Publications

2026

1. Revealing the Shape of Genome Space via-mer Topology

   Yuta Hozumi , and Guo-Wei Wei

   SIAM Journal on Life Sciences 2026
2. CAKR: commutative algebra k-mer representations for genomics

   Faisal Suwayyid, Yuta Hozumi , Mushal Zia, and 3 more authors

   Nature Communications 2026
3. Energy-filtered branching alternatives improve RNA secondary structure recall

   Yuta Hozumi , Svetlana Poznanović, and Christine Heitsch

   Biophysical Journal 2026

2025

1. CAML: Commutative Algebra Machine Learning A Case Study on Protein–Ligand Binding Affinity Prediction

   Hongsong Feng, Faisal Suwayyid, Mushal Zia, and 4 more authors

   Journal of Chemical Information and Modeling 2025
2. Cakl: Commutative algebra k-mer learning of genomics

   Faisal Suwayyid, Yuta Hozumi , Hongsong Feng, and 3 more authors

   ArXiv 2025
3. Commutative algebra neural network reveals genetic origins of diseases

   JunJie Wee, Faisal Suwayyid, Mushal Zia, and 3 more authors

   ArXiv 2025
4. CAP: Commutative algebra prediction of protein-nucleic acid binding affinities

   Mushal Zia, Faisal Suwayyid, Yuta Hozumi , and 3 more authors

   Machine learning: science and technology 2025

2024

1. K-nearest-neighbors induced topological PCA for single cell RNA-sequence data analysis

   Sean Cottrell, Yuta Hozumi , and Guo-Wei Wei

   Computers in biology and medicine 2024
2. Analyzing single cell RNA sequencing with topological nonnegative matrix factorization

   Yuta Hozumi , and Guo-Wei Wei

   Journal of Computational and Applied Mathematics 2024
3. Multiscale differential geometry learning of networks with applications to single-cell RNA sequencing data

   Hongsong Feng, Sean Cottrell, Yuta Hozumi , and 1 more author

   Computers in Biology and Medicine 2024
4. Analyzing scRNA-seq data by CCP-assisted UMAP and t-SNE

   Yuta Hozumi , and Guo-Wei Wei

   PLOS One 2024

2023

1. Analyzing scRNA-seq data by CCP-assisted UMAP and t-SNE

   Yuta Hozumi , and Gu-Wei Wei

   arXiv preprint arXiv:2306.13750 2023
2. Preprocessing of single cell RNA sequencing data using correlated clustering and projection

   Yuta Hozumi , Kiyoto Aramis Tanemura, and Guo-Wei Wei

   Journal of chemical information and modeling 2023

2022

1. Emerging vaccine-breakthrough SARS-CoV-2 variants

   Rui Wang, Jiahui Chen, Yuta Hozumi , and 2 more authors

   ACS infectious diseases 2022
2. Ccp: Correlated clustering and projection for dimensionality reduction

   Yuta Hozumi , Rui Wang, and Guo-Wei Wei

   arXiv preprint arXiv:2206.04189 2022
3. Emerging dominant SARS-CoV-2 variants

   Jiahui Chen, Rui Wang, Yuta Hozumi , and 4 more authors

   Journal of chemical information and modeling 2022

2021

1. UMAP-assisted K-means clustering of large-scale SARS-CoV-2 mutation datasets

   Yuta Hozumi , Rui Wang, Changchuan Yin, and 1 more author

   Computers in biology and medicine 2021
2. Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants

   Rui Wang, Jiahui Chen, Kaifu Gao, and 3 more authors

   Communications biology 2021

2020

1. Host immune response driving SARS-CoV-2 evolution

   Rui Wang, Yuta Hozumi , Yong-Hui Zheng, and 2 more authors

   Viruses 2020
2. Decoding SARS-CoV-2 transmission and evolution and ramifications for COVID-19 diagnosis, vaccine, and medicine

   Rui Wang, Yuta Hozumi , Changchuan Yin, and 1 more author

   Journal of chemical information and modeling 2020
3. Mutations on COVID-19 diagnostic targets

   Rui Wang, Yuta Hozumi , Changchuan Yin, and 1 more author

   Genomics 2020
4. Characterizing SARS-CoV-2 mutations in the United States

   Rui Wang, Jiahui Chen, Kaifu Gao, and 3 more authors

   Research square 2020
5. Decoding asymptomatic COVID-19 infection and transmission

   Rui Wang, Jiahui Chen, Yuta Hozumi , and 2 more authors

   The journal of physical chemistry letters 2020

preparation