Characterizing the Major Structural Variant Alleles of the Human Genome von Audano, Peter A., Sulovari, Arvis, Graves-Lindsay, Tina A., Cantsilieris, Stuart, Sorensen, Melanie, Welch, AnneMarie E., Dougherty, Max L., Nelson, Bradley J., Shah, Ankeeta, Dutcher, Susan K., Warren, Wesley C., Magrini, Vincent, McGrath, Sean D., Li, Yang I., Wilson, Richard K., Eichler, Evan E.

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Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement von Audano, 3rd, Peter A, Beck, Christine R

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Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants von 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

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Transposable element-mediated rearrangements are prevalent in human genomes von Balachandran, Parithi, Walawalkar, Isha A., Flores, Jacob I., Dayton, Jacob N., Audano, Peter A., Beck, Christine R.

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Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads von Vollger, Mitchell R., Logsdon, Glennis A., Audano, Peter A., Sulovari, Arvis, Porubsky, David, Peluso, Paul, Wenger, Aaron M., Concepcion, Gregory T., Kronenberg, Zev N., Munson, Katherine M., Baker, Carl, Sanders, Ashley D., Spierings, Diana C.J., Lansdorp, Peter M., Surti, Urvashi, Hunkapiller, Michael W., Eichler, Evan E.

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Mapping-free variant calling using haplotype reconstruction from k-mer frequencies von Audano, Peter A, Ravishankar, Shashidhar, Vannberg, Fredrik O

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes von Ebler, Jana, Ebert, Peter, Clarke, Wayne E., Rausch, Tobias, Audano, Peter A., Houwaart, Torsten, Mao, Yafei, Korbel, Jan O., Eichler, Evan E., Zody, Michael C., Dilthey, Alexander T., Marschall, Tobias

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Haplotype-resolved diverse human genomes and integrated analysis of structural variation von Ebert, Peter, Audano, Peter A., Zhu, Qihui, Rodriguez-Martin, Bernardo, Porubsky, David, Bonder, Marc Jan, Sulovari, Arvis, Ebler, Jana, Zhou, Weichen, Mari, Rebecca Serra, Yilmaz, Feyza, Zhao, Xuefang, Hsieh, PingHsun, Lee, Joyce, Kumar, Sushant, Lin, Jiadong, Rausch, Tobias, Chen, Yu, Ren, Jingwen, Santamarina, Martin, Hops, Wolfram, Ashraf, Hufsah, Chuang, Nelson T., Yang, Xiaofei, Munson, Katherine M., Lewis, Alexandra P., Fairley, Susan, Tallon, Luke J., Clarke, Wayne E., Basile, Anna O., Byrska-Bishop, Marta, Corvelo, Andre, Evani, Uday S., Lu, Tsung-Yu, Chaisson, Mark J. P., Chen, Junjie, Li, Chong, Brand, Harrison, Wenger, Aaron M., Ghareghani, Maryam, Harvey, William T., Raeder, Benjamin, Hasenfeld, Patrick, Regier, Allison A., Abel, Haley J., Hall, Ira M., Flicek, Paul, Stegle, Oliver, Gerstein, Mark B., Tubio, Jose M. C., Mu, Zepeng, Li, Yang, Shi, Xinghua, Hastie, Alex R., Ye, Kai, Chong, Zechen, Sanders, Ashley D., Zody, Michael C., Talkowski, Michael E., Mills, Ryan E., Devine, Scott E., Lee, Charles, Korbel, Jan O., Marschall, Tobias, Eichler, Evan E.

