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fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks [article]

Chengsheng Zhu, Yannick Mahlich, Yana Bromberg
2016 bioRxiv   pre-print
Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB  ...  Users can search fusionDB via combinations of organism names and metadata.  ...  Burkhard Rost (TU Munich), Max Haggblom and Tamar Barkay (both 10 Rutgers), and Tom O. Delmont (U Chicago) for all discussions and to those who  ... 
doi:10.1101/035923 fatcat:wfjyszjv3bh7vdjnmpun67kdtu

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks

Chengsheng Zhu, Yannick Mahlich, Maximilian Miller, Yana Bromberg
2017 Nucleic Acids Research  
Users can search fusionDB via combinations of organism names and metadata.  ...  Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB  ...  We are also grateful to all those who deposit their data in public databases -fusionDB wouldn't be possible without them.  ... 
doi:10.1093/nar/gkx1060 pmid:29112720 pmcid:PMC5753390 fatcat:ejqpk3qidvecraq3czdennosz4

Functional analysis of microbial genomes and metagenomes

Chengsheng Zhu
2017
We deposit the functional data in fusionDB, mapping bacteria and their functions to available metadata: habitat/niche, preferred temperature, and oxygen use.  ...  In the fusion (functional-repertoire similarity-based organism network) representation, organisms can be consistently assigned to groups based on a quantitative measure of their functional similarities  ...  It further places this microbe into a context of other reference organisms and relates the identified microbial function to the preferred environmental conditions.  ... 
doi:10.7282/t3dv1ntf fatcat:ispzaemtsndvtksnfrnd4osc3m

Burkholderia fungorum strain Rifle

Nicole Michele Koribanics
2017
The draft genome was assembled and annotated for prospective gene functions.  ...  To identify the capability of Burkholderia fungorum strain Rifle to precipitate elevated levels uranium, cultures were grown aerobically in the absence and presence of uranium (0-200 μM).  ...  the Burkholderia fungorum Rifle genome via BLAST to assess protein similarity and possible function.  ... 
doi:10.7282/t3cz3b9g fatcat:kz3uw5xwobcevjunkh4nqk36gm

Computational investigations of divalent heavy metal ion homeostasis [article]

Torsten Rozycki, Universitäts- Und Landesbibliothek Sachsen-Anhalt, Martin-Luther Universität, Nies, D. H., Prof. Dr., Krauss, G. J., Prof. Dr., Saier, M. H., Prof. Dr.
2018
preliminary genomic sequence of R. metallidurans, without which this study would not have been Acknowledgments This work was supported by Graduiertenkolleg ''Stress'' of the Deutsche Forschungsgemeinschaft and  ...  of DNA derived from diverse and mixed microbial communities (environmental genomics or ecogenomics) Metal Chelates Polydentate ring forming ligand groups working as chelating agents Metalloproteins Proteins  ...  Diversity of the Burkholderia cepacia complex and implications for risk assessment of biological control strains. Annu Rev Phytopathol. 39:225-258.  ... 
doi:10.25673/303 fatcat:abeyszkwuja2vfpvey2ownigze