Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data von Chin, Chen-Shan, Alexander, David H, Marks, Patrick, Klammer, Aaron A, Drake, James, Heiner, Cheryl, Clum, Alicia, Copeland, Alex, Huddleston, John, Eichler, Evan E, Turner, Stephen W, Korlach, Jonas

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Nextstrain: real-time tracking of pathogen evolution von Hadfield, James, Megill, Colin, Bell, Sidney M, Huddleston, John, Potter, Barney, Callender, Charlton, Sagulenko, Pavel, Bedford, Trevor, Neher, Richard A

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An Incomplete Understanding of Human Genetic Variation von Huddleston, John, Eichler, Evan E

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Resolving the complexity of the human genome using single-molecule sequencing von Chaisson, Mark J. P., Huddleston, John, Dennis, Megan Y., Sudmant, Peter H., Malig, Maika, Hormozdiari, Fereydoun, Antonacci, Francesca, Surti, Urvashi, Sandstrom, Richard, Boitano, Matthew, Landolin, Jane M., Stamatoyannopoulos, John A., Hunkapiller, Michael W., Korlach, Jonas, Eichler, Evan E.

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Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants von Lee, Juhye M., Huddleston, John, Doud, Michael B., Hooper, Kathryn A., Wu, Nicholas C., Bedford, Trevor, Bloom, Jesse D.

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Discovery and genotyping of structural variation from long-read haploid genome sequence data von 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

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Long-read sequence assembly of the gorilla genome von 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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Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA von Turner, Tychele N., Hormozdiari, Fereydoun, Duyzend, Michael H., McClymont, Sarah A., Hook, Paul W., Iossifov, Ivan, Raja, Archana, Baker, Carl, Hoekzema, Kendra, Stessman, Holly A., Zody, Michael C., Nelson, Bradley J., Huddleston, John, Sandstrom, Richard, Smith, Joshua D., Hanna, David, Swanson, James M., Faustman, Elaine M., Bamshad, Michael J., Stamatoyannopoulos, John, Nickerson, Deborah A., McCallion, Andrew S., Darnell, Robert, Eichler, Evan E.

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Global diversity, population stratification, and selection of human copy-number variation von Sudmant, Peter H., Mallick, Swapan, Nelson, Bradley J., Hormozdiari, Fereydoun, Krumm, Niklas, Huddleston, John, Coe, Bradley P., Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn B., Posukh, Olga L., Sahakyan, Hovhannes, Watkins, W. Scott, Yepiskoposyan, Levon, Abdullah, M. Syafiq, Bravi, Claudio M., Capelli, Cristian, Hervig, Tor, Wee, Joseph T. S., Tyler-Smith, Chris, van Driem, George, Romero, Irene Gallego, Jha, Aashish R., Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Henn, Brenna, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena B., Ayodo, George, Beall, Cynthia M., Di Rienzo, Anna, Hammer, Michael F., Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah A., Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, Eichler, Evan E.

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Long-read sequencing and de novo assembly of a Chinese genome von Shi, Lingling, Guo, Yunfei, Dong, Chengliang, Huddleston, John, Yang, Hui, Han, Xiaolu, Fu, Aisi, Li, Quan, Li, Na, Gong, Siyi, Lintner, Katherine E., Ding, Qiong, Wang, Zou, Hu, Jiang, Wang, Depeng, Wang, Feng, Wang, Lin, Lyon, Gholson J., Guan, Yongtao, Shen, Yufeng, Evgrafov, Oleg V., Knowles, James A., Thibaud-Nissen, Francoise, Schneider, Valerie, Yu, Chack-Yung, Zhou, Libing, Eichler, Evan E., So, Kwok-Fai, Wang, Kai

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Reconstructing complex regions of genomes using long-read sequencing technology von Huddleston, John, Ranade, Swati, Malig, Maika, Antonacci, Francesca, Chaisson, Mark, Hon, Lawrence, Sudmant, Peter H, Graves, Tina A, Alkan, Can, Dennis, Megan Y, Wilson, Richard K, Turner, Stephen W, Korlach, Jonas, Eichler, Evan E

