ArticleNature communications2022
Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
- Graph-based representations in modern protein science.The Biochemical journal · 2026Review
- Inference of fitness landscapes with heterogeneous patterns of epistasis across sites.bioRxiv : the preprint server for biology · 2026Article
- Probing the Specificity of Fluorescent Deoxyribozymes Using Single-Step Selections and Machine Learning.ACS chemical biology · 2026Article
- Inference and Visualization of Complex Genotype-Phenotype Maps.Molecular biology and evolution · 2026Article
- Using structured libraries, selection, and machine learning to rapidly explore the sequence space of a fluorescent deoxyribozyme.Nucleic acids research · 2025Article
- Inference and visualization of complex genotype-phenotype maps withbioRxiv : the preprint server for biology · 2025Article
- Exploring the space of self-reproducing ribozymes using generative models.Nature communications · 2025Article
- CHiTA: A scarless high-throughput pipeline for characterization of ribozymes.Methods (San Diego, Calif.) · 2025Article
- Bioengineering hybrid artificial life.Frontiers in bioinformatics · 2025Review
- Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.Nucleic acids research · 2024Article
- Evolution of the substrate specificity of an RNA ligase ribozyme from phosphorimidazole to triphosphate activation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity.PLoS computational biology · 2024Article
- Deep generative design of RNA family sequences.Nature methods · 2024Article
- Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis.RNA (New York, N.Y.) · 2023Article
- Random and Natural Non-Coding RNA Have Similar Structural Motif Patterns but Differ in Bulge, Loop, and Bond Counts.Life (Basel, Switzerland) · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A neutral network connects all genotypes with equivalent phenotypes in a fitness landscape and plays an important role in the mutational robustness and evolvability of biomolecules. In contrast to earlier theoretical works, evidence of large neutral networks has been lacking in recent experimental studies of fitness landscapes. This suggests that evolution could be constrained globally. Here, we demonstrate that a deep learning-guided evolutionary algorithm can efficiently identify neutral genotypes within the sequence space of an RNA ligase ribozyme. Furthermore, we measure the activities of all 2
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