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Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation Lawniczak, Mara K. N.; Kocot, Kevin M.; Astrin, Jonas J.; Blaxter, Mark; Sotero-Caio, Cibele G.; Barker, Katharine B.; Childers, Anna K.; Coddington, Jonathan; Davis, Paul; Howe, Kerstin; Johnson, Warren E.; Mckenna, Duane D.; Wideman, Jeremy G.; Pettersson, Olga Vinnere; Ras, Verena; Santos, Bernardo F. Share Save
Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia Al-Ajli, Farooq Omar; Formenti, Giulio; Fedrigo, Olivier; Tracey, Alan; Sims, Ying; Howe, Kerstin; Al-Karkhi, Ikdam M.; Althani, Asmaa Ali; Jarvis, Erich D.; Rahman, Sadequr; Ayub, Qasim Share Save
On the path to reference genomes for all biodiversity: laboratory protocols and lessons learned from processing over 2,000 species in the Sanger Tree of Life Howard, Caroline; Denton, Amy; Jackson, Benjamin W.; Bates, Adam; Jay, Jessie; Yatsenko, Halyna; Raman, Priyanka Sethu; Thomas, Abitha; Oatley, Graeme; do Amaral, Raquel Vionette; Goktan, Zeynep Ene; Gomez, Juan Pablo Narvaez; Clayton Lucey, Isabelle; Sinclair, Elizabeth; Quail, Michael A.; Blaxter, Mark; Howe, Kerstin; Lawniczak, Mara K. N. Share Save
A Complete Assembly and Annotation of the American Shad Genome Yields Insights into the Origins of Diadromy Velotta, Jonathan P.; Iqbal, Azwad R.; Glenn, Emma S.; Franckowiak, Ryan P.; Formenti, Giulio; Mountcastle, Jacquelyn; Balacco, Jennifer; Tracey, Alan; Sims, Ying; Howe, Kerstin; Fedrigo, Olivier; Jarvis, Erich D.; Therkildsen, Nina O. Share Save
Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding Li, Kai; Smith, Melissa L.; Blazier, J. Chris; Kochan, Kelli J.; Wood, Jonathan M. D.; Howe, Kerstin; Kwitek, Anne E.; Dwinell, Melinda R.; Chen, Hao; Ciosek, Julia L.; Masterson, Patrick; Murphy, Terence D.; Kalbfleisch, Theodore S.; Doris, Peter A. Share Save
Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure Ishigohoka, Jun; Bascon-Cardozo, Karen; Bours, Andrea; Fuss, Janina; Rhie, Arang; Mountcastle, Jacquelyn; Haase, Bettina; Chow, William; Collins, Joanna; Howe, Kerstin; Uliano-Silva, Marcela; Fedrigo, Olivier; Jarvis, Erich D.; Perez-Tris, Javier; Carlos Illera, Juan; Liedvogel, Miriam Share Save
Evolution and genetic architecture of sex-limited polymorphism in cuckoos Merondun, Justin; Marques, Cristiana I.; Andrade, Pedro; Meshcheryagina, Swetlana; Galvan, Ismael; Afonso, Sandra; Alves, Joel M.; Araujo, Pedro M.; Bachurin, Gennadiy; Balacco, Jennifer; Ban, Miklos; Fedrigo, Olivier; Formenti, Giulio; Fossoy, Frode; Fulop, Attila; Golovatin, Mikhail; Granja, Sofia; Hewson, Chris; Honza, Marcel; Howe, Kerstin; Larson, Greger; Marton, Attila; Moskat, Csaba; Mountcastle, Jacquelyn; Prochazka, Petr; Red'kin, Yaroslav; Sims, Ying; Sulc, Michal; Tracey, Alan; Wood, Jonathan M. D.; Jarvis, Erich D.; Hauber, Mark E.; Carneiro, Miguel; Wolf, Jochen B. W. Share Save
