Scaffolding of long read assemblies using long range contact information by Ghurye, Jay, Pop, Mihai, Koren, Sergey, Bickhart, Derek, Chin, Chen-Shan

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The complete sequence of a human genome by Nurk, Sergey, Koren, Sergey, Rhie, Arang, Rautiainen, Mikko, Bzikadze, Andrey V, Mikheenko, Alla, Vollger, Mitchell R, Altemose, Nicolas, Uralsky, Lev, Gershman, Ariel, Aganezov, Sergey, Hoyt, Savannah J, Diekhans, Mark, Logsdon, Glennis A, Alonge, Michael, Antonarakis, Stylianos E, Borchers, Matthew, Bouffard, Gerard G, Brooks, Shelise Y, Caldas, Gina V, Chen, Nae-Chyun, Cheng, Haoyu, Chin, Chen-Shan, Chow, William, de Lima, Leonardo G, Dishuck, Philip C, Durbin, Richard, Dvorkina, Tatiana, Fiddes, Ian T, Formenti, Giulio, Fulton, Robert S, Fungtammasan, Arkarachai, Garrison, Erik, Grady, Patrick G S, Graves-Lindsay, Tina A, Hall, Ira M, Hansen, Nancy F, Hartley, Gabrielle A, Haukness, Marina, Howe, Kerstin, Hunkapiller, Michael W, Jain, Chirag, Jain, Miten, Jarvis, Erich D, Kerpedjiev, Peter, Kirsche, Melanie, Kolmogorov, Mikhail, Korlach, Jonas, Kremitzki, Milinn, Li, Heng, Maduro, Valerie V, Marschall, Tobias, McCartney, Ann M, McDaniel, Jennifer, Miller, Danny E, Mullikin, James C, Myers, Eugene W, Olson, Nathan D, Paten, Benedict, Peluso, Paul, Pevzner, Pavel A, Porubsky, David, Potapova, Tamara, Rogaev, Evgeny I, Rosenfeld, Jeffrey A, Salzberg, Steven L, Schneider, Valerie A, Sedlazeck, Fritz J, Shafin, Kishwar, Shew, Colin J, Shumate, Alaina, Sims, Ying, Smit, Arian F A, Soto, Daniela C, Sović, Ivan, Storer, Jessica M, Streets, Aaron, Sullivan, Beth A, Thibaud-Nissen, Françoise, Torrance, James, Wagner, Justin, Walenz, Brian P, Wenger, Aaron, Wood, Jonathan M D, Xiao, Chunlin, Yan, Stephanie M, Young, Alice C, Zarate, Samantha, Surti, Urvashi, McCoy, Rajiv C, Dennis, Megan Y, Alexandrov, Ivan A, Gerton, Jennifer L, O'Neill, Rachel J, Timp, Winston, Zook, Justin M, Schatz, Michael C, Eichler, Evan E, Miga, Karen H, Phillippy, Adam M

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Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome by Wenger, Aaron M., Peluso, Paul, Rowell, William J., Chang, Pi-Chuan, Hall, Richard J., Concepcion, Gregory T., Ebler, Jana, Fungtammasan, Arkarachai, Kolesnikov, Alexey, Olson, Nathan D., Töpfer, Armin, Alonge, Michael, Mahmoud, Medhat, Qian, Yufeng, Chin, Chen-Shan, Phillippy, Adam M., Schatz, Michael C., Myers, Gene, DePristo, Mark A., Ruan, Jue, Marschall, Tobias, Sedlazeck, Fritz J., Zook, Justin M., Li, Heng, Koren, Sergey, Carroll, Andrew, Rank, David R., Hunkapiller, Michael W.

