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D

David Goodstein

Joint Genome Institute and Lawrence Berkeley National Laboratory

40H-index
197Paper Count
3.5WCitation Count
Published Papers 37
Publication Date
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A sorghum pangenome reference improves global crop trait discovery
errNature
IF48.5
err2026-03-11
err0
errOAAI
errGeoffrey P. Morris; Avril M. Harder; Adam L. Healey; Chloee M. McLaughlin; Joanna L. Rifkin; Clara Cruet-Burgos; Jerry W. Jenkins; Shengqiang Shu; John J. Spiekerman; Carl J. VanGessel; Erica Agnew; Alain Audebert; Kerrie Barry; Ivan Baxter; Gregory Beurier; Lori Beth Boston; Richard E. Boyles; Siobhan M. Brady; Victoria Bunting; Jacqueline M. Chaparro; Chaney Courtney; Joseph Sékou B. Dembele; Santosh Deshpande; Cyril Diatta; Nathaniel Eck; Andrea L. Eveland; Jacques M. Faye; Dave Flowers; Daniel Fonceka; Boubacar Gano; Marie de Gracia Coquerel; David Goodstein; Jane Grimwood; Matthew E. Hudson; Jana Kholova; Katherine Johnson; Kristen K. Johnson; Dorota Kawa; Mamoutou Kouressy; Stephen Kresovich; Scott Lee; Peggy G. Lemaux; Robert Lowery; Delphine Luquet; Fanna Maina; Sujan Mamidi; John K. McKay; Todd P. Michael; Taye T. Mindaye; John Mullet; Philip Ozersky; Christopher Plott; Jessica E. Prenni; Gael Pressoir; Jean-François Rami; Trevor W. Rife; Jocelyn Saxton; Bassirou Sine; Avinash Sreedasyam; Jayson Talag; Niaba Teme; Mitchell R. Tuinstra; Vincent Vadez; John P. Vogel; Rachel Walstead; Jianan Wang; Jenell Webber; Melissa Williams; Yuxing Xu; Todd C. Mockler; Jesse R. Lasky; Brian R. Rice; Jeremy Schmutz; Nadia Shakoor; John T. Lovell
errShare
errSave
Genomic approaches to accelerate American chestnut restoration
errScience
IF45.8
err2026-02-12
err0
PREAI
errJared W. Westbrook; Joanna Malukiewicz; Qian Zhang; Avinash Sreedasyam; Jerry W. Jenkins; Vasiliy Lakoba; Sara Fitzsimmons; Jamie Van Clief; Kendra Collins; Stephen Hoy; Cassie Stark; Lake Graboski; Eric Jenkins; Thomas M. Saielli; Benjamin T. Jarrett; Lucinda J. Wigfield; Lauren M. Kerwien; Ciera Wilbur; Alexander M. Sandercock; J. Hill Craddock; Susanna Keriö; Tetyana Zhebentyayeva; Shenghua Fan; Austin M. Thomas; Albert G. Abbott; C. Dana Nelson; Xiaoxia Xia; James R. McKenna; Caleb Kell; Melissa Williams; LoriBeth Boston; Christopher Plott; Florian Carle; Jack Swatt; Jack Ostroff; Steven N. Jeffers; Kathleen McKeever; Erica Smith; Thomas J. Ellis; Joseph B. James; Paul Sisco; Andrew Newhouse; Erik Carlson; William A. Powell; Frederick V. Hebard; John Scrivani; Caragh Heverly; Martin Cipollini; Brian Clark; Eric Evans; Bruce Levine; John E. Carlson; David Goodstein; Jack Orebaugh; Zamin K. Yang; Madhavi Z. Martin; Joanna Tannous; Tomás A. Rush; Nancy L. Engle; Timothy J. Tschaplinski; Jane Grimwood; Jeremy Schmutz; Jason A. Holliday; John T. Lovell
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errSave
Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae
errNature Communications
IF15.7
err2025-09-29
err0
errOAAI
