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For: Pei S, Dong R, He RL, Yau SST. Large-Scale Genome Comparison Based on Cumulative Fourier Power and Phase Spectra: Central Moment and Covariance Vector. Comput Struct Biotechnol J 2019;17:982-994. [PMID: 31384399 PMCID: PMC6661692 DOI: 10.1016/j.csbj.2019.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/24/2019] [Accepted: 07/10/2019] [Indexed: 01/04/2023]  Open
Number Cited by Other Article(s)
1
Shaukat MA, Nguyen TT, Hsu EB, Yang S, Bhatti A. Comparative study of encoded and alignment-based methods for virus taxonomy classification. Sci Rep 2023;13:18662. [PMID: 37907535 PMCID: PMC10618506 DOI: 10.1038/s41598-023-45461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]  Open
2
de Souza LC, Azevedo KS, de Souza JG, Barbosa RDM, Fernandes MAC. New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning. BMC Bioinformatics 2023;24:92. [PMID: 36906520 PMCID: PMC10007673 DOI: 10.1186/s12859-023-05188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/15/2023] [Indexed: 03/13/2023]  Open
3
Grønbæk C, Liang Y, Elliott D, Krogh A. Context dependent prediction in DNA sequence using neural networks. PeerJ 2022;10:e13666. [PMID: 36157058 PMCID: PMC9504454 DOI: 10.7717/peerj.13666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/10/2022] [Indexed: 01/17/2023]  Open
4
Li W, Yang L, Qiu Y, Yuan Y, Li X, Meng Z. FFP: joint Fast Fourier transform and fractal dimension in amino acid property-aware phylogenetic analysis. BMC Bioinformatics 2022;23:347. [PMID: 35986255 PMCID: PMC9392226 DOI: 10.1186/s12859-022-04889-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/11/2022] [Indexed: 11/10/2022]  Open
5
Dong R, Pei S, Guan M, Yau SC, Yin C, He RL, Yau SST. Full Chromosomal Relationships Between Populations and the Origin of Humans. Front Genet 2022;12:828805. [PMID: 35186019 PMCID: PMC8847220 DOI: 10.3389/fgene.2021.828805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022]  Open
6
Identification of HIV Rapid Mutations Using Differences in Nucleotide Distribution over Time. Genes (Basel) 2022;13:genes13020170. [PMID: 35205215 PMCID: PMC8872422 DOI: 10.3390/genes13020170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/08/2022] [Accepted: 01/12/2022] [Indexed: 02/07/2023]  Open
7
Kania A, Sarapata K. The robustness of the chaos game representation to mutations and its application in free-alignment methods. Genomics 2021;113:1428-1437. [PMID: 33713823 DOI: 10.1016/j.ygeno.2021.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
8
Li M, Sun X, Chen W. Patient-specific seizure detection method using nonlinear mode decomposition for long-term EEG signals. Med Biol Eng Comput 2020;58:3075-3088. [DOI: 10.1007/s11517-020-02279-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/20/2020] [Indexed: 11/30/2022]
9
Sun Z, Pei S, He RL, Yau SST. A novel numerical representation for proteins: Three-dimensional Chaos Game Representation and its Extended Natural Vector. Comput Struct Biotechnol J 2020;18:1904-1913. [PMID: 32774785 PMCID: PMC7390779 DOI: 10.1016/j.csbj.2020.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/04/2020] [Accepted: 07/05/2020] [Indexed: 12/16/2022]  Open
10
Dong R, Pei S, Yin C, He RL, Yau SST. Analysis of the Hosts and Transmission Paths of SARS-CoV-2 in the COVID-19 Outbreak. Genes (Basel) 2020;11:E637. [PMID: 32526937 PMCID: PMC7349679 DOI: 10.3390/genes11060637] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022]  Open
11
Sun N, Dong R, Pei S, Yin C, Yau SST. A New Method Based on Coding Sequence Density to Cluster Bacteria. J Comput Biol 2020;27:1688-1698. [PMID: 32392428 DOI: 10.1089/cmb.2019.0509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
12
Lichtblau D. Alignment-free genomic sequence comparison using FCGR and signal processing. BMC Bioinformatics 2019;20:742. [PMID: 31888438 PMCID: PMC6937637 DOI: 10.1186/s12859-019-3330-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/17/2019] [Indexed: 01/14/2023]  Open
13
Pei S, Dong W, Chen X, He RL, Yau SST. Fast and accurate genome comparison using genome images: The Extended Natural Vector Method. Mol Phylogenet Evol 2019;141:106633. [PMID: 31563612 DOI: 10.1016/j.ympev.2019.106633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 11/25/2022]
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