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SVision: a deep learning approach to resolve complex structural variants von Lin, Jiadong, Wang, Songbo, Audano, Peter A., Meng, Deyu, Flores, Jacob I., Kosters, Walter, Yang, Xiaofei, Jia, Peng, Marschall, Tobias, Beck, Christine R., Ye, Kai

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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads von Porubsky, David, Ebert, Peter, Audano, Peter A., Vollger, Mitchell R., Harvey, William T., Marijon, Pierre, Ebler, Jana, Munson, Katherine M., Sorensen, Melanie, Sulovari, Arvis, Haukness, Marina, Ghareghani, Maryam, Lansdorp, Peter M., Paten, Benedict, Devine, Scott E., Sanders, Ashley D., Lee, Charles, Chaisson, Mark J. P., Korbel, Jan O., Eichler, Evan E., Marschall, Tobias

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Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders von Porubsky, David, Höps, Wolfram, Ashraf, Hufsah, Hsieh, PingHsun, Rodriguez-Martin, Bernardo, Yilmaz, Feyza, Ebler, Jana, Hallast, Pille, Maria Maggiolini, Flavia Angela, Harvey, William T., Henning, Barbara, Audano, Peter A., Gordon, David S., Ebert, Peter, Hasenfeld, Patrick, Benito, Eva, Zhu, Qihui, Lee, Charles, Antonacci, Francesca, Steinrücken, Matthias, Beck, Christine R., Sanders, Ashley D., Marschall, Tobias, Eichler, Evan E., Korbel, Jan O.

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Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies von Zhao, Xuefang, Collins, Ryan L., Lee, Wan-Ping, Weber, Alexandra M., Jun, Yukyung, Zhu, Qihui, Weisburd, Ben, Huang, Yongqing, Audano, Peter A., Wang, Harold, Walker, Mark, Lowther, Chelsea, Fu, Jack, Gerstein, Mark B., Devine, Scott E., Marschall, Tobias, Korbel, Jan O., Eichler, Evan E., Chaisson, Mark J.P., Lee, Charles, Mills, Ryan E., Brand, Harrison, Talkowski, Michael E.

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Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility von Warren, Wesley C., Harris, R. Alan, Haukness, Marina, Fiddes, Ian T., Murali, Shwetha C., Fernandes, Jason, Dishuck, Philip C., Storer, Jessica M., Raveendran, Muthuswamy, Hillier, LaDeana W., Porubsky, David, Mao, Yafei, Gordon, David, Vollger, Mitchell R., Lewis, Alexandra P., Munson, Katherine M., DeVogelaere, Elizabeth, Armstrong, Joel, Diekhans, Mark, Walker, Jerilyn A., Tomlinson, Chad, Graves-Lindsay, Tina A., Kremitzki, Milinn, Salama, Sofie R., Audano, Peter A., Escalona, Merly, Maurer, Nicholas W., Antonacci, Francesca, Mercuri, Ludovica, Maggiolini, Flavia A. M., Catacchio, Claudia Rita, Underwood, Jason G., O'Connor, David H., Sanders, Ashley D., Korbel, Jan O., Ferguson, Betsy, Kubisch, H. Michael, Picker, Louis, Kalin, Ned H., Rosene, Douglas, Levine, Jon, Abbott, David H., Gray, Stanton B., Sanchez, Mar M., Kovacs-Balint, Zsofia A., Kemnitz, Joseph W., Thomasy, Sara M., Roberts, Jeffrey A., Kinnally, Erin L., Capitanio, John P., Skene, J. H. Pate, Platt, Michael, Cole, Shelley A., Green, Richard E., Ventura, Mario, Wiseman, Roger W., Paten, Benedict, Batzer, Mark A., Rogers, Jeffrey, Eichler, Evan E.

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Human-specific tandem repeat expansion and differential gene expression during primate evolution von Sulovari, Arvis, Li, Ruiyang, Audano, Peter A., Porubsky, David, Vollger, Mitchell R., Logsdon, Glennis A., Warren, Wesley C., Pollen, Alex A., Chaisson, Mark J. P., Eichler, Evan E.

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Familial long-read sequencing increases yield of de novo mutations von Noyes, Michelle D., Harvey, William T., Porubsky, David, Sulovari, Arvis, Li, Ruiyang, Rose, Nicholas R., Audano, Peter A., Munson, Katherine M., Lewis, Alexandra P., Hoekzema, Kendra, Mantere, Tuomo, Graves-Lindsay, Tina A., Sanders, Ashley D., Goodwin, Sara, Kramer, Melissa, Mokrab, Younes, Zody, Michael C., Hoischen, Alexander, Korbel, Jan O., McCombie, W. Richard, Eichler, Evan E.

