SARS-CoV-2 variants, spike mutations and immune escape von Harvey, William T., Carabelli, Alessandro M., Jackson, Ben, Gupta, Ravindra K., Thomson, Emma C., Harrison, Ewan M., Ludden, Catherine, Reeve, Richard, Rambaut, Andrew, Peacock, Sharon J., Robertson, David L.

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The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level von Rodriguez-R, Luis M, Gunturu, Santosh, Harvey, William T, Rosselló-Mora, Ramon, Tiedje, James M, Cole, James R, Konstantinidis, Konstantinos T

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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, Serra Mari, Rebecca, Yilmaz, Feyza, Zhao, Xuefang, Hsieh, PingHsun, Lee, Joyce, Kumar, Sushant, Lin, Jiadong, Rausch, Tobias, Chen, Yu, Ren, Jingwen, Santamarina, Martin, Höps, 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, André, 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 I, 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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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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A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses von Harvey, William T, Davies, Vinny, Daniels, Rodney S, Whittaker, Lynne, Gregory, Victoria, Hay, Alan J, Husmeier, Dirk, McCauley, John W, Reeve, Richard

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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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Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing von Henglin, Mir, Ghareghani, Maryam, Harvey, William T, Porubsky, David, Koren, Sergey, Eichler, Evan E, Ebert, Peter, Marschall, Tobias

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Inversion polymorphism in a complete human genome assembly von Porubsky, David, Harvey, William T, Rozanski, Allison N, Ebler, Jana, Höps, Wolfram, Ashraf, Hufsah, Hasenfeld, Patrick, Paten, Benedict, Sanders, Ashley D, Marschall, Tobias, Korbel, Jan O, Eichler, Evan E

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Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway von Zhou, Jie, Peacock, Thomas P., Brown, Jonathan C., Goldhill, Daniel H., Elrefaey, Ahmed M.E., Penrice-Randal, Rebekah, Cowton, Vanessa M., De Lorenzo, Giuditta, Furnon, Wilhelm, Harvey, William T., Kugathasan, Ruthiran, Frise, Rebecca, Baillon, Laury, Lassaunière, Ria, Thakur, Nazia, Gallo, Giulia, Goldswain, Hannah, Donovan-Banfield, I'ah, Dong, Xiaofeng, Randle, Nadine P., Sweeney, Fiachra, Glynn, Martha C., Quantrill, Jessica L., McKay, Paul F., Patel, Arvind H., Palmarini, Massimo, Hiscox, Julian A., Bailey, Dalan, Barclay, Wendy S.

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Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses von Harvey, William T, Benton, Donald J, Gregory, Victoria, Hall, James P J, Daniels, Rodney S, Bedford, Trevor, Haydon, Daniel T, Hay, Alan J, McCauley, John W, Reeve, Richard

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Common lizard microhabitat selection varies by sex, parity mode, and colouration von Recknagel, Hans, Harvey, William T, Layton, Megan, Elmer, Kathryn R

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Tracking the Antigenic Evolution of Foot-and-Mouth Disease Virus von Reeve, Richard, Borley, Daryl W, Maree, Francois F, Upadhyaya, Sasmita, Lukhwareni, Azwidowi, Esterhuysen, Jan J, Harvey, William T, Blignaut, Belinda, Fry, Elizabeth E, Parida, Satya, Paton, David J, Mahapatra, Mana

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Genomic and Immunogenic Protein Diversity of Erysipelothrix rhusiopathiae Isolated From Pigs in Great Britain: Implications for Vaccine Protection von Forde, Taya L, Kollanandi Ratheesh, Nichith, Harvey, William T, Thomson, Jill R, Williamson, Susanna, Biek, Roman, Opriessnig, Tanja

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The molecular basis of antigenic variation among A(H9N2) avian influenza viruses von Peacock, Thomas P., Harvey, William T., Sadeyen, Jean-Remy, Reeve, Richard, Iqbal, Munir

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SARS-CoV-2 variant biology: immune escape, transmission and fitness von Carabelli, Alessandro M., Peacock, Thomas P., Thorne, Lucy G., Harvey, William T., Hughes, Joseph, Peacock, Sharon J., Barclay, Wendy S., de Silva, Thushan I., Towers, Greg J., Robertson, David L.

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SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies von Cox, MacGregor, Peacock, Thomas P., Harvey, William T., Hughes, Joseph, Wright, Derek W., Willett, Brian J., Thomson, Emma, Gupta, Ravindra K., Peacock, Sharon J., Robertson, David L., Carabelli, Alessandro M.

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imGLAD: accurate detection and quantification of target organisms in metagenomes von Castro, Juan C, Rodriguez-R, Luis M, Harvey, William T, Weigand, Michael R, Hatt, Janet K, Carter, Michelle Q, Konstantinidis, Konstantinos T

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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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Genetic Basis of Antigenic Variation of SAT3 Foot-And-Mouth Disease Viruses in Southern Africa von Maake, Lorens, Harvey, William T, Rotherham, Lia, Opperman, Pamela, Theron, Jacques, Reeve, Richard, Maree, Francois F

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High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios von Byrska-Bishop, Marta, Evani, Uday S, Zhao, Xuefang, Basile, Anna O, Abel, Haley J, Regier, Allison A, Corvelo, André, Clarke, Wayne E, Musunuri, Rajeeva, Nagulapalli, Kshithija, Fairley, Susan, Runnels, Alexi, Winterkorn, Lara, Lowy, Ernesto, Paul Flicek, Germer, Soren, Brand, Harrison, Hall, Ira M, Talkowski, Michael E, Narzisi, Giuseppe, Zody, Michael C

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