List
of Stephen Yau's papers in Bioinformatics
March 21, 2023
1.
Yau lecture in
University of Notre Dame.pdf
2.
Utilizing the codon adaptation index (CAI) 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.
3.
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 (2023), 1-11.
4.
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.
5.
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.
6.
An efficient numerical representation of genome sequence:
natural vector with covariance component (with Nan Sun and Xin Zhao), Peer
J., Vol.. 10 :e13544
(2022), 1-23.
7.
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.
8.
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.
9.
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.
10.
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.
11.
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.
12.
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.
13.
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.
14.
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.
15.
Geometric construction of viral genome space and its
applications (with Nan Sun*, Shaojun Pei*, Lily
He, Changchuan Yin, Rong Lucy He), Computational and
Structural Biotechnology Journal, Vol. 19 (2021), 4226-4234.
16.
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.
17.
Amino acid torsion angles enable prediction of protein fold
classification (with Kun Tian* and Xin Zhao*), Scientific Reports,
10:21733, 2020, 1-8.
18.
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, DOI
10.7717/peerj.9625, 2020, 1-15.
19.
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.
20.
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.
21.
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.
22.
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.
23.
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.
24.
Splice sites detection using chaos game representation and
neural network (with Tung Hoang and Changchuan Yin), Genomics, Vol. 112,
No. 2 (2020), 1847-1852.
25.
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.
26.
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.
27.
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.
28.
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.
29.
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.
30.
Large-scale genome comparison based on cumulative Fourier power
and phase spectra: central moment and covariance vector (with Shao-jun Pei, Rui Dong and Rong Lucy He), Computational and Structural Biotechnology
Journal, Vol. 17 (2019), 982-994.
31.
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.
32.
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.
33.
Whole genome single nucleotide
polymorphism genotyping of Staphylococcus aureus (with Changchuan Yin),
Communications in Information and Systems, Vol. 19, No. 1 (2019), 57-80.
34.
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.
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.
36.
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.
37.
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.
38.
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.
39.
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.
40.
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.
41.
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.
42.
A
coevolution analysis for identifying protein-protein interactions by Fourier
transform (with
Changchuan Yin), PLoS ONE, Vol. 12, No. 4 (2017),
1-19.
43.
An
information-based network approach for protein classification (with Xiaogeng
Wan and Xin Zhao), PLoS ONE, Vol. 12, No. 3 (2017),
1-21.
44.
Zika and Flaviviruses
Phylogeny Based on the Alignment-Free Natural Vector Method (with Yongkun
Li, Lily He and Rong L. He), DNA and Cell Biology,
Vol. 36, No. 2 (2017), 109-116.
45.
Numerical
encoding of DNA sequences by chaos game representation with application in
similarity comparison
(with Tung Hoang and Changchuan Yin), Genomics, Vol. 108 (2016), 134-142.
46.
Virus
classification in 60-dimensional protein space (with Yongkun
Li, Kun Tian, Changchuan Yin and Rong L. He),
Molecular Phylogenetics and Evolution, Vol. 99
(2016), 53-62.
47.
A
New Method for Studying the Evolutionary Origin of the SAR11 Clade Marine
Bacteria (with Xin
Zhao, Xiaogeng Wan and Rong
L. He), Molecular Phylogenetics and Evolution, Vol.
98 (2016), 271-279.
48.
Two
Dimensional Yau-Hausdorff Distance with Applications
on Comparison of DNA and Protein Sequences (with Kun Tian, Xiaoqian
Yang, Qin Kong, Changchuan Yin, and Rong L. He), PLos ONE, DOI:10.1371/journal.pone.0136577
(2015), 1-19.
49.
Ebolaviruses
Classification Based on Natural Vectors (with Hui Zheng, Changchuan Yin, Tung Hoang, Rong Lucy He and Jie Yang), DNA
and Cell Biology, Vol. 34, No. 6 (2015), 1-11.
50.
An
improved model for whole genome phylogenetic analysis by Fourier transform (with Changchuan Yin), Journal of
Theoretical Biology, Vol. 382 (2015), 99-110.
51.
A
new method to cluster DNA sequences using Fourier power spectrum (with Tung Hoang, Changchuan Yin,
Hui Zheng, Chenglong Yu and Rong
Lucy He), Journal of Theoretical Biology, Vol. 372 (2015), 135-145.
52.
Distinguishing
Proteins From Arbitrary Amino Acid Sequences (with Wei-Guang Mao*, Max
Benson, and Rong Lucy He), Scientific Reports, Vol. 5
(2015), 1-8.
53.
Global
comparison of multiple-segmented viruses in 12-dimensional Genome space (with Hsin-Hsiung
Huang, Chenglong Yu, Hui Zheng; Troy Hernandez, Shek-Chung Yau; Rong Lucy He, and
Jie Yang), Molecular Phylogenetics
and Evolution, Vol. 81 (2014), 29-36.
54.
K-mer sparse matrix model for genetic sequence and its
applications in sequence comparison
(with Jia Wen and YuYan
Zhang), Journal of Theoretical Biology, Vol. 363 (2014), 145-150.
