ArticleGenome research2017
Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed, 70 citations in OpenAlex.
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- Draft genome of the endangered visayan spotted deer (GigaByte (Hong Kong, China) · 2025Article
- Proteogenomic Gene Structure Validation in the Pineapple Genome.Journal of proteome research · 2024Article
- Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis.Genome research · 2023Article
- DissectingACS omega · 2022Article
- Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges.Frontiers in bioengineering and biotechnology · 2022Article
- Proteotranscriptomics - A facilitator in omics research.Computational and structural biotechnology journal · 2022Review
- Advances in UnderstandingFrontiers in cell and developmental biology · 2021Review
- Novel Technologies in Studying Brain Immune Response.Oxidative medicine and cellular longevity · 2021Review
- Proteomics dataset of adultData in brief · 2020Article
- Recent advances and future perspectives in vector-omics.Current opinion in insect science · 2020Review
- Deciphering carbohydrate metabolism during wheat grain development via integrated transcriptome and proteome dynamics.Molecular biology reports · 2020Article
- The Cannabis Proteome Draft Map Project.International journal of molecular sciences · 2020Article
- Article
- Potential mechanisms of action of celastrol against rheumatoid arthritis: Transcriptomic and proteomic analysis.PloS one · 2020Article
- Combination of Proteogenomics with PeptidemBio · 2019Article
- Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives.Marine drugs · 2019Review
Corrections and comments
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Authors and funding
42 authors at 10 institutions in 2 countries.
Funding
Abstract
Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted "noncoding RNAs" to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.