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Protein Molecular Function Prediction by Bayesian Phylogenomics
2005
PLoS Computational Biology
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Citation: Engelhardt BE, Jordan MI, Muratore KE, Brenner SE (2005) Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol 1(5): e45. ...
Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled ...
Phylogenomics Phylogenomics is a methodology for annotating the specific molecular function of a protein using the evolutionary history of that protein as captured by a phylogenetic tree [17] . ...
doi:10.1371/journal.pcbi.0010045
pmid:16217548
pmcid:PMC1246806
fatcat:kjzqzpy3zng4xpoi6vkeuxqt4y
Phylogenomic inference of protein molecular function: advances and challenges
2004
Bioinformatics
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As a number of studies have shown, standard methods of protein function prediction produce systematic errors on these data. ...
The explicit integration of structure prediction and analysis in this framework, which we call structural phylogenomics, provides additional insights into protein superfamily evolution. ...
This work was supported in part by Grant no. 0238311 from the National Science Foundation, and by Grant no. R01 HG002769-01 from the National Institutes of Health. ...
doi:10.1093/bioinformatics/bth021
pmid:14734307
fatcat:juaxrnw2mngbfbflxh6kkvvwqu
Functional Classification Using Phylogenomic Inference
2006
PLoS Computational Biology
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Sequences without known function can be assigned a predicted molecular function using the tree topology to identify orthologs. ...
Fourth, phylogenomic approaches to protein function prediction have arisen only in the last few years, while database search methods have been available for much longer. ...
doi:10.1371/journal.pcbi.0020077
pmid:16846248
pmcid:PMC1484587
fatcat:hsmwraxff5aijbzs4abcpadm3u
Functional prediction through phylogenetic inference and structural classification of proteins
[chapter]
2006
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
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Acknowledgments This work was supported in part by Grant #0238311 from the National Science Foundation, and by Grant #R01 HG002769-01 from the National Institutes of Health to KS. ...
Phylogenomic inference of protein function has several distinct challenges. ...
This approach is called phylogenomic inference of protein function (Brown and Sjölander, 2006) . ...
doi:10.1002/047001153x.g306320
fatcat:hfc4hxrpgbempbltbb223ul4pi
Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae
2013
PLoS ONE
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A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. ...
In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the ...
As to molecular functions, 'protein binding', 'hydrolase activity', 'transferase activity', and 'structural molecule activity' were mostly represented. ...
doi:10.1371/journal.pone.0064642
pmid:23734211
pmcid:PMC3667173
fatcat:c34lxtq6tvglhdd2qbwjgin74y
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis
2007
Nucleic Acids Research
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Phylogenomic analysis addresses the limitations of function prediction based on annotation transfer, and has been shown to enable the highest accuracy in prediction of protein molecular function. ...
, subfamily identification and structure prediction. ...
The PhyloFacts resource is supported by a Presidential Early Career Award for Scientists and Engineers (PECASE) from the National Science Foundation (DBI-0238311), and by a grant from the National Human ...
doi:10.1093/nar/gkm325
pmid:17488835
pmcid:PMC1933202
fatcat:omacwxa4vvb5toaxahyhrolq3u
Evolutionary origin of a streamlined marine bacterioplankton lineage
2014
The ISME Journal
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Ancestral genome analysis suggests that the first evolved SAR11 cell had a small genome streamlined from its ancestor by a factor of two and coinciding with an ecological transition, followed by further ...
tree, whereas that based on the concatenation of 28 homogeneous proteins (including 19 ribosomal proteins) disassociated the lineages and placed SAR11 at the base of the non-endosymbiotic lineages. ...
This research was funded in part by the Gordon and Betty Moore Foundation through grant GBMF538.01 and a Direct Grant (4930062) of the Chinese University of Hong Kong. ...
doi:10.1038/ismej.2014.227
pmid:25431989
pmcid:PMC4438329
fatcat:cdzrhwa7i5bepcbxfja7zl4cza
A note on retrodiction and machine evolution
[article]
2023
arXiv
pre-print
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This allows description of the gradual evolutionary rise of structural and functional innovations in RNA and proteins. ...
For example, the accretion of rRNA substructures and ribosomal proteins can be traced in time and placed within a geological timescale. ...