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Chromosome-scale, haplotype-resolved assembly of human genomes by Garg, Shilpa, Fungtammasan, Arkarachai, Carroll, Andrew, Chou, Mike, Schmitt, Anthony, Zhou, Xiang, Mac, Stephen, Peluso, Paul, Hatas, Emily, Ghurye, Jay, Maguire, Jared, Mahmoud, Medhat, Cheng, Haoyu, Heller, David, Zook, Justin M., Moemke, Tobias, Marschall, Tobias, Sedlazeck, Fritz J., Aach, John, Chin, Chen-Shan, Church, George M., Li, Heng

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Ribbon: intuitive visualization for complex genomic variation by Nattestad, Maria, Aboukhalil, Robert, Chin, Chen-Shan, Schatz, Michael C

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Long-read sequence assembly of the gorilla genome by Gordon, David, Huddleston, John, Chaisson, Mark J. P., Hill, Christopher M., Kronenberg, Zev N., Munson, Katherine M., Malig, Maika, Raja, Archana, Fiddes, Ian, Hillier, LaDeana W., Dunn, Christopher, Baker, Carl, Armstrong, Joel, Diekhans, Mark, Paten, Benedict, Shendure, Jay, Wilson, Richard K., Haussler, David, Chin, Chen-Shan, Eichler, Evan E.

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Genomic variant benchmark: if you cannot measure it, you cannot improve it by Majidian, Sina, Agustinho, Daniel Paiva, Chin, Chen-Shan, Sedlazeck, Fritz J, Mahmoud, Medhat

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Multi-platform discovery of haplotype-resolved structural variation in human genomes by 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, Stütz, 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

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A complete reference genome improves analysis of human genetic variation by 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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HLA Typing for the Next Generation by Mayor, Neema P, Robinson, James, McWhinnie, Alasdair J M, Ranade, Swati, Eng, Kevin, Midwinter, William, Bultitude, Will P, Chin, Chen-Shan, Bowman, Brett, Marks, Patrick, Braund, Henny, Madrigal, J Alejandro, Latham, Katy, Marsh, Steven G E

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Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions by Butler, Daniel, Mozsary, Christopher, Meydan, Cem, Foox, Jonathan, Rosiene, Joel, Shaiber, Alon, Danko, David, Afshinnekoo, Ebrahim, MacKay, Matthew, Sedlazeck, Fritz J., Ivanov, Nikolay A., Sierra, Maria, Pohle, Diana, Zietz, Michael, Gisladottir, Undina, Ramlall, Vijendra, Sholle, Evan T., Schenck, Edward J., Westover, Craig D., Hassan, Ciaran, Ryon, Krista, Young, Benjamin, Bhattacharya, Chandrima, Ng, Dianna L., Granados, Andrea C., Santos, Yale A., Servellita, Venice, Federman, Scot, Ruggiero, Phyllis, Fungtammasan, Arkarachai, Chin, Chen-Shan, Pearson, Nathaniel M., Langhorst, Bradley W., Tanner, Nathan A., Kim, Youngmi, Reeves, Jason W., Hether, Tyler D., Warren, Sarah E., Bailey, Michael, Gawrys, Justyna, Meleshko, Dmitry, Xu, Dong, Couto-Rodriguez, Mara, Nagy-Szakal, Dorottya, Barrows, Joseph, Wells, Heather, O’Hara, Niamh B., Rosenfeld, Jeffrey A., Chen, Ying, Steel, Peter A. D., Shemesh, Amos J., Xiang, Jenny, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Iftner, Angelika, Bezdan, Daniela, Sanchez, Elizabeth, Campion, Thomas R., Sipley, John, Cong, Lin, Craney, Arryn, Velu, Priya, Melnick, Ari M., Shapira, Sagi, Hajirasouliha, Iman, Borczuk, Alain, Iftner, Thomas, Salvatore, Mirella, Loda, Massimo, Westblade, Lars F., Cushing, Melissa, Wu, Shixiu, Levy, Shawn, Chiu, Charles, Schwartz, Robert E., Tatonetti, Nicholas, Rennert, Hanna, Imielinski, Marcin, Mason, Christopher E.

