All papers authored by Adam M. Phillippy
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2024
Kateryna D. Makova 
,
Brandon D. Pickett ,
Robert S. Harris,
Gabrielle A. Hartley,
Monika Cechova,
Karol Pal ,
Sergey Nurk,
DongAhn Yoo ,
Qiuhui Li,
Prajna Hebbar,
Barbara C. McGrath,
Francesca Antonacci ,
Margaux Aubel ,
Arjun Biddanda,
Matthew Borchers
and 69 other authors
,
Brandon D. Pickett ,
Robert S. Harris,
Gabrielle A. Hartley,
Monika Cechova,
Karol Pal ,
Sergey Nurk,
DongAhn Yoo ,
Qiuhui Li,
Prajna Hebbar,
Barbara C. McGrath,
Francesca Antonacci ,
Margaux Aubel ,
Arjun Biddanda,
Matthew Borchers
and 69 other authors
The complete sequence and comparative analysis of ape sex chromosomes
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Delphine Larivière ,
Linelle Abueg,
Nadolina Brajuka,
Cristóbal Gallardo-Alba,
Bjorn Grüning ,
Byung June Ko,
Alex Ostrovsky,
Marc Palmada-Flores ,
Brandon D. Pickett ,
Keon Rabbani ,
Agostinho Antunes ,
Jennifer R. Balacco,
Mark J. P. Chaisson ,
Haoyu Cheng,
Joanna Collins
and 26 other authors
,
Linelle Abueg,
Nadolina Brajuka,
Cristóbal Gallardo-Alba,
Bjorn Grüning ,
Byung June Ko,
Alex Ostrovsky,
Marc Palmada-Flores ,
Brandon D. Pickett ,
Keon Rabbani ,
Agostinho Antunes ,
Jennifer R. Balacco,
Mark J. P. Chaisson ,
Haoyu Cheng,
Joanna Collins
and 26 other authors
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
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2023
Mikhail Kolmogorov ,
Kimberley J. Billingsley ,
Mira Mastoras ,
Melissa Meredith ,
Jean Monlong,
Ryan Lorig-Roach,
Mobin Asri,
Pilar Alvarez Jerez,
Laksh Malik,
Ramita Dewan ,
Xylena Reed,
Rylee M. Genner,
Kensuke Daida ,
Sairam Behera ,
Kishwar Shafin
and 15 other authors
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,
Kimberley J. Billingsley ,
Mira Mastoras ,
Melissa Meredith ,
Jean Monlong,
Ryan Lorig-Roach,
Mobin Asri,
Pilar Alvarez Jerez,
Laksh Malik,
Ramita Dewan ,
Xylena Reed,
Rylee M. Genner,
Kensuke Daida ,
Sairam Behera ,
Kishwar Shafin
and 15 other authors
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Arang Rhie ,
Sergey Nurk,
Monika Cechova,
Savannah J. Hoyt ,
Dylan J. Taylor ,
Nicolas Altemose ,
Paul W. Hook ,
Sergey Koren ,
Mikko Rautiainen,
Ivan A. Alexandrov,
Jamie Allen ,
Mobin Asri,
Andrey V. Bzikadze ,
Nae-Chyun Chen,
Chen-Shan Chin
and 72 other authors
,
Sergey Nurk,
Monika Cechova,
Savannah J. Hoyt ,
Dylan J. Taylor ,
Nicolas Altemose ,
Paul W. Hook ,
Sergey Koren ,
Mikko Rautiainen,
Ivan A. Alexandrov,
Jamie Allen ,
Mobin Asri,
Andrey V. Bzikadze ,
Nae-Chyun Chen,
Chen-Shan Chin
and 72 other authors
The complete sequence of a human Y chromosome
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2022
Nicolas Altemose ,
Pragya Sidhwani ,
Lev Uralsky ,
Fedor D. Ryabov ,
Colin J. Shew,
Michael E. G. Sauria ,
Valery A. Shepelev,
Mitchell R. Vollger ,
Arang Rhie ,
Glennis A. Logsdon ,
Kishwar Shafin ,
Andrey V. Bzikadze ,
Daniel Olson ,
Sasha A. Langley,
Leonardo Gomes de Lima
and 46 other authors
,
Pragya Sidhwani ,
Lev Uralsky ,
Fedor D. Ryabov ,
Colin J. Shew,
Michael E. G. Sauria ,
Valery A. Shepelev,
Mitchell R. Vollger ,
Arang Rhie ,
Glennis A. Logsdon ,
Kishwar Shafin ,
Andrey V. Bzikadze ,
Daniel Olson ,
Sasha A. Langley,
Leonardo Gomes de Lima
and 46 other authors
Complete genomic and epigenetic maps of human centromeres
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Savannah J. Hoyt ,
Jessica M. Storer ,
Gabrielle A. Hartley,
Patrick G. S. Grady ,
Ariel Gershman ,
Leonardo G. de Lima ,
Charles Limouse,
Reza Halabian ,
