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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

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

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

Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes

Vedran Franke
Sravya Ganesh
Rosa Karlic
Radek Malik
Josef Pasulka
Filip Horvat Maja Kuzman Helena Fulka Marketa Cernohorska Jana Urbanova Eliska Svobodova Jun Ma Yutaka Suzuki
... [+8 authors] ...,
Fugaku Aoki
Richard M. Schultz
Kristian Vlahovicek
Petr Svoboda

First Published May 18, 2017

A GC-rich sequence feature in the 3′ UTR directs UPF1-dependent mRNA decay in mammalian cells

Naoto Imamachi
Kazi Abdus Salam
Yutaka Suzuki
Nobuyoshi Akimitsu

First Published December 9, 2016

Callithrix jacchus genome" > Discovery of a new repeat family in the Callithrix jacchus genome

Miriam K. Konkel
Brygg Ullmer
Erika L. Arceneaux
Sreeja Sanampudi
Sarah A. Brantley
Robert Hubley
Arian F.A. Smit
Mark A. Batzer

First Published February 25, 2016

Ciona intestinalis" > Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis

Rui Yokomori
Kotaro Shimai
Koki Nishitsuji
Yutaka Suzuki
Takehiro G. Kusakabe
Kenta Nakai

First Published December 14, 2015

Plasmodium falciparum" > 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 4, 2014

Coelacanth genomes reveal signatures for evolutionary transition from water to land

Masato Nikaido
Hideki Noguchi
Hidenori Nishihara
Atsushi Toyoda
Yutaka Suzuki
Rei Kajitani Hikoyu Suzuki Miki Okuno Mitsuto Aibara Benjamin P. Ngatunga Semvua I. Mzighani Hassan W.J. Kalombo Kawilarang W.A. Masengi Josef Tuda Sadao Nogami Ryuichiro Maeda Masamitsu Iwata Yoshitaka Abe Koji Fujimura Masataka Okabe Takanori Amano Akiteru Maeno Toshihiko Shiroishi Takehiko Itoh
... [+19 authors] ...,
Sumio Sugano
Yuji Kohara
Asao Fujiyama
Norihiro Okada

First Published July 22, 2013

Alu insertions in diverse human populations" > Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations

David J. Witherspoon
Yuhua Zhang
Jinchuan Xing
W. Scott Watkins
Hongseok Ha
Mark A. Batzer
Lynn B. Jorde

First Published April 18, 2013

High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice

Hisato Kobayashi
Takayuki Sakurai
Fumihito Miura
Misaki Imai
Kentaro Mochiduki
Eikichi Yanagisawa Akihiko Sakashita Takuya Wakai
... [+3 authors] ...,
Yutaka Suzuki
Takashi Ito
Yasuhisa Matsui
Tomohiro Kono

First Published February 14, 2013

Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns

Wei Qu
Shin-ichi Hashimoto
Atsuko Shimada
Yoichiro Nakatani
Kazuki Ichikawa
Taro L. Saito Katsumi Ogoshi Kouji Matsushima
... [+3 authors] ...,
Yutaka Suzuki
Sumio Sugano
Hiroyuki Takeda
Shinichi Morishita

First Published June 11, 2012

Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

Hidenori Tani
Rena Mizutani
Kazi Abdus Salam
Keiko Tano
Kenichi Ijiri
Ai Wakamatsu
Takao Isogai
Yutaka Suzuki
Nobuyoshi Akimitsu

First Published February 27, 2012

Reading TE leaves: New approaches to the identification of transposable element insertions

David A. Ray
Mark A. Batzer

First Published June 1, 2011

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

Riu Yamashita
Nuankanya P. Sathira
Akinori Kanai
Kousuke Tanimoto
Takako Arauchi
Yoshiaki Tanaka
... [+1 authors] ...,
Shin-ichi Hashimoto
Sumio Sugano
Kenta Nakai
Yutaka Suzuki

First Published March 3, 2011

Nucleotide composition-linked divergence of vertebrate core promoter architecture

Simon J. van Heeringen
Waseem Akhtar
Ulrike G. Jacobi
Robert C. Akkers
Yutaka Suzuki
Gert Jan C. Veenstra

First Published January 10, 2011

5′-Transducing SVA retrotransposon groups spread efficiently throughout the human genome

