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Characterization and visualization of tandem repeats at genome scale Dolzhenko, Egor; English, Adam; Dashnow, Harriet; Brandine, Guilherme De Sena; Mokveld, Tom; Rowell, William J.; Karniski, Caitlin; Kronenberg, Zev; Danzi, Matt C.; Cheung, Warren A.; Bi, Chengpeng; Farrow, Emily; Wenger, Aaron; Chua, Khi Pin; Martinez-Cerdeno, Veronica; Bartley, Trevor D.; Jin, Peng; Nelson, David L.; Zuchner, Stephan; Pastinen, Tomi; Quinlan, Aaron R.; Sedlazeck, Fritz J.; Eberle, Michael A. Share Save
pbfusion: Detecting gene-fusion and other transcriptional abnormalities using PacBio HiFi data Volden, Roger; Kronenberg, Zev; Gillmor, Aaron; Verhey, Ted; Monument, Michael; Senger, Donna; Dhillon, Harsharan; Underwood, Jason; Tseng, Elizabeth; Baker, Daniel; Baybayan, Primo; Eberle, Michael A.; Korlach, Jonas; Morrissy, Sorana Share Save
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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C Kronenberg, Zev N.; Rhie, Arang; Koren, Sergey; Concepcion, Gregory T.; Peluso, Paul; Munson, Katherine M.; Porubsky, David; Kuhn, Kristen; Mueller, Kathryn A.; Low, Wai Yee; Hiendleder, Stefan; Fedrigo, Olivier; Liachko, Ivan; Hall, Richard J.; Phillippy, Adam M.; Eichler, Evan E.; Williams, John L.; Smith, Timothy P. L.; Jarvis, Erich D.; Sullivan, Shawn T.; Kingan, Sarah B. Share Save
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias) Sarver, Brice A. J.; Herrera, Nathanael D.; Sneddon, David; Hunter, Samuel S.; Settles, Matthew L.; Kronenberg, Zev; Demboski, John R.; Good, Jeffrey M.; Sullivan, Jack Share Save
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Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle Low, Wai Yee; Tearle, Rick; Liu, Ruijie; Koren, Sergey; Rhie, Arang; Bickhart, Derek M.; Rosen, Benjamin D.; Kronenberg, Zev N.; Kingan, Sarah B.; Tseng, Elizabeth; Thibaud-Nissen, Francoise; Martin, Fergal J.; Billis, Konstantinos; Ghurye, Jay; Hastie, Alex R.; Lee, Joyce; Pang, Andy W. C.; Heaton, Michael P.; Phillippy, Adam M.; Hiendleder, Stefan; Smith, Timothy P. L.; Williams, John L. Share Save
Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants He, Yaoxi; Luo, Xin; Zhou, Bin; Hu, Ting; Meng, Xiaoyu; Audano, Peter A.; Kronenberg, Zev N.; Eichler, Evan E.; Jin, Jie; Guo, Yongbo; Yang, Yanan; Qi, Xuebin; Su, Bing Share Save
Multi-platform discovery of haplotype-resolved structural variation in human genomes Chaisson, Mark J. P.; Sanders, Ashley D.; Zhao, Xuefang; Malhotra, Ankit; Porubsky, David; Rausch, Tobias; Gardner, Eugene J.; Rodriguez, Oscar L.; Guo, Li; Collins, Ryan L.; Fan, Xian; Wen, Jia; Handsaker, Robert E.; Fairley, Susan; Kronenberg, Zev N.; Kong, Xiangmeng; Hormozdiari, Fereydoun; Lee, Dillon; Wenger, Aaron M.; Hastie, Alex R.; Antaki, Danny; Anantharaman, Thomas; Audano, Peter A.; Brand, Harrison; Cantsilieris, Stuart; Cao, Han; Cerveira, Eliza; Chen, Chong; Chen, Xintong; Chin, Chen-Shan; Chong, Zechen; Chuang, Nelson T.; Lambert, Christine C.; Church, Deanna M.; Clarke, Laura; Farrell, Andrew; Flores, Joey; Galeev, Timur; Gorkin, David U.; Gujral, Madhusudan; Guryev, Victor; Heaton, William Haynes; Korlach, Jonas; Kumar, Sushant; Kwon, Jee Young; Lam, Ernest