Luke Wojenski ,
Matias Rodriguez ,
Nicolas Altemose ,
Arang Rhie ,
Leighton J. Core ,
Jennifer L. Gerton ,
Wojciech Makalowski
and 12 other authors
,
Jessica M. Storer ,
Gabrielle A. Hartley,
Patrick G. S. Grady ,
Ariel Gershman ,
Leonardo G. de Lima ,
Charles Limouse,
Reza Halabian ,
Luke Wojenski ,
Matias Rodriguez ,
Nicolas Altemose ,
Arang Rhie ,
Leighton J. Core ,
Jennifer L. Gerton ,
Wojciech Makalowski
and 12 other authors
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements
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Mitchell R. Vollger ,
Xavi Guitart ,
Philip C. Dishuck ,
Ludovica Mercuri ,
William T. Harvey ,
Ariel Gershman ,
Mark Diekhans ,
Arvis Sulovari ,
Katherine M. Munson ,
Alexandra P. Lewis,
Alexandra M. Lewis,
Kendra Hoekzema ,
David Porubsky ,
Ruiyang Li ,
Sergey Nurk
and 6 other authors
,
Xavi Guitart ,
Philip C. Dishuck ,
Ludovica Mercuri ,
William T. Harvey ,
Ariel Gershman ,
Mark Diekhans ,
Arvis Sulovari ,
Katherine M. Munson ,
Alexandra P. Lewis,
Alexandra M. Lewis,
Kendra Hoekzema ,
David Porubsky ,
Ruiyang Li ,
Sergey Nurk
and 6 other authors
Segmental duplications and their variation in a complete human genome
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Sergey Aganezov ,
Stephanie M. Yan ,
Daniela C. Soto ,
Melanie Kirsche ,
Samantha Zarate ,
Pavel Avdeyev ,
Dylan J. Taylor ,
Kishwar Shafin ,
Alaina Shumate ,
Chunlin Xiao ,
Justin Wagner,
Jennifer McDaniel ,
Nathan D. Olson ,
Michael E. G. Sauria ,
Mitchell R. Vollger
and 18 other authors
,
Stephanie M. Yan ,
Daniela C. Soto ,
Melanie Kirsche ,
Samantha Zarate ,
Pavel Avdeyev ,
Dylan J. Taylor ,
Kishwar Shafin ,
Alaina Shumate ,
Chunlin Xiao ,
Justin Wagner,
Jennifer McDaniel ,
Nathan D. Olson ,
Michael E. G. Sauria ,
Mitchell R. Vollger
and 18 other authors
A complete reference genome improves analysis of human genetic variation
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Ariel Gershman ,
Michael E. G. Sauria ,
Xavi Guitart ,
Mitchell R. Vollger ,
Paul W. Hook ,
Savannah J. Hoyt ,
Miten Jain ,
Alaina Shumate ,
Roham Razaghi ,
Sergey Koren ,
Nicolas Altemose ,
Gina V. Caldas,
Glennis A. Logsdon ,
Arang Rhie ,
Evan E. Eichler
and 5 other authors
,
Michael E. G. Sauria ,
Xavi Guitart ,
Mitchell R. Vollger ,
Paul W. Hook ,
Savannah J. Hoyt ,
Miten Jain ,
Alaina Shumate ,
Roham Razaghi ,
Sergey Koren ,
Nicolas Altemose ,
Gina V. Caldas,
Glennis A. Logsdon ,
Arang Rhie ,
Evan E. Eichler
and 5 other authors
Epigenetic patterns in a complete human genome
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Sergey Nurk ,
Sergey Koren ,
Arang Rhie ,
Mikko Rautiainen ,
Andrey V. Bzikadze ,
Alla Mikheenko,
Mitchell R. Vollger ,
Nicolas Altemose ,
Lev Uralsky ,
Ariel Gershman ,
Sergey Aganezov ,
Savannah J. Hoyt ,
Mark Diekhans ,
Glennis A. Logsdon ,
Michael Alonge
and 85 other authors
,
Sergey Koren ,
Arang Rhie ,
Mikko Rautiainen ,
Andrey V. Bzikadze ,
Alla Mikheenko,
Mitchell R. Vollger ,
Nicolas Altemose ,
Lev Uralsky ,
Ariel Gershman ,
Sergey Aganezov ,
Savannah J. Hoyt ,
Mark Diekhans ,
Glennis A. Logsdon ,
Michael Alonge
and 85 other authors
The complete sequence of a human genome
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Ann M. Mc Cartney ,
Kishwar Shafin ,
Michael Alonge,
Andrey V. Bzikadze,
Alaina Shumate,
Giulio Formenti ,
Chirag Jain,
Daniela C. Soto ,
Arkarachai Fungtammasan ,
Ivan Sović,
Sergey Koren ,
Jonathan Md D. Wood ,
Glennis A. Logsdon ,
Kerstin Howe ,
Justin M. Zook
and 6 other authors
,
Kishwar Shafin ,
Michael Alonge,
Andrey V. Bzikadze,
Alaina Shumate,