errZoltán Füssy; Robert H. Lampe; Kevin R. Arrigo; Kerrie Barry; Margaret M. Brisbin; Corina P. D. Brussaard; Johan Decelle; Colomban de Vargas; Giacomo R. DiTullio; Liam D. H. Elbourne; Marc E. Frischer; David M. Goodstein; Igor V. Grigoriev; Richard D. Hayes; Adam L. Healey; Chase C. James; Jerry W. Jenkins; Caroline Juery; Manish Kumar; Adam B. Kustka; Florian Maumus; Anna M. G. Novák Vanclová; Miroslav Oborník; Ian T. Paulsen; Ian Probert; Mak A. Saito; Jeremy Schmutz; Tomáš Skalický; Diego Tec-Campos; Hannah Tomelka; Pavlína Věchtová; Pratap Venepally; Brendan Wilson-Mortier; Karsten Zengler; Hong Zheng; Andrew E. Allen
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errSave
Comparative Analyses of Four Reference Genomes Reveal Exceptional Diversity and Weak Linked Selection in the Yellow Monkeyflower (Mimulus guttatus) Complex
errMolecular Ecology Resources
IF5.5
err2025-07-22
err0
errOAAI
errJohn T. Lovell; Rachel Walstead; Amelia Lawrence; Evan Stark-Dykema; Matthew C. Farnitano; Avril Harder; Tomáš Brůna; Kerrie Barry; David Goodstein; Jerry Jenkins; Anna Lipzen; LoriBeth Boston; Jenell Webber; Mansi Chovatia; Joanne Eichenberger; Jayson Talag; Jane Grimwood; Jeremy Schmutz; John K. Kelly; Andrea L. Sweigart; Lila Fishman; John H. Willis
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errSave
Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean
errPLANT JOURNAL
IF5.7
err2024-09-14
err3
errOAAI
errEspina, Mary Jane C.; Lovell, John T.; Jenkins, Jerry; Shu, Shengqiang; Sreedasyam, Avinash; Jordan, Brandon D.; Webber, Jenell; Boston, LoriBeth; Bruna, Tomas; Talag, Jayson; Goodstein, David; Grimwood, Jane; Stacey, Gary; Cannon, Steven B.; Lorenz, Aaron J.; Schmutz, Jeremy; Stupar, Robert M.
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errSave
Genome resources for three modern cotton lines guide future breeding efforts
errNATURE PLANTS
IF13.6
err2024-05-30
err1
errOAAI
errSreedasyam, Avinash; Lovell, John T.; Mamidi, Sujan; Khanal, Sameer; Jenkins, Jerry W.; Plott, Christopher; Bryan, Kempton B.; Li, Zhigang; Shu, Shengqiang; Carlson, Joseph; Goodstein, David; De Santiago, Luis; Kirkbride, Ryan C.; Calleja, Sebastian; Campbell, Todd; Koebernick, Jenny C.; Dever, Jane K.; Scheffler, Jodi A.; Pauli, Duke; Jenkins, Johnie N.; Mccarty, Jack C.; Williams, Melissa; Boston, Loribeth; Webber, Jenell; Udall, Joshua A.; Chen, Z. Jeffrey; Bourland, Fred; Stiller, Warwick N.; Saski, Christopher A.; Grimwood, Jane; Chee, Peng W.; Jones, Don C.; Schmutz, Jeremy
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errSave
JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom
errNUCLEIC ACIDS RESEARCH
IF13.1
err2023-08-01
err19
errOAAI
errSreedasyam, Avinash; Plott, Christopher; Hossain, Md Shakhawat; Lovell, John T.; Grimwood, Jane; Jenkins, Jerry W.; Daum, Christopher; Barry, Kerrie; Carlson, Joseph; Shu, Shengqiang; Phillips, Jeremy; Amirebrahimi, Mojgan; Zane, Matthew; Wang, Mei; Goodstein, David; Haas, Fabian B.; Hiss, Manuel; Perroud, Pierre-Francois; Jawdy, Sara S.; Yang, Yongil; Hu, Rongbin; Johnson, Jenifer; Kropat, Janette; Gallaher, Sean D.; Lipzen, Anna; Shakirov, Eugene, V; Weng, Xiaoyu; Torres-Jerez, Ivone; Weers, Brock; Conde, Daniel; Pappas, Marilia