas; M McElroy; Tom V Smulders; piero carninci; Yoshihide Hayashizaki; Fred S Dietrich; X Wu; Patrick McConnell; Jing Yu; P P Wang; Alexander J Hartemink; Simon Lin
A framework for integrating the songbird brain.
Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology 2002;188(11-12):961-80.
2002: Motoaki Seki; Junko Ishida; Mari Narusaka; Miki Fujita; Tokihiko Nanjo; Taishi Umezawa; Asako Kamiya; Maiko Nakajima; Akiko Enju; Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Kazuko Yamaguchi-Shinozaki; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Kazuo Shinozaki
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.
2002: A Sakurai; Shigeo Fujimori; Hiromi Kochiwa; S Kitamura-Abe; Takanori Washio; Rintaro Saito; piero carninci; Yoshihide Hayashizaki; Masaru Tomita
On biased distribution of introns in various eukaryotes.
Gene 2002;300(1-2):89-95.
2002: Y Ozawa; S Hanaoka; Rintaro Saito; Takanori Washio; S Nakano; A Shinagawa; Masayoshi Itoh; K Shibata; piero carninci; H Konno; Jun Kawai; Yoshihide Hayashizaki; Masaru Tomita
Comprehensive sequence analysis of translation termination sites in various eukaryotes.
Gene 2002;300(1-2):79-87.
2002: piero carninci; M Nakamura; K Sato; Y Hayashizaki; M J Brownstein
Cytoplasmic RNA extraction from fresh and frozen mammalian tissues.
BioTechniques 2002;33(2):306-9.
2002: Mark Stapleton; Guochun Liao; Peter Brokstein; Ling Hong; piero carninci; Toshiyuki Shiraki; Yoshihide Hayashizaki; Mark Champe; Joanne Pacleb; Ken Wan; Charles Yu; Joe Carlson; Reed George; Susan E Celniker; Gerald M Rubin
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes.
Genome research 2002;12(8):1294-300.
2002: Hiromi Kochiwa; Ryosuke Suzuki; Takanori Washio; Rintaro Saito; Hidemasa Bono; piero carninci; Yasushi Okazaki; Rika Miki; Yoshihide Hayashizaki; Masaru Tomita
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data.
Genome research 2002;12(8):1286-93.
2002: Motoaki Seki; Mari Narusaka; Junko Ishida; Tokihiko Nanjo; Miki Fujita; Youko Oono; Asako Kamiya; Maiko Nakajima; Akiko Enju; Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Teruaki Taji; Kazuko Yamaguchi-Shinozaki; piero carninci; Jun Kawai; Yoshihide Hayashizaki; Kazuo Shinozaki
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.
2002: Naoki Osato; Masayoshi Itoh; Hideaki Konno; Shinji Kondo; Kazuhiro Shibata; piero carninci; Toshiyuki Shiraki; Akira Shinagawa; Takahiro Arakawa; Shoshi Kikuchi; Kouji Sato; Jun Kawai; Yoshihide Hayashizaki
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.
2002: piero carninci; T Shiraki; Y Mizuno; M Muramatsu; Y Hayashizaki
Extra-long first-strand cDNA synthesis.
BioTechniques 2002;32(5):984-5.
2002: Motoaki Seki; Mari Narusaka; Asako Kamiya; Junko Ishida; Masakazu Satou; Tetsuya Sakurai; Maiko Nakajima; Akiko Enju; Kenji Akiyama; Youko Oono; Masami Muramatsu; Yoshihide Hayashizaki; Jun Kawai; piero carninci; Masayoshi Itoh; Yoshiyuki Ishii; Takahiro Arakawa; Kazuhiro Shibata; Akira Shinagawa; Kazuo Shinozaki
Functional annotation of a full-length Arabidopsis cDNA collection.
Science (New York, N.Y.) 2002;296(5565):141-5.
2002: Itaru Yamanaka; Hidenori Kiyosawa; Shinji Kondo; Tetsuya Saito; piero carninci; Akira Shinagawa; Katsunori Aizawa; Shiro Fukuda; Ayako Hara; Masayoshi Itoh; Jun Kawai; Kazuhiro Shibata; Takahiro Arakawa; Yoshiyuki Ishii; Yoshihide Hayashizaki
Mapping of 19032 mouse cDNAs on mouse chromosomes.
Journal of structural and functional genomics 2002;2(1):23-8.
2002: Jean-Marie Buerstedde; Hiroshi Arakawa; Akira Watahiki; piero carninci; Y Yoshihide Hayashizaki; Bernhard Korn; Jiri Plachy
The DT40 web site: sampling and connecting the genes of a B cell line.
