RaGOO: fast and accurate reference-guided scaffolding of draft genomes von Alonge, Michael, Soyk, Sebastian, Ramakrishnan, Srividya, Wang, Xingang, Goodwin, Sara, Sedlazeck, Fritz J, Lippman, Zachary B, Schatz, Michael C

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Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing von Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B, Schatz, Michael C, Soyk, Sebastian

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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato von Alonge, Michael, Wang, Xingang, Benoit, Matthias, Soyk, Sebastian, Pereira, Lara, Zhang, Lei, Suresh, Hamsini, Ramakrishnan, Srividya, Maumus, Florian, Ciren, Danielle, Levy, Yuval, Harel, Tom Hai, Shalev-Schlosser, Gili, Amsellem, Ziva, Razifard, Hamid, Caicedo, Ana L., Tieman, Denise M., Klee, Harry, Kirsche, Melanie, Aganezov, Sergey, Ranallo-Benavidez, T. Rhyker, Lemmon, Zachary H., Kim, Jennifer, Robitaille, Gina, Kramer, Melissa, Goodwin, Sara, McCombie, W. Richard, Hutton, Samuel, Van Eck, Joyce, Gillis, Jesse, Eshed, Yuval, Sedlazeck, Fritz J., van der Knaap, Esther, Schatz, Michael C., Lippman, Zachary B.

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Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies von Alonge, Michael, Shumate, Alaina, Puiu, Daniela, Zimin, Aleksey V, Salzberg, Steven L

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The bracteatus pineapple genome and domestication of clonally propagated crops von Chen, Li-Yu, VanBuren, Robert, Paris, Margot, Zhou, Hongye, Zhang, Xingtan, Wai, Ching Man, Yan, Hansong, Chen, Shuai, Alonge, Michael, Ramakrishnan, Srividya, Liao, Zhenyang, Liu, Juan, Lin, Jishan, Yue, Jingjing, Fatima, Mahpara, Lin, Zhicong, Zhang, Jisen, Huang, Lixian, Wang, Hao, Hwa, Teh-Yang, Kao, Shu-Min, Choi, Jae Young, Sharma, Anupma, Song, Jian, Wang, Lulu, Yim, Won C., Cushman, John C., Paull, Robert E., Matsumoto, Tracie, Qin, Yuan, Wu, Qingsong, Wang, Jianping, Yu, Qingyi, Wu, Jun, Zhang, Shaoling, Boches, Peter, Tung, Chih-Wei, Wang, Ming-Li, Coppens d’Eeckenbrugge, Geo, Sanewski, Garth M., Purugganan, Michael D., Schatz, Michael C., Bennetzen, Jeffrey L., Lexer, Christian, Ming, Ray

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A master regulator of regeneration von Alonge, Michael, Schatz, Michael C

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Natural Genetic Diversity in Tomato Flavor Genes von Pereira, Lara, Sapkota, Manoj, Alonge, Michael, Zheng, Yi, Zhang, Youjun, Razifard, Hamid, Taitano, Nathan K., Schatz, Michael C., Fernie, Alisdair R., Wang, Ying, Fei, Zhangjun, Caicedo, Ana L., Tieman, Denise M., van Der Knaap, Esther

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Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome von 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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The genetic and epigenetic landscape of the Arabidopsis centromeres von Naish, Matthew, Alonge, Michael, Wlodzimierz, Piotr, Tock, Andrew J., Abramson, Bradley W., Schmuecker, Anna, Mandakova, Terezie, Jamge, Bhagyshree, Lambing, Christophe, Kuo, Pallas, Yelina, Natasha, Hartwick, Nolan, Colt, Kelly, Smith, Lisa M., Ton, Jurriaan, Kakutani, Tetsuji, Martienssen, Robert A., Schneeberger, Korbinian, Lysak, Martin A., Berger, Frederic, Bousios, Alexandros, Michael, Todd P., Schatz, Michael C., Henderson, Ian R.

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Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome von He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan T, Hendelman, Anat, Van Eck, Joyce, Schatz, Michael C, Lippman, Zachary B

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Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies von Mc Cartney, Ann M., Shafin, Kishwar, Alonge, Michael, Bzikadze, Andrey V., Formenti, Giulio, Fungtammasan, Arkarachai, Howe, Kerstin, Jain, Chirag, Koren, Sergey, Logsdon, Glennis A., Miga, Karen H., Mikheenko, Alla, Paten, Benedict, Shumate, Alaina, Soto, Daniela C., Sović, Ivan, Wood, Jonathan M. D., Zook, Justin M., Phillippy, Adam M., Rhie, Arang

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Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato von Soyk, Sebastian, Lemmon, Zachary H., Sedlazeck, Fritz J., Jiménez-Gómez, José M., Alonge, Michael, Hutton, Samuel F., Van Eck, Joyce, Schatz, Michael C., Lippman, Zachary B.

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The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry) von Buti, Matteo, Moretto, Marco, Barghini, Elena, Mascagni, Flavia, Natali, Lucia, Brilli, Matteo, Lomsadze, Alexandre, Sonego, Paolo, Giongo, Lara, Alonge, Michael, Velasco, Riccardo, Varotto, Claudio, Šurbanovski, Nada, Borodovsky, Mark, Ward, Judson A, Engelen, Kristof, Cavallini, Andrea, Cestaro, Alessandro, Sargent, Daniel James

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Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies von Alonge, Michael, Shumate, Alaina, Puiu, Daniela, Zimin, Aleksey V, Salzberg, Steven L

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Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato von Soyk, Sebastian, Lemmon, Zachary H., Sedlazeck, Fritz J., Jiménez-Gómez, José M., Alonge, Michael, Hutton, Samuel F., Van Eck, Joyce, Schatz, Michael C., Lippman, Zachary B.

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The genetic and epigenetic landscape of the Arabidopsis centromeres von Naish, Matthew, Alonge, Michael, Wlodzimierz, Piotr, Tock, Andrew J, Abramson, Bradley W, Schmücker, Anna, Mandáková, Terezie, Jamge, Bhagyshree, Lambing, Christophe, Kuo, Pallas, Yelina, Natasha, Hartwick, Nolan, Colt, Kelly, Smith, Lisa M, Ton, Jurriaan, Kakutani, Tetsuji, Martienssen, Robert A, Schneeberger, Korbinian, Lysak, Martin A, Berger, Frédéric, Bousios, Alexandros, Michael, Todd P, Schatz, Michael C, Henderson, Ian R

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Additional file 2 of Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing von Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B., Schatz, Michael C., Soyk, Sebastian

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Additional file 3 of Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing von Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B., Schatz, Michael C., Soyk, Sebastian

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Additional file 4 of Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing von Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B., Schatz, Michael C., Soyk, Sebastian

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Additional file 5 of Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing von Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B., Schatz, Michael C., Soyk, Sebastian

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