HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads von Nurk, Sergey, Walenz, Brian P., Rhie, Arang, Vollger, Mitchell R., Logsdon, Glennis A., Grothe, Robert, Miga, Karen H., Eichler, Evan E., Phillippy, Adam M., Koren, Sergey

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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes von Shafin, Kishwar, Pesout, Trevor, Lorig-Roach, Ryan, Haukness, Marina, Olsen, Hugh E., Bosworth, Colleen, Armstrong, Joel, Tigyi, Kristof, Maurer, Nicholas, Koren, Sergey, Sedlazeck, Fritz J., Marschall, Tobias, Mayes, Simon, Costa, Vania, Zook, Justin M., Liu, Kelvin J., Kilburn, Duncan, Sorensen, Melanie, Munson, Katy M., Vollger, Mitchell R., Monlong, Jean, Garrison, Erik, Eichler, Evan E., Salama, Sofie, Haussler, David, Green, Richard E., Akeson, Mark, Phillippy, Adam, Miga, Karen H., Carnevali, Paolo, Jain, Miten, Paten, Benedict

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The structure, function and evolution of a complete human chromosome 8 von Logsdon, Glennis A., Vollger, Mitchell R., Hsieh, PingHsun, Mao, Yafei, Liskovykh, Mikhail A., Koren, Sergey, Nurk, Sergey, Mercuri, Ludovica, Dishuck, Philip C., Rhie, Arang, de Lima, Leonardo G., Dvorkina, Tatiana, Porubsky, David, Harvey, William T., Mikheenko, Alla, Bzikadze, Andrey V., Kremitzki, Milinn, Graves-Lindsay, Tina A., Jain, Chirag, Hoekzema, Kendra, Murali, Shwetha C., Munson, Katherine M., Baker, Carl, Sorensen, Melanie, Lewis, Alexandra M., Surti, Urvashi, Gerton, Jennifer L., Larionov, Vladimir, Ventura, Mario, Miga, Karen H., Phillippy, Adam M., Eichler, Evan E.

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Epigenetic patterns in a complete human genome von Gershman, Ariel, Sauria, Michael E G, Guitart, Xavi, Vollger, Mitchell R, Hook, Paul W, Hoyt, Savannah J, Jain, Miten, Shumate, Alaina, Razaghi, Roham, Koren, Sergey, Altemose, Nicolas, Caldas, Gina V, Logsdon, Glennis A, Rhie, Arang, Eichler, Evan E, Schatz, Michael C, O'Neill, Rachel J, Phillippy, Adam M, Miga, Karen H, Timp, Winston

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From telomere to telomere: The transcriptional and epigenetic state of human repeat elements von Hoyt, Savannah J, Storer, Jessica M, Hartley, Gabrielle A, Grady, Patrick G S, Gershman, Ariel, de Lima, Leonardo G, Limouse, Charles, Halabian, Reza, Wojenski, Luke, Rodriguez, Matias, Altemose, Nicolas, Rhie, Arang, Core, Leighton J, Gerton, Jennifer L, Makalowski, Wojciech, Olson, Daniel, Rosen, Jeb, Smit, Arian F A, Straight, Aaron F, Vollger, Mitchell R, Wheeler, Travis J, Schatz, Michael C, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Miga, Karen H, O'Neill, Rachel J

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Characterization of large-scale genomic differences in the first complete human genome von Yang, Xiangyu, Wang, Xuankai, Zou, Yawen, Zhang, Shilong, Xia, Manying, Fu, Lianting, Vollger, Mitchell R, Chen, Nae-Chyun, Taylor, Dylan J, Harvey, William T, Logsdon, Glennis A, Meng, Dan, Shi, Junfeng, McCoy, Rajiv C, Schatz, Michael C, Li, Weidong, Eichler, Evan E, Lu, Qing, Mao, Yafei

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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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Long-read human genome sequencing and its applications von Logsdon, Glennis A., Vollger, Mitchell R., Eichler, Evan E.

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Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes von Hsieh, PingHsun, Vollger, Mitchell R, Dang, Vy, Porubsky, David, Baker, Carl, Cantsilieris, Stuart, Hoekzema, Kendra, Lewis, Alexandra P, Munson, Katherine M, Sorensen, Melanie, Kronenberg, Zev N, Murali, Shwetha, Nelson, Bradley J, Chiatante, Giorgia, Maggiolini, Flavia Angela Maria, Blanché, Hélène, Underwood, Jason G, Antonacci, Francesca, Deleuze, Jean-François, Eichler, Evan E

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Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans von Hsieh, PingHsun, Dang, Vy, Vollger, Mitchell R., Mao, Yafei, Huang, Tzu-Hsueh, Dishuck, Philip C., Baker, Carl, Cantsilieris, Stuart, Lewis, Alexandra P., Munson, Katherine M., Sorensen, Melanie, Welch, AnneMarie E., Underwood, Jason G., Eichler, Evan E.

