ArticleNucleic acids research2021
A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 13 citations in OpenAlex.
- Discovery of diverse chimeric peptides in a eukaryotic proteome sets the stage for experimental validation of the mosaic translation hypothesis.Computational and structural biotechnology journal · 2025Article
- A universal pipeline MosaicProt enables large-scale modeling and detection of chimeric protein sequences for studies on programmed ribosomal frameshifting.Computational and structural biotechnology journal · 2025Article
- Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation.PLoS computational biology · 2023Article
- BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction.Functional & integrative genomics · 2022Article
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12 authors at 3 institutions in 3 countries.
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Abstract
Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association.
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