R.; Liu, Lifeng; Muchlinski, Andrew; Jiang, Hui; Shyu, Christine; Huang, Pu; Sebastian, Jose; Laiben, Carol; Medlin, Alyssa; Carey, Sankalpi; Carrell, Alyssa A.; Chen, Jin-Gui; Perales, Mariano; Swaminathan, Kankshita; Allona, Isabel; Grattapaglia, Dario; Cooper, Elizabeth A.; Tholl, Dorothea; Vogel, John P.; Weston, David J.; Yang, Xiaohan; Brutnell, Thomas P.; Kellogg, Elizabeth A.; Baxter, Ivan; Udvardi, Michael; Tang, Yuhong; Mockler, Todd C.; Juenger, Thomas E.; Mullet, John; Rensing, Stefan A.; Tuskan, Gerald A.; Merchant, Sabeeha S.; Stacey, Gary; Schmutz, Jeremy
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A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)
errPLANT GENOME
IF3.8
err2023-03-22
err15
errOAAI
errLiang, Qihua; Munoz-Amatriain, Maria; Shu, Shengqiang; Lo, Sassoum; Wu, Xinyi; Carlson, Joseph W.; Davidson, Patrick; Goodstein, David M.; Phillips, Jeremy; Janis, Nadia M.; Lee, Elaine J.; Liang, Chenxi; Morrell, Peter L.; Farmer, Andrew D.; Xu, Pei; Close, Timothy J.; Lonardi, Stefano
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errSave
The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory
errPLANT CELL
IF11.6
err2022-12-23
err34
errOAAI
errCraig, Rory J.; Gallaher, Sean D.; Shu, Shengqiang; Salome, Patrice A.; Jenkins, Jerry W.; Blaby-Haas, Crysten E.; Purvine, Samuel O.; O'Donnell, Samuel; Barry, Kerrie; Grimwood, Jane; Strenkert, Daniela; Kropat, Janette; Daum, Chris; Yoshinaga, Yuko; Goodstein, David M.; Vallon, Olivier; Schmutz, Jeremy; Merchant, Sabeeha S.
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errSave
Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium
errGENETICS
IF5.1
err2022-10-11
err8
errOAAI
errScarlett, Virginia T.; Lovell, John T.; Shao, Mingqin; Phillips, Jeremy; Shu, Shengqiang; Lusinska, Joanna; Goodstein, David M.; Jenkins, Jerry; Grimwood, Jane; Barry, Kerrie; Chalhoub, Boulos; Schmutz, Jeremy; Hasterok, Robert; Catalan, Pilar; Vogel, John P.
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errSave
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
errELIFE
IF0
err2022-09-09
err117
errOAAI
errLovell, John T.; Sreedasyam, Avinash; Schranz, M. Eric; Wilson, Melissa; Carlson, Joseph W.; Harkess, Alex; Emms, David; Goodstein, David M.; Schmutz, Jeremy
errShare
errSave
Chromosome evolution and the genetic basis of agronomically important traits in greater yam
errNATURE COMMUNICATIONS
IF15.7
err2022-04-14
err41
errOAAI
errBredeson, Jessen, V; Lyons, Jessica B.; Oniyinde, Ibukun O.; Okereke, Nneka R.; Kolade, Olufisayo; Nnabue, Ikenna; Nwadili, Christian O.; Hribova, Eva; Parker, Matthew; Nwogha, Jeremiah; Shu, Shengqiang; Carlson, Joseph; Kariba, Robert; Muthemba, Samuel; Knop, Katarzyna; Barton, Geoffrey J.; Sherwood, Anna, V; Lopez-Montes, Antonio; Asiedu, Robert; Jamnadass, Ramni; Muchugi, Alice; Goodstein, David; Egesi, Chiedozie N.; Featherston, Jonathan; Asfaw, Asrat; Simpson, Gordon G.; Dolezel, Jaroslav; Hendre, Prasad S.; Van Deynze, Allen; Kumar, Pullikanti Lava; Obidiegwu, Jude E.; Bhattacharjee, Ranjana; Rokhsar, Daniel S.
