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Method

Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit

  • David R. Lougheed
  • Tomi Pastinen
  • Guillaume Bourque
  • First Published January 15, 2026
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
Research

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

  • Theodore Gouliouris
  • Kathy E. Raven
  • Danesh Moradigaravand
  • Catherine Ludden
  • Francesc Coll
  • Beth Blane Plamena Naydenova Carolyne Horner Nicholas M. Brown
  • ... [+4 authors] ...,
  • Jukka Corander
  • Direk Limmathurotsakul
  • Julian Parkhill
  • Sharon J. Peacock
  • First Published March 21, 2019
Corrigendum

Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

  • Sandra Reuter
  • M. Estée Török
  • Matthew T.G. Holden
  • Rosy Reynolds
  • Kathy E. Raven
  • Beth Blane Tjibbe Donker Stephen D. Bentley David M. Aanensen Hajo Grundmann
  • ... [+5 authors] ...,
  • Edward J. Feil
  • Brian G. Spratt
  • Julian Parkhill
  • Sharon J. Peacock
  • First Published September 1, 2017
Research

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

  • Teemu Kallonen
  • Hayley J. Brodrick
  • Simon R. Harris
  • Jukka Corander
  • Nicholas M. Brown
  • Veronique Martin
  • Sharon J. Peacock
  • Julian Parkhill
  • First Published July 18, 2017
Research

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion

  • James Hadfield
  • Simon R. Harris
  • Helena M.B. Seth-Smith
  • Surendra Parmar
  • Patiyan Andersson
  • Philip M. Giffard Julius Schachter Jeanne Moncada Louise Ellison María Lucía Gallo Vaulet Marcelo Rodríguez Fermepin Frans Radebe Suyapa Mendoza Sander Ouburg Servaas A. Morré Konrad Sachse Mirja Puolakkainen Suvi J. Korhonen Chris Sonnex Rebecca Wiggins Hamid Jalal Tamara Brunelli Patrizia Casprini Rachel Pitt Cathy Ison Alevtina Savicheva Elena Shipitsyna Ronza Hadad Laszlo Kari Matthew J. Burton David Mabey Anthony W. Solomon David Lewis Peter Marsh
  • ... [+29 authors] ...,
  • Magnus Unemo
  • Ian N. Clarke
  • Julian Parkhill
  • Nicholas R. Thomson
  • First Published June 6, 2017
Research

Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently

  • Sophia David
  • Christophe Rusniok
  • Massimo Mentasti
  • Laura Gomez-Valero
  • Simon R. Harris
  • Pierre Lechat John Lees Christophe Ginevra Philippe Glaser Laurence Ma Christiane Bouchier Anthony Underwood
  • ... [+7 authors] ...,
  • Sophie Jarraud
  • Timothy G. Harrison
  • Julian Parkhill
  • Carmen Buchrieser
  • First Published September 23, 2016
Research

A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland

  • Kathy E. Raven
  • Sandra Reuter
  • Rosy Reynolds
  • Hayley J. Brodrick
  • Julie E. Russell
  • M. Estée Török
  • Julian Parkhill
  • Sharon J. Peacock
  • First Published August 15, 2016
Research

Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland

  • Danesh Moradigaravand
  • Christine J. Boinett
  • Veronique Martin
  • Sharon J. Peacock
  • Julian Parkhill
  • First Published July 18, 2016
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