Sequencing error profiles of Illumina sequencing instruments von Stoler, Nicholas, Nekrutenko, Anton

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Ten simple rules for reproducible computational research von Sandve, Geir Kjetil, Nekrutenko, Anton, Taylor, James, Hovig, Eivind

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Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees von Zaidi, Arslan A., Wilton, Peter R., Su, Marcia Shu-Wei, Paul, Ian M., Arbeithuber, Barbara, Anthony, Kate, Nekrutenko, Anton, Nielsen, Rasmus, Makova, Kateryna D.

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In memory of James Taylor: the birth of Galaxy von Nekrutenko, Anton, Schatz, Michael C

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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences von Goecks, Jeremy, Nekrutenko, Anton, Taylor, James

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Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA von Rebolledo-Jaramillo, Boris, Su, Marcia Shu-Wei, Stoler, Nicholas, McElhoe, Jennifer A., Dickins, Benjamin, Blankenberg, Daniel, Korneliussen, Thorfinn S., Chiaromonte, Francesca, Nielsen, Rasmus, Holland, Mitchell M., Paul, Ian M., Nekrutenko, Anton, Makova, Kateryna D.

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Galaxy CloudMan: delivering cloud compute clusters von Afgan, Enis, Baker, Dannon, Coraor, Nate, Chapman, Brad, Nekrutenko, Anton, Taylor, James

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Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists von Blankenberg, Daniel, Kuster, Gregory Von, Coraor, Nathaniel, Ananda, Guruprasad, Lazarus, Ross, Mangan, Mary, Nekrutenko, Anton, Taylor, James

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Galaxy: a platform for interactive large-scale genome analysis von Giardine, Belinda, Riemer, Cathy, Hardison, Ross C, Burhans, Richard, Elnitski, Laura, Shah, Prachi, Zhang, Yi, Blankenberg, Daniel, Albert, Istvan, Taylor, James, Miller, Webb, Kent, W James, Nekrutenko, Anton

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Ready-to-use public infrastructure for global SARS-CoV-2 monitoring von Maier, Wolfgang, Bray, Simon, van den Beek, Marius, Bouvier, Dave, Coraor, Nathan, Miladi, Milad, Singh, Babita, De Argila, Jordi Rambla, Baker, Dannon, Roach, Nathan, Gladman, Simon, Coppens, Frederik, Martin, Darren P., Lonie, Andrew, Grüning, Björn, Kosakovsky Pond, Sergei L., Nekrutenko, Anton

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Next-generation sequencing data interpretation: enhancing reproducibility and accessibility von Nekrutenko, Anton, Taylor, James

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Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City von Wertheim, Joel O., Wang, Jade C., Leelawong, Mindy, Martin, Darren P., Havens, Jennifer L., Chowdhury, Moinuddin A., Pekar, Jonathan E., Amin, Helly, Arroyo, Anthony, Awandare, Gordon A., Chow, Hoi Yan, Gonzalez, Edimarlyn, Luoma, Elizabeth, Morang’a, Collins M., Nekrutenko, Anton, Shank, Stephen D., Silver, Stefan, Quashie, Peter K., Rakeman, Jennifer L., Ruiz, Victoria, Torian, Lucia V., Vasylyeva, Tetyana I., Kosakovsky Pond, Sergei L., Hughes, Scott

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Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers von Grüning, Björn A, Rasche, Eric, Rebolledo-Jaramillo, Boris, Eberhard, Carl, Houwaart, Torsten, Chilton, John, Coraor, Nate, Backofen, Rolf, Taylor, James, Nekrutenko, Anton

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Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses von Larivière, Delphine, Wickham, Laura, Keiler, Kenneth, Nekrutenko, Anton

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RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis von Lucaci, Alexander G, Zehr, Jordan D, Shank, Stephen D, Bouvier, Dave, Ostrovsky, Alexander, Mei, Han, Nekrutenko, Anton, Martin, Darren P, Kosakovsky Pond, Sergei L

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No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics von Baker, Dannon, van den Beek, Marius, Blankenberg, Daniel, Bouvier, Dave, Chilton, John, Coraor, Nate, Coppens, Frederik, Eguinoa, Ignacio, Gladman, Simon, Grüning, Björn, Keener, Nicholas, Larivière, Delphine, Lonie, Andrew, Kosakovsky Pond, Sergei, Maier, Wolfgang, Nekrutenko, Anton, Taylor, James, Weaver, Steven

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Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy von Guerler, Aysam, Baker, Dannon, van den Beek, Marius, Gruening, Bjoern, Bouvier, Dave, Coraor, Nate, Shank, Stephen D, Zehr, Jordan D, Schatz, Michael C, Nekrutenko, Anton

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StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo von Tang, Yin, Bouvier, Emil, Kwok, Chun Kit, Ding, Yiliang, Nekrutenko, Anton, Bevilacqua, Philip C, Assmann, Sarah M

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Child Weight Gain Trajectories Linked To Oral Microbiota Composition von Craig, Sarah J. C., Blankenberg, Daniel, Parodi, Alice Carla Luisa, Paul, Ian M., Birch, Leann L., Savage, Jennifer S., Marini, Michele E., Stokes, Jennifer L., Nekrutenko, Anton, Reimherr, Matthew, Chiaromonte, Francesca, Makova, Kateryna D.

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Making whole genome multiple alignments usable for biologists von BLANKENBERG, Daniel, TAYLOR, James, NEKRUTENKO, Anton

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