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Towards a Dynamic Composability Approach for using Heterogeneous Systems in Remote Sensing

https://doi.org/10.1109/eScience55777.2022.00047

Altintas, Ilkay ; Perez, Ismael ; Mishin, Dmitry ; Trouillaud, Adrien ; Irving, Christopher ; Graham, John ; Tatineni, Mahidhar ; DeFanti, Thomas ; Strande, Shawn ; Smarr, Larry ; et al ( October 2022 , 2022 IEEE 18th International Conference on e-Science (e-Science))

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Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

https://doi.org/10.1186/s13059-019-1834-9

Sanders, Jon G. ; Nurk, Sergey ; Salido, Rodolfo A. ; Minich, Jeremiah ; Xu, Zhenjiang Z. ; Zhu, Qiyun ; Martino, Cameron ; Fedarko, Marcus ; Arthur, Timothy D. ; Chen, Feng ; et al ( December 2019 , Genome Biology)

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Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

https://doi.org/10.1038/s41467-019-13443-4

Zhu, Qiyun ; Mai, Uyen ; Pfeiffer, Wayne ; Janssen, Stefan ; Asnicar, Francesco ; Sanders, Jon G. ; Belda-Ferre, Pedro ; Al-Ghalith, Gabriel A. ; Kopylova, Evguenia ; McDonald, Daniel ; et al ( December 2019 , Nature Communications)

Abstract
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer “core” genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

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