Adam M. Phillippy - Publications, H-index & Citations

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Adam M. Phillippy

national institutes of health

94H-index

340Paper Count

7.7WCitation Count

Published Papers 91

Publication Date

Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet

Cell Genomics

IF9

2026-08-06

OAAI

Juhyun Kim; Benjamin D. Rosen; Sarah E. Fumagalli; Kristen L. Kuhn; Amy Long; Jeffrey J. Schoenebeck; Heather Schwartz; Lan Wu-Cavener; Aleksey V. Zimin; Douglas R. Cavener; Timothy P.L. Smith; Adam M. Phillippy; Sergey Koren; Arang Rhie

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Telomere-to-telomere genome assembly and a pangenome for the rat

Cell Genomics

IF9

2026-08-06

OAAI

Kai Li; Julia L. Ciosek; Sergey Koren; Adam M. Phillippy; Yaming Zhu; William A. Lauer; Shelise Y. Brooks; Gerard G. Bouffard; Brandon D. Pickett; Beth L. Dumont; Melissa L. Smith; Theodore S. Kalbfleisch; Peter A. Doris

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Harmonizing standards and resources for the medical genome

Nature

IF48.5

2026-07-01

PREAI

Euan A. Ashley; Ash A. Alizadeh; Hanae Armitage; Ami S. Bhatt; Yair Blumenfeld; Andrew Carroll; R. Martin Chavez; Petros Giannikopoulos; Megan E. Grove; Meghan C. Halley; Kiran Khush; Niall J. Lennon; Samantha Maragh; Alexander Marson; Benedict Paten; Adam M. Phillippy; Matthew H. Porteus; Heidi L. Rehm; Bradley R. Ringeisen; Julia Salzman; Valerie A. Schneider; Fritz J. Sedlazeck; Lars M. Steinmetz; Fyodor D. Urnov; Stacia K. Wyman; Justin M. Zook; Lloyd B. Minor; Jennifer A. Doudna

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Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes

Cell Genomics

IF9

2025-10-02

OAAI

Tamara A. Potapova; Paxton Kostos; Sean McKinney; Matthew Borchers; Jeff Haug; Andrea Guarracino; Steven J. Solar; Mark Mattingly; Graciela Monfort Anez; Leonardo Gomes de Lima; Yan Wang; Chongbei Zhao; Kate Hall; Madelaine Gogol; Sophie Hoffman; Dmitry Antipov; Arang Rhie; Monika Cechova; Karen H. Miga; Erik Garrison; Adam M. Phillippy; Jennifer L. Gerton

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The formation and propagation of human Robertsonian chromosomes

Nature

IF48.5

2025-09-24

OAAI

Leonardo Gomes de Lima; Andrea Guarracino; Sergey Koren; Tamara Potapova; Sean McKinney; Arang Rhie; Steven J. Solar; Chris Seidel; Brandon L. Fagen; Brian P. Walenz; Gerard G. Bouffard; Shelise Y. Brooks; Michael Peterson; Kate Hall; Juyun Crawford; Alice C. Young; Brandon D. Pickett; Erik Garrison; Adam M. Phillippy; Jennifer L. Gerton

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Analysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA

JOURNAL OF MOLECULAR EVOLUTION

IF0

2025-09-01

OAAI

Chen, Yaohui; Kim, Jung-Hyun; Lee, Hee-Sheung; Koren, Sergey; Larionov, Vladimir; Phillippy, Adam M.; Schlessinger, David; Nagaraja, Ramaiah

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Author Correction: Complex genetic variation in nearly complete human genomes

Nature

IF48.5

2025-08-26

OAAI

Glennis A. Logsdon; Peter Ebert; Peter A. Audano; Mark Loftus; David Porubsky; Jana Ebler; Feyza Yilmaz; Pille Hallast; Timofey Prodanov; DongAhn Yoo; Carolyn A. Paisie; William T. Harvey; Xuefang Zhao; Gianni V. Martino; Mir Henglin; Katherine M. Munson; Keon Rabbani; Chen-Shan Chin; Bida Gu; Hufsah Ashraf; Stephan Scholz; Olanrewaju Austine-Orimoloye; Parithi Balachandran; Marc Jan Bonder; Haoyu Cheng; Zechen Chong; Jonathan Crabtree; Mark Gerstein; Lisbeth A. Guethlein; Patrick Hasenfeld; Glenn Hickey; Kendra Hoekzema; Sarah E. Hunt; Matthew Jensen; Yunzhe Jiang; Sergey Koren; Youngjun Kwon; Chong Li; Heng Li; Jiaqi Li; Paul J. Norman; Keisuke K. Oshima; Benedict Paten; Adam M. Phillippy; Nicholas R. Pollock; Tobias Rausch; Mikko Rautiainen; Yuwei Song; Arda Söylev; Arvis Sulovari; Likhitha Surapaneni; Vasiliki Tsapalou; Weichen Zhou; Ying Zhou; Qihui Zhu; Michael C. Zody; Ryan E. Mills; Scott E. Devine; Xinghua Shi; Michael E. Talkowski; Mark J. P. Chaisson; Alexander T. Dilthey; Miriam K. Konkel; Jan O. Korbel; Charles Lee; Christine R. Beck; Evan E. Eichler; Tobias Marschall

