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A draft human pangenome reference
Author / Creator:Liao, Wen-Wei ; Ebler, Jana ; Doerr, Daniel ; Haukness, Marina ; Hickey, Glenn ; Lu, Shuangjia ; Lucas, Julian K. ; Monlong, Jean ; Abel, Haley J. ; Buonaiuto, Silvia ; Cheng, Haoyu ; Chu, Justin ; Colonna, Vincenza ; Eizenga, Jordan M. ; Feng, Xiaowen ; Fulton, Robert S. ; Garg, Shilpa ; Groza, Cristian ; Guarracino, Andrea ; Harvey, William T. ; Heumos, Simon ; Howe, Kerstin ; Jain, Miten ; Lu, Tsung-Yu ; Martin, Fergal J. ; Mitchell, Matthew W. ; Munson, Katherine M. ; Mwaniki, Moses Njagi ; Novak, Adam M. ; Olsen, Hugh E. ; Sirén, Jouni ; Tomlinson, Chad ; Villani, Flavia ; Vollger, Mitchell R. ; Antonacci-Fulton, Lucinda L. ; Baid, Gunjan ; Baker, Carl A. ; Belyaeva, Anastasiya ; Billis, Konstantinos ; Carroll, Andrew ; Chang, Pi-Chuan ; Cook, Daniel E. ; Cook-Deegan, Robert M. ; Diekhans, Mark ; Ebert, Peter ; Fedrigo, Olivier ; Frankish, Adam ; Gao, Yan ; Garrison, Nanibaa’ A. ; Giron, Carlos Garcia ; Green, Richard E. ; Haggerty, Leanne ; Hoekzema, Kendra ; Hourlier, Thibaut ; Ji, Hanlee P. ; Koenig, Barbara A. ; Korbel, Jan O. ; Kordosky, Jennifer ; Koren, Sergey ; Lee, HoJoon ; Magalhães, Hugo ; Marco-Sola, Santiago ; Marijon, Pierre ; McCartney, Ann ; McDaniel, Jennifer ; Mountcastle, Jacquelyn ; Nattestad, Maria ; Nurk, Sergey ; Olson, Nathan D. ; Popejoy, Alice B. ; Puiu, Daniela ; Rautiainen, Mikko ; Regier, Allison A. ; Rhie, Arang ; Sacco, Samuel ; Sanders, Ashley D. ; Schneider, Valerie A. ; Schultz, Baergen I. ; Shafin, Kishwar ; Sofia, Heidi J. ; Abou Tayoun, Ahmad N. ; Thibaud-Nissen, Françoise ; Tricomi, Francesca Floriana ; Wagner, Justin ; Wood, Jonathan M. D. ; Zimin, Aleksey V. ; Bourque, Guillaume ; Chaisson, Mark J. P. ; Flicek, Paul ; Phillippy, Adam M. ; Zook, Justin M. ; Eichler, Evan E. ; Haussler, David ; Wang, Ting ; Miga, Karen H. ; Garrison, Erik ; Marschall, Tobias ; Hall, Ira M. ; Li, Heng ; Paten, Benedict
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2023-05, Vol.617 (7960), p.312-324
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A pangenome reference of 36 Chinese populations
Author / Creator:Gao, Yang ; Yang, Xiaofei ; Chen, Hao ; Tan, Xinjiang ; Yang, Zhaoqing ; Deng, Lian ; Wang, Baonan ; Kong, Shuang ; Li, Songyang ; Cui, Yuhang ; Lei, Chang ; Wang, Yimin ; Pan, Yuwen ; Ma, Sen ; Sun, Hao ; Zhao, Xiaohan ; Shi, Yingbing ; Yang, Ziyi ; Wu, Dongdong ; Wu, Shaoyuan ; Zhao, Xingming ; Shi, Binyin ; Jin, Li ; Hu, Zhibin ; Lu, Yan ; Chu, Jiayou ; Ye, Kai ; Xu, Shuhua
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2023-07, Vol.619 (7968), p.112-121
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Graph pangenome captures missing heritability and empowers tomato breeding
Author / Creator:Zhou, Yao ; Zhang, Zhiyang ; Bao, Zhigui ; Li, Hongbo ; Lyu, Yaqing ; Zan, Yanjun ; Wu, Yaoyao ; Cheng, Lin ; Fang, Yuhan ; Wu, Kun ; Zhang, Jinzhe ; Lyu, Hongjun ; Lin, Tao ; Gao, Qiang ; Saha, Surya ; Mueller, Lukas ; Fei, Zhangjun ; Städler, Thomas ; Xu, Shizhong ; Zhang, Zhiwu ; Speed, Doug ; Huang, Sanwen
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2022-06, Vol.606 (7914), p.527-534
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The design and construction of reference pangenome graphs with minigraph
Author / Creator:Li, Heng ; Feng, Xiaowen ; Chu, Chong
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2020-10, Vol.21 (1), p.265-265, Article 265
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PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome
Author / Creator:Naz, Kanwal ; Naz, Anam ; Ashraf, Shifa Tariq ; Rizwan, Muhammad ; Ahmad, Jamil ; Baumbach, Jan ; Ali, Amjad
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2019-03, Vol.20 (1), p.123-10, Article 123
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Systematic discovery of antiphage defense systems in the microbial pangenome
Author / Creator:Doron, Shany ; Melamed, Sarah ; Ofir, Gal ; Leavitt, Azita ; Lopatina, Anna ; Keren, Mai ; Amitai, Gil ; Sorek, Rotem
Publisher:United States: The American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2018-03, Vol.359 (6379)