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Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity by Höijer, Ida, Johansson, Josefin, Gudmundsson, Sanna, Chin, Chen-Shan, Bunikis, Ignas, Häggqvist, Susana, Emmanouilidou, Anastasia, Wilbe, Maria, den Hoed, Marcel, Bondeson, Marie-Louise, Feuk, Lars, Gyllensten, Ulf, Ameur, Adam

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Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line by Nattestad, Maria, Goodwin, Sara, Ng, Karen, Baslan, Timour, Sedlazeck, Fritz J, Rescheneder, Philipp, Garvin, Tyler, Fang, Han, Gurtowski, James, Hutton, Elizabeth, Tseng, Elizabeth, Chin, Chen-Shan, Beck, Timothy, Sundaravadanam, Yogi, Kramer, Melissa, Antoniou, Eric, McPherson, John D, Hicks, James, McCombie, W Richard, Schatz, Michael C

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Heterogeneous resistance to quizartinib in acute myeloid leukemia revealed by single-cell analysis by Smith, Catherine C., Paguirigan, Amy, Jeschke, Grace R., Lin, Kimberly C., Massi, Evan, Tarver, Theodore, Chin, Chen-Shan, Asthana, Saurabh, Olshen, Adam, Travers, Kevin J., Wang, Susana, Levis, Mark J., Perl, Alexander E., Radich, Jerald P., Shah, Neil P.

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Effect of sequence depth and length in long-read assembly of the maize inbred NC358 by Ou, Shujun, Liu, Jianing, Chougule, Kapeel M., Fungtammasan, Arkarachai, Seetharam, Arun S., Stein, Joshua C., Llaca, Victor, Manchanda, Nancy, Gilbert, Amanda M., Wei, Sharon, Chin, Chen-Shan, Hufnagel, David E., Pedersen, Sarah, Snodgrass, Samantha J., Fengler, Kevin, Woodhouse, Margaret, Walenz, Brian P., Koren, Sergey, Phillippy, Adam M., Hannigan, Brett T., Dawe, R. Kelly, Hirsch, Candice N., Hufford, Matthew B., Ware, Doreen

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De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads by Korlach, Jonas, Gedman, Gregory, Kingan, Sarah B., Chin, Chen-Shan, Howard, Jason T., Audet, Jean-Nicolas, Cantin, Lindsey, Jarvis, Erich D.

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Extending reference assembly models by Church, Deanna M, Schneider, Valerie A, Steinberg, Karyn Meltz, Schatz, Michael C, Quinlan, Aaron R, Chin, Chen-Shan, Kitts, Paul A, Aken, Bronwen, Marth, Gabor T, Hoffman, Michael M, Herrero, Javier, Mendoza, M Lisandra Zepeda, Durbin, Richard, Flicek, Paul

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A diploid assembly-based benchmark for variants in the major histocompatibility complex by Chin, Chen-Shan, Wagner, Justin, Zeng, Qiandong, Garrison, Erik, Garg, Shilpa, Fungtammasan, Arkarachai, Rautiainen, Mikko, Aganezov, Sergey, Kirsche, Melanie, Zarate, Samantha, Schatz, Michael C., Xiao, Chunlin, Rowell, William J., Markello, Charles, Farek, Jesse, Sedlazeck, Fritz J., Bansal, Vikas, Yoo, Byunggil, Miller, Neil, Zhou, Xin, Carroll, Andrew, Barrio, Alvaro Martinez, Salit, Marc, Marschall, Tobias, Dilthey, Alexander T., Zook, Justin M.

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Ten simple rules for large-scale data processing by Fungtammasan, Arkarachai, Lee, Alexandra, Taroni, Jaclyn, Wheeler, Kurt, Chin, Chen-Shan, Davis, Sean, Greene, Casey

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Long-read whole-genome analysis of human single cells by Hård, Joanna, Mold, Jeff E., Eisfeldt, Jesper, Tellgren-Roth, Christian, Häggqvist, Susana, Bunikis, Ignas, Contreras-Lopez, Orlando, Chin, Chen-Shan, Nordlund, Jessica, Rubin, Carl-Johan, Feuk, Lars, Michaëlsson, Jakob, Ameur, Adam

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