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PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Jaime Huerta-Cepas, Salvador Capella-Gutiérrez, Leszek P. Pryszcz, Marina Marcet-Houben, Toni Gabaldón
2013 Nucleic Acids Research  
Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes).  ...  Here, we introduce a new release of PhylomeDB (, a public repository of phylomes.  ...  ACKNOWLEDGEMENTS The authors wish to thank members of Gabaldon's group, the quest for orthologs consortium and PhylomeDB users for their suggestions and feedback.  ... 
doi:10.1093/nar/gkt1177 pmid:24275491 pmcid:PMC3964985 fatcat:mlzwnhm3mfeynb4h46c4hh7phu

Insights into the molecular features of the von Hippel-Lindau like protein [article]

Federica Quaglia, Giovanni Minervini, Francesco Tabaro, Silvio C E Tosatto
2018 bioRxiv   pre-print
We present an in silico characterization of the von Hippel-Lindau like protein (VLP), the only known human paralogue of the von Hippel-Lindau tumor suppressor protein (pVHL).  ...  In particular, conservation of elements at the protein interfaces suggests VLP to be a functional pVHL homolog potentially possessing multiple functions beyond HIF-1α-dependent binding activity.  ...  Acknowledgements The authors are grateful to members of the BioComputingUP group for insightful discussions. Conflict of interest and funding  ... 
doi:10.1101/407353 fatcat:6poh6glfqvfzfa2kcrg6o7rejq

Matching tRNA modifications in humans to their known and predicted enzymes

Valérie de Crécy-Lagard, Pietro Boccaletto, Carl G Mangleburg, Puneet Sharma, Todd M Lowe, Sebastian A Leidel, Janusz M Bujnicki
2019 Nucleic Acids Research  
exception of the cerebellum.  ...  Only 48% of the candidate cytosolic tRNA modification enzymes have been experimentally validated in mammals (either directly or in a heterologous system).  ...  The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH and NINDS.  ... 
doi:10.1093/nar/gkz011 pmid:30698754 pmcid:PMC6412123 fatcat:j7nj2nqoxvbmhm7ueirdqajyp4

A study of protein coding genes in Enterobacteriaceae family: essentiality of genes and orthology [article]

Fatemeh Ashari Ghomi, University Of Canterbury
High-throughput sequencing technology has provided us with a wealth of data. The analysis of these sequenced genomes is not possible without di erent bioinformatics methods and tools.  ...  Finally, we present a visualisation method that can be used to facilitate the study of large datasets by making it possible to look at the relationships in a network in a single image.  ...  PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Research, 42(Database issue):D897-D902. [Hutchison et al., 1999] Hutchison, C. A., Peterson, S.  ... 
doi:10.26021/7562 fatcat:hbqvdo2kwvbwphum3t37xfwkzm