ArticleComputers in biology and medicine2022
Persistent Laplacian projected Omicron BA.4 and BA.5 to become new dominating variants.
Article in Computers in biology and medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers, 1 of them a synthesis that pooled it.
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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
62 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analysis and Topological Perturbation in Interactomic Network for Antiopioid Addiction Drug Repurposing.Journal of chemical information and modeling · 2025Pooled it
- Persistent sheaf Laplacian analysis of protein stability and solubility changes upon mutation.Protein science : a publication of the Protein Society · 2026Article
- Article
- Correlated clustering and projection for dimensionality reduction.Machine learning: science and technology · 2026Article
- Topological data analysis and topological deep learning beyond persistent homology: a review.Artificial intelligence review · 2026Article
- Leveraging knowledge graphs and large language models for integrating molecular variants and clinical insights in COVID-19 research.Biosafety and health · 2026Article
- Interpretability and Representability of Commutative Algebra, Algebraic Topology, and Topological Spectral Theory for Real-World Data.Advanced intelligent discovery · 2025Article
- A Review of Topological Data Analysis and Topological Deep Learning in Molecular Sciences.Journal of chemical information and modeling · 2025Review
- Topological machine learning for protein-nucleic acid binding affinity changes upon mutation.Machine learning: science and technology · 2025Article
- Topological deep learning for enhancing peptide-protein complex prediction.Communications chemistry · 2025Article
- PERSISTENT DIRECTED FLAG LAPLACIAN.Foundations of data science (Springfield, Mo.) · 2025Article
- PERSISTENT INTERACTION TOPOLOGY IN DATA ANALYSIS.Foundations of data science (Springfield, Mo.) · 2025Article
- How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors.PLoS computational biology · 2025Article
- PERSISTENT SHEAF LAPLACIANS.Foundations of data science (Springfield, Mo.) · 2025Article
- A review of machine learning methods for imbalanced data challenges in chemistry.Chemical science · 2025Review
- Persistent Directed Flag Laplacian (PDFL)-Based Machine Learning for Protein-Ligand Binding Affinity Prediction.Journal of chemical theory and computation · 2025Article
- Mayer-Homology Learning Prediction of Protein-Ligand Binding Affinities.Journal of computational biophysics and chemistry · 2025Article
- Decoding the functional impact of the cancer genome through protein-protein interactions.Nature reviews. Cancer · 2025Review
- Decoding the effects of mutation on protein interactions using machine learning.Biophysics reviews · 2025Review
- Persistent Topological Laplacians-A Survey.Mathematics (Basel, Switzerland) · 2025Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Due to its high transmissibility, Omicron BA.1 ousted the Delta variant to become a dominating variant in late 2021 and was replaced by more transmissible Omicron BA.2 in March 2022. An important question is which new variants will dominate in the future. Topology-based deep learning models have had tremendous success in forecasting emerging variants in the past. However, topology is insensitive to homotopic shape evolution in virus-human protein-protein binding, which is crucial to viral evolution and transmission. This challenge is tackled with persistent Laplacian, which is able to capture both the topological change and homotopic shape evolution of data. Persistent Laplacian-based deep learning models are developed to systematically evaluate variant infectivity. Our comparative analysis of Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron BA.1, BA.1.1, BA.2, BA.2.11, BA.2.12.1, BA.3, BA.4, and BA.5 unveils that Omicron BA.2.11, BA.2.12.1, BA.3, BA.4, and BA.5 are more contagious than BA.2. In particular, BA.4 and BA.5 are about 36% more infectious than BA.2 and are projected to become new dominant variants by natural selection. Moreover, the proposed models outperform the state-of-the-art methods on three major benchmark datasets for mutation-induced protein-protein binding free energy changes. Our key projection about BA4 and BA.5's dominance made on May 1, 2022 (see arXiv:2205.00532) became a reality in late June 2022.
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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 Socratic graph.