55.
A
measure of DNA sequence similarity by Fourier Transform with applications on
hierarchical clustering
(with Changchuan Yin, and Ying Chen), Journal of Theoretical Biology, Vol. 359
(2014), 18-28.
56.
DFA7,
A New Method to Distinguish between Intron-containing and Intronless
Genes (with Chenglong Yu, Mo Deng, Lu Zheng, Rong
Lucy He, and Jie Yang ), PLoS
ONE, Vol. 9, No. 7 (2014), 1-10.
57.
K-mer natural vector and its application to the phylogenetic
analysis of genetic sequences
(with Wen Jia, Raymond H.F. Chan, Shek-Chung
Yau, Rong L. He), Gene, Vol. 546, No. 1 (2014),
25-34.
58.
Viral
genome phylogeny based on Lempel-Ziv complexity and Hausdorff
distance (with Chenglong Yu, Rong Lucy He),
Journal of Theoretical Biology, Vol. 348 (2014), 12-20.
59.
Protein
sequence comparison based on K-string dictionary (with Chenglong
Yu and Rong L. He), Gene, Vol. 529 (2013), 250-256.
60.
Denoising the 3-Base Periodicity Walks of
DNA Sequences in Gene Finding
(with Changchuan Yin and Dongchul Yoo),
Journal of Medical and Bioengineering, Vol. 2, No. 2 (2013), 80-83.
61.
Real
Time Classification of Viruses in 12 Dimensions (with Chenglong
Yu, Troy Hernandez, Hui Zheng, Shek-Chung Yau, Hsin-Hsiung Huang, Rong Lucy He
and Jie Yang), PLoS ONE,
Vol. 8, No. 5 (2013), e64528, 1-10.
62.
Protein
space: A natural method for realizing the nature of protein universe (with Chenglong
Yu, Mo Deng, Shiu-Yuen Cheng, Shek-Chung
Yau, Rong L. He), Journal of Theoretical Biology,
Vol. 318 (2013), 197-204.
63.
Protein
map: An alignment-free sequence comparison method based on various properties
of amino acids
(with Chenglong Yu, ShiuYuen
Cheng, Rong L. He), Gene, Vol. 486 (2011), 110-118.
64.
A
novel clustering method via nucleotide-based Fourier power spectrum analysis (with Bo Zhao and Victor Duan), Journal of Theoretical Biology, Vol. 279 (2011),
83-89.
65.
A
new distribution vector and its application in genome clustering (with Bo Zhao and Rong L. He), Molecular Phylogenetics
and Evolution, Vol. 59 (2011), 438-443.
66.
A
Novel Method of Characterizing Genetic Sequences: genome space with biological
distance and applications
(with Mo Deng, Chenglong Yu, Qian Liang, Rong L. He), PLoS One, Vol. 6,
Issue 3, e17293, March 2011, 1-9.
67.
DNA
sequence comparison by a novel probabilistic method (with Chenglong
Yu and Mo Deng), Information Science, Vol. 181 (2011), 1484-1492.
68.
A
novel construction of genome space with biological geometry (with Chenglong
Yu, Qian Liang, Changchuan Yin, Rong He), DNA
Research, Vol. 17 (2010), 155-168.
69.
A
rapid method for characterization of protein relatedness using feature vectors (with Kareem Carr,
Eleanor Murray, Ebeneger Armah,
Rong He), PLoS ONE, Vol. 5,
issue 3 (2010), e9950, 1-10.
70.
Coding
region prediction based on a universal DNA sequence representative method (with Xianyang
Jiang and Dominique Lavenier), Journal of
Computational Biology, Vol. 15, No. 10 (2008), 1237-1256.
71.
A
protein map and its application
(with Chenglong Yu and Rong
He), DNA and Cell Biology, Vol. 27, No. 5 (2008), 241-250.
72.
Prediction
of Protein Coding Regions By the 3-Base Periodicity Analysis of a DNA Sequence (with ChangChuan
Yin), Journal of Theoretical Biology, Vol. 247 (2007), 687-694.
73.
Survey
on index based homology search algorithms (with Xianyang Jiang, Peiheng Zhang and Xinchun Liu),
Journal of Supercomputing, Vol. 40, No. 2 (2007), 185-212.
74.
Prediction
of Primate Splice Site Using Inhomogeneous Markov Chain and Neural Network (with Libin
Liu and Yee-Kin Ho), DNA and Cell Biology, Vol. 26, No. 7 (2007), 477-483.
75.
Clustering
DNA sequences by features vectors
(with Libin Liu and Yee-kin Ho), Molecular Phylogenetics and Evolution, Vol. 41 (2006), 64-69.
76.
A
Fourier characteristic of coding sequences: Origins and a non-Fourier
approximation
(with Changchuan Yin), Journal of Computation Biology, Vol. 12, No. 9 (2005),
1153-1165.
77.
DNA
sequence representation without degeneracy (with Jiasong Wang, Amir Niknejad, Chaoxiao Lu, Ning Jin and Yee-Kin Ho), Nucleic Acids Research, Vol. 31, No.
12 (2003), 3078-3080.