errShare
errSave
Genome sequence and evolution of Betula platyphylla
errHORTICULTURE RESEARCH
IF8.5
err2021-02-11
err74
errOAAI
errChen, Su; Wang, Yucheng; Yu, Lili; Zheng, Tao; Wang, Sui; Yue, Zhen; Jiang, Jing; Kumari, Sapna; Zheng, Chunfang; Tang, Ibao; Li, Jun; Li, Yuqi; Chen, Jiongjiong; Zhang, Wenbo; Kuang, Hanhui; Robertson, Jon S.; Zhao, Patrick X.; Li, Huiyu; Shu, Shengqiang; Yordanov, Yordan S.; Huang, Haijiao; Goodstein, David M.; Gai, Ying; Qi, Qi; Min, JiuMeng; Xu, ChunYan; Wang, SongBo; Qu, Guan-Zheng; Paterson, Andrew H.; Sankoff, David; Wei, Hairong; Liu, Guifeng; Yang, Chuanping
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errSave
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
errNATURE COMMUNICATIONS
IF15.7
err2020-07-29
err65
errOAAI
errGordon, Sean P.; Contreras-Moreira, Bruno; Levy, Joshua J.; Djamei, Armin; Czedik-Eysenberg, Angelika; Tartaglio, Virginia S.; Session, Adam; Martin, Joel; Cartwright, Amy; Katz, Andrew; Singan, Vasanth R.; Goltsman, Eugene; Barry, Kerrie; Vinh Ha Dinh-Thi; Chalhoub, Boulos; Diaz-Perez, Antonio; Sancho, Ruben; Lusinska, Joanna; Wolny, Elzbieta; Nibau, Candida; Doonan, John H.; Mur, Luis A. J.; Plott, Chris; Jenkins, Jerry; Hazen, Samuel P.; Lee, Scott J.; Shu, Shengqiang; Goodstein, David; Rokhsar, Daniel; Schmutz, Jeremy; Hasterok, Robert; Catalan, Pilar; Vogel, John P.
errShare
errSave
Construction and comparison of three reference-quality genome assemblies for soybean
errPLANT JOURNAL
IF5.7
err2019-10-28
err139
errOAAI
errValliyodan, Babu; Cannon, Steven B.; Bayer, Philipp E.; Shu, Shengqiang; Brown, Anne, V; Ren, Longhui; Jenkins, Jerry; Chung, Claire Y-L; Chan, Ting-Fung; Daum, Christopher G.; Plott, Christopher; Hastie, Alex; Baruch, Kobi; Barry, Kerrie W.; Huang, Wei; Patil, Gunvant; Varshney, Rajeev K.; Hu, Haifei; Batley, Jacqueline; Yuan, Yuxuan; Song, Qijian; Stupar, Robert M.; Goodstein, David M.; Stacey, Gary; Lam, Hon-Ming; Jackson, Scott A.; Schmutz, Jeremy; Grimwood, Jane; Edwards, David; Nguyen, Henry T.
