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Multisample motif discovery and visualization for tandem repeats

Yaran Zhang
Marc Hulsman
Alex Salazar
Niccolò Tesi
Lydian Knoop
Sven van der Lee
... [+1 authors] ...,
Sanduni Wijesekera
Jana Krizova
Erik-Jan Kamsteeg
Henne Holstege

First Published November 13, 2024

otter" > Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter

Niccoló Tesi
Alex Salazar
Yaran Zhang
Sven van der Lee
Marc Hulsman
Lydian Knoop Sanduni Wijesekera Jana Krizova Anne-Fleur Schneider Maartje Pennings
... [+5 authors] ...,
Kristel Sleegers
Erik-Jan Kamsteeg
Marcel Reinders
Henne Holstege

First Published October 15, 2024

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

A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci

Elisabeth J. van Bree
Rita L.F.P. Guimarães
Mischa Lundberg
Elena R. Blujdea
Jimi L. Rosenkrantz
Fred T.G. White Josse Poppinga Paula Ferrer-Raventós Anne-Fleur E. Schneider Isabella Clayton David Haussler Marcel J.T. Reinders
... [+7 authors] ...,
Henne Holstege
Adam D. Ewing
Colette Moses
Frank M.J. Jacobs

First Published March 24, 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

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

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis

Henne Holstege
Wayne Pfeiffer
Daoud Sie
Marc Hulsman
Thomas J. Nicholas
Clarence C. Lee Tristen Ross Jue Lin Mark A. Miller Bauke Ylstra Hanne Meijers-Heijboer Martijn H. Brugman Frank J.T. Staal Gert Holstege
... [+9 authors] ...,
Marcel J.T. Reinders
Timothy T. Harkins
Samuel Levy
Erik A. Sistermans

First Published April 23, 2014

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

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

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