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  • RaGOO: fast and accurate re... RaGOO: fast and accurate reference-guided scaffolding of draft genomes
    Alonge, Michael; Soyk, Sebastian; Ramakrishnan, Srividya ... Genome Biology, 10/2019, Volume: 20, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the ...
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2.
  • Automated assembly scaffold... Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
    Alonge, Michael; Lebeigle, Ludivine; Kirsche, Melanie ... Genome Biology, 12/2022, Volume: 23, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and ...
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  • Major Impacts of Widespread... Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
    Alonge, Michael; Wang, Xingang; Benoit, Matthias ... Cell, 07/2020, Volume: 182, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used ...
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  • Chromosome-Scale Assembly o... Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies
    Alonge, Michael; Shumate, Alaina; Puiu, Daniela ... Genetics (Austin), 10/2020, Volume: 216, Issue: 2
    Journal Article
    Peer reviewed
    Open access

    Abstract Bread wheat (Triticum aestivum) is a major food crop and an important plant system for agricultural genetics research. However, due to the complexity and size of its allohexaploid genome, ...
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5.
  • The bracteatus pineapple genome and domestication of clonally propagated crops
    Chen, Li-Yu; VanBuren, Robert; Paris, Margot ... Nature genetics, 10/2019, Volume: 51, Issue: 10
    Journal Article
    Peer reviewed
    Open access

    Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and ...
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  • A master regulator of regen... A master regulator of regeneration
    Alonge, Michael; Schatz, Michael C Science (American Association for the Advancement of Science), 03/2019, Volume: 363, Issue: 6432
    Journal Article
    Peer reviewed

    Study of panther worm reveals a pioneer transcription factor that regulates regeneration Hofstenia miamia , commonly called the three-banded panther worm, is a small flatworm that can be found along ...
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7.
  • Natural Genetic Diversity i... Natural Genetic Diversity in Tomato Flavor Genes
    Pereira, Lara; Sapkota, Manoj; Alonge, Michael ... Frontiers in plant science, 06/2021, Volume: 12
    Journal Article
    Peer reviewed
    Open access

    Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance ...
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  • Accurate circular consensus... Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
    Wenger, Aaron M; Peluso, Paul; Rowell, William J ... Nature biotechnology, 10/2019, Volume: 37, Issue: 10
    Journal Article
    Peer reviewed
    Open access

    The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the ...
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  • The genetic and epigenetic ... The genetic and epigenetic landscape of the Arabidopsis centromeres
    Naish, Matthew; Alonge, Michael; Wlodzimierz, Piotr ... Science (American Association for the Advancement of Science), 2021-Nov-12, 2021-11-12, 20211112, Volume: 374, Issue: 6569
    Journal Article
    Peer reviewed
    Open access

    Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used long-read ...
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10.
  • Establishing Physalis as a ... Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
    He, Jia; Alonge, Michael; Ramakrishnan, Srividya ... The Plant cell, 01/2023, Volume: 35, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. ...
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