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Research

Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved

Yang Li
Jianzhi Zhang

First Published February 18, 2025

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

Nascent RNA folding mitigates transcription-associated mutagenesis

Xiaoshu Chen
Jian-Rong Yang
Jianzhi Zhang

First Published October 30, 2015

Research

Genomic evidence for adaptation by gene duplication

Wenfeng Qian
Jianzhi Zhang

First Published June 5, 2014

LETTER

Evolutionary dynamics of nematode operons: Easy come, slow go

Wenfeng Qian
Jianzhi Zhang

First Published January 24, 2008

LETTER

Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land

Peng Shi
Jianzhi Zhang

First Published January 8, 2007

LETTER

Evolution of the complementary sex-determination gene of honey bees: Balancing selection and trans-species polymorphisms

Soochin Cho
Zachary Y. Huang
Daniel R. Green
Deborah R. Smith
Jianzhi Zhang

First Published October 25, 2006

LETTER

Testing the Chromosomal Speciation Hypothesis for Humans and Chimpanzees

Jianzhi Zhang
Xiaoxia Wang
Ondrej Podlaha

First Published May 3, 2004

LETTER

The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment

Sean M. Grimmond
Kevin C. Miranda
Zheng Yuan
Melissa J. Davis
David A. Hume
Ken Yagi Naoko Tominaga
... [+2 authors] ...,
Hidemasa Bono
Yoshihide Hayashizaki
Yasushi Okazaki
Rohan D. Teasdale

First Published June 2, 2003

LETTER

Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage

Christine A. Wells
Timothy Ravasi
Razvan Sultana
Ken Yagi
Piero Carninci
Hidemasa Bono Geoffrey Faulkner
... [+2 authors] ...,
Yasushi Okazaki
John Quackenbush
David A. Hume
Paul A. Lyons

First Published June 2, 2003

COMMENTARY

A Guide to the Mammalian Genome

Yasushi Okazaki
David A. Hume

First Published June 2, 2003

LETTER

Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays

Hidemasa Bono
Ken Yagi
Takeya Kasukawa
Itoshi Nikaido
Naoko Tominaga
Rika Miki Yosuke Mizuno Yasuhiro Tomaru Hitoshi Goto Hiroyuki Nitanda Daisuke Shimizu Hirochika Makino Tomoyuki Morita Junshin Fujiyama Takehito Sakai
... [+10 authors] ...,
Takashi Shimoji
David A. Hume
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

LETTER

Comprehensive Analysis of the Mouse Metabolome Based on the Transcriptome

Hidemasa Bono
Itoshi Nikaido
Takeya Kasukawa
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

RESOURCE

Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System

Takeya Kasukawa
Masaaki Furuno
Itoshi Nikaido
Hidemasa Bono
David A. Hume
Carol Bult David P. Hill Richard Baldarelli Julian Gough Alexander Kanapin Hideo Matsuda
... [+6 authors] ...,
Lynn M. Schriml
Yoshihide Hayashizaki
Yasushi Okazaki
John Quackenbush

First Published June 2, 2003

LETTER

CDS Annotation in Full-Length cDNA Sequence

Masaaki Furuno
Takeya Kasukawa
Rintaro Saito
Jun Adachi
Harukazu Suzuki
Richard Baldarelli
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

Methods

Human Disease Genes and Their Cloned Mouse Orthologs: Exploration of the FANTOM2 cDNA Sequence Data Set

Lynn M. Schriml
David P. Hill
Judith A. Blake
Hidemasa Bono
Anthony Wynshaw-Boris
William J. Pavan
... [+1 authors] ...,
Brian Z. Ring
Kirk Beisel
Mitsutoshi Setou
Yasushi Okazaki

