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Highly accurate assembly polishing with DeepPolisher

  • Mira Mastoras
  • Mobin Asri
  • Lucas Brambrink
  • Prajna Hebbar
  • Alexey Kolesnikov
  • Daniel E. Cook Maria Nattestad Julian Lucas Taylor S. Won Pi-Chuan Chang Andrew Carroll Benedict Paten Kishwar Shafin Ahmad Abou Tayoun Derek Albracht Jamie Allen Alawi A. Alsheikh-Ali Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Edward A. Belter Halle D. Bender Andrew P. Blair Silvia Buonaiuto Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Richard Durbin Jana Ebler Evan E Eichler Jordan M. Eizenga Parsa Eskandar Eddie Ferro Anna-Sophie Fiston-Lavier Sarah M. Ford Willard W. Ford Giulio Formenti Adam Frankish Mallory A. Freeberg Qichen Fu Stephanie M. Fullerton Robert S. Fulton Yan Gao Gage H. Garcia Obed A. Garcia Joshua M.V. Gardner Shilpa Garg Erik Garrison Nanibaa' A. Garrison John Garza Mohammadmersad Ghorbani Tina Graves-Lindsay Richard E. Green Cristian Groza Andrea Guarracino Melissa Gymrek Leanne Haggerty Ira M. Hall Nancy F. Hansen Mohammad Amiruddin Hashmi Maximilian Haeussler David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Juan Jiang Jonathan LoTempio Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Ben Langmead Xiaoyu Zhuo Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Juan F. Macias-Velasco Maximillian G. Marin Franco L. Marsico Kateryna D. Makova Christopher Markovic Tobias Marschall Fergal J. Martin Mira Mastoras Capucine Mayoud Brandy McNulty Jack A. Medico Julian M. Menendez Karen H. Miga Anna Minkina Matthew W. Mitchell Saswat K. Mohanty Younes Mokrab Jean Monlong Shabir Moosa Avelina Moreno-Ochando Shinichi Morishita Jonathan M. Mudge Katherine M. Munson Njagi Mwaniki Nasna Nassir Chiara Natali Shloka Negi Lingbin Ni Adam M. Novak Chie Owa Sadye Paez Benedict Paten Hiram Clawson Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Farnaz Salehi Samuel Sacco Michael C. Schatz Laura B. Scheinfeldt Aarushi Sehgal William E. Seligmann Mahsa Shabani Kishwar Shafin Shadi Shahatit Ruhollah Shemirani Vikram S. Shivakumar Swati Sinha Jouni Sirén Linnéa Smeds Steven J. Solar Marco Sollitto Nicole Soranzo Andrew B. Stergachis Marie-Marthe Suner Yoshihiko Suzuki Arda Söylev Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Mitchell R. Vollger Brian P. Walenz Charles Wang Lisa E. Wang Ting Wang Aaron M. Wenger Conor V. Whelan Zilan Xin Zheng Xu Kai Ye DongAhn Yoo
  • ... [+196 authors] ...,
  • Wenjin Zhang
  • Ying Zhou
  • Ivo Violich
  • Giulia Zunino
  • First Published May 19, 2025

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

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

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

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

  • Edward S. Rice
  • Satomi Kohno
  • John St. John
  • Son Pham
  • Jonathan Howard
  • Liana F. Lareau Brendan L. O'Connell Glenn Hickey Joel Armstrong Alden Deran Ian Fiddes Roy N. Platt Cathy Gresham Fiona McCarthy Colin Kern David Haan Tan Phan Carl Schmidt Jeremy R. Sanford
  • ... [+14 authors] ...,
  • David A. Ray
  • Benedict Paten
  • Louis J. Guillette
  • Richard E. Green
  • First Published January 30, 2017

Alignathon: a competitive assessment of whole-genome alignment methods

  • Dent Earl
  • Ngan Nguyen
  • Glenn Hickey
  • Robert S. Harris
  • Stephen Fitzgerald
  • Kathryn Beal Igor Seledtsov Vladimir Molodtsov Brian J. Raney Hiram Clawson Jaebum Kim Carsten Kemena Jia-Ming Chang Ionas Erb Alexander Poliakov Minmei Hou Javier Herrero William James Kent Victor Solovyev Aaron E. Darling Jian Ma Cedric Notredame
  • ... [+17 authors] ...,
  • Michael Brudno
  • Inna Dubchak
  • David Haussler
  • Benedict Paten
  • First Published October 1, 2014

