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Page 3 of 542
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Phenotype inference in an Escherichia coli strain panel

    Marco Galardini, Alexandra Koumoutsi ... Pedro Beltrao
    The mechanistic impact of genetic variants can be combined with previous knowledge on gene function to deliver conditional growth predictions and pave the way for personalized genetic interventions.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    TAF4, a subunit of transcription factor II D, directs promoter occupancy of nuclear receptor HNF4A during post-natal hepatocyte differentiation

    Daniil Alpern, Diana Langer ... Irwin Davidson
    Physical and functional interactions between HNF4A and TAF4 coordinate HNF4A genomic occupancy with pre-initiation complex formation to activate post-natal hepatocyte gene expression.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications

    Sebastià Franch-Expósito, Laia Bassaganyas ... Jordi Camps
    CNApp is a novel and unique web-based software that enables the performance of comprehensive and integrative analysis of genomic copy number alterations to uncover new associations with patient-oriented relevance.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    The mutational signatures of poor treatment outcomes on the drug-susceptible Mycobacterium tuberculosis genome

    Yiwang Chen, Qi Jiang ... Qian Gao
    There are fourteen genomic variants of Mycobacterium tuberculosis that are significantly associated with poor treatment outcomes in drug-susceptible TB patients, but their predictive value is limited.
    1. Microbiology and Infectious Disease

    Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni

    Wannaporn Ittiprasert, Victoria H Mann ... Paul J Brindley
    Gene knock-out of the omega-1 ribonuclease of Schistosoma mansoni eggs resulted in immunologically impaired phenotype, showcasing the novel application of CRISPR/Cas9 genome editing and utility for functional genomics in schistosomes.
    1. Computational and Systems Biology

    Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics

    Mayank Baranwal, Ryan L Clark ... Ophelia S Venturelli
    Recurrent neural network models enable prediction and design of health-relevant metabolite dynamics in synthetic human gut communities.
    1. Genetics and Genomics

    Firefly genomes illuminate parallel origins of bioluminescence in beetles

    Timothy R Fallon, Sarah E Lower ... Jing-Ke Weng
    The first genomic view of beetle luciferase evolution indicates evolutionary independence of luciferase between fireflies and click-beetles, and provide valuable datasets which will accelerate the discovery of new biotechnological tools.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learning

    Sion C Bayliss, Rebecca K Locke ... Lauren A Cowley
    Application of hierarchical machine learning to the geographical source attribution of Salmonella enteritidis indicates high utility for the rapid translation of raw pathogen genome sequencing data into accurate and actionable information for disease management in public health.
    1. Immunology and Inflammation

    A type I IFN-dependent DNA damage response regulates the genetic program and inflammasome activation in macrophages

    Abigail J Morales, Javier A Carrero ... Barry P Sleckman
    Activated macrophages initiate a robust DNA damage response that depends on type I IFN and regulates their genetic program and inflammasome activation, establishing a mechanistic link between DNA damage responses and innate immunity.
    1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen

    David E Cook, H Martin Kramer ... Bart P H J Thomma
    Assessment of DNA methylation, histone modifications, and DNA accessibility revealed that physical DNA characteristics are associated with adaptive genome evolution in the broad host range plant pathogenic fungus Verticillium dahliae.