Search | Genome Research

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

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

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

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Chao Cheng
Roger Alexander
Renqiang Min
Jing Leng
Kevin Y. Yip
Joel Rozowsky Koon-Kiu Yan Xianjun Dong Sarah Djebali Yijun Ruan Carrie A. Davis Piero Carninci Timo Lassman Thomas R. Gingeras Roderic Guigó
... [+10 authors] ...,
Ewan Birney
Zhiping Weng
Michael Snyder
Mark Gerstein

First Published September 5, 2012

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

Jie Wang
Jiali Zhuang
Sowmya Iyer
XinYing Lin
Troy W. Whitfield
Melissa C. Greven Brian G. Pierce Xianjun Dong Anshul Kundaje Yong Cheng Oliver J. Rando Ewan Birney
... [+7 authors] ...,
Richard M. Myers
William S. Noble
Michael Snyder
Zhiping Weng

First Published September 5, 2012

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

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

Bum-Kyu Lee
Akshay A. Bhinge
Anna Battenhouse
Ryan M. McDaniell
Zheng Liu
Lingyun Song Yunyun Ni Ewan Birney
... [+3 authors] ...,
Jason D. Lieb
Terrence S. Furey
Gregory E. Crawford
Vishwanath R. Iyer

First Published November 16, 2011

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

Lingyun Song
Zhancheng Zhang
Linda L. Grasfeder
Alan P. Boyle
Paul G. Giresi
Bum-Kyu Lee Nathan C. Sheffield Stefan Gräf Mikael Huss Damian Keefe Zheng Liu Darin London Ryan M. McDaniell Yoichiro Shibata Kimberly A. Showers Jeremy M. Simon Teresa Vales Tianyuan Wang Deborah Winter Zhuzhu Zhang Neil D. Clarke Ewan Birney
... [+17 authors] ...,
Vishwanath R. Iyer
Gregory E. Crawford
Jason D. Lieb
Terrence S. Furey

First Published July 12, 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

Efficient storage of high throughput DNA sequencing data using reference-based compression

Markus Hsi-Yang Fritz
Rasko Leinonen
Guy Cochrane
Ewan Birney

First Published January 18, 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

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

Alan P. Boyle
Lingyun Song
Bum-Kyu Lee
Darin London
Damian Keefe
Ewan Birney
Vishwanath R. Iyer
Gregory E. Crawford
Terrence S. Furey

First Published November 24, 2010

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

Santosh S. Atanur
İnanç Birol
Victor Guryev
Martin Hirst
Oliver Hummel
Catherine Morrissey Jacques Behmoaras Xose M. Fernandez-Suarez Michelle D. Johnson William M. McLaren Giannino Patone Enrico Petretto Charles Plessy Kathleen S. Rockland Charles Rockland Kathrin Saar Yongjun Zhao Piero Carninci Paul Flicek Ted Kurtz Edwin Cuppen Michal Pravenec
... [+17 authors] ...,
Norbert Hubner
Steven J.M. Jones
Ewan Birney
Timothy J. Aitman

First Published April 29, 2010

An effective model for natural selection in promoters

Michael M. Hoffman
Ewan Birney

First Published March 1, 2010

A new strategy for genome assembly using short sequence reads and reduced representation libraries

Andrew L. Young
Hatice Ozel Abaan
Daniel Zerbino
James C. Mullikin
Ewan Birney
Elliott H. Margulies

First Published February 1, 2010

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

Kim D. Pruitt
Jennifer Harrow
Rachel A. Harte
Craig Wallin
Mark Diekhans
Donna R. Maglott Steve Searle Catherine M. Farrell Jane E. Loveland Barbara J. Ruef Elizabeth Hart Marie-Marthe Suner Melissa J. Landrum Bronwen Aken Sarah Ayling Robert Baertsch Julio Fernandez-Banet Joshua L. Cherry Val Curwen Michael DiCuccio Manolis Kellis Jennifer Lee Michael F. Lin Michael Schuster Andrew Shkeda Clara Amid Garth Brown Oksana Dukhanina Adam Frankish Jennifer Hart Bonnie L. Maidak Jonathan Mudge Michael R. Murphy Terence Murphy Jeena Rajan Bhanu Rajput Lillian D. Riddick Catherine Snow Charles Steward David Webb Janet A. Weber Laurens Wilming Wenyu Wu Ewan Birney David Haussler
... [+40 authors] ...,
Tim Hubbard
James Ostell
Richard Durbin
David Lipman