Spark: A navigational paradigm for genomic data exploration

  • Cydney B. Nielsen
  • Hamid Younesy
  • Henriette O'Geen
  • Xiaoqin Xu
  • Andrew R. Jackson
  • Aleksandar Milosavljevic Ting Wang
  • ... [+2 authors] ...,
  • Joseph F. Costello
  • Martin Hirst
  • Peggy J. Farnham
  • Steven J.M. Jones
  • First Published September 7, 2012

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

  • Brad G. Hoffman
  • Gordon Robertson
  • Bogard Zavaglia
  • Mike Beach
  • Rebecca Cullum
  • Sam Lee Galina Soukhatcheva Leping Li Elizabeth D. Wederell Nina Thiessen Mikhail Bilenky Timothee Cezard Angela Tam Baljit Kamoh Inanc Birol Derek Dai YongJun Zhao Martin Hirst C. Bruce Verchere
  • ... [+14 authors] ...,
  • Cheryl D. Helgason
  • Marco A. Marra
  • Steven J.M. Jones
  • Pamela A. Hoodless
  • First Published June 15, 2010

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

  • Santosh S. Atanur
  • İnanç Birol
  • Victor Guryev
  • Martin Hirst
  • Oliver Hummel
  • Catherine Morrissey Jacques Behmoaras Xose M. Fernandez-Suarez Michelle D. Johnson William M. McLaren Giannino Patone Enrico Petretto Charles Plessy Kathleen S. Rockland Charles Rockland Kathrin Saar Yongjun Zhao Piero Carninci Paul Flicek Ted Kurtz Edwin Cuppen Michal Pravenec
  • ... [+17 authors] ...,
  • Norbert Hubner
  • Steven J.M. Jones
  • Ewan Birney
  • Timothy J. Aitman
  • First Published April 29, 2010

The completion of the Mammalian Gene Collection (MGC)

  • Gary Temple
  • Daniela S. Gerhard
  • Rebekah Rasooly
  • Elise A. Feingold
  • Peter J. Good
  • Cristen Robinson Allison Mandich Jeffrey G. Derge Jeanne Lewis Debonny Shoaf Francis S. Collins Wonhee Jang Lukas Wagner Carolyn M. Shenmen Leonie Misquitta Carl F. Schaefer Kenneth H. Buetow Tom I. Bonner Linda Yankie Ming Ward Lon Phan Alex Astashyn Garth Brown Catherine Farrell Jennifer Hart Melissa Landrum Bonnie L. Maidak Michael Murphy Terence Murphy Bhanu Rajput Lillian Riddick David Webb Janet Weber Wendy Wu Kim D. Pruitt Donna Maglott Adam Siepel Brona Brejova Mark Diekhans Rachel Harte Robert Baertsch Jim Kent David Haussler Michael Brent Laura Langton Charles L.G. Comstock Michael Stevens Chaochun Wei Marijke J. van Baren Kourosh Salehi-Ashtiani Ryan R. Murray Lila Ghamsari Elizabeth Mello Chenwei Lin Christa Pennacchio Kirsten Schreiber Nicole Shapiro Amber Marsh Elizabeth Pardes Troy Moore Anita Lebeau Mike Muratet Blake Simmons David Kloske Stephanie Sieja James Hudson Praveen Sethupathy Michael Brownstein Narayan Bhat Joseph Lazar Howard Jacob Chris E. Gruber Mark R. Smith John McPherson Angela M. Garcia Preethi H. Gunaratne Jiaqian Wu Donna Muzny Richard A. Gibbs Alice C. Young Gerard G. Bouffard Robert W. Blakesley Jim Mullikin Eric D. Green Mark C. Dickson Alex C. Rodriguez Jane Grimwood Jeremy Schmutz Richard M. Myers Martin Hirst Thomas Zeng Kane Tse Michelle Moksa Merinda Deng Kevin Ma Diana Mah Johnson Pang Greg Taylor Eric Chuah Athena Deng Keith Fichter Anne Go Stephanie Lee Jing Wang Malachi Griffith Ryan Morin Richard A. Moore Michael Mayo Sarah Munro Susan Wagner Steven J.M. Jones Robert A. Holt Marco A. Marra Sun Lu Shuwei Yang James Hartigan Marcus Graf Ralf Wagner Stanley Letovksy Jacqueline C. Pulido Keith Robison Dominic Esposito James Hartley
  • ... [+118 authors] ...,
  • Vanessa E. Wall
  • Ralph F. Hopkins
  • Osamu Ohara
  • Stefan Wiemann
  • First Published September 18, 2009
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