Nucleic acids research 2002;30(1):230-1.
2001: Y Shibata; piero carninci; K Sato; Norihito Hayatsu; Toshiyuki Shiraki; Y Ishii; Takahiro Arakawa; A Hara; N Ohsato; M Izawa; K Aizawa; Masayoshi Itoh; Kazuhiro Shibata; Akira Shinagawa; Jun Kawai; Y Ota; S Kikuchi; N Kishimoto; Masami Muramatsu; Yoshihide Hayashizaki
Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing.
BioTechniques 2001;31(5):1042, 1044, 1048-9.
2001: H Sakai; Takanori Washio; Rintaro Saito; A Shinagawa; Masayoshi Itoh; K Shibata; piero carninci; H Konno; Jun Kawai; Yoshihide Hayashizaki; Masaru Tomita
Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes.
Gene 2001;276(1-2):101-5.
2001: piero carninci; Y Shibata; Norihito Hayatsu; Masayoshi Itoh; Toshiyuki Shiraki; T Hirozane; Akira Watahiki; Kazuhiro Shibata; Hideaki Konno; Masami Muramatsu; Yoshihide Hayashizaki
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.
2001: Y Shibata; piero carninci; Akira Watahiki; Toshiyuki Shiraki; H Konno; Masami Muramatsu; Yoshihide Hayashizaki
Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method.
BioTechniques 2001;30(6):1250-4.
2001: Rika Miki; Koji Kadota; Hidemasa Bono; Yosuke Mizuno; Yasuhiro Tomaru; piero carninci; Masayoshi Itoh; Kazuhiro Shibata; Jun Kawai; H Konno; S Watanabe; K Sato; Y Tokusumi; N Kikuchi; Y Ishii; Yohei Hamaguchi; Itaru Nishizuka; Hitoshi Goto; Hiroyuki Nitanda; S Satomi; A Yoshiki; M Kusakabe; Joe L DeRisi; Michael B Eisen; Vishwanath R Iyer; P O Brown; Masami Muramatsu; Hiroshi Shimada; Yasushi Okazaki; Yoshihide Hayashizaki
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.
2001: J Kawai; A Shinagawa; K Shibata; M Yoshino; Masayoshi 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; Yasushi Okazaki; Takashi Gojobori; H Bono; T Kasukawa; R Saito; K Kadota; H Matsuda; Michael 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; John Quackenbush; Lynn 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; piero carninci; M F de Bonaldo; M J Brownstein; Carol Bult; C Fletcher; M Fujita; manuela gariboldi; S Gustincich; D Hill; Martin Hofmann-Apitius; D A Hume; M Kamiya; N H Lee; P Lyons; LUIGI MARCHIONNI; J Mashima; J Mazzarelli; P Mombaerts; P Nordone; B Ring; M Ringwald; ivan rodriguez; N Sakamoto; H Sasaki; K Sato; Christian Schönbach; Tsukasa 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; Hideya Kawaji; S Kohtsuki; Y Hayashizaki
Functional annotation of a full-length mouse cDNA collection.
Nature 2001;409(6821):685-90.
2001: Hideaki Konno; Y Fukunishi; Kazuhiro Shibata; Masayoshi Itoh; piero carninci; Y Sugahara; Yoshihide Hayashizaki
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.
2001: Y Sugahara; piero carninci; Masayoshi Itoh; K Shibata; H Konno; T Endo; M Muramatsu; Yoshihide Hayashizaki
Comparative evaluation of 5'-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries.
Gene 2001;263(1-2):93-102.
2001: Motoaki Seki; Mari Narusaka; H Abe; M Kasuga; Kazuko Yamaguchi-Shinozaki; piero carninci; Yoshihide Hayashizaki; Kazuo Shinozaki
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.
2000: K Shibata; M Itoh; K Aizawa; S Nagaoka; N Sasaki; piero carninci; H Konno; J Akiyama; K Nishi; T Kitsunai; H Tashiro; M Itoh; N Sumi; Y Ishii; S Nakamura; M Hazama; T Nishine; A Harada; R Yamamoto; H Matsumoto; S Sakaguchi; T Ikegami; K Kashiwagi; S Fujiwake; K Inoue; Y Togawa
RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.
Genome research 2000;10(11):1757-71.
2000: piero carninci; Y Shibata; Norihito Hayatsu; Y Sugahara; Kazuhiro Shibata; Masayoshi Itoh; Hideaki Konno; Yasushi Okazaki; Masami Muramatsu; Yoshihide Hayashizaki
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.
