ArticleBioinformatics (Oxford, England)2019
Pinetree: a step-wise gene expression simulator with codon-specific translation rates.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 13 citations in OpenAlex.
- Availability of Charged tRNAs Drives Maximal Protein Synthesis at Intermediate Levels of Codon Usage Bias.Bulletin of mathematical biology · 2026Article
- ΦX174 bacteriophage viability predicted by protein biophysical modeling.bioRxiv : the preprint server for biology · 2025Article
- Codon usage modulates the relationship between the burden and yield of protein overexpression.Journal of biological engineering · 2025Article
- Article
- spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.Nucleic acids research · 2023Article
- Generating dynamic gene expression patterns without the need for regulatory circuits.PloS one · 2022Article
- Transcript degradation and codon usage regulate gene expression in a lytic phage.Virus evolution · 2019Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
motivationStochastic gene expression simulations often assume steady-state transcript levels, or they model transcription in more detail than translation. Moreover, they lack accessible programing interfaces, which limit their utility.
resultsWe present Pinetree, a step-wise gene expression simulator with codon-specific translation rates. Pinetree models both transcription and translation in a stochastic framework with individual polymerase and ribosome-level detail. Written in C++ with a Python front-end, any user familiar with Python can specify a genome and simulate gene expression. Pinetree was designed to be efficient and scale to simulate large plasmids or viral genomes. AVAILABILITY AND IMPLEMENTATION: Pinetree is available on GitHub (https://github.com/benjaminjack/pinetree) and the Python Package Index (https://pypi.org/project/pinetree/).
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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.