Publications
Check Projects for more detail.
2025
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ProtSciPLD-Tree: Persistent Laplacian Decision Tree for Protein-Protein Binding Free Energy PredictionProtein Sciences 2025
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CISDimensionality reduction for k-means clustering of large-scale influenza mutation datasetsCommunication in Information and Systems 2025
2024
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CBMIntegration of persistent Laplacian and pre-trained transformer for proteinComputers in Biology and Medicine 2024
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SIAM RevGraph Combinatorial and Hodge Laplacians: Similarity and DifferenceSIAM Review 2024
2023
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arXivpersistent topological Laplacian analysis of SARS-CoV-2 variantsarXiv preprint arXiv:2301.10865 2023
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CBMTopological deep learning based deep mutational scanningComputers in Biology and Medicine 2023
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JCBCPersistent topological Laplacian analysis of SARS-CoV-2 variantsJournal of Computational Biophysics and Chemistry 2023
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SmallShape Anisotropy Governed High Performance Nanomagnetosol for In Vivo Magnetic Particle Imaging of LungsSmall 2023
2022
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ACS IDEmerging vaccine-breakthrough SARS-CoV-2 variantsACS infectious diseases 2022
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CJIMOmicron variant (B. 1.1. 529): infectivity, vaccine breakthrough, and antibody resistanceJournal of chemical information and modeling 2022
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JPCLOmicron BA. 2 (b. 1.1. 529.2): High potential for becoming the next dominant variantThe journal of physical chemistry letters 2022
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arXivGraph and Hodge Laplacians: Similarity and DifferencearXiv preprint arXiv:2204.12218 2022
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arXivMathematical artificial intelligence design of mutation-proof COVID-19 monoclonal antibodiesarXiv preprint arXiv:2204.09471 2022
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arXivPersistent Laplacian projected Omicron BA. 4 and BA. 5 to become new dominating variantsComputers in Biology and Medicine 2022
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CISComputing electrostatic binding energy with the TABI Poisson–Boltzmann solverCommunications in Information and Systems 2022
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JCIMEmerging dominant SARS-CoV-2 variantsJournal of Chemical Information and Modeling 2022
2021
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JCBCComputing protein pKas using the TABI Poisson-Boltzmann solverJournal of Computational Biophysics and Chemistry 2021
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FDSHERMES: Persistent spectral graph softwareFondations of data science (Springfield, Mo.) 2021
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CommBioAnalysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variantsCommunications biology 2021
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AppSciModeling the Effects of Calcium Overload on Mitochondrial Ultrastructural RemodelingApplied Sciences 2021
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CISSARS-CoV-2 becoming more infectious as revealed by algebraic topology and deep learningCommunications in Information and Systems 2021
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GenomicsVaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countriesGenomics 2021
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JMBRevealing the threat of emerging SARS-CoV-2 mutations to antibody therapiesJournal of molecular biology 2021
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arXivReview of the mechanisms of SARS-CoV-2 evolution and transmissionArXiv 2021
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CJCPMLIMC: Machine learning-based implicit-solvent Monte CarloChinese Journal of Chemical Physics 2021
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JPCLMechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and AmericaThe journal of physical chemistry letters 2021
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JMCPerspectives on SARS-CoV-2 main protease inhibitorsJournal of Medicinal Chemistry 2021
2020
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ACSRepositioning of 8565 existing drugs for COVID-19The journal of physical chemistry letters 2020
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JMBMutations strengthened SARS-CoV-2 infectivityJournal of Molecular Biology 2020
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AR of Biophy.Review of COVID-19 antibody therapiesAnnual Review of Biophysics 2020
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MathBioThe de Rham–Hodge Analysis and Modeling of BiomoleculesBulletin of Mathematical Biology 2020
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JPhysChemDecoding asymptomatic COVID-19 infection and transmissionThe journal of physical chemistry letters 2020
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ChemSciUnveiling the molecular mechanism of SARS-CoV-2 main protease inhibition from 137 crystal structures using algebraic topology and deep learningChemical Science 2020
2019
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SMUPARALLEL MULTIPOLE EXPANSION ALGORITHMS AND THEIR BIOLOGY APPLICATIONS2019
2018
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ProtSciImprovements to the APBS biomolecular solvation software suiteProtein Science 2018
2015
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Parallel computing of the adaptive n-body treecode algorithm for solving boundary integral Poisson-Boltzmann equationIn International Conference on High Performance Computing and Applications 2015