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Pangenome graph construction from genome alignments with Minigraph-Cactus
Author / Creator:Hickey, Glenn ; Monlong, Jean ; Ebler, Jana ; Novak, Adam M. ; Eizenga, Jordan M. ; Gao, Yan ; Marschall, Tobias ; Li, Heng ; Paten, Benedict
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2024-04, Vol.42 (4), p.663-673
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Estimating Pangenomes with Roary
Author / Creator:Farrah Sitto ; Battistuzzi, Fabia U
Publisher:Oxford: Oxford University Press
Journal title:Molecular biology and evolution, 2020-03, Vol.37 (3), p.933-939
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The rice pangenome branches out
Author / Creator:Olsen, Kenneth M.
Publisher:Singapore: Springer Nature Singapore
Journal title:Cell research, 2022-10, Vol.32 (10), p.867-868
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The pangenome of an agronomically important crop plant Brassica oleracea
Author / Creator:Golicz, Agnieszka A. ; Bayer, Philipp E. ; Barker, Guy C. ; Edger, Patrick P. ; Kim, HyeRan ; Martinez, Paula A. ; Chan, Chon Kit Kenneth ; Severn-Ellis, Anita ; McCombie, W. Richard ; Parkin, Isobel A. P. ; Paterson, Andrew H. ; Pires, J. Chris ; Sharpe, Andrew G. ; Tang, Haibao ; Teakle, Graham R. ; Town, Christopher D. ; Batley, Jacqueline ; Edwards, David
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2016-11, Vol.7 (1), p.13390-8, Article 13390
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Trait associations in the pangenome of pigeon pea (Cajanus cajan)
Author / Creator:Zhao, Junliang ; Bayer, Philipp E. ; Ruperao, Pradeep ; Saxena, Rachit K. ; Khan, Aamir W. ; Golicz, Agnieszka A. ; Nguyen, Henry T. ; Batley, Jacqueline ; Edwards, David ; Varshney, Rajeev K.
Publisher:England: John Wiley & Sons, Inc
Journal title:Plant biotechnology journal, 2020-09, Vol.18 (9), p.1946-1954
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Genotyping structural variants in pangenome graphs using the vg toolkit
Author / Creator:Hickey, Glenn ; Heller, David ; Monlong, Jean ; Sibbesen, Jonas A. ; Sirén, Jouni ; Eizenga, Jordan ; Dawson, Eric T. ; Garrison, Erik ; Novak, Adam M. ; Paten, Benedict
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2020-02, Vol.21 (1), p.35-35, Article 35
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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
Author / Creator:Gautreau, Guillaume ; Bazin, Adelme ; Gachet, Mathieu ; Planel, Rémi ; Burlot, Laura ; Dubois, Mathieu ; Perrin, Amandine ; Médigue, Claudine ; Calteau, Alexandra ; Cruveiller, Stéphane ; Matias, Catherine ; Ambroise, Christophe ; Rocha, Eduardo P. C. ; Vallenet, David
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2020-03, Vol.16 (3), p.e1007732-e1007732
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Why prokaryotes have pangenomes
Author / Creator:McInerney, James O. ; McNally, Alan ; O'Connell, Mary J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature microbiology, 2017-03, Vol.2 (4), p.17040-17040, Article 17040
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The Human Pangenome Project: a global resource to map genomic diversity
Author / Creator:Wang, Ting ; Antonacci-Fulton, Lucinda ; Howe, Kerstin ; Lawson, Heather A. ; Lucas, Julian K. ; Phillippy, Adam M. ; Popejoy, Alice B. ; Asri, Mobin ; Carson, Caryn ; Chaisson, Mark J. P. ; Chang, Xian ; Cook-Deegan, Robert ; Felsenfeld, Adam L. ; Fulton, Robert S. ; Garrison, Erik P. ; Garrison, Nanibaa’ A. ; Graves-Lindsay, Tina A. ; Ji, Hanlee ; Kenny, Eimear E. ; Koenig, Barbara A. ; Li, Daofeng ; Marschall, Tobias ; McMichael, Joshua F. ; Novak, Adam M. ; Purushotham, Deepak ; Schneider, Valerie A. ; Schultz, Baergen I. ; Smith, Michael W. ; Sofia, Heidi J. ; Weissman, Tsachy ; Flicek, Paul ; Li, Heng ; Miga, Karen H. ; Paten, Benedict ; Jarvis, Erich D. ; Hall, Ira M. ; Eichler, Evan E. ; Haussler, David
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2022-04, Vol.604 (7906), p.437-446
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One pangenome to bind them all
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2022-09, Vol.40 (9), p.1301-1301
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Graphtyper enables population-scale genotyping using pangenome graphs