A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats de Jong, Tristan V.; Pan, Yanchao; Rastas, Pasi; Munro, Daniel; Tutaj, Monika; Akil, Huda; Benner, Chris; Chen, Denghui; Chitre, Apurva S.; Chow, William; Colonna, Vincenza; Dalgard, Clifton L.; Demos, Wendy M.; Doris, Peter A.; Garrison, Erik; Geurts, Aron M.; Gunturkun, Hakan M.; Guryev, Victor; Hourlier, Thibaut; Howe, Kerstin; Huang, Jun; Kalbfleisch, Ted; Kim, Panjun; Li, Ling; Mahaffey, Spencer; Martin, Fergal J.; Mohammadi, Pejman; Ozel, Ayse Bilge; Polesskaya, Oksana; Pravenec, Michal; Prins, Pjotr; Sebat, Jonathan; Smith, Jennifer R.; Woods, Leah C. Solberg; Tabakoff, Boris; Tracey, Alan; Uliano-Silva, Marcela; Villani, Flavia; Wang, Hongyang; Sharp, Burt M.; Telese, Francesca; Jiang, Zhihua; Saba, Laura; Wang, Xusheng; Murphy, Terence D.; Palmer, Abraham A.; Kwitek, Anne E.; Dwinell, Melinda R.; Williams, Robert W.; Li, Jun Z.; Chen, Hao Share Save
A region of suppressed recombination misleads neoavian phylogenomics Mirarab, Siavash; Rivas-Gonzalez, Iker; Feng, Shaohong; Stiller, Josefin; Fang, Qi; Mai, Uyen; Hickey, Glenn; Chen, Guangji; Brajuka, Nadolina; Fedrigo, Olivier; Formenti, Giulio; Wolf, Jochen B. W.; Howe, Kerstin; Antunes, Agostinho; Schierup, Mikkel H.; Paten, Benedict; Jarvis, Erich D.; Zhang, Guojie; Braun, Edward L. Share Save
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography 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 Share Save
The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes Bond, Donna M.; Ortega-Recalde, Oscar; Laird, Melanie K.; Hayakawa, Takashi; Richardson, Kyle S.; Reese, Finlay. C. B.; Kyle, Bruce; McIsaac-Williams, Brooke E.; Robertson, Bruce C.; Van Heezik, Yolanda; Adams, Amy L.; Chang, Wei-Shan; Haase, Bettina; Mountcastle, Jacquelyn; Driller, Maximilian; Collins, Joanna; Howe, Kerstin; Go, Yasuhiro; Thibaud-Nissen, Francoise; Lister, Nicholas C.; Waters, Paul D.; Fedrigo, Olivier; Jarvis, Erich D.; Gemmell, Neil J.; Alexander, Alana; Hore, Timothy A. Share Save
Genomics of cold adaptations in the Antarctic notothenioid fish radiation Bista, Iliana; Wood, Jonathan M. D.; Desvignes, Thomas; McCarthy, Shane A.; Matschiner, Michael; Ning, Zemin; Tracey, Alan; Torrance, James; Sims, Ying; Chow, William; Smith, Michelle; Oliver, Karen; Haggerty, Leanne; Salzburger, Walter; Postlethwait, John H.; Howe, Kerstin; Clark, Melody S.; Detrich, H. William, III; Cheng, C. -H. Christina; Miska, Eric A.; Durbin, Richard Share Save
Pangenome graph construction from genome alignments with Minigraph-Cactus 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. Share Save
An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes Timoshevskaya, Nataliya; Eskut, Kaan, I; Timoshevskiy, Vladimir A.; Robb, Sofia M. C.; Holt, Carson; Hess, Jon E.; Parker, Hugo J.; Baker, Cindy F.; Miller, Allison K.; Saraceno, Cody; Yandell, Mark; Krumlauf, Robb; Narum, Shawn R.; Lampman, Ralph T.; Gemmell, Neil J.; Mountcastle, Jacquelyn; Haase, Bettina; Balacco, Jennifer R.; Formenti, Giulio; Pelan, Sarah; Sims, Ying; Howe, Kerstin; Fedrigo, Olivier; Jarvis, Erich D.; Smith, Jeramiah J. Share Save
Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories Bentley, Blair P.; Carrasco-Valenzuela, Tomas; Ramos, Elisa K. S.; Pawar, Harvinder; Arantes, Larissa Souza; Alexander, Alana; Banerjee, Shreya M.; Masterson, Patrick; Kuhlwilm, Martin; Pippel, Martin; Mountcastle, Jacquelyn; Haase, Bettina; Uliano-Silva, Marcela; Formenti, Giulio; Howe, Kerstin; Chow, William; Tracey, Alan; Sims, Ying; Pelan, Sarah; Wood, Jonathan; Yetsko, Kelsey; Perrault, Justin R.; Stewart, Kelly; Benson, Scott R.; Levy, Yaniv; V. Todd, Erica; Shaffer, H. Bradley; Scott, Peter; Henen, Brian T.; Murphy, Robert W.; Mohr, David W.; Scott, Alan F.; Duffy, David J.; Gemmell, Neil J.; Suh, Alexander; Winkler, Sylke; Thibaud-Nissen, Francoise; Nery, Mariana F.; Marques-Bonet, Tomas; Antunes, Agostinho; Tikochinski, Yaron; Dutton, Peter H.; Fedrigo, Olivier; Myers, Eugene W.; Jarvis, Erich D.; Mazzoni, Camila J.; Komoroske, Lisa M. Share Save
The swan genome and transcriptome, it is not all black and white Karawita, Anjana C.; Cheng, Yuanyuan; Chew, Keng Yih; Challagulla, Arjun; Kraus, Robert; Mueller, Ralf C.; Tong, Marcus Z. W.; Hulme, Katina D.; Bielefeldt-Ohmann, Helle; Steele, Lauren E.; Wu, Melanie; Sng, Julian; Noye, Ellesandra; Bruxner, Timothy J.; Au, Gough G.; Lowther, Suzanne; Blommaert, Julie; Suh, Alexander; McCauley, Alexander J.; Kaur, Parwinder; Dudchenko, Olga; Aiden, Erez; Fedrigo, Olivier; Formenti, Giulio; Mountcastle, Jacquelyn; Chow, William; Martin, Fergal J.; Ogeh, Denye N.; Thiaud-Nissen, Francoise; Howe, Kerstin; Tracey, Alan; Smith, Jacqueline; Kuo, Richard I.; Renfree, Marilyn B.; Kimura, Takashi; Sakoda, Yoshihiro; McDougall, Mathew; Spencer, Hamish G.; Pyne, Michael; Tolf, Conny; Waldenstroem, Jonas; Jarvis, Erich D.; Baker, Michelle L.; Burt, David W.; Short, Kirsty R. Share Save
A chromosome-level reference genome and pangenome for barn swallow population genomics Secomandi, Simona; Gallo, Guido R.; Sozzoni, Marcella; Iannucci, Alessio; Galati, Elena; Abueg, Linelle; Balacco, Jennifer; Caprioli, Manuela; Chow, William; Ciofi, Claudio; Collins, Joanna; Fedrigo, Olivier; Ferretti, Luca; Fungtammasan, Arkarachai; Haase, Bettina; Howe, Kerstin; Kwak, Woori; Lombardo, Gianluca; Masterson, Patrick; Messina, Graziella; Moller, Anders P.; Mountcastle, Jacquelyn; Mousseau, Timothy A.; Obiol, Joan Ferrer; Olivieri, Anna; Rhie, Arang; Rubolini, Diego; Saclier, Marielle; Stanyon, Roscoe; Stucki, David; Thibaud-Alquati, Francoise; Torrance, James; Torroni, Antonio; Weber, Kristina; Ambrosini, Roberto; Bonisoli-Alquati, Andrea; Jarvis, Erich D.; Gianfranceschi, Luca; Formenti, Giulio Share Save
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats 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. Share Save
Widespread false gene gains caused by duplication errors in genome assemblies Ko, Byung June; Lee, Chul; Kim, Juwan; Rhie, Arang; Yoo, Dong Ahn; Howe, Kerstin; Wood, Jonathan; Cho, Seoae; Brown, Samara; Formenti, Giulio; Jarvis, Erich D.; Kim, Heebal Share Save
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