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Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus von Maggiolini, Flavia A M, Cantsilieris, Stuart, D'Addabbo, Pietro, Manganelli, Michele, Coe, Bradley P, Dumont, Beth L, Sanders, Ashley D, Pang, Andy Wing Chun, Vollger, Mitchell R, Palumbo, Orazio, Palumbo, Pietro, Accadia, Maria, Carella, Massimo, Eichler, Evan E, Antonacci, Francesca

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StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps von Vollger, Mitchell R, Kerpedjiev, Peter, Phillippy, Adam M, Eichler, Evan E

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Segmental duplications and their variation in a complete human genome von Vollger, Mitchell R, Guitart, Xavi, Dishuck, Philip C, Mercuri, Ludovica, Harvey, William T, Gershman, Ariel, Diekhans, Mark, Sulovari, Arvis, Munson, Katherine M, Lewis, Alexandra P, Hoekzema, Kendra, Porubsky, David, Li, Ruiyang, Nurk, Sergey, Koren, Sergey, Miga, Karen H, Phillippy, Adam M, Timp, Winston, Ventura, Mario, Eichler, Evan E

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A complete reference genome improves analysis of human genetic variation von Aganezov, Sergey, Yan, Stephanie M, Soto, Daniela C, Kirsche, Melanie, Zarate, Samantha, Avdeyev, Pavel, Taylor, Dylan J, Shafin, Kishwar, Shumate, Alaina, Xiao, Chunlin, Wagner, Justin, McDaniel, Jennifer, Olson, Nathan D, Sauria, Michael E G, Vollger, Mitchell R, Rhie, Arang, Meredith, Melissa, Martin, Skylar, Lee, Joyce, Koren, Sergey, Rosenfeld, Jeffrey A, Paten, Benedict, Layer, Ryan, Chin, Chen-Shan, Sedlazeck, Fritz J, Hansen, Nancy F, Miller, Danny E, Phillippy, Adam M, Miga, Karen H, McCoy, Rajiv C, Dennis, Megan Y, Zook, Justin M, Schatz, Michael C

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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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Long-read sequence and assembly of segmental duplications von Vollger, Mitchell R., Dishuck, Philip C., Sorensen, Melanie, Welch, AnneMarie E., Dang, Vy, Dougherty, Max L., Graves-Lindsay, Tina A., Wilson, Richard K., Chaisson, Mark J. P., Eichler, Evan E.

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Gaps and complex structurally variant loci in phased genome assemblies von Porubsky, David, Vollger, Mitchell R, Harvey, William T, Rozanski, Allison N, Ebert, Peter, Hickey, Glenn, Hasenfeld, Patrick, Sanders, Ashley D, Stober, Catherine, Korbel, Jan O, Paten, Benedict, Marschall, Tobias, Eichler, Evan E

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STR mutations on chromosome 15q cause thyrotropin resistance by activating a primate-specific enhancer of MIR7-2/MIR1179 von Grasberger, Helmut, Dumitrescu, Alexandra M., Liao, Xiao-Hui, Swanson, Elliott G., Weiss, Roy E., Srichomkwun, Panudda, Pappa, Theodora, Chen, Junfeng, Yoshimura, Takashi, Hoffmann, Phillip, França, Monica Malheiros, Tagett, Rebecca, Onigata, Kazumichi, Costagliola, Sabine, Ranchalis, Jane, Vollger, Mitchell R., Stergachis, Andrew B., Chong, Jessica X., Bamshad, Michael J., Smits, Guillaume, Vassart, Gilbert, Refetoff, Samuel

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Telomere-to-telomere assembly of a complete human X chromosome von Miga, Karen H., Koren, Sergey, Rhie, Arang, Vollger, Mitchell R., Gershman, Ariel, Bzikadze, Andrey, Brooks, Shelise, Howe, Edmund, Porubsky, David, Logsdon, Glennis A., Schneider, Valerie A., Potapova, Tamara, Wood, Jonathan, Chow, William, Armstrong, Joel, Fredrickson, Jeanne, Pak, Evgenia, Tigyi, Kristof, Kremitzki, Milinn, Markovic, Christopher, Maduro, Valerie, Dutra, Amalia, Bouffard, Gerard G., Chang, Alexander M., Hansen, Nancy F., Wilfert, Amy B., Thibaud-Nissen, Françoise, Schmitt, Anthony D., Belton, Jon-Matthew, Selvaraj, Siddarth, Dennis, Megan Y., Soto, Daniela C., Sahasrabudhe, Ruta, Kaya, Gulhan, Quick, Josh, Loman, Nicholas J., Holmes, Nadine, Loose, Matthew, Surti, Urvashi, Risques, Rosa ana, Graves Lindsay, Tina A., Fulton, Robert, Hall, Ira, Paten, Benedict, Howe, Kerstin, Timp, Winston, Young, Alice, Mullikin, James C., Pevzner, Pavel A., Gerton, Jennifer L., Sullivan, Beth A., Eichler, Evan E., Phillippy, Adam M.

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Complete genomic and epigenetic maps of human centromeres von Altemose, Nicolas, Logsdon, Glennis A, Bzikadze, Andrey V, Sidhwani, Pragya, Langley, Sasha A, Caldas, Gina V, Hoyt, Savannah J, Uralsky, Lev, Ryabov, Fedor D, Shew, Colin J, Sauria, Michael E G, Borchers, Matthew, Gershman, Ariel, Mikheenko, Alla, Shepelev, Valery A, Dvorkina, Tatiana, Kunyavskaya, Olga, Vollger, Mitchell R, Rhie, Arang, McCartney, Ann M, Asri, Mobin, Lorig-Roach, Ryan, Shafin, Kishwar, Lucas, Julian K, Aganezov, Sergey, Olson, Daniel, de Lima, Leonardo Gomes, Potapova, Tamara, Hartley, Gabrielle A, Haukness, Marina, Kerpedjiev, Peter, Gusev, Fedor, Tigyi, Kristof, Brooks, Shelise, Young, Alice, Nurk, Sergey, Koren, Sergey, Salama, Sofie R, Paten, Benedict, Rogaev, Evgeny I, Streets, Aaron, Karpen, Gary H, Dernburg, Abby F, Sullivan, Beth A, Straight, Aaron F, Wheeler, Travis J, Gerton, Jennifer L, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Dennis, Megan Y, O'Neill, Rachel J, Zook, Justin M, Schatz, Michael C, Pevzner, Pavel A, Diekhans, Mark, Langley, Charles H, Alexandrov, Ivan A, Miga, Karen H

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