errShare
errSave
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
errPLANT JOURNAL
IF5.7
err2018-01-19
err338
errOAAI
errLang, Daniel; Ullrich, Kristian K.; Murat, Florent; Fuchs, Joerg; Jenkins, Jerry; Haas, Fabian B.; Piednoel, Mathieu; Gundlach, Heidrun; Van Bel, Michiel; Meyberg, Rabea; Vives, Cristina; Morata, Jordi; Symeonidi, Aikaterini; Hiss, Manuel; Muchero, Wellington; Kamisugi, Yasuko; Saleh, Omar; Blanc, Guillaume; Decker, Eva L.; van Gessel, Nico; Grimwood, Jane; Hayes, Richard D.; Graham, Sean W.; Gunter, Lee E.; McDaniel, Stuart F.; Hoernstein, Sebastian N. W.; Larsson, Anders; Li, Fay-Wei; Perroud, Pierre-Francois; Phillips, Jeremy; Ranjan, Priya; Rokshar, Daniel S.; Rothfels, Carl J.; Schneider, Lucas; Shu, Shengqiang; Stevenson, Dennis W.; Thummler, Fritz; Tillich, Michael; Aguilar, Juan C. Villarreal; Widiez, Thomas; Wong, Gane Ka-Shu; Wymore, Ann; Zhang, Yong; Zimmer, Andreas D.; Quatrano, Ralph S.; Mayer, Klaus F. X.; Goodstein, David; Casacuberta, Josep M.; Vandepoele, Klaas; Reski, Ralf; Cuming, Andrew C.; Tuskan, Gerald A.; Maumus, Florian; Salse, Jerome; Schmutz, Jeremy; Rensing, Stefan A.
errShare
errSave
Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure
errNATURE COMMUNICATIONS
IF15.7
err2017-12-19
err250
errOAAI
errGordon, Sean P.; Contreras-Moreira, Bruno; Woods, Daniel P.; Marais, David L. Des; Burgess, Diane; Shu, Shengqiang; Stritt, Christoph; Roulin, Anne C.; Schackwitz, Wendy; Tyler, Ludmila; Martin, Joel; Lipzen, Anna; Dochy, Niklas; Phillips, Jeremy; Barry, Kerrie; Geuten, Koen; Budak, Hikmet; Juenger, Thomas E.; Amasino, Richard; Caicedo, Ana L.; Goodstein, David; Davidson, Patrick; Mur, Luis A. J.; Figueroa, Melania; Freeling, Michael; Catalan, Pilar; Vogel, John P.
errShare
errSave
The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism
errNATURE COMMUNICATIONS
IF15.7
err2017-12-01
err138
errOAAI
errYang, Xiaohan; Hu, Rongbin; Yin, Hengfu; Jenkins, Jerry; Shu, Shengqiang; Tang, Haibao; Liu, Degao; Weighill, Deborah A.; Yim, Won Cheol; Ha, Jungmin; Heyduk, Karolina; Goodstein, David M.; Guo, Hao-Bo; Moseley, Robert C.; Fitzek, Elisabeth; Jawdy, Sara; Zhang, Zhihao; Xie, Meng; Hartwell, James; Grimwood, Jane; Abraham, Paul E.; Mewalal, Ritesh; Beltran, Juan D.; Boxall, Susanna F.; Dever, Louisa V.; Palla, Kaitlin J.; Albion, Rebecca; Garcia, Travis; Mayer, Jesse A.; Lim, Sung Don; Wai, Ching Man; Peluso, Paul; Van Buren, Robert; De Paoli, Henrique Cestari; Borland, Anne M.; Guo, Hong; Chen, Jin-Gui; Muchero, Wellington; Yin, Yanbin; Jacobson, Daniel A.; Tschaplinski, Timothy J.; Hettich, Robert L.; Ming, Ray; Winter, Klaus; Leebens-Mack, James H.; Smith, J. Andrew C.; Cushman, John C.; Schmutz, Jeremy; Tuskan, Gerald A.
