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  • Exploring amino acid functi... Exploring amino acid functions in a deep mutational landscape
    Dunham, Alistair S; Beltrao, Pedro Molecular systems biology, July 2021, Volume: 17, Issue: 7
    Journal Article
    Peer reviewed
    Open access

    Amino acids fulfil a diverse range of roles in proteins, each utilising its chemical properties in different ways in different contexts to create required functions. For example, cysteines form ...
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  • High-throughput deep learni... High-throughput deep learning variant effect prediction with Sequence UNET
    Dunham, Alistair S; Beltrao, Pedro; AlQuraishi, Mohammed Genome Biology, 05/2023, Volume: 24, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    Understanding coding mutations is important for many applications in biology and medicine but the vast mutation space makes comprehensive experimental characterisation impossible. Current predictors ...
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  • The impact of the genetic b... The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae
    Galardini, Marco; Busby, Bede P; Vieitez, Cristina ... Molecular systems biology, December 2019, Volume: 15, Issue: 12
    Journal Article
    Peer reviewed
    Open access

    Loss‐of‐function (LoF) mutations associated with disease do not manifest equally in different individuals. The impact of the genetic background on the consequences of LoF mutations remains poorly ...
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4.
  • Towards a structurally reso... Towards a structurally resolved human protein interaction network
    Burke, David F; Bryant, Patrick; Barrio-Hernandez, Inigo ... Nature structural & molecular biology, 02/2023, Volume: 30, Issue: 2
    Journal Article
    Peer reviewed
    Open access

    Cellular functions are governed by molecular machines that assemble through protein-protein interactions. Their atomic details are critical to studying their molecular mechanisms. However, fewer than ...
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  • Population Structure, Strat... Population Structure, Stratification, and Introgression of Human Structural Variation
    Almarri, Mohamed A.; Bergström, Anders; Prado-Martinez, Javier ... Cell, 07/2020, Volume: 182, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of ...
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  • SARS-CoV-2 variants evolve ... SARS-CoV-2 variants evolve convergent strategies to remodel the host response
    Bouhaddou, Mehdi; Reuschl, Ann-Kathrin; Polacco, Benjamin J. ... Cell, 10/2023, Volume: 186, Issue: 21
    Journal Article
    Peer reviewed

    SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces driving VOC evolution. We discovered that VOCs ...
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  • Inferring Fitness Effects f... Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model
    Nené, Nuno R; Dunham, Alistair S; Illingworth, Christopher J R Genetics, 05/2018, Volume: 209, Issue: 1
    Journal Article
    Peer reviewed
    Open access

    A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. ...
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