Literature DB >> 30670797

Reply to 'Errors in long-read assemblies can critically affect protein prediction'.

Sergey Koren1, Adam M Phillippy1, Jared T Simpson2, Nicholas J Loman3, Matthew Loose4.   

Abstract

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Year:  2019        PMID: 30670797     DOI: 10.1038/s41587-018-0005-y

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  11 in total

Review 1.  Centromere studies in the era of 'telomere-to-telomere' genomics.

Authors:  Karen H Miga
Journal:  Exp Cell Res       Date:  2020-06-03       Impact factor: 3.905

Review 2.  Long-read human genome sequencing and its applications.

Authors:  Glennis A Logsdon; Mitchell R Vollger; Evan E Eichler
Journal:  Nat Rev Genet       Date:  2020-06-05       Impact factor: 53.242

3.  Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands.

Authors:  Joanna Warwick-Dugdale; Natalie Solonenko; Karen Moore; Lauren Chittick; Ann C Gregory; Michael J Allen; Matthew B Sullivan; Ben Temperton
Journal:  PeerJ       Date:  2019-04-25       Impact factor: 2.984

4.  ntEdit: scalable genome sequence polishing.

Authors:  René L Warren; Lauren Coombe; Hamid Mohamadi; Jessica Zhang; Barry Jaquish; Nathalie Isabel; Steven J M Jones; Jean Bousquet; Joerg Bohlmann; Inanç Birol
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

5.  Telomere-to-telomere assembly of a complete human X chromosome.

Authors:  Karen H Miga; Sergey Koren; Arang Rhie; Mitchell R Vollger; Ariel Gershman; Andrey Bzikadze; Shelise Brooks; Edmund Howe; David Porubsky; Glennis A Logsdon; Valerie A Schneider; Tamara Potapova; Jonathan Wood; William Chow; Joel Armstrong; Jeanne Fredrickson; Evgenia Pak; Kristof Tigyi; Milinn Kremitzki; Christopher Markovic; Valerie Maduro; Amalia Dutra; Gerard G Bouffard; Alexander M Chang; Nancy F Hansen; Amy B Wilfert; Françoise Thibaud-Nissen; Anthony D Schmitt; Jon-Matthew Belton; Siddarth Selvaraj; Megan Y Dennis; Daniela C Soto; Ruta Sahasrabudhe; Gulhan Kaya; Josh Quick; Nicholas J Loman; Nadine Holmes; Matthew Loose; Urvashi Surti; Rosa Ana Risques; Tina A Graves Lindsay; Robert Fulton; Ira Hall; Benedict Paten; Kerstin Howe; Winston Timp; Alice Young; James C Mullikin; Pavel A Pevzner; Jennifer L Gerton; Beth A Sullivan; Evan E Eichler; Adam M Phillippy
Journal:  Nature       Date:  2020-07-14       Impact factor: 49.962

6.  Oxford Nanopore sequencing: new opportunities for plant genomics?

Authors:  Kathryn Dumschott; Maximilian H-W Schmidt; Harmeet Singh Chawla; Rod Snowdon; Björn Usadel
Journal:  J Exp Bot       Date:  2020-09-19       Impact factor: 6.992

