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Research

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
Method

Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm" > Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

  • Aleksey V. Zimin
  • Daniela Puiu
  • Ming-Cheng Luo
  • Tingting Zhu
  • Sergey Koren
  • Guillaume Marçais
  • James A. Yorke
  • Jan Dvořák
  • Steven L. Salzberg
  • First Published January 27, 2017
Resource

Improved definition of the mouse transcriptome via targeted RNA sequencing

  • Giovanni Bussotti
  • Tommaso Leonardi
  • Michael B. Clark
  • Tim R. Mercer
  • Joanna Crawford
  • Lorenzo Malquori
  • ... [+1 authors] ...,
  • Cedric Notredame
  • Marcel E. Dinger
  • John S. Mattick
  • Anton J. Enright
  • First Published May 2, 2016
Resource

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
Resource

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

  • Thomas Derrien
  • Rory Johnson
  • Giovanni Bussotti
  • Andrea Tanzer
  • Sarah Djebali
  • Hagen Tilgner Gregory Guernec David Martin Angelika Merkel David G. Knowles Julien Lagarde Lavanya Veeravalli Xiaoan Ruan Yijun Ruan Timo Lassmann Piero Carninci James B. Brown Leonard Lipovich Jose M. Gonzalez Mark Thomas Carrie A. Davis Ramin Shiekhattar Thomas R. Gingeras
  • ... [+18 authors] ...,
  • Tim J. Hubbard
  • Cedric Notredame
  • Jennifer Harrow
  • Roderic Guigó
  • First Published September 5, 2012
Resource

GAGE: A critical evaluation of genome assemblies and assembly algorithms

  • Steven L. Salzberg
  • Adam M. Phillippy
  • Aleksey Zimin
  • Daniela Puiu
  • Tanja Magoc
  • Sergey Koren Todd J. Treangen Michael C. Schatz Arthur L. Delcher
  • ... [+4 authors] ...,
  • Michael Roberts
  • Guillaume Marçais
  • Mihai Pop
  • James A. Yorke
  • First Published December 6, 2011
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