About Evolutionary Bioinformatics
Evolutionary Bioinformatics
About this Collection
This collection aims to publish articles (e.g., research articles, brief reports, software tool articles, method articles, and reviews) highlighting the diverse portfolio of our Evolutionary and Comparative Genomics COSI of ISMB (Intelligent Systems for Molecular Biology, Flagship meeting of the International Society for Computational Biology).
Whether it is to fight against the spread of cancerous tumors, develop antiviral drugs and vaccines against the novel coronavirus, exploit the molecular scissors CRISPR-Cas9 for biotechnological advances, or trace back the root of the tree of life, it is critical to acquire a deep understanding of the evolution of the corresponding viruses, cancer tissues, genes, protein domains, or genomes.
This collection will focus on the contemporary challenges in Evolutionary Bioinformatics. First, the widespread use of next-generation sequencing technology allows phylogenetic studies to span hundreds of thousands of taxa, such large-scale phylogenies being essential for understanding the genomic epidemiology of pathogens such as SARS-CoV-2. On the other hand, the increasing availability of full-genome sequences requires phylogenetic analyses based on very long sequences. Dealing with such datasets requires novel alignment and phylogenetic prediction tools outperforming existing ones in time complexity and accuracy. These new challenges have accelerated the emergence of machine learning-driven methods in phylogenetics. Another critical challenge is the ever-increasing volume of available multi-modal, multi-omics, and heterogeneous biological datasets raising the question of benchmarking datasets and designing appropriate simulations to compare and evaluate the reliability of different methods. Recent years have also seen a shift in paradigm regarding the representation of evolution, moving from the traditional tree structure for vertical transmission of the genetic material to network structures or other complex models that relax the hierarchy between the species tree and gene trees. The newer models account for incomplete lineage sorting, horizontal transfer, recombination, or other species diversification mechanisms such as hybridization, introgression, or lineage fusion.
The Evolutionary Bioinformatics perspectives at F1000 will provide an avenue for these new challenges, the latest algorithmic and methodological advances, and the open software technologies that address them. We invite you to submit your proposal.
Keywords: Comparative genomics; Pangenomics; Population genetics; Phylogenetic analysis; Phylogenetic trees and networks; Gene tree/Species tree Reconciliation; Horizontal transfer; Recombination; Incomplete lineage sorting; Molecular evolution
Submission deadline: This Collection is now closed for submissions.
Any questions about this collection? Please get in contact directly with research@f1000.com.
This collection is part of the Bioinformatics Gateway.
Image source: HUGE-B 500-NCBI PGT by Elena Regina, 2015
Whether it is to fight against the spread of cancerous tumors, develop antiviral drugs and vaccines against the novel coronavirus, exploit the molecular scissors CRISPR-Cas9 for biotechnological advances, or trace back the root of the tree of life, it is critical to acquire a deep understanding of the evolution of the corresponding viruses, cancer tissues, genes, protein domains, or genomes.
This collection will focus on the contemporary challenges in Evolutionary Bioinformatics. First, the widespread use of next-generation sequencing technology allows phylogenetic studies to span hundreds of thousands of taxa, such large-scale phylogenies being essential for understanding the genomic epidemiology of pathogens such as SARS-CoV-2. On the other hand, the increasing availability of full-genome sequences requires phylogenetic analyses based on very long sequences. Dealing with such datasets requires novel alignment and phylogenetic prediction tools outperforming existing ones in time complexity and accuracy. These new challenges have accelerated the emergence of machine learning-driven methods in phylogenetics. Another critical challenge is the ever-increasing volume of available multi-modal, multi-omics, and heterogeneous biological datasets raising the question of benchmarking datasets and designing appropriate simulations to compare and evaluate the reliability of different methods. Recent years have also seen a shift in paradigm regarding the representation of evolution, moving from the traditional tree structure for vertical transmission of the genetic material to network structures or other complex models that relax the hierarchy between the species tree and gene trees. The newer models account for incomplete lineage sorting, horizontal transfer, recombination, or other species diversification mechanisms such as hybridization, introgression, or lineage fusion.
The Evolutionary Bioinformatics perspectives at F1000 will provide an avenue for these new challenges, the latest algorithmic and methodological advances, and the open software technologies that address them. We invite you to submit your proposal.
Keywords: Comparative genomics; Pangenomics; Population genetics; Phylogenetic analysis; Phylogenetic trees and networks; Gene tree/Species tree Reconciliation; Horizontal transfer; Recombination; Incomplete lineage sorting; Molecular evolution
Submission deadline: This Collection is now closed for submissions.
Any questions about this collection? Please get in contact directly with research@f1000.com.
This collection is part of the Bioinformatics Gateway.
Image source: HUGE-B 500-NCBI PGT by Elena Regina, 2015
Collection Advisors
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Nadia El-Mabrouk
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Lars Arvestad
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Janani Ravi
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