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Research

Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T

  • Luis F. Paulin
  • Jeremy Fan
  • Kieran O'Neill
  • Erin Pleasance
  • Vanessa L. Porter
  • Steven J.M. Jones
  • Fritz J. Sedlazeck
  • First Published March 17, 2025
Research

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation

  • Vanessa L. Porter
  • Michelle Ng
  • Kieran O'Neill
  • Signe MacLennan
  • Richard D. Corbett
  • Luka Culibrk Zeid Hamadeh Marissa Iden Rachel Schmidt Shirng-Wern Tsaih Carolyn Nakisige Martin Origa Jackson Orem Glenn Chang Jeremy Fan Ka Ming Nip Vahid Akbari Simon K. Chan James Hopkins Richard A. Moore Eric Chuah Karen L. Mungall Andrew J. Mungall
  • ... [+18 authors] ...,
  • Inanc Birol
  • Steven J.M. Jones
  • Janet S. Rader
  • Marco A. Marra
  • First Published December 5, 2024
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
Corrigendum

Drosophila" > Corrigendum: Tempo and mode of regulatory evolution in Drosophila

  • Joseph D. Coolon
  • C. Joel McManus
  • Kraig R. Stevenson
  • Brenton R. Graveley
  • Patricia J. Wittkopp
  • First Published November 1, 2018
Resource

Drosophila by 56 RNA binding proteins" > Regulation of alternative splicing in Drosophila by 56 RNA binding proteins

  • Angela N. Brooks
  • Michael O. Duff
  • Gemma May
  • Li Yang
  • Mohan Bolisetty
  • Jane Landolin Ken Wan Jeremy Sandler
  • ... [+3 authors] ...,
  • Benjamin W. Booth
  • Susan E. Celniker
  • Brenton R. Graveley
  • Steven E. Brenner
  • First Published August 20, 2015
Research

Drosophila" > Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila

  • Marcus H. Stoiber
  • Sara Olson
  • Gemma E. May
  • Michael O. Duff
  • Jan Manent
  • Robert Obar K.G. Guruharsha Peter J. Bickel
  • ... [+3 authors] ...,
  • Spyros Artavanis-Tsakonas
  • James B. Brown
  • Brenton R. Graveley
  • Susan E. Celniker
  • First Published August 20, 2015
Resource

D. melanogaster modENCODE transcriptome annotation" > Comparative validation of the D. melanogaster modENCODE transcriptome annotation

  • Zhen-Xia Chen
  • David Sturgill
  • Jiaxin Qu
  • Huaiyang Jiang
  • Soo Park
  • Nathan Boley Ana Maria Suzuki Anthony R. Fletcher David C. Plachetzki Peter C. FitzGerald Carlo G. Artieri Joel Atallah Olga Barmina James B. Brown Kerstin P. Blankenburg Emily Clough Abhijit Dasgupta Sai Gubbala Yi Han Joy C. Jayaseelan Divya Kalra Yoo-Ah Kim Christie L. Kovar Sandra L. Lee Mingmei Li James D. Malley John H. Malone Tittu Mathew Nicolas R. Mattiuzzo Mala Munidasa Donna M. Muzny Fiona Ongeri Lora Perales Teresa M. Przytycka Ling-Ling Pu Garrett Robinson Rebecca L. Thornton Nehad Saada Steven E. Scherer Harold E. Smith Charles Vinson Crystal B. Warner Kim C. Worley Yuan-Qing Wu Xiaoyan Zou Peter Cherbas Manolis Kellis Michael B. Eisen Fabio Piano Karin Kionte David H. Fitch Paul W. Sternberg Asher D. Cutter Michael O. Duff Roger A. Hoskins Brenton R. Graveley Richard A. Gibbs Peter J. Bickel Artyom Kopp
  • ... [+54 authors] ...,
  • Piero Carninci
  • Susan E. Celniker
  • Brian Oliver
  • Stephen Richards
  • First Published July 1, 2014
Research

Drosophila" > Tempo and mode of regulatory evolution in Drosophila

  • Joseph D. Coolon
  • C. Joel McManus
  • Kraig R. Stevenson
  • Brenton R. Graveley
  • Patricia J. Wittkopp
  • First Published February 24, 2014
Research

Drosophila" > Evolution of splicing regulatory networks in Drosophila

  • C. Joel McManus
  • Joseph D. Coolon
  • Jodi Eipper-Mains
  • Patricia J. Wittkopp
  • Brenton R. Graveley
  • First Published February 10, 2014
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