Blar i forfatter "Mäklin, Tommi"

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    • Bacterial genomic epidemiology with mixed samples 

      Mäklin, Tommi; Kallonen, Teemu; Alanko, Jarno; Samuelsen, Ørjan; Hegstad, Kristin; Mäkinen, Veli; Corander, Jukka; Heinz, Eva; Honkela, Antti (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-11-15)
      Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for ...

    • Strong pathogen competition in neonatal gut colonisation 

      Mäklin, Tommi; Thorpe, Harry Arthur Frank Wright; Pöntinen, Anna Kaarina; Gladstone, Rebecca Ashley; Shao, Yan; Pesonen, Maiju; McNally, Alan; Johnsen, Pål Jarle; Samuelsen, Ørjan; Lawley, Trevor D.; Honkela, Antti; Corander, Jukka (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-12-01)
      Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors ...