Publications | Bioinformatics

Publications List

Automated recognition of chromosome fusion using an alignment-free natural vector method (with Hongyu Yu ) , Frontiers in Genetics, section Computational Genomics ,Vol. 15 :1364951 ,No. 2024 (2024) , 1-10 DOI

CAPE: a deep learning framework with Chaos-Attention net for Promoter Evolution (with Ruohan Ren* , Hongyu Yu* , Jiahao Teng , Sihui Mao , Zixuan Bian and Yangtianze Tao ) , Briefings in Bioinformatics ,Vol. 25 ,No. 5 (2024) , 1-12 DOI

Exploring geometry of genome space via Grassmann manifolds (with Xiaoguang Li* , Tao Zhou* , Xingdong Feng and Shing-Tung Yau ) , The Innovation ,Vol. 5 :100677 ,No. 5 (2024) , 1-8 DOI

New Virus Variant Detection Based on the Optimal Natural Metric (with Hongyu Yu ) , Genes ,Vol. 15 :891 (2024) , 1-12 DOI

A Novel Natural Graph for Efficient Clustering of Virus Genome Sequences (with Harris Song* , Nan Sun* and Wenping Yu ) , Current Bioinformatics ,Vol. 19 (2024) , 687-703 DOI

The optimal metric for viral genome space (with Hongyu Yu ) , Computational and Structural Biotechnology Journal ,Vol. 23 (2024) , 2083-2096 DOI

Geometric Analysis of SARS-CoV-2 Variants (with Mengcen Guan and Nan Sun ) , Gene ,Vol. 909 :148291 (2024) , 1-11 DOI

Yau's slide in the conference "first Symposium of Geometry and Statistics" in Beijing , China (2023) , on July 29-31

Quantitative proteomics profiling reveals the inhibition of trastuzumab antitumor efficacy by phosphorylated RPS6 in gastric carcinoma (with Chun-Ting Hu* , Shao-Jun Pei* , Jing-Long Wang , Li-Dong Zu , Wei-Wei Shen , Lin Yuan , Feng Gao , Li-Ren Jiang and Guo-Hui Fu ) , Cancer Chemotherapy and Pharmacology ,Vol. 92 (2023) , 341-355 DOI

Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans (with Haoyu Zhou* and Ruohan Ren* ) , Frontiers in Cellular and Infection Microbiology, section Virus and Host ,Vol. 12 :1085397 (2023) , 1-19

Generating Minimal Models of H1N1 NS1 Gene Sequences Using Alignment-based and Alignment-free Algorithms (with Meng Fang* , Jiawei Xu* and Nan Sun ) , Genes ,Vol. 14 :186 ,No. 186 (2023) , 1-11 DOI

Yau's slide in University of Notre Dam , USA (2022) , in 2022 October

Classification of Protein Sequences by a Novel Alignment-Free Method on Bacterial and Virus Families (with Mengcen Guan and Leqi Zhao ) , Genes ,Vol. 13 :1744 (2022) , 1-12 DOI

In-depth Investigation of the Point Mutation Pattern of HIV-1 (with Nan Sun ) , Frontiers in Cellular and Infection Microbiology-Extra-intestinal Microbiome ,Vol. 12 :1033481 (2022) , 1-11 DOI

An efficient numerical representation of genome sequence: natural vector with covariance component (with Nan Sun and Xin Zhao ) , Peer J ,Vol. 10 :e13544 ,No. 2022 (2022) , 1-23 DOI

Biomolecular Topology: Modelling and Analysis (with Jian Liu , Ke-Lin Xia , Jie Wu and Guo-Wei Wei ) , Acta Mathematica Sinica ,Vol. 38 ,No. 10 (2022) , 1901-1938

Nucleotide Amino Acid K-mer Vector: An alignment-free method for comparing genomic sequences (with Xiaona Bao , Lily He and Jingan Cui ) , Communications in Information and Systems ,Vol. 22 ,No. 3 (2022) , 317-337

kmer2vec: a novel method for comparing DNA sequences by word2vec embedding (with Ruohan Ren and Changchuan Yin ) , Journal of Computational Biology ,Vol. 29 ,No. 9 (2022) , 1001-1021 DOI

