Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England von Eales, Oliver, de Oliveira Martins, Leonardo, Page, Andrew J., Wang, Haowei, Bodinier, Barbara, Tang, David, Haw, David, Jonnerby, Jakob, Atchison, Christina, Ashby, Deborah, Barclay, Wendy, Taylor, Graham, Cooke, Graham, Ward, Helen, Darzi, Ara, Riley, Steven, Elliott, Paul, Donnelly, Christl A., Chadeau-Hyam, Marc

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CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes von Baker, Dave J, Aydin, Alp, Le-Viet, Thanh, Kay, Gemma L, Rudder, Steven, de Oliveira Martins, Leonardo, Tedim, Ana P, Kolyva, Anastasia, Diaz, Maria, Alikhan, Nabil-Fareed, Meadows, Lizzie, Bell, Andrew, Gutierrez, Ana Victoria, Trotter, Alexander J, Thomson, Nicholas M, Gilroy, Rachel, Griffith, Luke, Adriaenssens, Evelien M, Stanley, Rachael, Charles, Ian G, Elumogo, Ngozi, Wain, John, Prakash, Reenesh, Meader, Emma, Mather, Alison E, Webber, Mark A, Dervisevic, Samir, Page, Andrew J, O'Grady, Justin

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Scalable neighbour search and alignment with uvaia von de Oliveira Martins, Leonardo, Mather, Alison E, Page, Andrew J

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Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs von Trampari, Eleftheria, Holden, Emma R., Wickham, Gregory J., Ravi, Anuradha, Martins, Leonardo de Oliveira, Savva, George M., Webber, Mark A.

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Evolutionary process of deep-sea bathymodiolus mussels von Miyazaki, Jun-Ichi, de Oliveira Martins, Leonardo, Fujita, Yuko, Matsumoto, Hiroto, Fujiwara, Yoshihiro

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Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing von de Oliveira Martins, Leonardo, Page, Andrew J, Mather, Alison E, Charles, Ian G

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Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine von Ereqat, Suheir, Alikhan, Nabil-Fareed, Al-Jawabreh, Amer, Matthews, Michaela, Al-Jawabreh, Ahmed, de Oliveira Martins, Leonardo, Trotter, Alexander J, Al-Kaila, Mai, Page, Andrew J, Pallen, Mark J, Nasereddin, Abedelmajeed

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Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern von Mashe, Tapfumanei, Takawira, Faustinos Tatenda, Gumbo, Hlanai, Juru, Agnes, Nyagupe, Charles, Maeka, Kenneth K, Mtapuri-Zinyowera, Sekesai, Gudza-Mugabe, Muchaneta, de Oliveira Martins, Leonardo, O'Grady, Justin, Kingsley, Robert A, Page, Andrew J, Simbi, Raiva

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Tatajuba: exploring the distribution of homopolymer tracts von de Oliveira Martins, Leonardo, Bloomfield, Samuel, Stoakes, Emily, Grant, Andrew J, Page, Andrew J, Mather, Alison E

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SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees von Mallo, Diego, De Oliveira Martins, Leonardo, Posada, David

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Phylogenetic detection of recombination with a Bayesian prior on the distance between trees von Martins, Leonardo de Oliveira, Leal, Elcio, Kishino, Hirohisa

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A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction von De Oliveira Martins, Leonardo, Mallo, Diego, Posada, David

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Nanoneedle-Mediated Stimulation of Cell Mechanotransduction Machinery von Hansel, Catherine S, Crowder, Spencer W, Cooper, Samuel, Gopal, Sahana, João Pardelha da Cruz, Maria, de Oliveira Martins, Leonardo, Keller, Debora, Rothery, Stephen, Becce, Michele, Cass, Anthony E. G, Bakal, Chris, Chiappini, Ciro, Stevens, Molly M

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Species Tree Estimation from Genome-Wide Data with guenomu von de Oliveira Martins, Leonardo, Posada, David

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Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites von Sawai, Hiromi, Otani, Hiroto, Arisue, Nobuko, Palacpac, Nirianne, de Oliveira Martins, Leonardo, Pathirana, Sisira, Handunnetti, Shiroma, Kawai, Satoru, Kishino, Hirohisa, Horii, Toshihiro, Tanabe, Kazuyuki

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Testing for Universal Common Ancestry von de Oliveira Martins, Leonardo, Posada, David

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Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing von Raphenya, Amogelang R., Robertson, James, Jamin, Casper, de Oliveira Martins, Leonardo, Maguire, Finlay, McArthur, Andrew G., Hays, John P.

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Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data von Mashe, Tapfumanei, Takawira, Faustinos Tatenda, de Oliveira Martins, Leonardo, Gudza-Mugabe, Muchaneta, Chirenda, Joconiah, Munyanyi, Manes, Chaibva, Blessmore V, Tarupiwa, Andrew, Gumbo, Hlanai, Juru, Agnes, Nyagupe, Charles, Ruhanya, Vurayai, Phiri, Isaac, Manangazira, Portia, Goredema, Alexander, Danda, Sydney, Chabata, Israel, Jonga, Janet, Munharira, Rutendo, Masunda, Kudzai, Mukeredzi, Innocent, Mangwanya, Douglas, Trotter, Alex, Le Viet, Thanh, Rudder, Steven, Kay, Gemma, Baker, David, Thilliez, Gaetan, Gutierrez, Ana Victoria, O'Grady, Justin, Hove, Maxwell, Mutapuri-Zinyowera, Sekesai, Page, Andrew J, Kingsley, Robert A, Mhlanga, Gibson

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Phylogeography of Loaches of the Genus Lefua (Balitoridae, Cypriniformes) Inferred from Mitochondrial DNA Sequences von Mihara, Motohiro, Sakai, Takehiko, Nakao, Koushin, de Oliveira Martins, Leonardo, Hosoya, Kazumi, Miyazaki, Jun-Ichi

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SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021 von Sarwar, Muhammad Bilal, Yasir, Muhammad, Alikhan, Nabil-Fareed, Afzal, Nadeem, de Oliveira Martins, Leonardo, Le Viet, Thanh, Trotter, Alexander J, Prosolek, Sophie J, Kay, Gemma L, Foster-Nyarko, Ebenezer, Rudder, Steven, Baker, David J, Muntaha, Sidra Tul, Roman, Muhammad, Webber, Mark A, Shafiq, Almina, Shabbir, Bilquis, Akram, Javed, Page, Andrew J, Jahan, Shah

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