ArticleCommunications biology2021
Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Rhobot-Screen: an integrated robotic platform for functional screening of rhodopsin variants.BMC biology · 2026Article
- Accessible and robust machine learning approaches to improve the opsin genotype-phenotype map.Molecular biology and evolution · 2026Article
- Light-harvesting by antenna-containing xanthorhodopsin from an Antarctic Pseudanabaenaceae cyanobacterium.Communications biology · 2025Article
- Harnessing light the retinal way.Nature chemistry · 2025Article
- CryoRhodopsins: A comprehensive characterization of a group of microbial rhodopsins from cold environments.Science advances · 2025Article
- Optogenetic engineering for ion channel modulation.Current opinion in chemical biology · 2025Review
- Solid-state NMR of the retinal protonated Schiff base in microbial rhodopsins.Magnetic resonance letters · 2024Review
- Tetherless Optical Neuromodulation: Wavelength from Orange-red to Mid-infrared.Neuroscience bulletin · 2024Review
- Rhodopsin-based light-harvesting system for sustainable synthetic biology.Microbial biotechnology · 2024Article
- RhoMax: Computational Prediction of Rhodopsin Absorption Maxima Using Geometric Deep Learning.Journal of chemical information and modeling · 2024Article
- Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD).GigaScience · 2024Article
- Efficient model selection for predictive pattern mining model by safe pattern pruning.Patterns (New York, N.Y.) · 2023Article
- Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites.Microbial ecology · 2023Article
- Article
- Review
- Rhodopsin driven microbial COEnvironmental microbiology · 2023Article
- Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins.Molecular biology and evolution · 2022Article
- Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering.Frontiers in chemistry · 2022Review
- Red Light Optogenetics in Neuroscience.Frontiers in cellular neuroscience · 2021Review
- Emerging Diversity of Channelrhodopsins and Their Structure-Function Relationships.Frontiers in cellular neuroscience · 2021Review
Corrections and comments
- Erratum issued
Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial rhodopsins are photoreceptive membrane proteins, which are used as molecular tools in optogenetics. Here, a machine learning (ML)-based experimental design method is introduced for screening rhodopsins that are likely to be red-shifted from representative rhodopsins in the same subfamily. Among 3,022 ion-pumping rhodopsins that were suggested by a protein BLAST search in several protein databases, the ML-based method selected 65 candidate rhodopsins. The wavelengths of 39 of them were able to be experimentally determined by expressing proteins with the Escherichia coli system, and 32 (82%, p = 7.025 × 10
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