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errSave
JBrowse: a dynamic web platform for genome visualization and analysis
errGENOME BIOLOGY
IF9.4
err2016-04-12
err572
errOAAI
errBuels, Robert; Yao, Eric; Diesh, Colin M.; Hayes, Richard D.; Munoz-Torres, Monica; Helt, Gregg; Goodstein, David M.; Elsik, Christine G.; Lewis, Suzanna E.; Stein, Lincoln; Holmes, Ian H.
errShare
errSave
The BioMart community portal: an innovative alternative to large, centralized data repositories
errNUCLEIC ACIDS RESEARCH
IF13.1
err2015-04-20
err578
errOAAI
errSmedley, Damian; Haider, Syed; Durinck, Steffen; Pandini, Luca; Provero, Paolo; Allen, James; Arnaiz, Olivier; Awedh, Mohammad Hamza; Baldock, Richard; Barbiera, Giulia; Bardou, Philippe; Beck, Tim; Blake, Andrew; Bonierbale, Merideth; Brookes, Anthony J.; Bucci, Gabriele; Buetti, Iwan; Burge, Sarah; Cabau, Cedric; Carlson, Joseph W.; Chelala, Claude; Chrysostomou, Charalambos; Cittaro, Davide; Collin, Olivier; Cordova, Raul; Cutts, Rosalind J.; Dassi, Erik; Di Genova, Alex; Djari, Anis; Esposito, Anthony; Estrella, Heather; Eyras, Eduardo; Fernandez-Banet, Julio; Forbes, Simon; Free, Robert C.; Fujisawa, Takatomo; Gadaleta, Emanuela; Garcia-Manteiga, Jose M.; Goodstein, David; Gray, Kristian; Guerra-Assuncao, JoseE Afonso; Haggarty, Bernard; Han, Dong-Jin; Han, Byung Woo; Harris, Todd; Harshbarger, Jayson; Hastings, Robert K.; Hayes, Richard D.; Hoede, Claire; Hu, Shen; Hu, Zhi-Liang; Hutchins, Lucie; Kan, Zhengyan; Kawaji, Hideya; Keliet, Aminah; Kerhornou, Arnaud; Kim, Sunghoon; Kinsella, Rhoda; Klopp, Christophe; Kong, Lei; Lawson, Daniel; Lazarevic, Dejan; Lee, Ji-Hyun; Letellier, Thomas; Li, Chuan-Yun; Lio, Pietro; Liu, Chu-Jun; Luo, Jie; Maass, Alejandro; Mariette, Jerome; Maurel, Thomas; Merella, Stefania; Mohamed, Azza Mostafa; Moreews, Francois; Nabihoudine, Ibounyamine; Ndegwa, Nelson; Noirot, Celine; Perez-Llamas, Cristian; Primig, Michael; Quattrone, Alessandro; Quesneville, Hadi; Rambaldi, Davide; Reecy, James; Riba, Michela; Rosanoff, Steven; Saddiq, Amna Ali; Salas, Elisa; Sallou, Olivier; Shepherd, Rebecca; Simon, Reinhard; Sperling, Linda; Spooner, William; Staines, Daniel M.; Steinbach, Delphine; Stone, Kevin; Stupka, Elia; Teague, Jon W.; Ullah, Abu Z. Dayem; Wang, Jun; Ware, Doreen; Wong-Erasmus, Marie; Youens-Clark, Ken; Zadissa, Amonida; Zhang, Shi-Jian; Kasprzyk, Arek
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errSave

Research Directions

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Co-authors
Cooperation Journals
王
王军 (Jun Wang)
H-index: 222 · Papers: 3.2K
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Rajeev K. Varshney
H-index: 139 · Papers: 1.5K
A
Andrew H. Paterson
H-index: 125 · Papers: 646
I
Ian T. Paulsen
H-index: 125 · Papers: 514
Y
Yuri I. Wolf
H-index: 121 · Papers: 518
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