First Published June 4, 2009

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

Albert J. Vilella
Jessica Severin
Abel Ureta-Vidal
Li Heng
Richard Durbin
Ewan Birney

First Published November 24, 2008

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

Benedict Paten
Javier Herrero
Kathryn Beal
Stephen Fitzgerald
Ewan Birney

First Published October 10, 2008

Genome-wide nucleotide-level mammalian ancestor reconstruction

Benedict Paten
Javier Herrero
Stephen Fitzgerald
Kathryn Beal
Paul Flicek
Ian Holmes
Ewan Birney

First Published October 10, 2008

Confounding between recombination and selection, and the Ped/Pop method for detecting selection

Paul F. O’Reilly
Ewan Birney
David J. Balding

First Published July 10, 2008

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

Vardhman K. Rakyan
Thomas A. Down
Natalie P. Thorne
Paul Flicek
Eugene Kulesha
Stefan Gräf Eleni M. Tomazou Liselotte Bäckdahl Nathan Johnson Marlis Herberth Kevin L. Howe David K. Jackson Marcos M. Miretti Heike Fiegler John C. Marioni Ewan Birney
... [+11 authors] ...,
Tim J.P. Hubbard
Nigel P. Carter
Simon Tavaré
Stephan Beck

First Published June 24, 2008

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

Daniel R. Zerbino
Ewan Birney

First Published March 18, 2008

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Elliott H. Margulies
Gregory M. Cooper
George Asimenos
Daryl J. Thomas
Colin N. Dewey
Adam Siepel Ewan Birney Damian Keefe Ariel S. Schwartz Minmei Hou James Taylor Sergey Nikolaev Juan I. Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham James B. Brown Peter Bickel Ian Holmes James C. Mullikin Abel Ureta-Vidal Benedict Paten Eric A. Stone Kate R. Rosenbloom W. James Kent Gerard G. Bouffard Xiaobin Guan Nancy F. Hansen Jacquelyn R. Idol Valerie V.B. Maduro Baishali Maskeri Jennifer C. McDowell Morgan Park Pamela J. Thomas Alice C. Young Robert W. Blakesley Donna M. Muzny Erica Sodergren David A. Wheeler Kim C. Worley Huaiyang Jiang George M. Weinstock Richard A. Gibbs Tina Graves Robert Fulton Elaine R. Mardis Richard K. Wilson Michele Clamp James Cuff Sante Gnerre David B. Jaffe Jean L. Chang Kerstin Lindblad-Toh Eric S. Lander Angie Hinrichs Heather Trumbower Hiram Clawson Ann Zweig Robert M. Kuhn Galt Barber Rachel Harte Donna Karolchik Matthew A. Field Richard A. Moore Carrie A. Matthewson Jacqueline E. Schein Marco A. Marra Stylianos E. Antonarakis Serafim Batzoglou Nick Goldman Ross Hardison David Haussler
... [+68 authors] ...,
Webb Miller
Lior Pachter
Eric D. Green
Arend Sidow

First Published June 13, 2007

The landscape of histone modifications across 1% of the human genome in five human cell lines

Christoph M. Koch
Robert M. Andrews
Paul Flicek
Shane C. Dillon
Ulaş Karaöz
Gayle K. Clelland Sarah Wilcox David M. Beare Joanna C. Fowler Phillippe Couttet Keith D. James Gregory C. Lefebvre Alexander W. Bruce Oliver M. Dovey Peter D. Ellis Pawandeep Dhami Cordelia F. Langford Zhiping Weng
... [+13 authors] ...,
Ewan Birney
Nigel P. Carter
David Vetrie
Ian Dunham

First Published June 13, 2007

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

Identification of novel peptide hormones in the human proteome by hidden Markov model screening

Olivier Mirabeau
Emerald Perlas
Cinzia Severini
Enrica Audero
Olivier Gascuel
Roberta Possenti
Ewan Birney
Nadia Rosenthal
Cornelius Gross

First Published February 6, 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

Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

Simon J. Hubbard
Darren V. Grafham
Kevin J. Beattie
Ian M. Overton
Stuart R. McLaren
Michael D.R. Croning Paul E. Boardman James K. Bonfield Joan Burnside Robert M. Davies Elizabeth R. Farrell Matthew D. Francis Sam Griffiths-Jones Sean J. Humphray Christopher Hyland Carol E. Scott Haizhou Tang Ruth G. Taylor Cheryll Tickle
... [+14 authors] ...,
William R.A. Brown
Ewan Birney
Jane Rogers
Stuart A. Wilson

First Published December 8, 2004

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

The Ensembl Core Software Libraries

Arne Stabenau
Graham McVicker
Craig Melsopp
Glenn Proctor
Michele Clamp
Ewan Birney

First Published May 3, 2004

Sockeye: A 3D Environment for Comparative Genomics

Stephen B. Montgomery
Tamara Astakhova
Mikhail Bilenky
Ewan Birney
Tony Fu
Maik Hassel Craig Melsopp Marcin Rak
... [+3 authors] ...,
A. Gordon Robertson
Monica Sleumer
Asim S. Siddiqui
Steven J.M. Jones

First Published May 3, 2004

GeneWise and Genomewise

Ewan Birney
Michele Clamp
Richard Durbin

First Published May 3, 2004

An Overview of Ensembl

Ewan Birney
T. Daniel Andrews
Paul Bevan
Mario Caccamo
Yuan Chen
Laura Clarke Guy Coates James Cuff Val Curwen Tim Cutts Thomas Down Eduardo Eyras Xose M. Fernandez-Suarez Paul Gane Brian Gibbins James Gilbert Martin Hammond Hans-Rudolf Hotz Vivek Iyer Kerstin Jekosch Andreas Kahari Arek Kasprzyk Damian Keefe Stephen Keenan Heikki Lehvaslaiho Graham McVicker Craig Melsopp Patrick Meidl Emmanuel Mongin Roger Pettett Simon Potter Glenn Proctor Mark Rae Steve Searle Guy Slater Damian Smedley James Smith Will Spooner Arne Stabenau James Stalker Roy Storey Abel Ureta-Vidal K. Cara Woodwark Graham Cameron
... [+39 authors] ...,
Richard Durbin
Anthony Cox
Tim Hubbard
Michele Clamp

First Published April 12, 2004

Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment

Emmanouil T. Dermitzakis
Ewen Kirkness
Scott Schwarz
Ewan Birney
Alexandre Reymond
Stylianos E. Antonarakis

First Published April 12, 2004

EnsMart: A Generic System for Fast and Flexible Access to Biological Data

Arek Kasprzyk
Damian Keefe
Damian Smedley
Darin London
William Spooner
Craig Melsopp
... [+1 authors] ...,
Martin Hammond
Philippe Rocca-Serra
Tony Cox
Ewan Birney

First Published January 5, 2004

cis-Regulatory Motifs Using Functional Networks" > Discovering Novel cis-Regulatory Motifs Using Functional Networks

Laurence M. Ettwiller
Johan Rung
Ewan Birney

First Published May 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

The Bioperl Toolkit: Perl Modules for the Life Sciences

Jason E. Stajich
David Block
Kris Boulez
Steven E. Brenner
Stephen A. Chervitz
Chris Dagdigian Georg Fuellen James G.R. Gilbert Ian Korf Hilmar Lapp Heikki Lehväslaiho Chad Matsalla Chris J. Mungall Brian I. Osborne Matthew R. Pocock Peter Schattner Martin Senger
... [+12 authors] ...,
Lincoln D. Stein
Elia Stupka
Mark D. Wilkinson
Ewan Birney

First Published October 1, 2002

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

GeneWise in the Drosophila Annotation Experiment" > Using `GeneWise` in the Drosophila Annotation Experiment

Ewan Birney
Richard Durbin

First Published April 1, 2000

Comparative Analysis of Noncoding Regions of 77 Orthologous Mouse and Human Gene Pairs

Niclas Jareborg
Ewan Birney
Richard Durbin

First Published September 1, 1999

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