Computational pan-genomics: status, promises and challenges
By Computational Pan-Genomics Consortium. bioRxiv, 2016
388 citations recorded by the source corpus.
Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic datasets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this paper, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies, and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/bc86cc7b512c468df18cdc65dab3a582a975c34b
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In Molecular Biology
Citations in the corpus
- CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions (2024, background): “Pangenome and graph representation efforts ( 85–87 ) will provide an interesting D 1152 Nucleic Acids Research , 2024, Vol. 52, Database issue framework, with major challenges for the mapping and representation of existing gene and transcript annotations, sequence conservation, or biochemical…”