Annette Damert
Julija Raiz
Axel V. Horn
Johannes Löwer
Hui Wang
Jinchuan Xing
Mark A. Batzer
Roswitha Löwer
Gerald G. Schumann

First Published August 3, 2009

Mobile elements create structural variation: Analysis of a complete human genome

Jinchuan Xing
Yuhua Zhang
Kyudong Han
Abdel Halim Salem
Shurjo K. Sen
Chad D. Huff Qiong Zhou
... [+2 authors] ...,
Ewen F. Kirkness
Samuel Levy
Mark A. Batzer
Lynn B. Jorde

First Published May 13, 2009

Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes

Katsuki Tsuritani
Takuma Irie
Riu Yamashita
Yuta Sakakibara
Hiroyuki Wakaguri
Akinori Kanai
... [+1 authors] ...,
Junko Mizushima-Sugano
Sumio Sugano
Kenta Nakai
Yutaka Suzuki

First Published June 13, 2007

Monodelphis domestica" > Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica

Andrew J. Gentles
Matthew J. Wakefield
Oleksiy Kohany
Wanjun Gu
Mark A. Batzer
David D. Pollock
Jerzy Jurka

First Published May 10, 2007

Toxoplasma gondii" > Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii

Asis Khan
Ulrike Böhme
Krystyna A. Kelly
Ellen Adlem
Karen Brooks
Mark Simmonds Karen Mungall Michael A. Quail Claire Arrowsmith Tracey Chillingworth Carol Churcher David Harris Matthew Collins Nigel Fosker Audrey Fraser Zahra Hance Kay Jagels Sharon Moule Lee Murphy Susan O'Neil Marie-Adele Rajandream David Saunders Kathy Seeger Sally Whitehead Thomas Mayr Xuenan Xuan Junichi Watanabe Yutaka Suzuki Hiroyuki Wakaguri Sumio Sugano Chihiro Sugimoto Ian Paulsen Aaron J. Mackey David S. Roos Neil Hall
... [+30 authors] ...,
Matthew Berriman
Bart Barrell
L. David Sibley
James W. Ajioka

First Published August 10, 2006

Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes

Kouichi Kimura
Ai Wakamatsu
Yutaka Suzuki
Toshio Ota
Tetsuo Nishikawa
Riu Yamashita Jun-ichi Yamamoto Mitsuo Sekine Katsuki Tsuritani Hiroyuki Wakaguri Shizuko Ishii Tomoyasu Sugiyama Kaoru Saito Yuko Isono Ryotaro Irie Norihiro Kushida Takahiro Yoneyama Rie Otsuka Katsuhiro Kanda Takahide Yokoi Hiroshi Kondo Masako Wagatsuma Katsuji Murakawa Shinichi Ishida Tadashi Ishibashi Asako Takahashi-Fujii Tomoo Tanase Keiichi Nagai
... [+23 authors] ...,
Hisashi Kikuchi
Kenta Nakai
Takao Isogai
Sumio Sugano

First Published December 12, 2005

Alu amplification" > Under the genomic radar: The Stealth model of Alu amplification

Kyudong Han
Jinchuan Xing
Hui Wang
Dale J. Hedges
Randall K. Garber
Richard Cordaux
Mark A. Batzer

First Published May 2, 2005

Analysis of Small Human Proteins Reveals the Translation of Upstream Open Reading Frames of mRNAs

Masaaki Oyama
Chiharu Itagaki
Hiroko Hata
Yutaka Suzuki
Tomonori Izumi
Tohru Natsume
Toshiaki Isobe
Sumio Sugano

First Published October 15, 2004

Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions

Yutaka Suzuki
Riu Yamashita
Matsuyuki Shirota
Yuta Sakakibara
Joe Chiba
Junko Mizushima-Sugano
Kenta Nakai
Sumio Sugano

First Published September 1, 2004

Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages" > Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages

Dale J. Hedges
Pauline A. Callinan
Richard Cordaux
Jinchuan Xing
Erin Barnes
Mark A. Batzer

First Published June 1, 2004

Alu Insertion Polymorphisms" > Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms

W. Scott Watkins
Alan R. Rogers
Christopher T. Ostler
Steve Wooding
Michael J. Bamshad
Anna-Marie E. Brassington Marion L. Carroll Son V. Nguyen Jerilyn A. Walker B.V. Ravi Prasad
... [+5 authors] ...,
P. Govinda Reddy
Pradipta K. Das
Mark A. Batzer
Lynn B. Jorde

First Published June 12, 2003

Y Chromosome STR Haplotypes and the Genetic Structure of U.S. Populations of African, European, and Hispanic Ancestry

Manfred Kayser
Silke Brauer
Hiltrud Schädlich
Mechthild Prinz
Mark A. Batzer
Peter A. Zimmerman
B. A. Boatin
Mark Stoneking

First Published April 1, 2003

Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation" > Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation

Melody S. Clark
Yvonne J.K. Edwards
Dan Peterson
Sandra W. Clifton
Amanda J. Thompson
Masahide Sasaki Yutaka Suzuki Kiyoshi Kikuchi Shugo Watabe
... [+4 authors] ...,
Koichi Kawakami
Sumio Sugano
Greg Elgar
Stephen L. Johnson

First Published January 1, 2003

Mammalian Retroelements

Prescott L. Deininger
Mark A. Batzer

First Published October 1, 2002

Active Alu Element “A-Tails”: Size Does Matter

Astrid M. Roy-Engel
Abdel-Halim Salem
Oluwatosin O. Oyeniran
Lisa Deininger
Dale J. Hedges
Gail E. Kilroy
Mark A. Batzer
Prescott L. Deininger

First Published August 21, 2002

Patterns of Human Diversity, within and among Continents, Inferred from Biallelic DNA Polymorphisms

Chiara Romualdi
David Balding
Ivane S. Nasidze
Gregory Risch
Myles Robichaux
Stephen T. Sherry
Mark Stoneking
Mark A. Batzer
Guido Barbujani

First Published April 1, 2002

Genetic Evidence on the Origins of Indian Caste Populations

Michael Bamshad
Toomas Kivisild
W. Scott Watkins
Mary E. Dixon
Chris E. Ricker
Baskara B. Rao J. Mastan Naidu B.V. Ravi Prasad P. Govinda Reddy Arani Rasanayagam Surinder S. Papiha Richard Villems Alan J. Redd Michael F. Hammer
... [+9 authors] ...,
Son V. Nguyen
Marion L. Carroll
Mark A. Batzer
Lynn B. Jorde

First Published May 8, 2001

Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes

Yutaka Suzuki
Tatsuhiko Tsunoda
Jun Sese
Hirotoshi Taira
Junko Mizushima-Sugano
Hiroko Hata Toshio Ota Takao Isogai Toshihiro Tanaka Yusuke Nakamura Akira Suyama
... [+6 authors] ...,
Yoshiyuki Sakaki
Shinichi Morishita
Kousaku Okubo
Sumio Sugano

First Published April 11, 2001

CART Classification of Human 5′ UTR Sequences

Ramana V. Davuluri
Yutaka Suzuki
Sumio Sugano
Michael Q. Zhang

First Published November 8, 2000

Potential Gene Conversion and Source Genes for Recently Integrated Alu Elements

Astrid M. Roy
Marion L. Carroll
Son V. Nguyen
Abdel-Halim Salem
Michael Oldridge
Andrew O. M. Wilkie
Mark A. Batzer
Prescott L. Deininger

First Published October 1, 2000

Reading between the LINEs: Human Genomic Variation Induced by LINE-1 Retrotransposition

Fang-miin Sheen
Stephen T. Sherry
Gregory M. Risch
Myles Robichaux
Ivane Nasidze
Mark Stoneking
Mark A. Batzer
Gary D. Swergold

First Published October 1, 2000

AluInsertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa " > AluInsertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa

Mark Stoneking
Jennifer J. Fontius
Stephanie L. Clifford
Himla Soodyall
Santosh S. Arcot
Nilmani Saha
... [+1 authors] ...,
Trefor Jenkins
Mohammad A. Tahir
Prescott L. Deininger
Mark A. Batzer

First Published November 1, 1997

Modeling Human Evolution—To Tree or Not to Tree?

Stephen T. Sherry
Mark A. Batzer

First Published October 1, 1997