Author / Creator:Eggertsson, Hannes P ; Jonsson, Hakon ; Kristmundsdottir, Snaedis ; Hjartarson, Eirikur ; Kehr, Birte ; Masson, Gisli ; Zink, Florian ; Hjorleifsson, Kristjan E ; Jonasdottir, Aslaug ; Jonasdottir, Adalbjorg ; Jonsdottir, Ingileif ; Gudbjartsson, Daniel F ; Melsted, Pall ; Stefansson, Kari ; Halldorsson, Bjarni V
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2017-11, Vol.49 (11), p.1654-1660
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Producing polished prokaryotic pangenomes with the Panaroo pipeline
Author / Creator:Tonkin-Hill, Gerry ; MacAlasdair, Neil ; Ruis, Christopher ; Weimann, Aaron ; Horesh, Gal ; Lees, John A. ; Gladstone, Rebecca A. ; Lo, Stephanie ; Beaudoin, Christopher ; Floto, R. Andres ; Frost, Simon D.W. ; Corander, Jukka ; Bentley, Stephen D. ; Parkhill, Julian
Publisher:London: BioMed Central Ltd
Journal title:Genome Biology, 2020-07, Vol.21 (1), p.180-180, Article 180
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A super-pangenome of the North American wild grape species
Author / Creator:Cochetel, Noé ; Minio, Andrea ; Guarracino, Andrea ; Garcia, Jadran F. ; Figueroa-Balderas, Rosa ; Massonnet, Mélanie ; Kasuga, Takao ; Londo, Jason P. ; Garrison, Erik ; Gaut, Brandon S. ; Cantu, Dario
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2023-12, Vol.24 (1), p.290-290, Article 290
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Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
Author / Creator:Li, Ning ; He, Qiang ; Wang, Juan ; Wang, Baike ; Zhao, Jiantao ; Huang, Shaoyong ; Yang, Tao ; Tang, Yaping ; Yang, Shengbao ; Aisimutuola, Patiguli ; Xu, Ruiqiang ; Hu, Jiahui ; Jia, Chunping ; Ma, Kai ; Li, Zhiqiang ; Jiang, Fangling ; Gao, Jie ; Lan, Haiyan ; Zhou, Yongfeng ; Zhang, Xinyan ; Huang, Sanwen ; Fei, Zhangjun ; Wang, Huan ; Li, Hongbo ; Yu, Qinghui
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2023-05, Vol.55 (5), p.852-860
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A draft human pangenome reference

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A pangenome reference of 36 Chinese populations

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Graph pangenome captures missing heritability and empowers tomato breeding

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The design and construction of reference pangenome graphs with minigraph

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PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome

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Systematic discovery of antiphage defense systems in the microbial pangenome

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Pangenome graph construction from genome alignments with Minigraph-Cactus

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Estimating Pangenomes with Roary

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The rice pangenome branches out

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The pangenome of an agronomically important crop plant Brassica oleracea

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Trait associations in the pangenome of pigeon pea (Cajanus cajan)

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Genotyping structural variants in pangenome graphs using the vg toolkit

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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

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Why prokaryotes have pangenomes

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The Human Pangenome Project: a global resource to map genomic diversity

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One pangenome to bind them all

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Graphtyper enables population-scale genotyping using pangenome graphs

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Producing polished prokaryotic pangenomes with the Panaroo pipeline

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A super-pangenome of the North American wild grape species

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Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

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