New Genome Sequence Detection via Natural Vector Convex Hull Method (with Ruzhang Zhao and Shaojun Pei ) , IEEE/ACM Transactions on Computational Biology and Bioinformatics ,Vol. 19 ,No. 3 (2022) , 1782-1793

Full chromosomal relationships between populations and the origin of humans (with Rui Dong , Shaojun Pei , Mengcen Guan , Shek-Chung Yau , Changchuan Yin and Rong L He ) , Frontiers in Genetics ,Vol. 12 (2022) , 1-10 DOI

Identification of HIV rapid mutations using differences in nucleotide distribution over time (with Nan Sun and Jie Yang ) , Genes ,Vol. 13 ,No. 170 (2022) , 1-15 DOI

Analysis of the Genomic Distance between Bat Coronavirus RaTG13 and SARS-COV-2 Reveals Multiple Origins of Covid-19 (with Shaojun Pei ) , Acta Mathematica Scientia ,Vol. 41 ,No. 3 (2021) , 1017-1022 DOI

Geometric construction of viral genome space and its applications (with Nan Sun* , Shaojun Pei* , Lily He , Changchuan Yin and Rong Lucy He ) , Computational and Structural Biotechnology Journal ,Vol. 19 (2021) , 4226-4234 DOI Journal Homepage

Determination of the nucleotide or amino acid composition of genome or protein sequences by using natural vector method and convex hull principle (with Xiaopei Jiao* , Shaojun Pei* , Zeju Sun and Jiayi Kang ) , Fundamental Research ,Vol. 1 (2021) , 559-564 DOI Journal Homepage

Inverted Repeats in Coronavirus SARS-CoV-2 Genome and Implications in Evolution (with Changchuan Yin ) , Communications in Information and Systems ,Vol. 21 ,No. 1 (2021) , 125-145

Splice sites detection using chaos game representation and neural network (with Tung Hoang and Changchuan Yin ) , Genomics ,Vol. 112 ,No. 2 (2020) , 1847-1852 DOI Journal Homepage

A novel alignment-free method for HIV-1 subtype classification (with Lily He* , Rui Dong* and Rong Lucy He ) , Infection, Genetics and Evolution ,Vol. 77 (2020) , 1-11 DOI

Analysis of the hosts and transmission paths of SARS-CoV-2 in the COVID-19 outbreak (with Rui Dong* , Shaojun Pei* , Changchuan Yin and Rong Lucy He ) , Genes ,Vol. 11:637 (2020) , 1-16 DOI

Positional Correlation Natural Vector: A Novel Method for Genome Comparison (with Lily He , Rui Dong and Rong Lucy He ) , International Journal of Molecular Sciences ,Vol. 21:3859 (2020) , 1-19 DOI

A novel numerical representation for proteins: three-dimensional Chaos Game Representation and its Extended Natural Vector (with Zeju Sun* , Shaojun Pei* and Rong Lucy He ) , Computational and Structural Biotechnology Journal ,Vol. 18 (2020) , 1904-1913 DOI

A new method based on coding sequence density to cluster bacteria (with Nan Sun* , Rui Dong* , Shaojun Pei and Changchuan Yin ) , Journal of Computational Biology ,Vol. 127 ,No. 12 (2020) , 1688-1698 DOI

Classification of genomic components and prediction of genes of Begomovirus based on subsequence natural vector and support vector machine (with Shaojun Pei , Rui Dong , Yiming Bao and Rong He ) , Peer J (2020) , 1-15 DOI

Amino acid torsion angles enable prediction of protein fold classification (with Kun Tian* and Xin Zhao* ) , Scientific Reports ,Vol. 10:21733 (2020) , 1-8 DOI

Virus classification based on Q-vectors (with Hui Zheng , Jie Yang and Rong L. He ) , Communications in Information and Systems ,Vol. 19 ,No. 1 (2019) , 81-94

