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Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations

  • Yasine Malki
  • Guannan Kang
  • W.K. Jacky Lam
  • Qing Zhou
  • Suk Hang Cheng
  • Peter P.H. Cheung Jinyue Bai Ming Lok Chan Chui Ting Lee Wenlei Peng Yiqiong Zhang Wanxia Gai Winsome W.S. Wong Mary-Jane L. Ma Wenshuo Li Xinzhou Xu Zhuoran Gao Irene O.L. Tse Huimin Shang
  • ... [+14 authors] ...,
  • L.Y. Lois Choy
  • Peiyong Jiang
  • K.C. Allen Chan
  • Y.M. Dennis Lo
  • First Published November 27, 2024

Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma

  • Huiwen Che
  • Peiyong Jiang
  • L.Y. Lois Choy
  • Suk Hang Cheng
  • Wenlei Peng
  • Rebecca W.Y. Chan Jing Liu Qing Zhou W.K. Jacky Lam Stephanie C.Y. Yu So Ling Lau Tak Y. Leung John Wong Vincent Wai-Sun Wong
  • ... [+9 authors] ...,
  • Grace L.H. Wong
  • Stephen L. Chan
  • K.C. Allen Chan
  • Y.M. Dennis Lo
  • First Published February 26, 2024

Gaps and complex structurally variant loci in phased genome assemblies

  • David Porubsky
  • Mitchell R. Vollger
  • William T. Harvey
  • Allison N. Rozanski
  • Peter Ebert
  • Glenn Hickey Patrick Hasenfeld Ashley D. Sanders Catherine Stober Jan O. Korbel Benedict Paten Tobias Marschall Evan E. Eichler Haley J. Abel Lucinda L. Antonacci-Fulton Mobin Asri Gunjan Baid Carl A. Baker Anastasiya Belyaeva Konstantinos Billis Guillaume Bourque Silvia Buonaiuto Andrew Carroll Mark J.P. Chaisson Pi-Chuan Chang Xian H. Chang Haoyu Cheng Justin Chu Sarah Cody Vincenza Colonna Daniel E. Cook Robert M. Cook-Deegan Omar E. Cornejo Mark Diekhans Daniel Doerr Peter Ebert Jana Ebler Evan E. Eichler Jordan M. Eizenga Susan Fairley Olivier Fedrigo Adam L. Felsenfeld Xiaowen Feng Christian Fischer Paul Flicek Giulio Formenti Adam Frankish Robert S. Fulton Yan Gao Shilpa Garg Erik Garrison Nanibaa’ A. Garrison Carlos Garcia Giron Richard E. Green Cristian Groza Andrea Guarracino Leanne Haggerty Ira M. Hall William T. Harvey Marina Haukness David Haussler Simon Heumos Glenn Hickey Kendra Hoekzema Thibaut Hourlier Kerstin Howe Miten Jain Erich D. Jarvis Hanlee P. Ji Eimear E. Kenny Barbara A. Koenig Alexey Kolesnikov Jan O. Korbel Jennifer Kordosky Sergey Koren HoJoon Lee Alexandra P. Lewis Heng Li Wen-Wei Liao Shuangjia Lu Tsung-Yu Lu Julian K. Lucas Hugo Magalhães Santiago Marco-Sola Pierre Marijon Charles Markello Tobias Marschall Fergal J. Martin Ann McCartney Jennifer McDaniel Karen H. Miga Matthew W. Mitchell Jean Monlong Jacquelyn Mountcastle Katherine M. Munson Moses Njagi Mwaniki Maria Nattestad Adam M. Novak Sergey Nurk Hugh E. Olsen Nathan D. Olson Benedict Paten Trevor Pesout Adam M. Phillippy Alice B. Popejoy David Porubsky Pjotr Prins Daniela Puiu Mikko Rautiainen Allison A. Regier Arang Rhie Samuel Sacco Ashley D. Sanders Valerie A. Schneider Baergen I. Schultz Kishwar Shafin Jonas A. Sibbesen Jouni Sirén Michael W. Smith Heidi J. Sofia Ahmad N. Abou Tayoun Françoise Thibaud-Nissen Chad Tomlinson Francesca Floriana Tricomi Flavia Villani Mitchell R. Vollger Justin Wagner Brian Walenz
  • ... [+123 authors] ...,
  • Ting Wang
  • Jonathan M.D. Wood
  • Aleksey V. Zimin
  • Justin M. Zook
  • First Published May 10, 2023

Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera

  • Peter O. Mulhair
  • Liam Crowley
  • Douglas H. Boyes
  • Amber Harper
  • Owen T. Lewis
  • Peter W.H. Holland Mark Blaxter Nova Mieszkowska Federica Di Palma Peter Holland Richard Durbin Thomas Richards Matthew Berriman Paul Kersey Peter Hollingsworth Willie Wilson Alex Twyford Ester Gaya Mara Lawniczak Owen Lewis Gavin Broad
  • ... [+16 authors] ...,
  • Kevin Howe
  • Michelle Hart
  • Paul Flicek
  • Ian Barnes
  • First Published December 8, 2022

Nuclease deficiencies alter plasma cell-free DNA methylation profiles

  • Diana S.C. Han
  • Meng Ni
  • Rebecca W.Y. Chan
  • Danny K.L. Wong
  • Linda T. Hiraki
  • Stefano Volpi Peiyong Jiang
  • ... [+2 authors] ...,
  • Kathy O. Lui
  • K.C. Allen Chan
  • Rossa W.K. Chiu
  • Y.M. Dennis Lo
  • First Published September 1, 2021

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

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

Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma

  • Raquel Ordoñez
  • Marta Kulis
  • Nuria Russiñol
  • Vicente Chapaprieta
  • Arantxa Carrasco-Leon
  • Beatriz García-Torre Stella Charalampopoulou Guillem Clot Renée Beekman Cem Meydan Martí Duran-Ferrer Núria Verdaguer-Dot Roser Vilarrasa-Blasi Paula Soler-Vila Leire Garate Estíbaliz Miranda Edurne San José-Enériz Juan R. Rodriguez-Madoz Teresa Ezponda Rebeca Martínez-Turrilas Amaia Vilas-Zornoza David Lara-Astiaso Daphné Dupéré-Richer Joost H.A. Martens Halima El-Omri Ruba Y. Taha Maria J. Calasanz Bruno Paiva Jesus San Miguel Paul Flicek Ivo Gut Ari Melnick Constantine S. Mitsiades Jonathan D. Licht Elias Campo
  • ... [+30 authors] ...,
  • Hendrik G. Stunnenberg
  • Xabier Agirre
  • Felipe Prosper
  • Jose I. Martin-Subero
  • First Published August 20, 2020

Detection and characterization of jagged ends of double-stranded DNA in plasma

  • Peiyong Jiang
  • Tingting Xie
  • Spencer C. Ding
  • Ze Zhou
  • Suk Hang Cheng
  • Rebecca W.Y. Chan Wing-Shan Lee Wenlei Peng John Wong Vincent W.S. Wong Henry L.Y. Chan Stephen L. Chan Liona C.Y. Poon
  • ... [+8 authors] ...,
  • Tak Y. Leung
  • K.C. Allen Chan
  • Rossa W.K. Chiu
  • Y.M. Dennis Lo
  • First Published August 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
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