Giulio Formenti ,
Chirag Jain,
Daniela C. Soto ,
Arkarachai Fungtammasan ,
Ivan Sović,
Sergey Koren ,
Jonathan Md D. Wood ,
Glennis A. Logsdon ,
Kerstin Howe ,
Justin M. Zook
and 6 other authors
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
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Mara K. N. Lawniczak,
Richard Durbin,
Paul Flicek,
Kerstin Lindblad-Toh ,
Xiaofeng Wei,
John M. Archibald ,
William J. Baker ,
Katherine Belov,
Mark L. Blaxter,
Tomas Marques Bonet ,
Anna K. Childers ,
Jonathan A. Coddington ,
Keith A. Crandall ,
Andrew J. Crawford,
Robert P. Davey
and 30 other authors
,
Xiaofeng Wei,
John M. Archibald ,
William J. Baker ,
Katherine Belov,
Mark L. Blaxter,
Tomas Marques Bonet ,
Anna K. Childers ,
Jonathan A. Coddington ,
Keith A. Crandall ,
Andrew J. Crawford,
Robert P. Davey
and 30 other authors
Standards recommendations for the Earth BioGenome Project
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2021
Chentao Yang,
Yang Zhou ,
Stephanie Marcus,
Giulio Formenti ,
Lucie A. Bergeron,
Zhenzhen Song,
Xupeng Bi,
Juraj Bergman ,
Marjolaine Marie C. Rousselle,
Chengran Zhou ,
Long Zhou,
Yuan Deng,
Miaoquan Fang,
Duo Xie ,
Yuanzhen Zhu
and 18 other authors
,
Stephanie Marcus,
Giulio Formenti ,
Lucie A. Bergeron,
Zhenzhen Song,
Xupeng Bi,
Juraj Bergman ,
Marjolaine Marie C. Rousselle,
Chengran Zhou ,
Long Zhou,
Yuan Deng,
Miaoquan Fang,
Duo Xie ,
Yuanzhen Zhu
and 18 other authors
Evolutionary and biomedical insights from a marmoset diploid genome assembly
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Arang Rhie ,
Shane A. McCarthy,
Olivier Fedrigo ,
Joana Damas ,
Giulio Formenti ,
Sergey Koren ,
Marcela Uliano-Silva ,
William Chow ,
Arkarachai Fungtammasan ,
Gregory L. Gedman,
Mark Chaisson,
Lindsey J. Cantin,
Chul Lee,
Francoise Thibaud-Nissen ,
Leanne Haggerty
and 114 other authors
,
Shane A. McCarthy,
Olivier Fedrigo ,
Joana Damas ,
Giulio Formenti ,
Sergey Koren ,
Marcela Uliano-Silva ,
William Chow ,
Arkarachai Fungtammasan ,
Gregory L. Gedman,
Mark Chaisson,
Lindsey J. Cantin,
Chul Lee,
Francoise Thibaud-Nissen ,
Leanne Haggerty
and 114 other authors
Towards complete and error-free genome assemblies of all vertebrate species
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Glennis A. Logsdon ,
Mitchell R. Vollger ,
PingHsun Hsieh,
Yafei Mao ,
Mikhail A. Liskovykh,
Sergey Koren ,
Sergey Nurk,
Ludovica Mercuri ,
Philip C. Dishuck ,
Arang Rhie ,
Leonardo G. de Lima ,
Tatiana Dvorkina,
David Porubsky ,
William T. Harvey,
Alla Mikheenko
and 17 other authors
,
Mitchell R. Vollger ,
PingHsun Hsieh,
Yafei Mao ,
Mikhail A. Liskovykh,
Sergey Koren ,
Sergey Nurk,
Ludovica Mercuri ,
Philip C. Dishuck ,
Arang Rhie ,
Leonardo G. de Lima ,
Tatiana Dvorkina,
David Porubsky ,
William T. Harvey,
Alla Mikheenko
and 17 other authors
The structure, function and evolution of a complete human chromosome 8
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Yang Zhou ,
Linda Shearwin-Whyatt ,
Jing Li,
Zhenzhen Song,
Takashi Hayakawa ,
David Stevens,
Jane C. Fenelon ,
Emma Peel ,
Yuanyuan Cheng ,
Filip Pajpach,
Natasha Bradley,
Hikoyu Suzuki,
Masato Nikaido,
Joana Damas ,
Tasman Daish
and 27 other authors
,
Linda Shearwin-Whyatt ,
Jing Li,
Zhenzhen Song,
Takashi Hayakawa ,
David Stevens,
Jane C. Fenelon ,
Emma Peel ,
Yuanyuan Cheng ,
Filip Pajpach,
Natasha Bradley,
Hikoyu Suzuki,
Masato Nikaido,
Joana Damas ,
Tasman Daish
and 27 other authors
Platypus and echidna genomes reveal mammalian biology and evolution
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