7.  Towards complete and error-free genome assemblies of all vertebrate species.

Authors:  Arang Rhie; Shane A McCarthy; Olivier Fedrigo; Joana Damas; Giulio Formenti; Sergey Koren; Marcela Uliano-Silva; William Chow; Arkarachai Fungtammasan; Juwan Kim; Chul Lee; Byung June Ko; Mark Chaisson; Gregory L Gedman; Lindsey J Cantin; Francoise Thibaud-Nissen; Leanne Haggerty; Iliana Bista; Michelle Smith; Bettina Haase; Jacquelyn Mountcastle; Sylke Winkler; Sadye Paez; Jason Howard; Sonja C Vernes; Tanya M Lama; Frank Grutzner; Wesley C Warren; Christopher N Balakrishnan; Dave Burt; Julia M George; Matthew T Biegler; David Iorns; Andrew Digby; Daryl Eason; Bruce Robertson; Taylor Edwards; Mark Wilkinson; George Turner; Axel Meyer; Andreas F Kautt; Paolo Franchini; H William Detrich; Hannes Svardal; Maximilian Wagner; Gavin J P Naylor; Martin Pippel; Milan Malinsky; Mark Mooney; Maria Simbirsky; Brett T Hannigan; Trevor Pesout; Marlys Houck; Ann Misuraca; Sarah B Kingan; Richard Hall; Zev Kronenberg; Ivan Sović; Christopher Dunn; Zemin Ning; Alex Hastie; Joyce Lee; Siddarth Selvaraj; Richard E Green; Nicholas H Putnam; Ivo Gut; Jay Ghurye; Erik Garrison; Ying Sims; Joanna Collins; Sarah Pelan; James Torrance; Alan Tracey; Jonathan Wood; Robel E Dagnew; Dengfeng Guan; Sarah E London; David F Clayton; Claudio V Mello; Samantha R Friedrich; Peter V Lovell; Ekaterina Osipova; Farooq O Al-Ajli; Simona Secomandi; Heebal Kim; Constantina Theofanopoulou; Michael Hiller; Yang Zhou; Robert S Harris; Kateryna D Makova; Paul Medvedev; Jinna Hoffman; Patrick Masterson; Karen Clark; Fergal Martin; Kevin Howe; Paul Flicek; Brian P Walenz; Woori Kwak; Hiram Clawson; Mark Diekhans; Luis Nassar; Benedict Paten; Robert H S Kraus; Andrew J Crawford; M Thomas P Gilbert; Guojie Zhang; Byrappa Venkatesh; Robert W Murphy; Klaus-Peter Koepfli; Beth Shapiro; Warren E Johnson; Federica Di Palma; Tomas Marques-Bonet; Emma C Teeling; Tandy Warnow; Jennifer Marshall Graves; Oliver A Ryder; David Haussler; Stephen J O'Brien; Jonas Korlach; Harris A Lewin; Kerstin Howe; Eugene W Myers; Richard Durbin; Adam M Phillippy; Erich D Jarvis
Journal:  Nature       Date:  2021-04-28       Impact factor: 49.962

8.  Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size.

Authors:  Francesco Cicconardi; James J Lewis; Simon H Martin; Robert D Reed; Charles G Danko; Stephen H Montgomery
Journal:  Mol Biol Evol       Date:  2021-09-27       Impact factor: 16.240

Review 9.  Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.

Authors:  Ole K Tørresen; Bastiaan Star; Pablo Mier; Miguel A Andrade-Navarro; Alex Bateman; Patryk Jarnot; Aleksandra Gruca; Marcin Grynberg; Andrey V Kajava; Vasilis J Promponas; Maria Anisimova; Kjetill S Jakobsen; Dirk Linke
Journal:  Nucleic Acids Res       Date:  2019-12-02       Impact factor: 16.971

10.  Highly contiguous assemblies of 101 drosophilid genomes.

Authors:  Bernard Y Kim; Jeremy R Wang; Daniel R Matute; Dmitri A Petrov; Danny E Miller; Olga Barmina; Emily Delaney; Ammon Thompson; Aaron A Comeault; David Peede; Emmanuel R R D'Agostino; Julianne Pelaez; Jessica M Aguilar; Diler Haji; Teruyuki Matsunaga; Ellie E Armstrong; Molly Zych; Yoshitaka Ogawa; Marina Stamenković-Radak; Mihailo Jelić; Marija Savić Veselinović; Marija Tanasković; Pavle Erić; Jian-Jun Gao; Takehiro K Katoh; Masanori J Toda; Hideaki Watabe; Masayoshi Watada; Jeremy S Davis; Leonie C Moyle; Giulia Manoli; Enrico Bertolini; Vladimír Košťál; R Scott Hawley; Aya Takahashi; Corbin D Jones; Donald K Price; Noah Whiteman; Artyom Kopp
Journal:  Elife       Date:  2021-07-19       Impact factor: 8.713

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