First Published June 2, 2003

LETTER

Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System

Stefano Gustincich
Serge Batalov
Kirk W. Beisel
Hidemasa Bono
Piero Carninci
Colin F. Fletcher Sean Grimmond Nobutaka Hirokawa Erich D. Jarvis Tim Jegla Yuka Kawasawa Julianna LeMieux Harukata Miki Elio Raviola Rohan D. Teasdale Naoko Tominaga
... [+11 authors] ...,
Ken Yagi
Andreas Zimmer
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

LETTER

Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling

Itoshi Nikaido
Chika Saito
Yosuke Mizuno
Makiko Meguro
Hidemasa Bono
Moritoshi Kadomura Tomohiro Kono Gerard A. Morris
... [+3 authors] ...,
Paul A. Lyons
Mitsuo Oshimura
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

ARTICLE

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

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 Camper Junji Hirota Peter Mombaerts
... [+38 authors] ...,
Masami Muramatsu
Yasushi Okazaki
Jun Kawai
Yoshihide Hayashizaki

First Published June 2, 2003

RESOURCE

Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data

Hiromi Kochiwa
Ryosuke Suzuki
Takanori Washio
Rintaro Saito
The RIKEN Genome Exploration Research Group Phase
Hidemasa Bono Piero Carninci
... [+2 authors] ...,
Yasushi Okazaki
Rika Miki
Yoshihide Hayashizaki
Masaru Tomita

First Published July 19, 2002

LETTER

Exploration of Novel Motifs Derived from Mouse cDNA Sequences

Hideya Kawaji
Christian Schönbach
Yo Matsuo
Jun Kawai
Yasushi Okazaki
Yoshihide Hayashizaki
Hideo Matsuda

First Published February 15, 2002

METHODS

Protein–Protein Interaction Panel Using Mouse Full-Length cDNAs

Harukazu Suzuki
Yoshifumi Fukunishi
Ikuko Kagawa
Rintaro Saito
Hiroshi Oda
Toshinori Endo
... [+1 authors] ...,
Shinji Kondo
Hidemasa Bono
Yasushi Okazaki
Yoshihide Hayashizaki

First Published September 20, 2001

LETTER

RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

Kazuhiro Shibata
Masayoshi Itoh
Katsunori Aizawa
Sumiharu Nagaoka
Nobuya Sasaki
Piero Carninci Hideaki Konno Junichi Akiyama Katsuo Nishi Tokuji Kitsunai Hideo Tashiro Mari Itoh Noriko Sumi Yoshiyuki Ishii Shin Nakamura Makoto Hazama Tsutomu Nishine Akira Harada Rintaro Yamamoto Hiroyuki Matsumoto Sumito Sakaguchi Takashi Ikegami Katsuya Kashiwagi Syuji Fujiwake Kouji Inoue Yoshiyuki Togawa Masaki Izawa Eiji Ohara Masanori Watahiki Yuko Yoneda Tomokazu Ishikawa Kaori Ozawa Takumi Tanaka Shuji Matsuura Jun Kawai Yasushi Okazaki
... [+31 authors] ...,
Masami Muramatsu
Yorinao Inoue
Akira Kira
Yoshihide Hayashizaki

First Published November 1, 2000

METHODS

Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes

Piero Carninci
Yuko Shibata
Norihito Hayatsu
Yuichi Sugahara
Kazuhiro Shibata
Masayoshi Itoh
... [+1 authors] ...,
Hideaki Konno
Yasushi Okazaki
Masami Muramatsu
Yoshihide Hayashizaki

First Published October 1, 2000

LETTER

Automated Filtration-Based High-Throughput Plasmid Preparation System

Masayoshi Itoh
Tokuji Kitsunai
Junichi Akiyama
Kazuhiro Shibata
Masaki Izawa
Jun Kawai Yasuhiro Tomaru Piero Carninci Yuko Shibata
... [+4 authors] ...,
Yasuhiro Ozawa
Masami Muramatsu
Yasushi Okazaki
Yoshihide Hayashizaki

First Published May 1, 1999

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