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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

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

Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs

Severin Berger
Mikhail Pachkov
Phil Arnold
Saeed Omidi
Nicholas Kelley
Silvia Salatino
Erik van Nimwegen

First Published May 28, 2019

The frequent evolutionary birth and death of functional promoters in mouse and human

Robert S. Young
Yoshihide Hayashizaki
Robin Andersson
Albin Sandelin
Hideya Kawaji
Masayoshi Itoh Timo Lassmann
... [+2 authors] ...,
Piero Carninci
Wendy A. Bickmore
Alistair R. Forrest
Martin S. Taylor

First Published July 30, 2015

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

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

Piotr J. Balwierz
Mikhail Pachkov
Phil Arnold
Andreas J. Gruber
Mihaela Zavolan
Erik van Nimwegen

First Published February 10, 2014

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

Phil Arnold
Anne Schöler
Mikhail Pachkov
Piotr J. Balwierz
Helle Jørgensen
Michael B. Stadler
Erik van Nimwegen
Dirk Schübeler

First Published September 10, 2012

Promoter architecture of mouse olfactory receptor genes

Charles Plessy
Giovanni Pascarella
Nicolas Bertin
Altuna Akalin
Claudia Carrieri
Anne Vassalli Dejan Lazarevic Jessica Severin Christina Vlachouli Roberto Simone Geoffrey J. Faulkner Jun Kawai Carsten O. Daub Silvia Zucchelli Yoshihide Hayashizaki
... [+10 authors] ...,
Peter Mombaerts
Boris Lenhard
Stefano Gustincich
Piero Carninci

First Published December 22, 2011

Unamplified cap analysis of gene expression on a single-molecule sequencer

Mutsumi Kanamori-Katayama
Masayoshi Itoh
Hideya Kawaji
Timo Lassmann
Shintaro Katayama
Miki Kojima Nicolas Bertin Ai Kaiho Noriko Ninomiya
... [+4 authors] ...,
Carsten O. Daub
Piero Carninci
Alistair R.R. Forrest
Yoshihide Hayashizaki

First Published May 19, 2011

A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness

A. Maxwell Burroughs
Yoshinari Ando
Michiel J.L. de Hoon
Yasuhiro Tomaru
Takahiro Nishibu
Ryo Ukekawa Taku Funakoshi
... [+2 authors] ...,
Tsutomu Kurokawa
Harukazu Suzuki
Yoshihide Hayashizaki
Carsten O. Daub

First Published August 18, 2010

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