T.; Lee, Jong Eun; Lee, Joyce; Lee, Wan-Ping; Lee, Sau Peng; Li, Shantao; Marks, Patrick; Viaud-Martinez, Karine; Meiers, Sascha; Munson, Katherine M.; Navarro, Fabio C. P.; Nelson, Bradley J.; Nodzak, Conor; Noor, Amina; Kyriazopoulou-Panagiotopoulou, Sofia; Pang, Andy W. C.; Qiu, Yunjiang; Rosanio, Gabriel; Ryan, Mallory; Stuetz, Adrian; Spierings, Diana C. J.; Ward, Alistair; Welch, AnneMarie E.; Xiao, Ming; Xu, Wei; Zhang, Chengsheng; Zhu, Qihui; Zheng-Bradley, Xiangqun; Lowy, Ernesto; Yakneen, Sergei; McCarroll, Steven; Jun, Goo; Ding, Li; Koh, Chong Lek; Ren, Bing; Flicek, Paul; Chen, Ken; Gerstein, Mark B.; Kwok, Pui-Yan; Lansdorp, Peter M.; Marth, Gabor T.; Sebat, Jonathan; Shi, Xinghua; Bashir, Ali; Ye, Kai; Devine, Scott E.; Talkowski, Michael E.; Mills, Ryan E.; Marschall, Tobias; Korbel, Jan O.; Eichler, Evan E.; Lee, Charles Share Save
Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon Vickrey, Anna I.; Bruders, Rebecca; Kronenberg, Zev; Mackey, Emma; Bohlender, Ryan J.; Maclary, Emily T.; Maynez, Raquel; Osborne, Edward J.; Johnson, Kevin P.; Huff, Chad D.; Yandell, Mark; Shapiro, Michael D. Share Save
Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation Fiddes, Ian T.; Armstrong, Joel; Diekhans, Mark; Nachtweide, Stefanie; Kronenberg, Zev N.; Underwood, Jason G.; Gordon, David; Earl, Dent; Keane, Thomas; Eichler, Evan E.; Haussler, David; Stanke, Mario; Paten, Benedict Share Save
Discovery and genotyping of structural variation from long-read haploid genome sequence data (vol 27, pg 677, 2017) Huddleston, John; Chaisson, Mark J. P.; Steinberg, Karyn Meltz; Warren, Wes; Hoekzema, Kendra; Gordon, David; Graves-Lindsay, Tina A.; Munson, Katherine M.; Kronenberg, Zev N.; Vives, Laura; Peluso, Paul; Boitano, Matthew; Chin, Chen-Shin; Korlach, Jonas; Wilson, Richard K.; Eichler, Evan E. Share Save
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Discovery and genotyping of structural variation from long-read haploid genome sequence data Huddleston, John; Chaisson, Mark J. P.; Steinberg, Karyn Meltz; Warren, Wes; Hoekzema, Kendra; Gordon, David; Graves-Lindsay, Tina A.; Munson, Katherine M.; Kronenberg, Zev N.; Vives, Laura; Peluso, Paul; Boitano, Matthew; Chin, Chen-Shin; Korlach, Jonas; Wilson, Richard K.; Eichler, Evan E. Share Save
De novo genic mutations among a Chinese autism spectrum disorder cohort Wang, Tianyun; Guo, Hui; Xiong, Bo; Stessman, Holly A. F.; Wu, Huidan; Coe, Bradley P.; Turner, Tychele N.; Liu, Yanling; Zhao, Wenjing; Hoekzema, Kendra; Vives, Laura; Xia, Lu; Tang, Meina; Ou, Jianjun; Chen, Biyuan; Shen, Yidong; Xun, Guanglei; Long, Min; Lin, Janice; Kronenberg, Zev N.; Peng, Yu; Bai, Ting; Li, Honghui; Ke, Xiaoyan; Hu, Zhengmao; Zhao, Jingping; Zou, Xiaobing; Xia, Kun; Eichler, Evan E. Share Save
Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region Mohajeri, Kiana; Cantsilieris, Stuart; Huddleston, John; Nelson, Bradley J.; Coe, Bradley P.; Campbell, Catarina D.; Baker, Carl; Harshman, Lana; Munson, Katherine M.; Kronenberg, Zev N.; Kremitzki, Milinn; Raja, Archana; Catacchio, Claudia Rita; Graves, Tina A.; Wilson, Richard K.; Ventura, Mario; Eichler, Evan E. Share Save
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