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ALPACA ITN Project

ALPACA ITN Project

Algorithms for Pangenome Computational Analysis is an EU funded Innovative Training Network (ITN)

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    Pan-genome representations for deep machine learning applications

    Pan-genome representations for deep machine learning applications

    The amount of sequenced genomes, and in many areas of application also the amount of annotations, have reached a mass – hundreds of thousands of sequenced genomes – that is critical for successful application of deep learning pipelines. However, …

    dg December 15, 2020November 7, 2022 Jobs Read more

    Measures and algorithms for alignment-free comparative pan-genomics

    Measures and algorithms for alignment-free comparative pan-genomics

    A pan-genome stored as a graph data structure can be characterized by various attributes, such as the graph’s structural properties (average node degree, diameter, density), sequence attributes (k-mer diversity or distribution), or its functional …

    dg December 15, 2020November 7, 2022 Jobs Read more

    Pan-genome graph update strategies

    Pan-genome graph update strategies

    We propose to explore distinct approaches when creating or adding information to a pan-genome graph. The simplest approach is to map new sequences, indicating newly discovered variants and annotating existing ones. However, when the graph …

    dg November 13, 2020November 8, 2022 Jobs Read more

    Adapting the Positional Burrows Wheeler Transform to pan-genome graphs

    Adapting the Positional Burrows Wheeler Transform to pan-genome graphs

    The Positional Burrows Wheeler Transform (PBWT) is a data structure that enables efficient storage and local haplotype matching over large collections of aligned linear genome sequences with genetic variation. Recently, we …

    dg November 13, 2020November 7, 2022 Jobs Read more

    Pan-genomes of viruses

    Pan-genomes of viruses

    The role of viruses is key for understanding the environment (e.g., in the sea, the soil or the air) or the functioning of humans, animals and plants’ microbiomes. Despite their comparatively small genome sizes, viruses pose specific challenges for …

    dg November 13, 2020November 7, 2022 Jobs Read more

    Matching to and between pan-genomes

    Matching to and between pan-genomes

    In the specific case of a set of very closely related genomes, a pan-genome can be represented by a so-called (elastic)-degenerate text that actually corresponds to the .vcf file format or, alternatively for slightly less closely related …

    dg November 13, 2020November 7, 2022 Jobs Read more

    Representations for the comparative and hierarchical analysis of pan-genomes

    Representations for the comparative and hierarchical analysis of pan-genomes

    The main goal is to study new representations of pan-genomes that allow fast and space-efficient queries of multiple pan-genomes, allowing their comparison and exploiting the eventual ancestral relationships. We want to overcome the limitations …

    dg November 13, 2020November 8, 2022 Jobs Read more

    Comparing/aligning two pan-genomes with applications in transcriptomics and microbiomics

    Comparing/aligning two pan-genomes with applications in transcriptomics and microbiomics

    Comparing pan-genomes amounts to comparing two graphs, generalizing the idea to align two genomes. We aim at developing algorithms and software for ‘whole-pan-genome alignment’. Though for aligning two networks approaches already …

    dg November 13, 2020November 8, 2022 Jobs Read more

    Pan-genomics of complex loci in the human genome

    Pan-genomics of complex loci in the human genome

    Despite tremendous progress in genome assembly, recalcitrant genomic loci remain whose sequences cannot be resolved. Such regions are often variable in copy number and such copy number variants (CNVs) have been linked to various disorders, including neuropsychiatric conditions and autism …

    dg November 13, 2020November 7, 2022 Jobs Read more

    Integrating the bacterial pan-genome with GWAS and machine learning approaches to study antibiotic resistance

    Integrating the bacterial pan-genome with GWAS and machine learning approaches to study antibiotic resistance

    Antibiotic resistance (ABR) is a global threat to public health, and is a property primarily conferred to bacteria either by horizontal transfer of a gene or by mutational evolution. Predictions suggest ABR will kill more people than cancer by 2050, as it …

    dg November 13, 2020November 7, 2022 Jobs Read more
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    This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 956229

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