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Research

Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development

  • Patricia Gerdes
  • Dorothy Chan
  • Mischa Lundberg
  • Francisco J. Sanchez-Luque
  • Gabriela O. Bodea
  • Adam D. Ewing
  • Geoffrey J. Faulkner
  • Sandra R. Richardson
  • First Published October 5, 2023
Research

Somatic retrotransposition in the developing rhesus macaque brain

  • Victor Billon
  • Francisco J. Sanchez-Luque
  • Jay Rasmussen
  • Gabriela O. Bodea
  • Daniel J. Gerhardt
  • Patricia Gerdes Seth W. Cheetham Stephanie N. Schauer Prabha Ajjikuttira Thomas J. Meyer Cora E. Layman Kimberly A. Nevonen Natasha Jansz Jose L. Garcia-Perez
  • ... [+9 authors] ...,
  • Sandra R. Richardson
  • Adam D. Ewing
  • Lucia Carbone
  • Geoffrey J. Faulkner
  • First Published June 21, 2022
Research

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
Corrigendum

Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

  • Jordan A. Ramilowski
  • Chi Wai Yip
  • Saumya Agrawal
  • Jen-Chien Chang
  • Yari Ciani
  • Ivan V. Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F. Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V. Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher J.F. Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L. Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S. Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J. Makeev Luigi Marchionni Yulia A. Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R. Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J.C. Parr Owen J.L. Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A.M. Semple Youtaro Shibayama Divya M. Sivaraman Takahiro Suzuki Suzannah C. Szumowski Michihira Tagami Martin S. Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E. Vorontsov Chinatsu Yamamoto Robert S. Young J. Kenneth Baillie Alistair R.R. Forrest Roderic Guigó Michael M. Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki
  • ... [+107 authors] ...,
  • Ken Yagi
  • Michiel J.L. de Hoon
  • Jay W. Shin
  • Piero Carninci
  • First Published September 14, 2020
Resource

Functional annotation of human long noncoding RNAs via molecular phenotyping

  • Jordan A. Ramilowski
  • Chi Wai Yip
  • Saumya Agrawal
  • Jen-Chien Chang
  • Yari Ciani
  • Ivan V. Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F. Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V. Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher J.F. Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L. Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S. Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J. Makeev Luigi Marchionni Yulia A. Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R. Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J.C. Parr Owen J.L. Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A.M. Semple Youtaro Shibayama Divya M. Sivaraman Takahiro Suzuki Suzannah C. Szumowski Michihira Tagami Martin S. Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E. Vorontsov Chinatsu Yamamoto Robert S. Young J. Kenneth Baillie Alistair R.R. Forrest Roderic Guigó Michael M. Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki
  • ... [+107 authors] ...,
  • Ken Yagi
  • Michiel J.L. de Hoon
  • Jay W. Shin
  • Piero Carninci
  • First Published July 27, 2020
Method

Ancestry-agnostic estimation of DNA sample contamination from sequence reads

  • Fan Zhang
  • Matthew Flickinger
  • Sarah A. Gagliano Taliun
  • Gonçalo R. Abecasis
  • Laura J. Scott
  • Steven A. McCaroll
  • Carlos N. Pato
  • Michael Boehnke
  • Hyun Min Kang
  • First Published January 24, 2020
Research

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

  • Stephanie N. Schauer
  • Patricia E. Carreira
  • Ruchi Shukla
  • Daniel J. Gerhardt
  • Patricia Gerdes
  • Francisco J. Sanchez-Luque Paola Nicoli Michaela Kindlova Serena Ghisletti Alexandre Dos Santos Delphine Rapoud Didier Samuel
  • ... [+7 authors] ...,
  • Jamila Faivre
  • Adam D. Ewing
  • Sandra R. Richardson
  • Geoffrey J. Faulkner
  • First Published April 11, 2018
Research

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

  • Sandra R. Richardson
  • Patricia Gerdes
  • Daniel J. Gerhardt
  • Francisco J. Sanchez-Luque
  • Gabriela-Oana Bodea
  • Martin Muñoz-Lopez J. Samuel Jesuadian Marie-Jeanne H.C. Kempen Patricia E. Carreira Jeffrey A. Jeddeloh
  • ... [+5 authors] ...,
  • Jose L. Garcia-Perez
  • Haig H. Kazazian
  • Adam D. Ewing
  • Geoffrey J. Faulkner
  • First Published May 8, 2017
Research

Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution

  • Adam D. Ewing
  • Anthony Gacita
  • Laura D. Wood
  • Florence Ma
  • Dongmei Xing
  • Min-Sik Kim Srikanth S. Manda Gabriela Abril Gavin Pereira Alvin Makohon-Moore Leendert H.J. Looijenga Ad J.M. Gillis Ralph H. Hruban Robert A. Anders Katharine E. Romans Akhilesh Pandey Christine A. Iacobuzio-Donahue
  • ... [+12 authors] ...,
  • Bert Vogelstein
  • Kenneth W. Kinzler
  • Haig H. Kazazian
  • Szilvia Solyom
  • First Published August 10, 2015
Method

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data

  • Goo Jun
  • Mary Kate Wing
  • Gonçalo R. Abecasis
  • Hyun Min Kang
  • First Published April 16, 2015
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