Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies von Roach, Michael J, Schmidt, Simon A, Borneman, Anthony R

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New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species von Roach, Michael J, Borneman, Anthony R

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Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay von Roach, Michael J, Johnson, Daniel L, Bohlmann, Joerg, van Vuuren, Hennie J J, Jones, Steven J M, Pretorius, Isak S, Schmidt, Simon A, Borneman, Anthony R

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The human gut virome: composition, colonization, interactions, and impacts on human health von Pargin, Evan, Roach, Michael J, Skye, Amber, Papudeshi, Bhavya, Inglis, Laura K, Mallawaarachchi, Vijini, Grigson, Susanna R, Harker, Clarice, Edwards, Robert A, Giles, Sarah K

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Ten simple rules and a template for creating workflows-as-applications von Roach, Michael J, Pierce-Ward, N Tessa, Suchecki, Radoslaw, Mallawaarachchi, Vijini, Papudeshi, Bhavya, Handley, Scott A, Brown, C Titus, Watson-Haigh, Nathan S, Edwards, Robert A

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Englacial drainage structures in an East Antarctic outlet glacier von Schaap, Thomas, Roach, Michael J., Peters, Leo E., Cook, Sue, Kulessa, Bernd, Schoof, Christian

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Phables: from fragmented assemblies to high-quality bacteriophage genomes von Mallawaarachchi, Vijini, Roach, Michael J, Decewicz, Przemyslaw, Papudeshi, Bhavya, Giles, Sarah K, Grigson, Susanna R, Bouras, George, Hesse, Ryan D, Inglis, Laura K, Hutton, Abbey L K, Dinsdale, Elizabeth A, Edwards, Robert A

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Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice von Onetto, Cristobal A, Schmidt, Simon A, Roach, Michael J, Borneman, Anthony R

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Prophages: an integral but understudied component of the human microbiome von Inglis, Laura K, Roach, Michael J, Edwards, Robert A

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Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies von Bouras, George, Houtak, Ghais, Wick, Ryan R, Mallawaarachchi, Vijini, Roach, Michael J, Papudeshi, Bhavya, Judd, Lousie M, Sheppard, Anna E, Edwards, Robert A, Vreugde, Sarah

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Hecatomb: an integrated software platform for viral metagenomics von Roach, Michael J, Beecroft, Sarah J, Mihindukulasuriya, Kathie A, Wang, Leran, Paredes, Anne, Cárdenas, Luis Alberto Chica, Henry-Cocks, Kara, Lima, Lais Farias Oliveira, Dinsdale, Elizabeth A, Edwards, Robert A, Handley, Scott A

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Philympics 2021: Prophage Predictions Perplex Programs [version 1; peer review: 1 approved with reservations, 1 not approved] von Roach, Michael J, McNair, Katelyn, Giles, Sarah K, Inglis, Laura K, Pargin, Evan, Roux, Simon, Decewicz, Przemysław, Edwards, Robert A

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Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2 von Papudeshi, Bhavya, Vega, Alejandro A, Souza, Cole, Giles, Sarah K, Mallawaarachchi, Vijini, Roach, Michael J, An, Michelle, Jacobson, Nicole, McNair, Katelyn, Fernanda Mora, Maria, Pastrana, Karina, Boling, Lance, Leigh, Christopher, Harker, Clarice, Plewa, Will S, Grigson, Susanna R, Bouras, George, Decewicz, Przemysław, Luque, Antoni, Droit, Lindsay, Handley, Scott A, Wang, David, Segall, Anca M, Dinsdale, Elizabeth A, Edwards, Robert A

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snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives von Wang, Taopeng, Roach, Michael J., Harvey, Kate, Morlanes, Javier Escudero, Kiedik, Beata, Al-Eryani, Ghamdan, Greenwald, Alissa, Kalavros, Nikolaos, Dezem, Felipe Segato, Ma, Yuling, Pita-Juarez, Yered H., Wise, Kellie, Degletagne, Cyril, Elz, Anna, Hadadianpour, Azi, Johanneson, Jack, Pakiam, Fiona, Ryu, Heeju, Newell, Evan W., Tonon, Laurie, Kohlway, Andrew, Drennon, Tingsheng, Abousoud, Jawad, Stott, Ryan, Lund, Paul, Durruthy, Jens, Vallejo, Andres F., Li, Wenyan, Salomon, Robert, Kaczorowski, Dominik, Warren, Joanna, Butler, Lisa M., O’Toole, Sandra, Plummer, Jasmine, Vlachos, Ioannis S., Lundeberg, Joakim, Swarbrick, Alexander, Martelotto, Luciano G.

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Thoracoscopic diaphragm plication von Kara, H. Volkan, Roach, Michael J., Balderson, Stafford S., D’Amico, Thomas A.

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Ten simple rules and a template for creating workflows-as-applications von Michael J Roach, N Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi, Bhavya Papudeshi, Scott A Handley, C Titus Brown, Nathan S Watson-Haigh, Robert A Edwards

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Dnaapler: A tool to reorient circular microbial genomes von Bouras, George, Grigson, Susanna R., Papudeshi, Bhavya, Mallawaarachchi, Vijini, Roach, Michael J.

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Koverage: Read-coverage analysis for massive (meta)genomics datasets von Roach, Michael J., Hart, Bradley J., Beecroft, Sarah J., Papudeshi, Bhavya, Inglis, Laura K., Grigson, Susanna R., Mallawaarachchi, Vijini, Bouras, George, Edwards, Robert A.

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Philympics 2021: Prophage Predictions Perplex Programs [version 2; peer review: 1 approved, 1 approved with reservations] von Roach, Michael J., McNair, Katelyn, Michalczyk, Maciej, Giles, Sarah K, Inglis, Laura K, Pargin, Evan, Barylski, Jakub, Roux, Simon, Decewicz, Przemysław, Edwards, Robert A.

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Chardonnay genome assembly and annotations von Roach, Michael J.

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