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3C sites in poly(A) RNA" > Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA

Shuhei Mitsutomi
Anzu Sugawara
Masahide Seki
Yutaka Suzuki
Sotaro Miyao
Haozhe Du
... [+1 authors] ...,
Kenji Takahashi
Yusuke Mizukami
Kenzui Taniue
Nobuyoshi Akimitsu

First Published October 30, 2025

Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq

Alejandro Paniagua
Cristina Agustín-García
Francisco J. Pardo-Palacios
Thomas Brown
Maite De Maria
Nancy D. Denslow
Camila J. Mazzoni
Ana Conesa

First Published December 23, 2024

Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data

Kaixuan Luo
Jianling Zhong
Alexias Safi
Linda K. Hong
Alok K. Tewari
Lingyun Song
... [+1 authors] ...,
Timothy E. Reddy
Li Ma
Gregory E. Crawford
Alexander J. Hartemink

First Published May 24, 2022

Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants

Kazumasa Shirai
Mitsuhiko P. Sato
Ranko Nishi
Masahide Seki
Yutaka Suzuki
Kousuke Hanada

First Published May 18, 2021

Long-read sequencing for non-small-cell lung cancer genomes

Yoshitaka Sakamoto
Liu Xu
Masahide Seki
Toshiyuki T. Yokoyama
Masahiro Kasahara
Yukie Kashima Akihiro Ohashi Yoko Shimada Noriko Motoi Katsuya Tsuchihara Susumu S. Kobayashi
... [+6 authors] ...,
Takashi Kohno
Yuichi Shiraishi
Ayako Suzuki
Yutaka Suzuki

First Published September 4, 2020

Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates

Kentaro Kawata
Hiroyasu Wakida
Toshimichi Yamada
Kenzui Taniue
Han Han
Masahide Seki
Yutaka Suzuki
Nobuyoshi Akimitsu

First Published August 25, 2020

cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants" > Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants

Dongwon Lee
Ashish Kapoor
Alexias Safi
Lingyun Song
Marc K. Halushka
Gregory E. Crawford
Aravinda Chakravarti

First Published August 23, 2018

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

Ian C. McDowell
Alejandro Barrera
Anthony M. D'Ippolito
Christopher M. Vockley
Linda K. Hong
Sarah M. Leichter Luke C. Bartelt William H. Majoros Lingyun Song Alexias Safi D. Dewran Koçak Charles A. Gersbach
... [+7 authors] ...,
Alexander J. Hartemink
Gregory E. Crawford
Barbara E. Engelhardt
Timothy E. Reddy

First Published August 10, 2018

Plasmodium falciparum" > Corrigendum: Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum

Junya Yamagishi
Anna Natori
Mohammed E.M. Tolba
Arthur E. Mongan
Chihiro Sugimoto
Toshiaki Katayama Shuichi Kawashima Wojciech Makalowski
... [+3 authors] ...,
Ryuichiro Maeda
Yuki Eshita
Josef Tuda
Yutaka Suzuki

First Published August 1, 2018

Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

Juan L. Mateo
Debbie L.C. van den Berg
Maximilian Haeussler
Daniela Drechsel
Zachary B. Gaber
Diogo S. Castro Paul Robson Q. Richard Lu Gregory E. Crawford Paul Flicek
... [+5 authors] ...,
Laurence Ettwiller
Joachim Wittbrodt
François Guillemot
Ben Martynoga

First Published December 1, 2017

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