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Method

Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs

  • Michiel de Hoon
  • Alessandro Bonetti
  • Charles Plessy
  • Yoshinari Ando
  • Chung-Chau Hon
  • Yuri Ishizu Masayoshi Itoh Sachi Kato Dongyan Lin Sho Maekawa Mitsuyoshi Murata Hiromi Nishiyori Jay W. Shin Jens Stolte Ana Maria Suzuki Michihira Tagami Hazuki Takahashi Supat Thongjuea
  • ... [+13 authors] ...,
  • Alistair R.R. Forrest
  • Yoshihide Hayashizaki
  • Juha Kere
  • Piero Carninci
  • First Published August 12, 2022
Corrigendum

Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

  • Jordan A. Ramilowski
  • Chi Wai Yip
  • Saumya Agrawal
  • Jen-Chien Chang
  • Yari Ciani
  • Ivan V. Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F. Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V. Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher J.F. Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L. Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S. Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J. Makeev Luigi Marchionni Yulia A. Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R. Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J.C. Parr Owen J.L. Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A.M. Semple Youtaro Shibayama Divya M. Sivaraman Takahiro Suzuki Suzannah C. Szumowski Michihira Tagami Martin S. Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E. Vorontsov Chinatsu Yamamoto Robert S. Young J. Kenneth Baillie Alistair R.R. Forrest Roderic Guigó Michael M. Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki
  • ... [+107 authors] ...,
  • Ken Yagi
  • Michiel J.L. de Hoon
  • Jay W. Shin
  • Piero Carninci
  • First Published September 14, 2020
Resource

Functional annotation of human long noncoding RNAs via molecular phenotyping

  • Jordan A. Ramilowski
  • Chi Wai Yip
  • Saumya Agrawal
  • Jen-Chien Chang
  • Yari Ciani
  • Ivan V. Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F. Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V. Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher J.F. Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L. Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S. Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J. Makeev Luigi Marchionni Yulia A. Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R. Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J.C. Parr Owen J.L. Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A.M. Semple Youtaro Shibayama Divya M. Sivaraman Takahiro Suzuki Suzannah C. Szumowski Michihira Tagami Martin S. Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E. Vorontsov Chinatsu Yamamoto Robert S. Young J. Kenneth Baillie Alistair R.R. Forrest Roderic Guigó Michael M. Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki
  • ... [+107 authors] ...,
  • Ken Yagi
  • Michiel J.L. de Hoon
  • Jay W. Shin
  • Piero Carninci
  • First Published July 27, 2020
Research

Comparative transcriptomics of primary cells in vertebrates

  • Tanvir Alam
  • Saumya Agrawal
  • Jessica Severin
  • Robert S. Young
  • Robin Andersson
  • Erik Arner Akira Hasegawa Marina Lizio Jordan A. Ramilowski Imad Abugessaisa Yuri Ishizu Shohei Noma Hiroshi Tarui Martin S. Taylor Timo Lassmann Masayoshi Itoh Takeya Kasukawa Hideya Kawaji Luigi Marchionni Guojun Sheng Alistair R.R. Forrest
  • ... [+16 authors] ...,
  • Levon M. Khachigian
  • Yoshihide Hayashizaki
  • Piero Carninci
  • Michiel J.L. de Hoon
  • First Published July 27, 2020
Research

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

  • Kosuke Hashimoto
  • Ana Maria Suzuki
  • Alexandre Dos Santos
  • Christophe Desterke
  • Agnese Collino
  • Serena Ghisletti Emilie Braun Alessandro Bonetti Alexandre Fort Xian-Yang Qin Enrico Radaelli Bogumil Kaczkowski Alistair R.R. Forrest Soichi Kojima Didier Samuel
  • ... [+10 authors] ...,
  • Gioacchino Natoli
  • Marie Annick Buendia
  • Jamila Faivre
  • Piero Carninci
  • First Published October 28, 2015
Method

Read clouds uncover variation in complex regions of the human genome

  • Alex Bishara
  • Yuling Liu
  • Ziming Weng
  • Dorna Kashef-Haghighi
  • Daniel E. Newburger
  • Robert West
  • Arend Sidow
  • Serafim Batzoglou
  • First Published August 18, 2015
Method

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

  • Hideya Kawaji
  • Marina Lizio
  • Masayoshi Itoh
  • Mutsumi Kanamori-Katayama
  • Ai Kaiho
  • Hiromi Nishiyori-Sueki Jay W. Shin Miki Kojima-Ishiyama Mitsuoki Kawano Mitsuyoshi Murata Noriko Ninomiya-Fukuda Sachi Ishikawa-Kato Sayaka Nagao-Sato
  • ... [+8 authors] ...,
  • Shohei Noma
  • Yoshihide Hayashizaki
  • Alistair R.R. Forrest
  • Piero Carninci
  • First Published March 27, 2014
Method

Discovery of recurrent structural variants in nasopharyngeal carcinoma

  • Anton Valouev
  • Ziming Weng
  • Robert T. Sweeney
  • Sushama Varma
  • Quynh-Thu Le
  • Christina Kong
  • Arend Sidow
  • Robert B. West
  • First Published November 8, 2013
Research

Genome evolution during progression to breast cancer

  • Daniel E. Newburger
  • Dorna Kashef-Haghighi
  • Ziming Weng
  • Raheleh Salari
  • Robert T. Sweeney
  • Alayne L. Brunner Shirley X. Zhu Xiangqian Guo Sushama Varma
  • ... [+4 authors] ...,
  • Megan L. Troxell
  • Robert B. West
  • Serafim Batzoglou
  • Arend Sidow
  • First Published April 8, 2013
Research

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

  • Stephen B. Montgomery
  • David L. Goode
  • Erika Kvikstad
  • Cornelis A. Albers
  • Zhengdong D. Zhang
  • Xinmeng Jasmine Mu Guruprasad Ananda Bryan Howie Konrad J. Karczewski Kevin S. Smith Vanessa Anaya Rhea Richardson Joe Davis Daniel G. MacArthur Arend Sidow Laurent Duret Mark Gerstein
  • ... [+12 authors] ...,
  • Kateryna D. Makova
  • Jonathan Marchini
  • Gil McVean
  • Gerton Lunter
  • First Published March 11, 2013
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