ArticlePLoS computational biology2021
Balrog: A universal protein model for prokaryotic gene prediction.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed, 32 citations in OpenAlex.
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- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- PSAURON: a tool for assessing protein annotation across a broad range of species.NAR genomics and bioinformatics · 2025Article
- Optimizing bacteriophage treatment of resistantmSphere · 2024Article
- Small proteins in Gram-positive bacteria.FEMS microbiology reviews · 2023Article
- Accurate and fast graph-based pangenome annotation and clustering with ggCaller.Genome research · 2023Article
- Challenges in prokaryote pangenomics.Microbial genomics · 2023Review
- Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence.FEMS microbiology reviews · 2023Review
- ProkBERT family: genomic language models for microbiome applications.Frontiers in microbiology · 2023Article
- A toolbox of machine learning software to support microbiome analysis.Frontiers in microbiology · 2023Review
- Evaluating Plant Gene Models Using Machine Learning.Plants (Basel, Switzerland) · 2022Article
- Article
- RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria.Briefings in bioinformatics · 2022Article
- Adaptive lifestyle of bacteria determines phage-bacteria interaction.Frontiers in microbiology · 2022Article
- Metagenomics: a path to understanding the gut microbiome.Mammalian genome : official journal of the International Mammalian Genome Society · 2021Review
- A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data.Computational and structural biotechnology journal · 2021Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Low-cost, high-throughput sequencing has led to an enormous increase in the number of sequenced microbial genomes, with well over 100,000 genomes in public archives today. Automatic genome annotation tools are integral to understanding these organisms, yet older gene finding methods must be retrained on each new genome. We have developed a universal model of prokaryotic genes by fitting a temporal convolutional network to amino-acid sequences from a large, diverse set of microbial genomes. We incorporated the new model into a gene finding system, Balrog (Bacterial Annotation by Learned Representation Of Genes), which does not require genome-specific training and which matches or outperforms other state-of-the-art gene finding tools. Balrog is freely available under the MIT license at https://github.com/salzberg-lab/Balrog.
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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.