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r-index-based pangenome indexing" > Accurate short-read alignment through r-index-based pangenome indexing

  • Rahul Varki
  • Massimiliano Rossi
  • Eddie Ferro
  • Marco Oliva
  • Erik Garrison
  • Ben Langmead
  • Christina Boucher
  • First Published June 12, 2025

Efficient taxa identification using a pangenome index

  • Omar Ahmed
  • Massimiliano Rossi
  • Christina Boucher
  • Ben Langmead
  • First Published May 31, 2023

C. Thomas Caskey (1938–2022)

  • Richard A. Gibbs
  • Aravinda Chakravarti
  • Evan E. Eichler
  • Eric D. Green
  • Richard M. Myers
  • Anne C. Ferguson-Smith
  • Kateryna D. Makova
  • Hillary E. Sussman
  • First Published February 17, 2022

Deborah A. Nickerson (1954 –2021)

  • Aravinda Chakravarti
  • Evan E. Eichler
  • Richard A. Gibbs
  • Eric D. Green
  • Richard M. Myers
  • Hillary E. Sussman
  • First Published January 24, 2022

Enhancers with tissue-specific activity are enriched in intronic regions

  • Beatrice Borsari
  • Pablo Villegas-Mirón
  • Sílvia Pérez-Lluch
  • Isabel Turpin
  • Hafid Laayouni
  • Alba Segarra-Casas
  • Jaume Bertranpetit
  • Roderic Guigó
  • Sandra Acosta
  • First Published July 21, 2021

Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages" > Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

  • Jennifer F. Hughes
  • Helen Skaletsky
  • Tatyana Pyntikova
  • Natalia Koutseva
  • Terje Raudsepp
  • Laura G. Brown Daniel W. Bellott Ting-Jan Cho Shannon Dugan-Rocha Ziad Khan Colin Kremitzki Catrina Fronick Tina A. Graves-Lindsay Lucinda Fulton Wesley C. Warren Richard K. Wilson Elaine Owens James E. Womack William J. Murphy Donna M. Muzny
  • ... [+15 authors] ...,
  • Kim C. Worley
  • Bhanu P. Chowdhary
  • Richard A. Gibbs
  • David C. Page
  • First Published November 18, 2020

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

A limited set of transcriptional programs define major cell types

  • Alessandra Breschi
  • Manuel Muñoz-Aguirre
  • Valentin Wucher
  • Carrie A. Davis
  • Diego Garrido-Martín
  • Sarah Djebali Jesse Gillis Dmitri D. Pervouchine Anna Vlasova Alexander Dobin Chris Zaleski Jorg Drenkow Cassidy Danyko Alexandra Scavelli
  • ... [+9 authors] ...,
  • Ferran Reverter
  • Michael P. Snyder
  • Thomas R. Gingeras
  • Roderic Guigó
  • First Published July 29, 2020

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

Dynamics of microRNA expression during mouse prenatal development

  • Sorena Rahmanian
  • Rabi Murad
  • Alessandra Breschi
  • Weihua Zeng
  • Mark Mackiewicz
  • Brian Williams Carrie A. Davis Brian Roberts Sarah Meadows Dianna Moore Diane Trout Chris Zaleski Alex Dobin Lei-Hoon Sei Jorg Drenkow Alex Scavelli Thomas R. Gingeras
  • ... [+12 authors] ...,
  • Barbara J. Wold
  • Richard M. Myers
  • Roderic Guigó
  • Ali Mortazavi
  • First Published October 23, 2019
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