Fast and accurate genome comparison using genome images: the Extended Natural Vector (with Shaojun Pei* , Wenhui Dong* , Xiuqiong Chen and Rong Lucy He ) , Molecular Phylogenetics and Evolution ,Vol. 141 (2019) , 1-7 DOI Journal Homepage

A Novel Approach to Clustering Genome Sequences Using Inter-Nucleotide Covariance (with Rui Dong , Lily He and Rong Lucy He ) , Frontiers in Genetics, section Bioinformatics and Computational Biology ,Vol. 10 (2019) , 1-12 DOI

Convex hull principle for classification and phylogeny of eukaryotic proteins (with Xin Zhao* , Kun Tian* and Rong L. He ) , Genomics ,Vol. 111 ,No. 6 (2019) , 1777-1784 DOI Journal Homepage

Phylogenetic analysis of protein sequences based on a novel k-mer natural vector method (with Yuyan Zhang and Jia Wen ) , Genomics ,Vol. 111 ,No. 6 (2019) , 1298-1305 DOI Journal Homepage

Comparing protein structures and inferring functions with a novel three-dimensional Yau-Hausdorff method (with Kun Tian* , Xin Zhao* and Yuning Zhang ) , Journal of Biomolecular Structure and Dynamics ,Vol. 37 ,No. 16 (2019) , 4115-4160 DOI Journal Homepage

Large-scale genome comparison based on cumulative Fourier power and phase spectra: central moment and covariance vector (with Shaojun Pei , Rui Dong and Rong Lucy He ) , Computational and Structural Biotechnology Journal ,Vol. 17 (2019) , 982-994 DOI Journal Homepage

Protein Sequence Classification Using Natural Vector and Convex Hull Method (with Yi Wang and Kun Tian ) , Journal of Computational Biology ,Vol. 26 ,No. 4 (2019) , 315-321 DOI

Whole genome single nucleotide polymorphism genotyping of Staphylococcus aureus (with Changchuan Yin ) , Communications in Information and Systems ,Vol. 19 ,No. 1 (2019) , 57-80

Assessment of kmer degeneration method for complicated genomes (with Shuai Liu* , Shaojun Pei* and Qi Wu ) , Communications in Information and Systems ,Vol. 19 ,No. 1 (2019) , 17-35

A new efficient method for analyzing fungi species using correlations between nucleotides (with Xin Zhao and Kun Tian ) , BMC Evolutionary Biology ,Vol. 18:200 (2018) , 1-13 DOI

Convex hull analysis of evolutionary and phylogenetic relationships between biological groups (with Kun Tian* and Xin Zhao* ) , Journal of Theoretical Biology ,Vol. 456 ,No. 7 (2018) , 34-40 DOI Journal Homepage

A new method to cluster genomes based on cumulative Fourier power spectrum (with Rui Dong* , Ziyue Zhu* , Changchuan Yin and Rong L. He ) , Gene ,Vol. 673 (2018) , 239-250 DOI

A novel fast vector method for genetic sequence comparison (with Yongkun Li , Lily He and Rong L. He ) , Scientific Reports ,Vol. 7 (2017) , 1-11 DOI

Virus Database and Online Inquiry System Based on Natural Vectors (with Rui Dong , Hui Zheng , Kun Tian , Shek-Chung Yau , Weiguang Mao , Wenping Yu , Changchuan Yin , Chenglong Yu , Rong L. He and Jie Yang ) , Evolutionary Bioinformatics ,Vol. 13 (2017) , 1-7 DOI

Establishing the phylogeny of Prochlorococcus with a new alignment-free method (with Xin Zhao* , Kun Tian* and Rong L. He ) , Ecology and Evolution ,Vol. 7 (2017) , 11057-11065 DOI

A novel alignment-free vector method to cluster protein sequences (with Lily He* , Yongkun Li* and Rong L. He ) , Journal of Theoretical Biology ,Vol. 427 (2017) , 41-52 DOI Journal Homepage