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Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall von Harvey, William T, Ebert, Peter, Ebler, Jana, Audano, Peter A, Munson, Katherine M, Hoekzema, Kendra, Porubsky, David, Beck, Christine R, Marschall, Tobias, Garimella, Kiran, Eichler, Evan E

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Assembly of 43 human Y chromosomes reveals extensive complexity and variation von Hallast, Pille, Ebert, Peter, Loftus, Mark, Yilmaz, Feyza, Audano, Peter A., Logsdon, Glennis A., Bonder, Marc Jan, Zhou, Weichen, Höps, Wolfram, Kim, Kwondo, Li, Chong, Hoyt, Savannah J., Dishuck, Philip C., Porubsky, David, Tsetsos, Fotios, Kwon, Jee Young, Zhu, Qihui, Munson, Katherine M., Hasenfeld, Patrick, Harvey, William T., Lewis, Alexandra P., Kordosky, Jennifer, Hoekzema, Kendra, O’Neill, Rachel J., Korbel, Jan O., Tyler-Smith, Chris, Eichler, Evan E., Shi, Xinghua, Beck, Christine R., Marschall, Tobias, Konkel, Miriam K., Lee, Charles

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Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation von Yilmaz, Feyza, Karageorgiou, Charikleia, Kim, Kwondo, Pajic, Petar, Scheer, Kendra, Beck, Christine R, Torregrossa, Ann-Marie, Lee, Charles, Gokcumen, Omer, Audano, Peter A, Austine-Orimoloye, Olanrewaju, Beck, Christine R, Eichler, Evan E, Hallast, Pille, Harvey, William T, Hastie, Alex R, Hoekzema, Kendra, Hunt, Sarah, Korbel, Jan O, Kordosky, Jennifer, Lee, Charles, Lewis, Alexandra P, Marschall, Tobias, Munson, Katherine M, Pang, Andy, Yilmaz, Feyza

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Structurally divergent and recurrently mutated regions of primate genomes von Mao, Yafei, Harvey, William T., Porubsky, David, Munson, Katherine M., Hoekzema, Kendra, Lewis, Alexandra P., Audano, Peter A., Rozanski, Allison, Yang, Xiangyu, Zhang, Shilong, Yoo, DongAhn, Gordon, David S., Fair, Tyler, Wei, Xiaoxi, Logsdon, Glennis A., Haukness, Marina, Dishuck, Philip C., Jeong, Hyeonsoo, del Rosario, Ricardo, Bauer, Vanessa L., Fattor, Will T., Wilkerson, Gregory K., Mao, Yuxiang, Shi, Yongyong, Sun, Qiang, Lu, Qing, Paten, Benedict, Bakken, Trygve E., Pollen, Alex A., Feng, Guoping, Sawyer, Sara L., Warren, Wesley C., Carbone, Lucia, Eichler, Evan E.

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A high-quality bonobo genome refines the analysis of hominid evolution von Mao, Yafei, Catacchio, Claudia R., Hillier, LaDeana W., Porubsky, David, Li, Ruiyang, Sulovari, Arvis, Fernandes, Jason D., Montinaro, Francesco, Gordon, David S., Storer, Jessica M., Haukness, Marina, Fiddes, Ian T., Murali, Shwetha Canchi, Dishuck, Philip C., Hsieh, PingHsun, Harvey, William T., Audano, Peter A., Mercuri, Ludovica, Piccolo, Ilaria, Antonacci, Francesca, Munson, Katherine M., Lewis, Alexandra P., Baker, Carl, Underwood, Jason G., Hoekzema, Kendra, Huang, Tzu-Hsueh, Sorensen, Melanie, Walker, Jerilyn A., Hoffman, Jinna, Thibaud-Nissen, Françoise, Salama, Sofie R., Pang, Andy W. C., Lee, Joyce, Hastie, Alex R., Paten, Benedict, Batzer, Mark A., Diekhans, Mark, Ventura, Mario, Eichler, Evan E.

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