(B) The biphasic history of the ribosome is showcased by an evolutionary timeline of ribosomal RNA (rRNA) and proteins (r-proteins) inferred directly from phylogenomic data. ...
arXiv:2303.14590v1
fatcat:qyh54lxd5fa5noo6qd2ckkvnzy
Early photosynthetic eukaryotes inhabited low-salinity habitats
2017
Proceedings of the National Academy of Sciences of the United States of America
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We present phylogenomic and molecular clock analyses, including data from cyanobacterial and chloroplast genomes using a Bayesian approach, with the aim of estimating the age for the primary endosymbiotic ...
event, the ages of crown groups for photosynthetic eukaryotes, and the independent incorporation of a cyanobacterial endosymbiont by Paulinella. ...
We thank Martin Brasier for in-depth discussions on the early fossil record, John Huelsenbeck for discussion on the implementation of molecular clocks, and Sam Price for advice on stochastic mapping analyses ...
doi:10.1073/pnas.1620089114
pmid:28808007
pmcid:PMC5603991
fatcat:plq3wmni3vatvam74bxyxwytfm
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification
2006
Genome Biology
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The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional ...
PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary ...
Acknowledgements This work was supported by a Presidential Early Career Award for Scientists and Engineers (PECASE) from the National Science Foundation, and by an R01 from the National Human Genome Research ...
doi:10.1186/gb-2006-7-9-r83
pmid:16973001
pmcid:PMC1794543
fatcat:uib3z34bjzfcneno7favzrp6ri
Phylogenetic Analysis of General Bacterial Porins: A Phylogenomic Case Study
2006
Journal of Molecular Microbiology and Biotechnology
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Altogether, our results support the potential for phylogenomics to increase the accuracy of sequence annotations. ...
This work was supported by a grant from the California State University Program for Education and Research in Biotechnology (CSUPERB). Phylogenetic Analysis of General Bacterial Porins ...
Discussion The results of our phylogenetic study showed the potential for phylogenomics to enhance our understanding of protein evolution and improve protein function prediction. ...
doi:10.1159/000095631
pmid:17114893
fatcat:s24r7ouepjbpnkqy7ukyl4razu
Parasitism and Mutualism in Wolbachia: What the Phylogenomic Trees Can and Cannot Say
2008
Molecular biology and evolution
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Ecological and evolutionary theories predict that parasitism and mutualism are not fixed endpoints of the symbiotic spectrum. ...
Rather, parasitism and mutualism may be host or environment dependent, induced by the same genetic machinery, and shifted due to selection. ...
Bayesian nucleotide analyses were performed with the same running conditions as the protein analyses. ...
doi:10.1093/molbev/msn243
pmid:18974066
pmcid:PMC2721558
fatcat:onfqkryqdra4dpd3usj2xnbomq
Evolution of Divergent Life History Strategies in Marine Alphaproteobacteria
2013
mBio
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The timing of the first Roseobacter genome expansion was coincident with the predicted radiation of modern marine eukaryotic phytoplankton of sufficient size to create nutrient-enriched microzones and ...
on a concatenation of 60 orthologous protein sequences using the P4 Bayesian software
Fig. 3A; see also Fig. ...
The genetic composition was determined by mapping the gene families to COG functional categories. ...
doi:10.1128/mbio.00373-13
pmid:23839216
pmcid:PMC3735120
fatcat:4ldmxdhau5dprp7wjb5e2la5nq
Overview of the First Phylogenomics Conference
2007
BMC Evolutionary Biology
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The First Phylogenomics Conference was held in Ste-Adèle (Québec, Canada) in March 2006. Selected papers appear in this special issue of BMC Evolutionary Biology. ...
This article has been published as part of BMC Evolutionary Biology Volume 7, Supplement 1, 2007: First International Conference on Phylogenomics. ...
The word phylogenomics was first introduced in 1998 in the context of an "approach to the prediction of gene function" for genome-scale data [1] , and soon after in the context of phylogenetic inference ...
doi:10.1186/1471-2148-7-s1-s1
pmid:17288567
pmcid:PMC1796603
fatcat:u2wdc2hlv5bexor3j5g77kx4g4
Novel evolutionary relationship among four fish model systems
2004
Trends in Genetics
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A sophisticated application of phylogenomics is to improve functional predictions for uncharacterized genes [44] . ...
The composition of many taxonomic groups of fish at the ordinal and supra-ordinal level requires validation by rigorous molecular phylogenetic study. ...
Acknowledgements Part of this work was supported by grants from the Deutsche Forschungsgemeinschaft to A.M., and the National Science Foundation (DEB 9985045) to G.O. We thank E. ...
doi:10.1016/j.tig.2004.07.005
pmid:15313551
fatcat:nymtvmgbm5dxlctx24td324sva
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