Publications List
A coevolution analysis for identifying protein-protein interactions by Fourier transform
(with
Changchuan Yin
)
, PLoS ONE
,Vol. 12
,No. 4
(2017)
, 1-19
DOI
An information-based network approach for protein classification
(with
Xiaogeng Wan
and Xin Zhao
)
, PLoS ONE
,Vol. 12
,No. 3
(2017)
, 1-21
DOI
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
DOI
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
DOI
Other
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
DOI
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
DOI
Journal Homepage
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
(2015)
, 1-19
DOI
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
DOI
An improved model for whole genome phylogenetic analysis by Fourier transform
(with
Changchuan Yin
)
, Journal of Theoretical Biology
,Vol. 382
(2015)
, 99-110
DOI
A new method to cluster DNA sequences using Fourier power spectrum
(with
Tung Hoang
, Changchuan Yin
, Chenglong Yu
and Rong Lucy He
)
, Journal of Theoretical Biology
,Vol. 372
(2015)
, 135-145
DOI
Distinguishing Proteins From Arbitrary Amino Acid Sequences
(with
Wei-Guang Mao*
, Max Benson
and Rong Lucy He
)
, Scientific Reports
,Vol. 5
(2015)
, 1-8
DOI
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
:e64528
,No. 5
(2014)
, 1-10
Viral genome phylogeny based on Lempel-Ziv complexity and Hausdorff distance
(with
Chenglong Yu
and Rong Lucy He
)
, Journal of Theoretical Biology
,Vol. 348
(2014)
, 12-20
K-mer natural vector and its application to the phylogenetic analysis of genetic sequences
(with
Wen Jia
, Raymond H.F. Chan
, Shek-Chung Yau
and Rong L. He
)
, Gene
,Vol. 546
,No. 1
(2014)
, 25-34
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
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
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
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
Protein sequence comparison based on K-string dictionary
(with
Chenglong Yu
and Rong L. He
)
, Gene
,Vol. 529
(2013)
, 250-256
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
Protein space: A natural method for realizing the nature of protein universe
(with
Chenglong Yu
, Mo Deng
, Shiu-Yuen Cheng
, Shek-Chung Yau
and Rong L. He
)
, Journal of Theoretical Biology,
,Vol. 318
(2013)
, 197-204
A Novel Method of Characterizing Genetic Sequences: genome space with biological distance and applications
(with
Mo Deng
, Chenglong Yu
, Qian Liang
and Rong L. He
)
, PLoS One
,Vol. 6
:e17293
,No. 3
(2011)
, 1-9
DNA sequence comparison by a novel probabilistic method
(with
Chenglong Yu
and Mo Deng
)
, Information Science
,Vol. 181
(2011)
, 1484-1492
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
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
Protein map: An alignment-free sequence comparison method based on various properties of amino acids
(with
Chenglong Yu
, ShiuYuen Cheng
and Rong L. He
)
, Gene
,Vol. 486
(2011)
, 110-118
A novel construction of genome space with biological geometry
(with
Chenglong Yu
, Qian Liang
, Changchuan Yin
and Rong He
)
, DNA Research
,Vol. 17
(2010)
, 155-168
A rapid method for characterization of protein relatedness using feature vectors
, PLoS ONE
,Vol. 5
:e9950
,No. 3
(2010)
, 1-10
A protein map and its application
(with
Chenglong Yu
and Rong He
)
, DNA and Cell Biology
,Vol. 27
,No. 5
(2008)
, 241-250
Coding region prediction based on a universal DNA sequence representative method
(with
Xianyang Jiang
and Dominique Lavenier
)
, Journal of Computational Biology
,Vol. 15
(2008)
, 1237-1256
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
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
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
Clustering DNA sequences by features vectors
(with
Libin Liu
and Yee-kin Ho
)
, Molecular Phylogenetics and Evolution
,Vol. 41
(2006)
, 64-69
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
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