1999: Masayoshi Itoh; T Kitsunai; J Akiyama; Kazuhiro Shibata; M Izawa; Jun Kawai; Yasuhiro Tomaru; piero carninci; Y Shibata; Y Ozawa; Masami Muramatsu; Yasushi Okazaki; Yoshihide Hayashizaki
Automated filtration-based high-throughput plasmid preparation system.
Genome research 1999;9(5):463-70.
1999: Y Mizuno; piero carninci; Yasushi Okazaki; M Tateno; J Kawai; H Amanuma; M Muramatsu; Yoshihide Hayashizaki
Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display.
Nucleic acids research 1999;27(5):1345-9.
1999: piero carninci; Yoshihide Hayashizaki
High-efficiency full-length cDNA cloning.
Methods in enzymology 1999;303():19-44.
1998: M Seki; piero carninci; Y Nishiyama; Y Hayashizaki; Kazuo Shinozaki
High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper.
The Plant journal : for cell and molecular biology 1998;15(5):707-20.
1998: N Sasaki; S Nagaoka; Masayoshi Itoh; M Izawa; H Konno; piero carninci; A Yoshiki; M Kusakabe; T Moriuchi; M Muramatsu; Yasushi Okazaki; Yoshihide Hayashizaki
Characterization of gene expression in mouse blastocyst using single-pass sequencing of 3995 clones.
Genomics 1998;49(2):167-79.
1998: N Sasaki; M Izawa; Masanori Watahiki; K Ozawa; T Tanaka; Y Yoneda; S Matsuura; piero carninci; M Muramatsu; Yasushi Okazaki; Yoshihide Hayashizaki
Transcriptional sequencing: A method for DNA sequencing using RNA polymerase.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(7):3455-60.
1998: piero carninci; Y Nishiyama; A Westover; Masayoshi Itoh; S Nagaoka; N Sasaki; Yasushi Okazaki; M Muramatsu; Yoshihide Hayashizaki
Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(2):520-4.
1997: N Sasaki; M Izawa; M Shimojo; K Shibata; J Akiyama; Masayoshi Itoh; S Nagaoka; piero carninci; Yasushi Okazaki; T Moriuchi; M Muramatsu; S Watanabe; Yoshihide Hayashizaki
A novel control system for polymerase chain reaction using a RIKEN GS384 thermalcycler.
DNA research : an international journal for rapid publication of reports on genes and genomes 1997;4(6):387-91.
1997: Y Nishiyama; piero carninci; S Yoneya; Yoshihide Hayashizaki
[New approach for an analysis of full-length cDNA library].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 1997;42(17 Suppl):2858-63.
1997: Masayoshi Itoh; piero carninci; S Nagaoka; N Sasaki; Yasushi Okazaki; T Ohsumi; M Muramatsu; Yoshihide Hayashizaki
Simple and rapid preparation of plasmid template by a filtration method using microtiter filter plates.
Nucleic acids research 1997;25(6):1315-6.
1997: piero carninci; A Westover; Y Nishiyama; T Ohsumi; Masayoshi Itoh; S Nagaoka; N Sasaki; Yasushi Okazaki; M Muramatsu; C Schneider; Yoshihide Hayashizaki
High efficiency selection of full-length cDNA by improved biotinylated cap trapper.
DNA research : an international journal for rapid publication of reports on genes and genomes 1997;4(1):61-6.
1996: piero carninci; C Kvam; A Kitamura; T Ohsumi; Yasushi Okazaki; Masayoshi Itoh; M Kamiya; K Shibata; N Sasaki; M Izawa; M Muramatsu; Yoshihide Hayashizaki; C Schneider
High-efficiency full-length cDNA cloning by biotinylated CAP trapper.
Genomics 1996;37(3):327-36.
1995: piero carninci; F Volpatti; C Schneider
A discontinuous buffer system increasing resolution and reproducibility in DNA sequencing on high voltage horizontal ultrathin-layer electrophoresis.
Electrophoresis 1995;16(10):1836-45.
1991: S Gustincich; G Manfioletti; Giannino Del Sal; Claudio Schneider; piero carninci
A fast method for high-quality genomic DNA extraction from whole human blood.
BioTechniques 1991;11(3):298-300, 302.
1990: piero carninci; S Gustincich; S Bottega; C Patrosso; Giannino Del Sal; G Manfioletti; Claudio Schneider
A simple discontinuous buffer system for increased resolution and speed in gel electrophoretic analysis of DNA sequence.
Nucleic acids research 1990;18(1):204.