@article {razban2018proteomevis,
	title = {ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms{\textquoteright} proteomes},
	journal = {Bioinformatics},
	volume = {1},
	year = {2018},
	pages = {9},
	publisher = {Oxford University Press},
	abstract = {<p>Motivation:\&nbsp;Protein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the\&nbsp;Saccharomyces cerevisiae\&nbsp;and\&nbsp;Escherichia coli\&nbsp;proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution are studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level.</p><p>Results:\&nbsp;We demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determi- nants.\&nbsp;S.cerevisiae\&nbsp;and\&nbsp;E.coli\&nbsp;oPCUGs are scale-free with scaling constants of 1.79 and 1.56, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution. Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of {\textendash}0.49 (P-value\&nbsp;\&lt;\&nbsp;10<sup>-10</sup>) and {\textendash}0.46 (P-value\&lt;10<sup>-10</sup>) for\&nbsp;S.cerevisiae\&nbsp;and\&nbsp;E.coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant.</p>},
	url = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/bty370/25018003/bty370.pdf},
	author = {Razban, Rostam M and Gilson, Amy I and Durfee, Niamh and Strobelt, Hendrik and Dinkla, Kasper and Jeong-Mo Choi and Hanspeter Pfister and Shakhnovich, EugeneI.}
}