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Evolution and diversity of copy number variation in the great ape lineage von Sudmant, Peter H, Huddleston, John, Catacchio, Claudia R, Malig, Maika, Hillier, Ladeana W, Baker, Carl, Mohajeri, Kiana, Kondova, Ivanela, Bontrop, Ronald E, Persengiev, Stephan, Antonacci, Francesca, Ventura, Mario, Prado-Martinez, Javier, Marques-Bonet, Tomas, Eichler, Evan E

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Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation von Watson, Corey T., Steinberg, Karyn M., Huddleston, John, Warren, Rene L., Malig, Maika, Schein, Jacqueline, Willsey, A. Jeremy, Joy, Jeffrey B., Scott, Jamie K., Graves, Tina A., Wilson, Richard K., Holt, Robert A., Eichler, Evan E., Breden, Felix

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Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility von Nuttle, Xander, Giannuzzi, Giuliana, Duyzend, Michael H., Schraiber, Joshua G., Narvaiza, Iñigo, Sudmant, Peter H., Penn, Osnat, Chiatante, Giorgia, Malig, Maika, Huddleston, John, Benner, Chris, Camponeschi, Francesca, Ciofi-Baffoni, Simone, Stessman, Holly A. F., Marchetto, Maria C. N., Denman, Laura, Harshman, Lana, Baker, Carl, Raja, Archana, Penewit, Kelsi, Janke, Nicolette, Tang, W. Joyce, Ventura, Mario, Banci, Lucia, Antonacci, Francesca, Akey, Joshua M., Amemiya, Chris T., Gage, Fred H., Reymond, Alexandre, Eichler, Evan E.

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Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution von Huddleston, John, Barnes, John R., Rowe, Thomas, Xu, Xiyan, Kondor, Rebecca, Wentworth, David E., Whittaker, Lynne, Ermetal, Burcu, Daniels, Rodney Stuart, McCauley, John W., Fujisaki, Seiichiro, Nakamura, Kazuya, Kishida, Noriko, Watanabe, Shinji, Hasegawa, Hideki, Barr, Ian, Subbarao, Kanta, Barrat-Charlaix, Pierre, Neher, Richard A., Bedford, Trevor

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Single haplotype assembly of the human genome from a hydatidiform mole von Steinberg, Karyn Meltz, Schneider, Valerie A, Graves-Lindsay, Tina A, Fulton, Robert S, Agarwala, Richa, Huddleston, John, Shiryev, Sergey A, Morgulis, Aleksandr, Surti, Urvashi, Warren, Wesley C, Church, Deanna M, Eichler, Evan E, Wilson, Richard K

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Homotypic protection against influenza in a pediatric cohort in Managua, Nicaragua von Wraith, Steph, Balmaseda, Angel, Carrillo, Fausto Andres Bustos, Kuan, Guillermina, Huddleston, John, Kubale, John, Lopez, Roger, Ojeda, Sergio, Schiller, Amy, Lopez, Brenda, Sanchez, Nery, Webby, Richard, Nelson, Martha I., Harris, Eva, Gordon, Aubree

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Bovine NK-lysin: Copy number variation and functional diversification von Chen, Junfeng, Huddleston, John, Buckley, Reuben M, Malig, Maika, Lawhon, Sara D, Skow, Loren C, Lee, Mi Ok, Eichler, Evan E, Andersson, Leif, Womack, James E

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Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H (CFH) gene family von Cantsilieris, Stuart, Nelson, Bradley J., Huddleston, John, Baker, Carl, Harshman, Lana, Penewit, Kelsi, Munson, Katherine M., Sorensen, Melanie, Welch, AnneMarie E., Dang, Vy, Grassmann, Felix, Richardson, Andrea J., Guymer, Robyn H., Graves-Lindsay, Tina A., Wilson, Richard K., Weber, Bernhard H. F., Baird, Paul N., Allikmets, Rando, Eichler, Evan E.

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An evolutionary driver of interspersed segmental duplications in primates von Cantsilieris, Stuart, Sunkin, Susan M., Johnson, Matthew E., Anaclerio, Fabio, Huddleston, John, Baker, Carl, Dougherty, Max L., Underwood, Jason G., Sulovari, Arvis, Hsieh, PingHsun, Mao, Yafei, Catacchio, Claudia Rita, Malig, Maika, Welch, AnneMarie E., Sorensen, Melanie, Munson, Katherine M., Jiang, Weihong, Girirajan, Santhosh, Ventura, Mario, Lamb, Bruce T., Conlon, Ronald A., Eichler, Evan E.

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