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Complex genetic variation in nearly complete human genomes

Nature

IF48.5

2025-07-23

OAAI

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Integrated analysis of the complete sequence of a macaque genome

NATURE

IF48.5

2025-02-26

PREAI

Zhang, Shilong; Xu, Ning; Fu, Lianting; Yang, Xiangyu; Ma, Kaiyue; Li, Yamei; Yang, Zikun; Li, Zhengtong; Feng, Yu; Jiang, Xinrui; Han, Junmin; Hu, Ruixing; Zhang, Lu; Lian, Da; de Gennaro, Luciana; Paparella, Annalisa; Ryabov, Fedor; Meng, Dan; He, Yaoxi; Wu, Dongya; Yang, Chentao; Mao, Yuxiang; Bian, Xinyan; Lu, Yong; Antonacci, Francesca; Ventura, Mario; Shepelev, Valery A.; Miga, Karen H.; Alexandrov, Ivan A.; Logsdon, Glennis A.; Phillippy, Adam M.; Su, Bing; Zhang, Guojie; Eichler, Evan E.; Lu, Qing; Shi, Yongyong; Sun, Qiang; Mao, Yafei

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Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

GENOME RESEARCH

IF5.5

2024-11-06

OAAI

Koren, Sergey; Bao, Zhigui; Guarracino, Andrea; Ou, Shujun; Goodwin, Sara; Jenike, Katharine M.; Lucas, Julian; Mcnulty, Brandy; Park, Jimin; Rautiainen, Mikko; Rhie, Arang; Roelofs, Dick; Schneiders, Harrie; Vrijenhoek, Ilse; Nijbroek, Koen; Nordesjo, Olle; Nurk, Sergey; Vella, Mike; Lawrence, Katherine R.; Ware, Doreen; Schatz, Michael C.; Garrison, Erik; Huang, Sanwen; Mccombie, William Richard; Miga, Karen H.; Wittenberg, Alexander H. J.; Phillippy, Adam M.

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The Ruminant Telomere-to-Telomere (RT2T) Consortium

NATURE GENETICS

IF31.8

2024-08-05

PREAI

Kalbfleisch, Theodore S.; McKay, Stephanie D.; Murdoch, Brenda M.; Adelson, David L.; Almansa-Villa, Diego; Becker, Gabrielle; Beckett, Linda M.; Benitez-Galeano, Maria Jose; Biase, Fernando; Casey, Theresa; Chuong, Edward; Clark, Emily; Clarke, Shannon; Cockett, Noelle; Couldrey, Christine; Davis, Brian W.; Elsik, Christine G.; Faraut, Thomas; Gao, Yahui; Genet, Carine; Grady, Patrick; Green, Jonathan; Green, Richard; Guan, Dailu; Hagen, Darren; Hartley, Gabrielle A.; Heaton, Mike; Hoyt, Savannah J.; Huang, Wen; Jarvis, Erich; Kalleberg, Jenna; Khatib, Hasan; Koepfi, Klaus-Peter; Koltes, James; Koren, Sergey; Kuehn, Christa; Leeb, Tosso; Leonard, Alexander; Liu, George E.; Low, Wai Yee; Mcconnell, Hunter; Mcrae, Kathryn; Miga, Karen; Mousel, Michelle; Neibergs, Holly; Olagunju, Temitayo; Pennell, Matt; Petry, Bruna; Pewsner, Mirjam; Phillippy, Adam M.; Pickett, Brandon D.; Pineda, Paulene; Potapova, Tamara; Rachagani, Satyanarayana; Rhie, Arang; Rijnkels, Monique; Robic, Annie; Rodriguez Osorio, Nelida; Safonova, Yana; Schettini, Gustavo; Schnabel, Robert D.; Sirpu Natesh, Nagabhishek; Stegemiller, Morgan; Storer, Jessica; Stothard, Paul; Stull, Caleb; Tosser-Klopp, Gwenola; Traglia, German M.; Tuggle, Christopher K.; Van Tassell, Curtis P.; Watson, Corey; Weikard, Rosemarie; Wimmers, Klaus; Xie, Shangqian; Yang, Liu; Smith, Timothy P. L.; O'Neill, Rachel J.; Rosen, Benjamin D.

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A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

MOLECULAR BIOLOGY AND EVOLUTION

IF5.3

2024-02-20

OAAI

Bukhman, Yury, V; Morin, Phillip A.; Meyer, Susanne; Chu, Li-Fang; Jacobsen, Jeff K.; Antosiewicz-Bourget, Jessica; Mamott, Daniel; Gonzales, Maylie; Argus, Cara; Bolin, Jennifer; Berres, Mark E.; Fedrigo, Olivier; Steill, John; Swanson, Scott A.; Jiang, Peng; Rhie, Arang; Formenti, Giulio; Phillippy, Adam M.; Harris, Robert S.; Wood, Jonathan M. D.; Howe, Kerstin; Kirilenko, Bogdan M.; Munegowda, Chetan; Hiller, Michael; Jain, Aashish; Kihara, Daisuke; Johnston, J. Spencer; Ionkov, Alexander; Raja, Kalpana; Toh, Huishi; Lang, Aimee; Wolf, Magnus; Jarvis, Erich D.; Thomson, James A.; Chaisson, Mark J. P.; Stewart, Ron

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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

NATURE BIOTECHNOLOGY

IF41.7

2024-01-26

OAAI

Lariviere, Delphine; Abueg, Linelle; Brajuka, Nadolina; Gallardo-Alba, Cristobal; Gruening, Bjorn; Ko, Byung June; Ostrovsky, Alex; Palmada-Flores, Marc; Pickett, Brandon D.; Rabbani, Keon; Antunes, Agostinho; Balacco, Jennifer R.; Chaisson, Mark J. P.; Cheng, Haoyu; Collins, Joanna; Couture, Melanie; Denisova, Alexandra; Fedrigo, Olivier; Gallo, Guido Roberto; Giani, Alice Maria; Gooder, Grenville MacDonald; Horan, Kathleen; Jain, Nivesh; Johnson, Cassidy; Kim, Heebal; Lee, Chul; Marques-Bonet, Tomas; O'Toole, Brian; Rhie, Arang; Secomandi, Simona; Sozzoni, Marcella; Tilley, Tatiana; Uliano-Silva, Marcela; van den Beek, Marius; Williams, Robert W.; Waterhouse, Robert M.; Phillippy, Adam M.; Jarvis, Erich D.; Schatz, Michael C.; Nekrutenko, Anton; Formenti, Giulio

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High-quality metagenome assembly from long accurate reads with metaMDBG

NATURE BIOTECHNOLOGY

IF41.7

2024-01-02

OAAI

Benoit, Gaetan; Raguideau, Sebastien; James, Robert; Phillippy, Adam M.; Chikhi, Rayan; Quince, Christopher

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Improved sequence mapping using a complete reference genome and lift-over

NATURE METHODS

IF32.1

2023-11-30

OAAI

Chen, Nae-Chyun; Paulin, Luis F.; Sedlazeck, Fritz J.; Koren, Sergey; Phillippy, Adam M.; Langmead, Ben

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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

NATURE METHODS

IF32.1

2023-09-14

OAAI

Kolmogorov, Mikhail; Billingsley, Kimberley J.; Mastoras, Mira; Meredith, Melissa; Monlong, Jean; Lorig-Roach, Ryan; Asri, Mobin; Alvarez Jerez, Pilar; Malik, Laksh; Dewan, Ramita; Reed, Xylena; Genner, Rylee M.; Daida, Kensuke; Behera, Sairam; Shafin, Kishwar; Pesout, Trevor; Prabakaran, Jeshuwin; Carnevali, Paolo; Yang, Jianzhi; Rhie, Arang; Scholz, Sonja W.; Traynor, Bryan J.; Miga, Karen H.; Jain, Miten; Timp, Winston; Phillippy, Adam M.; Chaisson, Mark; Sedlazeck, Fritz J.; Blauwendraat, Cornelis; Paten, Benedict

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Pangenome graph construction from genome alignments with Minigraph-Cactus

NATURE BIOTECHNOLOGY

IF41.7

2023-05-10

OAAI

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

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Telomere-to-telomere assembly of diploid chromosomes with Verkko

NATURE BIOTECHNOLOGY

IF41.7

2023-02-16

103

OAAI

Rautiainen, Mikko; Nurk, Sergey; Walenz, Brian P.; Logsdon, Glennis A.; Porubsky, David; Rhie, Arang; Eichler, Evan E.; Phillippy, Adam M.; Koren, Sergey

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A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

DNA RESEARCH

IF2.9

2022-10-05

OAAI

McGrath, J. Mitchell; Funk, Andrew; Galewski, Paul; Ou, Shujun; Townsend, Belinda; Davenport, Karen; Daligault, Hajnalka; Johnson, Shannon; Lee, Joyce; Hastie, Alex; Darracq, Aude; Willems, Glenda; Barnes, Steve; Liachko, Ivan; Sullivan, Shawn; Koren, Sergey; Phillippy, Adam; Wang, Jie; Liu, Tiffany; Pulman, Jane; Childs, Kevin; Shu, Shengqiang; Yocum, Anastasia; Fermin, Damian; Mutasa-Gottgens, Effie; Stevanato, Piergiorgio; Taguchi, Kazunori; Naegele, Rachel; Dorn, Kevin M.

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False gene and chromosome losses in genome assemblies caused by GC content variation and repeats

GENOME BIOLOGY

IF9.4

2022-09-27

OAAI

Kim, Juwan; Lee, Chul; Ko, Byung June; Yoo, Dong Ahn; Won, Sohyoung; Phillippy, Adam M.; Fedrigo, Olivier; Zhang, Guojie; Howe, Kerstin; Wood, Jonathan; Durbin, Richard; Formenti, Giulio; Brown, Samara; Cantin, Lindsey; Mello, Claudio V.; Cho, Seoae; Rhie, Arang; Kim, Heebal; Jarvis, Erich D.

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Research Directions